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1.
Zhonghua Yi Xue Za Zhi ; 100(2): 97-103, 2020 Jan 14.
Artigo em Chinês | MEDLINE | ID: mdl-31937047

RESUMO

Objective: To explore the role of pulmonary arterial pressure in chronic obstructive pulmonary disease (COPD) phenotypes based on cluster analysis and its prognostic value. Methods: Three hundred and nineteen patients admitted to Beijing Chaoyang Hospital and Xuanwu Hospital from April 2013 to April 2016 were recruited in the study. All the patients were older than 40 years old and in stable COPD. One-year follow-up was performed and the endpoint was acute exacerbation of COPD or all-cause mortality. Age, body mass index (BMI), smoking index, history of exacerbation, modified British medical research council (mMRC), forced expiratory volume in first second (FEV(1)), pulmonary arterial pressure and right ventricular transverse diameter measured by echocardiography were selected as cluster indicators to classify patients, survival analysis was performed. Results: Eight cluster indexes were converted into four independent principal components by principal component analysis (PCA), with a cumulative contribution rate of 70.1%. The extracted principal components were used for cluster analysis. Patients were divided into four categories, each contained different GOLD grades and had statistically significant differences in age, symptoms, degree of pulmonary function impairment and pulmonary arterial pressure (all P<0.001). The four categories were: class 1: young, pulmonary function damage was medium, lower pulmonary arterial pressure, good prognosis; class 2: elderly, pulmonary function damage was mild, higher pulmonary arterial pressure, poor prognosis; class 3: young, pulmonary function damage was serious, normal pulmonary arterial pressure, the best prognosis; class 4: elderly, pulmonary function damage was medium, pulmonary arterial pressure increased significantly, the worst prognosis. Conclusion: Cluster analysis based on pulmonary artery pressure can be used to identify COPD patients with different risk of acute exacerbation or death, suggesting that pulmonary hypertension as a COPD phenotype plays a role in prognostic assessment.


Assuntos
Pressão Arterial , Doença Pulmonar Obstrutiva Crônica , Adulto , Idoso , Análise por Conglomerados , Volume Expiratório Forçado , Humanos , Fenótipo , Prognóstico
2.
Anticancer Res ; 40(1): 413-419, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892595

RESUMO

BACKGROUND/AIM: In patients with lung cancer, there has been no study that treated 'distant metastases' as 'metastatic patterns'. This study aimed to evaluate if specific 'metastatic patterns' exist in lung cancer patients. PATIENTS AND METHODS: Data were collected from lung cancer patients between 2009 and 2018. Metastatic patterns were analyzed using cluster analysis in patients with epidermal growth factor receptor (EGFR) mutation-positive lung adenocarcinoma, those with small cell lung cancer (SCLC), and those with squamous cell lung cancer (SqCLC). RESULTS: In 313 patients (127 patients with EGFR mutation, 87 patients with SCLC, and 99 patients with SqCLC), metastatic patterns existed in each of the three subset groups, and metastatic patterns of these groups were statistically different. CONCLUSION: The knowledge of the metastatic patterns might be useful for clinical practice in the foreseeable future, as it enables a more efficient detection of metastatic disease through imaging, and a more effective treatment at predicted metastatic sites.


Assuntos
Neoplasias Pulmonares/patologia , Adenocarcinoma de Pulmão/genética , Idoso , Idoso de 80 Anos ou mais , Análise por Conglomerados , Receptores ErbB/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Mutação/genética , Metástase Neoplásica , Probabilidade
3.
Sports Health ; 12(1): 80-87, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31710819

RESUMO

BACKGROUND: The prevalence of musculoskeletal (MSK) conditions is increasing, and although current guidelines for physical activity attempt to combat this, many fail to achieve the recommended targets. The present study sought to investigate whether regular tennis participation is more effective at enhancing MSK function than meeting the current international physical activity guidelines. HYPOTHESIS: Tennis players will display significantly enhanced MSK function when compared with age-matched healthy active nonplayers. STUDY DESIGN: Cross-sectional study. LEVEL OF EVIDENCE: Level 3. METHODS: Ninety participants (age range, 18-65 years) took part in this study; there were 43 tennis players (18 men, 25 women) and 47 nonplayers (26 men, 21 women). MSK function was assessed by cluster analysis of 3 factors: (1) electromyographic fatigability of prime movers during handgrip, knee extension, and knee flexion; (2) isometric strength in the aforementioned movements; and (3) body composition measured by bioelectrical impedance analysis. Maximal oxygen uptake was also assessed to characterize cardiorespiratory fitness. RESULTS: Tennis players displayed significantly greater upper body MSK function than nonplayers when cluster scores of body fat percentage, handgrip strength, and flexor carpi radialis fatigue were compared by analysis of covariance, using age as a covariate (tennis players, 0.33 ± 1.93 vs nonplayers, -0.26 ± 1.66; P < 0.05). Similarly, tennis players also demonstrated greater lower extremity function in a cluster of body fat percentage, knee extension strength, and rectus femoris fatigue (tennis players, 0.17 ± 1.76 vs nonplayers, -0.16 ± 1.70; P < 0.05). CONCLUSION: The present study offers support for improved MSK functionality in tennis players when compared with age-matched healthy active nonplayers. This may be due to the hybrid high-intensity interval training nature of tennis. CLINICAL RELEVANCE: The findings suggest tennis is an excellent activity mode to promote MSK health and should therefore be more frequently recommended as a viable alternative to existing physical activity guidelines.


Assuntos
Músculo Esquelético/fisiologia , Tênis/fisiologia , Adolescente , Adulto , Idoso , Composição Corporal , Aptidão Cardiorrespiratória/fisiologia , Análise por Conglomerados , Estudos Transversais , Feminino , Força da Mão , Humanos , Joelho/fisiologia , Masculino , Pessoa de Meia-Idade , Fadiga Muscular/fisiologia , Força Muscular/fisiologia , Consumo de Oxigênio/fisiologia , Adulto Jovem
4.
Bioresour Technol ; 298: 122495, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31830658

RESUMO

Machine learning has emerges as a novel method for model development and has potential to be used to predict and control the performance of anaerobic digesters. In this study, several machine learning algorithms were applied in regression and classification models on digestion performance to identify determinant operational parameters and predict methane production. In the regression models, k-nearest neighbors (KNN) algorithm demonstrates optimal prediction accuracy (root mean square error = 26.6, with the dataset range of 259.0-573.8), after narrowing prediction coverage by excluding extreme outliers from the validation set. In the classification models, logistic regression multiclass algorithm yields the best prediction accuracy of 0.73. Feature importance reveals that total carbon was the determinant operational parameter. These results demonstrate the great potential of using machine learning algorithms to predict anaerobic digestion performance.


Assuntos
Algoritmos , Aprendizado de Máquina , Anaerobiose , Análise por Conglomerados , Modelos Logísticos
5.
Food Chem ; 307: 125521, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-31655264

RESUMO

The essential oils and antioxidant activity of four Thymus species were evaluated under five light spectra (namely, red, blue, red-blue, white, and greenhouse condition). The highest essential oil yield (4.17%) was observed under red light in T. migricus, while the lowest (1.05%) was observed in T. carmanicus under greenhouse conditions. Light quality also led to difference in essential oil constituents. The highest thymol (66%) was found in T. migricus exposed to blue light, while the least (1.69%) was observed in T. kotschyanus grown under red-blue light. The LED treatments did not induce any significant effect on carvacrol of Thymus species in comparison to the greenhouse condition. Finally, the analysis of variance indicates that the effect of light varied with the studied species. T. migricus performed the highest antioxidant capacity (IC50 = 176.8 µg/mL) under blue light. Overall, essential oil components as well as antioxidants showed significant responses to light emitting diodes wavelengths.


Assuntos
Antioxidantes/metabolismo , Luz , Timol/metabolismo , Thymus (Planta)/química , Análise de Variância , Antioxidantes/química , Cromatografia Gasosa , Análise por Conglomerados , Efeito Estufa , Óleos Voláteis/química , Análise de Componente Principal , Timol/química , Thymus (Planta)/crescimento & desenvolvimento , Thymus (Planta)/metabolismo
6.
Sci Total Environ ; 698: 133999, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31499345

RESUMO

When water and solutes enter the plant root through the epidermis, organic contaminants in solution either cross the root membranes and transport through the vascular pathways to the aerial tissues or accumulate in the plant roots. The accumulation of contaminants in plant roots and edible tissues is measured by root concentration factor (RCF) and fruit concentration factor (FCF). In this paper, 1) a neural network (NN) was applied to model RCF based on physicochemical properties of organic compounds, 2) correlation and significance of physicochemical properties were assessed using statistical analysis, 3) fuzzy logic was used to examine the simultaneous impacts of significant compound properties on RCF and FCF, 4) a clustering algorithm (k-means) was used to identify unique groups and discover hidden relationships within contaminants in various parts of the plants. The physicochemical cutoffs achieved by fuzzy logic for the RCF and the FCF were compared versus the cutoffs for compounds that crossed the plant root membranes and found their way into transpiration stream (measured by transpiration stream concentration factor, TSCF). The NN predicted the RCF with improved accuracy compared to mechanistic models. The analysis indicated that log Kow, molecular weight, and rotatable bonds are the most important properties for predicting the RCF. These significant compound properties are positively correlated with RCF while they are negatively correlated with TSCF. Comparing the relationships between compound properties in various plant tissues showed that compounds detected in the edible parts have physicochemical cutoffs that are more like the compounds crossing the plant root membranes (into xylem tissues) than the compounds accumulating in the plant roots, with clear relationships to food security. The cluster analysis placed the contaminants into three meaningful groups that were in agreement with the results of fuzzy logic.


Assuntos
Abastecimento de Alimentos , Aprendizado de Máquina , Plantas/metabolismo , Poluentes do Solo/metabolismo , Análise por Conglomerados , Lógica Fuzzy , Xilema
7.
J Sci Food Agric ; 100(1): 245-257, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31512244

RESUMO

BACKGROUND: This study was conducted to assess whether there are differences in consumer liking of beef. Samples were collected from different groups and analyses were conducted, including quantitative descriptive analysis, consumer panels and instrumental analyses. Palatability traits, such as aroma liking, tenderness, juiciness, flavour liking and overall liking (OL), were rated by consumers. RESULTS: Warner-Bratzler shear force was negatively associated with tender mouthfeel and consumer tenderness score. Cluster analysis identified four groups of clusters, which were described as 'easily pleased', 'bull beef liker', 'tender beef liker' and 'fastidious' consumers. Cluster group 2 awarded a higher score for bulls and located in a separate region on the external preference map. CONCLUSION: External preference mapping showed the association between consumer liking of beef and sensory attributes. © 2019 Society of Chemical Industry.


Assuntos
Comportamento do Consumidor , Carne/análise , Animais , Bovinos , Análise por Conglomerados , Feminino , Aromatizantes/análise , Preferências Alimentares , Humanos , Masculino , Paladar
8.
BMC Bioinformatics ; 20(Suppl 26): 628, 2019 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-31839008

RESUMO

BACKGROUND: Development of new drugs is a time-consuming and costly process, and the cost is still increasing in recent years. However, the number of drugs approved by FDA every year per dollar spent on development is declining. Drug repositioning, which aims to find new use of existing drugs, attracts attention of pharmaceutical researchers due to its high efficiency. A variety of computational methods for drug repositioning have been proposed based on machine learning approaches, network-based approaches, matrix decomposition approaches, etc. RESULTS: We propose a novel computational method for drug repositioning. We construct and decompose three-dimensional tensors, which consist of the associations among drugs, targets and diseases, to derive latent factors reflecting the functional patterns of the three kinds of entities. The proposed method outperforms several baseline methods in recovering missing associations. Most of the top predictions are validated by literature search and computational docking. Latent factors are used to cluster the drugs, targets and diseases into functional groups. Topological Data Analysis (TDA) is applied to investigate the properties of the clusters. We find that the latent factors are able to capture the functional patterns and underlying molecular mechanisms of drugs, targets and diseases. In addition, we focus on repurposing drugs for cancer and discover not only new therapeutic use but also adverse effects of the drugs. In the in-depth study of associations among the clusters of drugs, targets and cancer subtypes, we find there exist strong associations between particular clusters. CONCLUSIONS: The proposed method is able to recover missing associations, discover new predictions and uncover functional clusters of drugs, targets and diseases. The clustering of drugs, targets and diseases, as well as the associations among the clusters, provides a new guiding framework for drug repositioning.


Assuntos
Biologia Computacional , Reposicionamento de Medicamentos , Análise por Conglomerados , Biologia Computacional/métodos , Reposicionamento de Medicamentos/métodos , Humanos , Aprendizado de Máquina
9.
Environ Monit Assess ; 192(1): 5, 2019 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-31797222

RESUMO

Lake Cajititlán is a shallow body of water located in an endorheic basin in western Mexico. This lake receives excess fertilizer runoff from agriculture and approximately 2.3 Hm3 per year of poorly treated wastewater from three municipal treatment plants. Thirteen water quality parameters were monitored at five sampling points within the lake over 9 years. The objective of this work was to characterize the spatial and temporal variations of the water quality and to identify the sources of data variability in order to assess the influence and the impact of different natural and anthropogenic processes. One-way ANOVA tests, principal component analysis (PCA), cluster analysis (CA), and discriminant analysis (DA) were implemented. The one-way ANOVA showed that biochemical oxygen demand and pH present statistically significant spatial variations and that alkalinity, total chloride, conductivity, chemical oxygen demand, total hardness, ammonia, pH, total dissolved solids, and temperature present statistically significant temporal variations. PCA results explained both natural and anthropogenic processes and their relationship with water quality data. The CA results suggested there is no significant spatial variation in the water quality of the lake because of lake mixing caused by wind. The most significant parameters for spatial variations were pH, NO3-, and NO2-, consistent with the configuration of point and nonpoint sources that affect the lake's water quality. The temporal DA results suggested that conductivity, hardness, NO2-, pH, and temperature were the most significant parameters to discriminate between seasons. The temporal behavior of these parameters was associated with the transport pathways of seasonal contaminants.


Assuntos
Monitoramento Ambiental , Lagos/química , Análise Multivariada , Qualidade da Água , Análise por Conglomerados , Análise Discriminante , Monitoramento Ambiental/métodos , México , Análise de Componente Principal , Estações do Ano , Poluentes Químicos da Água/análise
10.
Phys Rev Lett ; 123(20): 208002, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31809118

RESUMO

Active particles such as swimming bacteria or self-propelled colloids spontaneously self-organize into large-scale dynamic structures. The emergence of these collective states from the motility pattern of the individual particles, typically a random walk, is yet to be probed in a well-defined synthetic system. Here, we report the experimental realization of tunable colloidal motion that reproduces run-and-tumble and Lévy trajectories. We utilize the Quincke effect to achieve controlled sequences of repeated particle runs and random reorientations. We find that a population of these random walkers exhibit behaviors reminiscent of bacterial suspensions such as dynamic clusters and mesoscale turbulentlike flows.


Assuntos
Coloides/química , Modelos Teóricos , Análise por Conglomerados , Movimento (Física)
11.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 36(6): 978-985, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31875372

RESUMO

Accurate segmentation of pulmonary nodules is an important basis for doctors to determine lung cancer. Aiming at the problem of incorrect segmentation of pulmonary nodules, especially the problem that it is difficult to separate adhesive pulmonary nodules connected with chest wall or blood vessels, an improved random walk method is proposed to segment difficult pulmonary nodules accurately in this paper. The innovation of this paper is to introduce geodesic distance to redefine the weights in random walk combining the coordinates of the nodes and seed points in the image with the space distance. The improved algorithm is used to achieve the accurate segmentation of pulmonary nodules. The computed tomography (CT) images of 17 patients with different types of pulmonary nodules were selected for segmentation experiments. The experimental results are compared with the traditional random walk method and those of several literatures. Experiments show that the proposed method has good accuracy in the segmentation of pulmonary nodule, and the accuracy can reach more than 88% with segmentation time is less than 4 seconds. The results could be used to assist doctors in the diagnosis of benign and malignant pulmonary nodules and improve clinical efficiency.


Assuntos
Análise por Conglomerados , Neoplasias Pulmonares , Nódulos Pulmonares Múltiplos , Algoritmos , Humanos , Interpretação de Imagem Radiográfica Assistida por Computador , Tomografia Computadorizada por Raios X
12.
Zhongguo Zhong Yao Za Zhi ; 44(21): 4670-4676, 2019 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-31872663

RESUMO

This research was performed to establish the HPLC fingerprint of Sabia parviflora. HPLC method was carried out on a Thermo Accucore-C18(4. 6 mm×150 mm,2. 6 µm) column by 30% tetrahydrofuran in methyl alcohol-acetonitrile-0. 1% phosphate solution as mobile phase at a flow rate of 1. 0 m L·min-1,the column temperature was 30 ℃ and the detection wavelength was 360 nm. The fingerprints were further evaluated by chemometrics methods including similarity analysis,hierarchical clustering analysis,and principal component analysis. In HPLC fingerprint,15 common peaks were selected as the common peaks,and 6 contents of them were identified. The similarity degrees of 38 batches of the samples was more than 0. 710,and the samples were divided into 6 clusters by their quality difference. The method was precision,repeatable,stable,simple and reliable,which could be used for quality control and evaluation of S. parviflora.


Assuntos
Medicamentos de Ervas Chinesas , Cromatografia Líquida de Alta Pressão , Análise por Conglomerados , Análise de Componente Principal , Controle de Qualidade
13.
BMC Infect Dis ; 19(1): 925, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31666015

RESUMO

BACKGROUND: Ruili is a border city in southwest China along the heroin trafficking route. In recent decades, the city has witnessed increased in HIV transmission. The current study aims to explore the spatiotemporal trends in HIV prevalence identify and map the spatial variation and clustering of factors associated with HIV transmission through drug use and heterosexual contact transmissions at the village level from 1989 through 2016. METHODS: Geographic information system-based spatiotemporal analyses, including global and local spatial autocorrelation analyses and space-time scanning statistics, were applied to detect the location and extent of HIV/AIDS high-risk areas. RESULTS: Drug use and heterosexual contact were identified as the major transmission routes causing infection in Ruili. Results of global spatial analysis showed significant clustering throughout the city caused by transmission via drug use in the early phase of the epidemic and transmission via heterosexual contact in the late phase of the epidemic during the study period. Hotspots of transmission from drug use were randomly distributed throughout the city. However, the hotspots of transmission by heterosexual contact were located in the central area only around the Jiegao China-Myanmar land port. Space-time scanning showed that transmission from drug use clustered in the southwest area between 1989 and 1990, while transmission by heterosexual contact clustered in the central area between 2004 and 2014. CONCLUSIONS: Heterosexual contact has become the dominant mode of transmission. Interventions should focus on highly clustered area where is around the Jiegao land port.


Assuntos
Infecções por HIV/epidemiologia , Transtornos Relacionados ao Uso de Substâncias/epidemiologia , Síndrome de Imunodeficiência Adquirida/epidemiologia , Síndrome de Imunodeficiência Adquirida/transmissão , Adulto , China/epidemiologia , Cidades , Análise por Conglomerados , Epidemias , Feminino , Sistemas de Informação Geográfica , Infecções por HIV/transmissão , Heterossexualidade , Humanos , Masculino , Mianmar , Prevalência , Comportamento Sexual , Análise Espaço-Temporal , Transtornos Relacionados ao Uso de Substâncias/virologia
14.
Environ Monit Assess ; 191(12): 729, 2019 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-31705319

RESUMO

Managers of water quality and water monitoring programs are often faced with constraints in terms of budget, time, and laboratory capacity for sample analysis. In such situation, the ideal solution is to reduce the number of sampling sites and/or monitored variables. In this case, selecting appropriate monitoring sites is a challenge. To overcome this problem, this study was conducted to statistically assess and identify the appropriate sampling stations of monitoring network under the monitored parameters. To achieve this goal, two sets of water quality data acquired from two different monitoring networks were used. The hierarchical agglomerative cluster analysis (HACA) were used to group stations with similar characteristics in the networks, the time series analysis was then performed to observe the temporal variation of water quality within the station clusters, and the geo-statistical analysis associated Kendall's coefficient of concordance were finally applied to identify the most appropriate and least appropriate sampling stations. Based on the overall result, five stations were identified in the networks that contribute the most to the knowledge of water quality status of the entire river. In addition, five stations deemed less important were identified and could therefore be considered as redundant in the network. This result demonstrated that geo-statistical technique coupled with Kendall's coefficient of concordance can be a reliable method for water resource managers to identify appropriate sampling sites in a river monitoring network.


Assuntos
Monitoramento Ambiental , Rios/química , Poluentes Químicos da Água/análise , Análise por Conglomerados , Água/análise , Qualidade da Água , Recursos Hídricos
15.
Medicine (Baltimore) ; 98(46): e17687, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31725611

RESUMO

To analyze the factors that affecting the help-seeking behavior of bipolar disorder (BD) patients by conducting interviews BD individuals in Hunan province of China.In 2015, 72,999 people from 123 counties of Hunan province of China were interviewed through multistage stratified random sampling. Twelve items of general health questionnaire (GHQ-12) and abnormal behavioral clue questionnaire were used as screening tools. The Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV) (SCID) was used as a diagnostic tool.Among the 75 BD patients, 36% (27/75) sought help. Compared with help-seekers, non-help-seekers were more likely to be older, divorced, or widowed, mostly illiterate or elementary education, family monthly income at least 3000 ¥, more physically consulted in the past year, able to effective work or study, at a stable illness status. 70.4% help-seekers firstly sought help from a medical institution. The main reasons that patients did not seek help were economic problem, did not know where to seek help, unsatisfied with medical services, afraid of mental health stigma, and other problems, such as traffic inconvenience.Non-help-seekers were faced with more difficulties in their social functions and social interactions.


Assuntos
Transtorno Bipolar/psicologia , Comportamento de Busca de Ajuda , Aceitação pelo Paciente de Cuidados de Saúde/psicologia , Adulto , Idoso , China , Análise por Conglomerados , Feminino , Humanos , Masculino , Pessoa de Meia-Idade
16.
BMC Bioinformatics ; 20(Suppl 9): 367, 2019 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-31757198

RESUMO

MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths. RESULTS: In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.


Assuntos
Algoritmos , Mapeamento de Sequências Contíguas , Metagenoma , Metagenômica , Probabilidade , Estatística como Assunto , Análise por Conglomerados , Bases de Dados Genéticas , Microbiota/genética
17.
BMC Genomics ; 20(1): 769, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31646964

RESUMO

BACKGROUND: Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatellite markers. However, the instability is identified by comparing the length of microsatellite repeats in tumor and normal samples. In this work, we developed a qualitative transcriptional signature to individually predict MSI status for right-sided colon cancer (RCC) based on tumor samples. RESULTS: Using RCC samples, based on the relative expression orderings (REOs) of gene pairs, we extracted a signature consisting of 10 gene pairs (10-GPS) to predict MSI status for RCC through a feature selection process. A sample is predicted as MSI when the gene expression orderings of at least 7 gene pairs vote for MSI; otherwise the microsatellite stability (MSS). The classification performance reached the largest F-score in the training dataset. This signature was verified in four independent datasets of RCCs with the F-scores of 1, 0.9630, 0.9412 and 0.8798, respectively. Additionally, the hierarchical clustering analyses and molecular features also supported the correctness of the reclassifications of the MSI status by 10-GPS. CONCLUSIONS: The qualitative transcriptional signature can be used to classify MSI status of RCC samples at the individualized level.


Assuntos
Neoplasias do Colo/genética , Instabilidade de Microssatélites , Transcriptoma , Algoritmos , Análise por Conglomerados , Biologia Computacional , Humanos
18.
J Chem Theory Comput ; 15(12): 6752-6759, 2019 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-31647864

RESUMO

Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This has remained a formidable task, despite a plethora of existing clustering methods. We present InfleCS, a novel method for extracting well-defined core states from free energy landscapes. The method is based on a Gaussian mixture free energy estimator and exploits the shape of the estimated density landscape. The core states that naturally arise from the clustering allow for detailed characterization of the conformational ensemble. The clustering quality is evaluated on three toy models with different properties, where the method is shown to consistently outperform other conventional and state-of-the-art clustering methods. Finally, the method is applied to a temperature enhanced molecular dynamics simulation of Ca2+-bound Calmodulin. Through the free energy landscape, we discover a pathway between a canonical and a compact state, revealing conformational changes driven by electrostatic interactions.


Assuntos
Calmodulina/química , Entropia , Simulação de Dinâmica Molecular , Análise por Conglomerados , Estrutura Molecular , Eletricidade Estática
19.
Parasit Vectors ; 12(1): 473, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31604471

RESUMO

BACKGROUND: A considerable amount of evidence has favored ecological host-fitting, rather than coevolution, as the main mechanism responsible for trypanosome divergence. Nevertheless, beyond the study of human pathogenic trypanosomes, the genetic basis of host specificity among trypanosomes isolated from forest-inhabiting hosts remains largely unknown. METHODS: To test possible scenarios on ecological host-fitting and coevolution, we combined a host capture recapture strategy with parasite genetic data and studied the genetic variation, population dynamics and phylogenetic relationships of Trypanosoma terrestris, a recently described trypanosome species isolated from lowland tapirs in the Brazilian Pantanal and Atlantic Forest biomes. RESULTS: We made inferences of T. terrestris population structure at three possible sources of genetic variation: geography, tapir hosts and 'putative' vectors. We found evidence of a bottleneck affecting the contemporary patterns of parasite genetic structure, resulting in little genetic diversity and no evidence of genetic structure among hosts or biomes. Despite this, a strongly divergent haplotype was recorded at a microgeographical scale in the landscape of Nhecolândia in the Pantanal. However, although tapirs are promoting the dispersion of the parasites through the landscape, neither geographical barriers nor tapir hosts were involved in the isolation of this haplotype. Taken together, these findings suggest that either host-switching promoted by putative vectors or declining tapir population densities are influencing the current parasite population dynamics and genetic structure. Similarly, phylogenetic analyses revealed that T. terrestris is strongly linked to the evolutionary history of its perissodactyl hosts, suggesting a coevolving scenario between Perissodactyla and their trypanosomes. Additionally, T. terrestris and T. grayi are closely related, further indicating that host-switching is a common feature promoting trypanosome evolution. CONCLUSIONS: This study provides two lines of evidence, both micro- and macroevolutionary, suggesting that both host-switching by ecological fitting and coevolution are two important and non-mutually-exclusive processes driving the evolution of trypanosomes. In line with other parasite systems, our results support that even in the face of host specialization and coevolution, host-switching may be common and is an important determinant of parasite diversification.


Assuntos
Perissodáctilos/parasitologia , Trypanosoma/classificação , Jacarés e Crocodilos/parasitologia , Animais , Teorema de Bayes , Coevolução Biológica , Análise por Conglomerados , Fenômenos Ecológicos e Ambientais , Ecossistema , Variação Genética , Genética Populacional , Interações Hospedeiro-Parasita , Filogenia , Dinâmica Populacional , Trypanosoma/genética , Trypanosoma/crescimento & desenvolvimento
20.
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi ; 31(4): 368-373, 2019 Sep 25.
Artigo em Chinês | MEDLINE | ID: mdl-31612670

RESUMO

OBJECTIVE: To develop a method for designing schistosomiasis surveillance sites, so as to improve the efficiency and quality of schitsosomiasis surveillance. METHODS: By using the minimum spanning tree-based Spatial Kluster Analysis by Tree Edge Removal (SKATER) method, spatially constrained clustering was performed upon 31 historical schistosomiasis-endemic counties (districts) in Anhui Province. A surveillance site was selected from each cluster to evaluate the representativeness and surveillance efficiency of these cluster-based surveillance sites for the endemic situation of schistosomiassi in Anhui Province, and to compare the surveillance efficiency with local national schistosomiasis surveillance sites. RESULTS: There was no significant difference in the environmental factors between the cluster-based schistosomiasis surveillance sites and the whole region, showing a high homogeneity. If the same number of schistosomiasis surveillance sites was selected, there was no significant difference between the cluster-based surveillance sites and national schistosomiasis surveillance sites in the efficiency of the mean risk and long-term trend of schistosomiasis surveillance in Anhui Province; however, the cluster-based surveillance sites were superior to the national schistosomiasis surveillance sites for the prediction and estimation of the endemic situation of schistosomiasis in the unmonitored areas. CONCLUSIONS: The SKATER-based selection of schistosomiasis surveillance sites may better represent the endemic situation of schistosomiasis in Anhui Province, which may serve as an effective supplement for the conventional method of selecting schistosomiasis surveillance sites.


Assuntos
Métodos Epidemiológicos , Vigilância da População , Esquistossomose , Caramujos , Animais , China/epidemiologia , Análise por Conglomerados , Humanos , Vigilância da População/métodos , Schistosoma/fisiologia , Esquistossomose/epidemiologia , Esquistossomose/prevenção & controle , Caramujos/parasitologia , Análise Espacial
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