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1.
BMC Ophthalmol ; 19(1): 169, 2019 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-31376834

RESUMO

BACKGROUND: Accurate alignment of toric intraocular lens (TIOL) to steep corneal astigmatic axis is important to achieve effective postoperative results. The authors compare the accuracy of astigmatism correction using automated and manual marking in TIOL implantation during cataract surgery. METHODS: One hundred thirty-two eyes with nuclear density from Grade 2 to 4 were randomly subdivided into 2 groups (automated and manual marking). All patients underwent manual marking and the steep axis was compared to SensoMotoric Instruments (SMI). After phacoemulsification, 62 patients underwent toric IOL implantation using the SMI and 70 patients underwent toric IOL implantation using manual marking. Intraoperative measurement was the steep axis difference. Clinical measurements included preoperative and postoperative best corrected visual acuity (BCVA), and TIOL axis. RESULTS: The intraoperative steep axis difference between SMI and manual marking was 7.86 ± 6.4 degrees. The difference between the preoperative steep axis and the postoperative TIOL axis using SMI (3.63 ± 1.12 degrees) was significantly lower than that using manual marking (8.29 ± 2.23 degrees) (P < 0.05). CONCLUSIONS: The steep axis measurements may be different when using SMI vs. manual marking. The SMI is more accurate than manual marking for TIOL implantation during cataract surgery. TRIAL REGISTRATION: Current Controlled Trials ISRCTN12294725 , Retrospectively registered, on 20 July 2018.


Assuntos
Automação/métodos , Catarata/fisiopatologia , Lentes Intraoculares , Cuidados Pré-Operatórios/métodos , Refração Ocular/fisiologia , Acuidade Visual , Biometria/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Desenho de Prótese
2.
Stud Health Technol Inform ; 264: 45-49, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31437882

RESUMO

The aim of the study was to build a proof-of-concept demonstratrating that big data technology could improve drug safety monitoring in a hospital and could help pharmacovigilance professionals to make data-driven targeted hypotheses on adverse drug events (ADEs) due to drug-drug interactions (DDI). We developed a DDI automatic detection system based on treatment data and laboratory tests from the electronic health records stored in the clinical data warehouse of Rennes academic hospital. We also used OrientDb, a graph database to store informations from five drug knowledge databases and Spark to perform analysis of potential interactions betweens drugs taken by hospitalized patients. Then, we developed a machine learning model to identify the patients in whom an ADE might have occurred because of a DDI. The DDI detection system worked efficiently and computation time was manageable. The system could be routinely employed for monitoring.


Assuntos
Interações de Medicamentos , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Registros Eletrônicos de Saúde , Automação , Big Data , Humanos , Farmacovigilância
4.
J Chromatogr A ; 1602: 350-358, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31257039

RESUMO

This work describes development of a quick and accurate online solid-phase extraction (SPE) liquid chromatography tandem mass spectrometry method for simultaneous determination of 87 emerging organic compounds, including 22 per- and polyfluoroalkyl substances, 58 pharmaceuticals and personal care products, and 7 organophosphorus flame retardants, in diverse water matrices. Considering the wide range of physicochemical properties for the target contaminants, efficient analysis in one injection is challenging. Thus, key extraction and analytical parameters, including online SPE sorbent, mobile phase additives, sample pH, loading solvent pH and composition, injection volume, and valve-switching time, were systematically optimized. The final conditions, namely a polymeric reversed-phase column with alkaline samples and an acidic loading solvent, provided satisfactory results for all target analytes compared to conventional methods that employ acidic samples for multi-residue analysis. The method detection limits (MDLs) ranged from 0.16 to 5.13 ng L-1 with 85% of MDLs lower than 2 ng L-1 for sample volumes of just 1.8 mL. The method also demonstrated satisfactory accuracy with 82% of analytes exhibiting 70-130% recovery. Importantly, only 30 min was required per sample. The optimized method was successfully applied to investigate the removal efficiency of emerging contaminants in a drinking water treatment plant and to analyze the environmental occurrence of target analytes. The method is sensitive, reliable, labor-saving, and cost effective, and therefore has the potential to advance large-scale environmental monitoring programs.


Assuntos
Cromatografia Líquida/métodos , Retardadores de Chama/análise , Fluorcarbonetos/análise , Produtos Domésticos/análise , Preparações Farmacêuticas/análise , Extração em Fase Sólida/métodos , Espectrometria de Massas em Tandem/métodos , Poluentes Químicos da Água/análise , Automação , Monitoramento Ambiental , Concentração de Íons de Hidrogênio , Internet , Limite de Detecção , Solventes/química , Fatores de Tempo
5.
J Chromatogr A ; 1602: 160-167, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31280942

RESUMO

An automatic flow-based system as a front end to liquid chromatography (LC) for on-line dynamic leaching of microplastic materials (polyethylene of medium density and poly(vinyl chloride)) with incurred phthalates and bisphenol A is herein presented. The microplastic particles were packed in a metal column holder, through which seawater was pumped continuously by resorting to advanced flow methodology. Each milliliter of the leachable (bioaccessible) fraction of chemical additives was preconcentrated on-line using a 10 mm-long octadecyl monolithic silica column placed in the sampling loop of the injection valve of a HPLC system that served concomitantly for analyte uptake and removal of the seawater matrix. After loading of the leachate fraction, the LC valve was switched to the inject position and the analytes were eluted and separated by a monolithic column (Onyx C18HD 100 × 4.6 mm) using an optimized acetonitrile/water gradient with UV detection at 240 nm. The automatic flow method including dynamic flow-through extraction, on-line sorptive preconcentration, and matrix clean-up was synchronized with the HPLC separation, which lasted ca. 9 min. The only two currently available multi-component certified reference materials (CRM) of microplastics (CRM-PE002 and CRM-PVC001) were used for method development and validation. Out of the eight regulated phthalates contained in the two CRMs, only the 2 most polar species, namely, dimethyl phthalate and diethyl phthalate as well as bisphenol A, were leached significantly by the seawater in less than 2 h, with bioaccessibility percentages of 51-100%. The leaching profiles were monitored and modeled with a first-order kinetic equation so as to determine the rate constants for desorption in a risk assessment scenario. Intermediate precision values of bioaccessibility data for three batches of CRMs were for the suite of targeted compounds ≤22%. This work for the first time reports a fully automatic flow method with infinite sink capacity (i.e., using a surplus of extracting solution) for the target species able to mimic the leaching of additives from plastic debris across the water body in marine settings under worst-case extraction conditions.


Assuntos
Cromatografia Líquida/métodos , Plásticos/análise , Água do Mar/química , Poluentes Químicos da Água/análise , Automação , Cromatografia Líquida de Alta Pressão , Cinética
6.
High Blood Press Cardiovasc Prev ; 26(4): 293-303, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31290085

RESUMO

INTRODUCTION: Automated office blood pressure (AOBP) has been proposed for blood pressure (BP) assessment in the office because it shows a strong association with the awake ambulatory BP. However, it remains unknown whether the presence or absence of an observer modulates AOBP readings. AIM: To determine the difference between unattended and attended AOBP measurements through systematic review and meta-analysis. METHODS: We searched the PubMed and the Cochrane Collaboration Library and we screened the references' list of relevant reports to identify potentially eligible articles. For included studies, quality was assessed by using the Quality Assessment for Diagnostic Accuracy Studies 2. The weighted pooled BP difference with 95% confidence interval (CI) between unattended and attended AOBP was estimated under the random effects model. RESULTS: Twelve studies (1762 subjects) were included. The systolic and diastolic BP difference between unattended and attended AOBP measurements was - 3.66 (- 6.58 to - 0.75) and - 1.67 (- 2.78 to - 0.55) mmHg, respectively. Heterogeneity across studies was high (I2 = 97,1% for systolic and I2 = 89% for diastolic BP, P < 0.001) and was partially determined by the sequence of performing unattended and attended BP measurements, the device used for AOBP, the geographic region in which studies were performed and the presence of a resting period before unattended AOBP. CONCLUSIONS: Due to the high heterogeneity, we cannot rely on the weighted pooled estimate. However, the available evidence suggests that attended AOBP yielded higher systolic and diastolic BP levels and it seems that the procedural methodology determines partially the statistical heterogeneity across studies.


Assuntos
Determinação da Pressão Arterial/métodos , Pressão Sanguínea , Hipertensão/diagnóstico , Visita a Consultório Médico , Hipertensão do Jaleco Branco/prevenção & controle , Adolescente , Adulto , Idoso , Automação , Determinação da Pressão Arterial/efeitos adversos , Feminino , Humanos , Hipertensão/fisiopatologia , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Reprodutibilidade dos Testes , Fatores de Risco , Hipertensão do Jaleco Branco/diagnóstico , Hipertensão do Jaleco Branco/etiologia , Hipertensão do Jaleco Branco/fisiopatologia , Adulto Jovem
8.
Stud Health Technol Inform ; 262: 47-50, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31349262

RESUMO

The use of automated dispensing cabinets (ADCs) to enhance medication processes in hospitals has been increasing recently. Studies evaluated the effects of this technology on patient safety, workflow efficiency and cost reduction. To evaluate factors affecting nurses' attitudes and acceptance of using ADCs, an online survey, including seven categories with closed-ended questions and one open-ended question, was developed based on technology acceptance model and instruments used in previous studies. Response rate was 29.4% of 1,062 nurses at King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia. Perceived usefulness, perceived ease of use, perceived usefulness to enhance control systems and training have positive effects on improving nurses' attitudes and increasing acceptance of using ADCs. Perceived risks had negative effects. The qualitative analysis of the open-ended responses supported these results and helped to identify many areas for improvement, especially in addressing perceived risks associated with the use of this technology.


Assuntos
Atitude do Pessoal de Saúde , Sistemas de Medicação no Hospital , Enfermeiras e Enfermeiros , Segurança do Paciente , Atitude , Automação , Humanos , Arábia Saudita , Inquéritos e Questionários
9.
Brain Nerve ; 71(7): 695-704, 2019 Jul.
Artigo em Japonês | MEDLINE | ID: mdl-31289243

RESUMO

There are strong expectations for automated driving. Whether the purpose is accident prevention or driver shortage, it is technically difficult to move fully automatically anywhere, and it is also difficult to establish business potential and merchantability through reasonable cost. In this paper, to properly understand automated driving, I will explain the current conditions and prospects.


Assuntos
Automação , Condução de Veículo , Automação/economia
10.
Medicine (Baltimore) ; 98(28): e16350, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31305425

RESUMO

Most of the recent studies have used fixed tube current while few investigators use automatic current selection (ACS) with iterative reconstruction (IR) techniques to reduce effective dose (ED) to < 1 mSv in low-dose chest computed tomography (LDCCT). We investigated whether image quality of lungs as produced by a fixed tube current (FTC) of 35 mAs can be maintained with ED < 1 mSv produced by ACS with IR techniques in LDCCT. A total of 32 participants were included. The LDCCT was performed by a FTC 35 mAs (with a kilovoltage peak of 120 kVp) in 16 participants (Group A), and by a DoseRight ACS in 16 participants (Group B). Their images were improved by IR technique. The ED was estimated by multiplying the individual dose length product (DLP) by the dose conversion factor. The image quality was assessed by the CT number, noise levels, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) of the regions of interest in the apex, upper lobe, and lower lobe of lung regions in the CT images. A t-test was used to evaluate the LDCCT image quality between the groups. The ED was significantly 49.2% lower in Group B than in Group A (0.71 ±â€Š0.05 mSv vs 1.40 ±â€Š0.02 mSv, P < .001). However, noise level, SNR, and CNR were not significantly different between Groups A and B, indicating the image quality was similar between two groups, or our setting parameters for DoseRight ACS with IR technique can achieve the image quality as good as obtained on the FTC 35 mAs with IR techniques. Our results suggest that the DoseRight ACS with IR technique reduces ED to lower than 1 mSv (averagely 0.71 mSv) yet maintains an image quality as good as produced by FTC 35 mAs with IR technique in normal BMI persons. The ACS setup thus is more preferable than the FTC to achieve the ALARA (as low as reasonably achievable) principle.


Assuntos
Pulmão/diagnóstico por imagem , Doses de Radiação , Tomografia Computadorizada por Raios X/métodos , Adulto , Idoso , Automação/métodos , Índice de Massa Corporal , Eletricidade , Feminino , Humanos , Pneumopatias/diagnóstico por imagem , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos
11.
BMC Bioinformatics ; 20(1): 393, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311505

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are small RNAs that regulate gene expression at a post-transcriptional level and are emerging as potentially important biomarkers for various disease states, including pancreatic cancer. In silico-based functional analysis of miRNAs usually consists of miRNA target prediction and functional enrichment analysis of miRNA targets. Since miRNA target prediction methods generate a large number of false positive target genes, further validation to narrow down interesting candidate miRNA targets is needed. One commonly used method correlates miRNA and mRNA expression to assess the regulatory effect of a particular miRNA. The aim of this study was to build a bioinformatics pipeline in R for miRNA functional analysis including correlation analyses between miRNA expression levels and its targets on mRNA and protein expression levels available from the cancer genome atlas (TCGA) and the cancer proteome atlas (TCPA). TCGA-derived expression data of specific mature miRNA isoforms from pancreatic cancer tissue was used. RESULTS: Fifteen circulating miRNAs with significantly altered expression levels detected in pancreatic cancer patients were queried separately in the pipeline. The pipeline generated predicted miRNA target genes, enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Predicted miRNA targets were evaluated by correlation analyses between each miRNA and its predicted targets. MiRNA functional analysis in combination with Kaplan-Meier survival analysis suggest that hsa-miR-885-5p could act as a tumor suppressor and should be validated as a potential prognostic biomarker in pancreatic cancer. CONCLUSIONS: Our miRNA functional analysis (miRFA) pipeline can serve as a valuable tool in biomarker discovery involving mature miRNAs associated with pancreatic cancer and could be developed to cover additional cancer types. Results for all mature miRNAs in TCGA pancreatic adenocarcinoma dataset can be studied and downloaded through a shiny web application at https://emmbor.shinyapps.io/mirfa/ .


Assuntos
MicroRNAs/metabolismo , Neoplasias Pancreáticas/genética , Proteínas/genética , Interface Usuário-Computador , Automação , Humanos , Estimativa de Kaplan-Meier , MicroRNAs/genética , Neoplasias Pancreáticas/mortalidade , Neoplasias Pancreáticas/patologia , Mapas de Interação de Proteínas , Proteínas/metabolismo , RNA Mensageiro/metabolismo
12.
J Chromatogr A ; 1602: 458-466, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31153601

RESUMO

Bioanalytical questions are more and more solved by bioassays directly in situ the planar separation. If compared to chemical derivatization in situ, several reagent applications on the same chromatogram make the workflow for enzymatic and biological assays more complex. Hence, if compared to piezoelectric spraying of chemical derivatization reagents, an assay transfer to the piezoelectric spraying technique was much more challenging. Important aspects were investigated, i.e., plate pre-wetting, spraying nozzle type and applied volumes for microorganism suspension as well as enzyme and substrate-chromogenic solutions. Finally, with the newly developed piezoelectric spraying procedures for the application of biological (Aliivibrio fischeri) and enzymatic (acetyl- and butyrylcholinesterase) assays, several obstacles of the state-of-the-art automated immersion were avoided such as the (1) required high volumes of solutions, (2) tailing of highly water-soluble zones upon slow plate withdrawal, (3) zone distortion or shift observed after previous buffer salt applications or long/slow immersion times/speeds, (4) gradual inactivation of the enzyme solution along with its ongoing re-use, and (5) lack of covering the whole plate surface. The benchmarking of both techniques also showed that simplicity remains the key argument for immersion. As proof of concept, piezoelectrically sprayed autograms were compared with those of immersion, by taking the example of Peganum harmala (P. h.) seed extract. The plate background and thus homogeneity of the applied solutions were found to be almost comparable. Three bands among the pronounced fluorescent bands were responsible for the most antibacterial activity of P. h. seed extract in the A. fischeri bioassay and were also inhibiting the AChE. These AChE and three further BChE inhibitors were detected, whereby the AChE inhibition was twice as strong as the BChE inhibition. By their in situ HRMS spectra, the active zones in the P. h. seed extract were assigned to be the AChE-inhibiting ß-carboline alkaloids, harmine, harmaline and ruine, as well as the BChE-inhibiting quinazoline alkaloids, vasicine and deoxyvasicine, and the ß-carboline alkaloid harmol. For the first time, the found inhibitors were calculated equivalently to the well-known ChE-inhibitor physostigmine, and thus, piezoelectric spraying was proven to be suited for quantifications.


Assuntos
Cromatografia/métodos , Eletricidade , Ensaios Enzimáticos/métodos , Sementes/química , Acetilcolinesterase/metabolismo , Aliivibrio fischeri/fisiologia , Automação , Bioensaio , Butirilcolinesterase/metabolismo , Cromatografia em Camada Delgada , Espectrometria de Massas , Peganum/química , Extratos Vegetais/química
13.
Biochem Med (Zagreb) ; 29(2): 021002, 2019 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-31223268

RESUMO

Introduction: Blood coagulation tests (BCT) are very important for clinicians to diagnose bleeding or thrombotic disorders and to monitor anticoagulant therapy. Case description: On a Saturday morning, a laboratory technician noted an abrupt rise in the number of coagulation error messages on our ALC TOP analysers. Visual inspection revealed the presence of partially and/or fully clotted citrate tubes and prompted the clinical biologist to further investigate a potential preanalytical cause. Considered causes: Partially or fully clotted blood in citrate tubes can have multiple causes including improper mixing of the tube, under- or overfilling or combining blood samples from different tubes into one citrate tube. What happened: The affected citrate tubes originated mostly from the same clinical departments. Moreover, all the affected tubes shared the same lot number (1 of 7 in use at the time). Visual inspection of 7 unopened boxes of 100 citrate tubes of this lot number revealed one box with nine completely empty and two partially filled tubes and one box with two partially filled tubes. No under-filled tubes were found in the other 5 boxes. Discussion: The blood to additive ratio is crucial for BCT. A sudden rise in clot errors should trigger a thorough investigation to identify the cause. Main lesson: Laboratories should regularly monitor and evaluate the percentage of clotted samples as a quality indicator at scheduled time points. A problem with the volume of additive in citrate tubes should be considered as a possible cause.


Assuntos
Automação , Testes de Coagulação Sanguínea , Anticoagulantes/farmacologia , Coagulação Sanguínea/efeitos dos fármacos , Coleta de Amostras Sanguíneas , Humanos
14.
BMC Bioinformatics ; 20(1): 364, 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31253090

RESUMO

BACKGROUND: Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as versed in programing language, but want to perform these operations hands on, there is a lengthy learning curve to utilize the vast number of programs available for these analyses. RESULTS: In an effort to streamline the entire process with easy-to-use steps for scientists working with big data, the Odyssey pipeline was developed. Odyssey is a simplified, efficient, semi-automated genome-wide imputation and analysis pipeline, which prepares raw genetic data, performs pre-imputation quality control, phasing, imputation, post-imputation quality control, population stratification analysis, and genome-wide association with statistical data analysis, including result visualization. Odyssey is a pipeline that integrates programs such as PLINK, SHAPEIT, Eagle, IMPUTE, Minimac, and several R packages, to create a seamless, easy-to-use, and modular workflow controlled via a single user-friendly configuration file. Odyssey was built with compatibility in mind, and thus utilizes the Singularity container solution, which can be run on Linux, MacOS, and Windows platforms. It is also easily scalable from a simple desktop to a High-Performance System (HPS). CONCLUSION: Odyssey facilitates efficient and fast genome-wide association analysis automation and can go from raw genetic data to genome: phenome association visualization and analyses results in 3-8 h on average, depending on the input data, choice of programs within the pipeline and available computer resources. Odyssey was built to be flexible, portable, compatible, scalable, and easy to setup. Biologists less familiar with programing can now work hands on with their own big data using this easy-to-use pipeline.


Assuntos
Biologia Computacional/métodos , Interpretação Estatística de Dados , Estudo de Associação Genômica Ampla , Automação , Software
15.
BMC Bioinformatics ; 20(1): 343, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208323

RESUMO

BACKGROUND: Protein based therapeutics are one of the fastest growing classes of novel medical interventions in areas such as cancer, infectious disease, and inflammation. Protein engineering plays an important role in the optimization of desired therapeutic properties such as reducing immunogenicity, increasing stability for storage, increasing target specificity, etc. One category of protein therapeutics is nature-inspired bioengineered cystine-dense peptides (CDPs) for various biological targets. These engineered proteins are often further modified by synthetic chemistry. For example, candidate mini-proteins can be conjugated into active small molecule drugs. We refer to modified mini-proteins as "Optides" (Optimized peptides). To efficiently serve the multidisciplinary lab scientists with varied therapeutic portfolio research goals in a non-commercial setting, a cost effective extendable laboratory information management system (LIMS) is/was needed. RESULTS: We have developed a LIMS named Optide-Hunter for a generalized engineered protein compounds workflow that tracks entities and assays from creation to preclinical experiments. The implementation and custom modules are built using LabKey server, which is an Open Source platform for scientific data integration and analysis. Optide-Hunter contains a compound registry, in-silico assays, high throughput production, large-scale production, in vivo assays and data extraction from a specimen-tracking database. It is used to store, extract, and view data for various therapeutics projects. Optide-Hunter also includes external processing stand-alone software (HPLCPeakClassifierApp) for automated chromatogram classification. The HPLCPeakClassifierApp is used for pre-processing of HPLC data prior to loading to Optide-Hunter. The custom implementation is done using data transformation modules in R, SQL, javascript, and java and is Open Source to assist new users in customizing it for their unique workflows. Instructions for exploring a deployed version of Optide-Hunter can be found at https://www.labkey.com/case%20study/optide-hunter CONCLUSION: The Optide-Hunter LIMS system is designed and built to track the process of engineering, producing and prioritizing protein therapeutic candidates. It can be easily adapted and extended for use in small or large research laboratories where multidisciplinary scientists are collaborating to engineer compounds for potential therapeutic or protein science applications. Open Source exploration of Optide-Hunter can help any bioinformatics scientist adapt, extend, and deploy an equivalent system tailored to each laboratory's workflow.


Assuntos
Laboratórios , Engenharia de Proteínas , Proteínas/uso terapêutico , Software , Automação , Humanos , Gestão da Informação , Interface Usuário-Computador , Fluxo de Trabalho
16.
BMC Bioinformatics ; 20(1): 326, 2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31195977

RESUMO

BACKGROUND: An important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Due to the necessity of human involvement in the process, current particle picking techniques are time consuming and often result in many false positives and negatives. Adjusting the parameters to eliminate false positives often excludes true particles in certain orientations. The supervised machine learning (e.g. deep learning) methods for particle picking often need a large training dataset, which requires extensive manual annotation. Other reference-dependent methods rely on low-resolution templates for particle detection, matching and picking, and therefore, are not fully automated. These issues motivate us to develop a fully automated, unbiased framework for particle picking. RESULTS: We design a fully automated, unsupervised approach for single particle picking in cryo-EM micrographs. Our approach consists of three stages: image preprocessing, particle clustering, and particle picking. The image preprocessing is based on multiple techniques including: image averaging, normalization, cryo-EM image contrast enhancement correction (CEC), histogram equalization, restoration, adaptive histogram equalization, guided image filtering, and morphological operations. Image preprocessing significantly improves the quality of original cryo-EM images. Our particle clustering method is based on an intensity distribution model which is much faster and more accurate than traditional K-means and Fuzzy C-Means (FCM) algorithms for single particle clustering. Our particle picking method, based on image cleaning and shape detection with a modified Circular Hough Transform algorithm, effectively detects the shape and the center of each particle and creates a bounding box encapsulating the particles. CONCLUSIONS: AutoCryoPicker can automatically and effectively recognize particle-like objects from noisy cryo-EM micrographs without the need of labeled training data or human intervention making it a useful tool for cryo-EM protein structure determination.


Assuntos
Algoritmos , Microscopia Crioeletrônica/métodos , Processamento de Imagem Assistida por Computador/métodos , Aprendizado de Máquina não Supervisionado , Automação , Análise por Conglomerados , Software
17.
Anal Bioanal Chem ; 411(17): 3789-3800, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31161320

RESUMO

MicroRNAs (miRNAs) in a blood sample are usually measured by quantitative reverse transcription PCR (qRT-PCR), microarray, and next-generation sequencing (NGS) which requires time-consuming pre-treatment, manual operation, and a stand-alone instrument. To overcome these disadvantages, miRNA testing has been developed using the automated analyzers routinely used in clinical laboratories. An isothermal DNA amplification reaction was adapted to a fully automated immunoassay analyzer that conducts extraction, amplification, and detection processes at 37 °C in 44 min. In a reaction vessel, a pre-designed single-stranded signal DNA was amplified in the presence of miRNA, using DNA templates, DNA polymerase, and nicking endonuclease. Then, the amplified signal DNA was hybridized by one DNA probe attached to a magnetic particle and another DNA probe labeled with acridinium ester. After the chemiluminescence reaction, luminescence intensity was automatically measured. The automated assays of cancer-related miRNAs were implemented on the analyzer with throughput of 66 tests per hour. In the assays with one-step amplification, three miRNAs (miR-21-5p, miR-18a-5p, and miR-500a-3p) at concentrations lower than 100 fM were automatically detected and the cross reactivity for miR-21-5p with fifteen similar miRNAs was not higher than 0.02%. In the assay with two-step amplification, detection sensitivity and amplification rate for miR-21-5p were 3 fM and 103-fold, respectively. The coefficient of variations (CVs) in the measurement at the target concentrations from 5 fM to 1000 pM were less than 8%. Furthermore, we also achieved automated nucleic acid detection in human serum. The proposed fully automated miRNA assays showed high sensitivity, low cross reactivity, and reproducibility suitable for clinical use. Graphical abstract.


Assuntos
Imunoensaio/métodos , MicroRNAs/análise , Técnicas de Amplificação de Ácido Nucleico/métodos , Automação , Humanos , Luminescência
18.
J Chromatogr A ; 1602: 419-424, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31160094

RESUMO

This paper reports on an automated temperature-programmed headspace GC technique for the determination of gelatinization temperature of starch. 1-butanol was used as a tracer and added to the starch-solution for the test. Based on measuring the GC signal of 1-butanol in the headspace with the temperature increasing, two transition points (corresponding to the onset temperature and the ending temperature of starch gelatinization) were observed by plotting the GC signal of 1-butanol vs. the temperature. The results showed that the method has a good measurement precision (the standard deviation < 1 °C) and accuracy (the average relative differences = 3.9%, compared to a standard reference method). The present method is simple and suitable for the gelatinization temperature testing for starch samples.


Assuntos
Cromatografia Gasosa/métodos , Amido/química , Temperatura Ambiente , 1-Butanol/química , Automação , Reprodutibilidade dos Testes , Fatores de Tempo
19.
J Chromatogr A ; 1601: 95-103, 2019 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-31208795

RESUMO

Fully automated dried blood spot (DBS) extraction systems, online coupled to standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) configurations, decrease the hands-on time associated with conventional DBS analysis, resulting in a higher sample throughput, making the technique more compatible with a high-capacity bioanalytical workflow. The aim of this study was to develop and validate an LC-MS/MS method, using a DBS-MS 500 autosampler, for the determination and quantification of four anti-epileptic drugs (carbamazepine, valproic acid, phenobarbital and phenytoin) and one active metabolite (carbamazepine-10,11-epoxide) in DBS samples. Method development included thorough optimization of the fully automated extraction procedure (i.e. extraction solvent, extraction (loop) volume, internal standard application, internal standard drying time, etc.). The method was fully validated based on international guidelines. Accuracy (%bias), as well as precision (%RSD) (with a single exception) were below 13%. Neither carry-over nor unacceptable interferences were observed. All compounds were stable in DBS for at least 1 month when stored at room temperature, 4 °C and -20 °C and for at least 4 days when stored at 60 °C. Internal standard-corrected matrix effects were below 8%, with %RSDs below 9.1%. Reproducible relative recovery values (around 60% for all analytes) were obtained and the effect of the hematocrit on the relative recovery was overall limited. Successful application on capillary patient samples originating from developing countries demonstrated the applicability of the developed procedure in a remote setting.


Assuntos
Anticonvulsivantes/análise , Teste em Amostras de Sangue Seco , Monitoramento de Medicamentos/métodos , Anticonvulsivantes/sangue , Automação , Cromatografia Líquida , Teste em Amostras de Sangue Seco/normas , Monitoramento de Medicamentos/instrumentação , Humanos , Reprodutibilidade dos Testes , Espectrometria de Massas em Tandem
20.
Talanta ; 200: 177-185, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31036171

RESUMO

Paper based assays are paving the way to automated, simplified, robust and cost-effective point of care testing (POCT). We propose a method for fabricating three dimensional (3D) microfluidic paper based analytical devices (µPADs) via combining thin adhesive films and paper folding, which avoids the use of cellulose powders and the complex folding sequence and simultaneously permits assays in several layers. To demonstrate the effectiveness of this approach, a 3DµPADs was designed to conduct more assays on a small footprint, allowing dual colorimetric and electrochemical detections. More importantly, we further developed a 3D platform for implementing automated and multiplexed ELISA in parallel, since ELISA, a routine and standard laboratory method, has rarely been used in practical analyses outside of the laboratory. In this configuration, complex and multistep diagnostic assays can be carried out with the addition of the sample and buffer in a simple fashion. Using Troponin I as model, the device showed a broad dynamic range of detection with a detection limit of 0.35 ng/mL. Thus, the developed platforms allow for various assays to be cost-effectively carried out on a single 3D device, showing great potential in an academic setting and point of care testing under resource-poor conditions.


Assuntos
Automação , Papel , Troponina I/análise , Colorimetria/economia , Colorimetria/instrumentação , Técnicas Eletroquímicas/economia , Técnicas Eletroquímicas/instrumentação , Técnicas Analíticas Microfluídicas/economia , Técnicas Analíticas Microfluídicas/instrumentação
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