Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 28.623
Filtrar
3.
PLoS One ; 15(11): e0241959, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33166373

RESUMO

The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In pooled sample testing, multiple samples are combined (or pooled) together and tested as a single unit. If the pool is positive, the individual samples can then be individually tested to identify the positive case(s). Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert® Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the limit of detection of this assay was comparable to laboratory-developed reverse-transcription quantitative PCR SARS-CoV-2 tests, with observed detection below 100 copies/mL. The Xpert® Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were pooled in groups of six. Based on these data, we recommend the adoption of pooled testing with the Xpert® Xpress SARS-CoV-2 assay where warranted based on public health needs. The suggested number of samples per pool, or the pooling depth, is unique for each point-of-care testing site and can be determined by the positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , RNA Viral/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Humanos , Pandemias , Pneumonia Viral/virologia , Testes Imediatos , RNA Viral/genética , Kit de Reagentes para Diagnóstico , Manejo de Espécimes , Carga Viral
5.
PLoS One ; 15(11): e0240652, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33147228

RESUMO

In the current COVID19 crisis many national healthcare systems are confronted with an acute shortage of tests for confirming SARS-CoV-2 infections. For low overall infection levels in the population the pooling of samples can drastically amplify the testing capacity. Here we present a formula to estimate the optimal group-size for pooling, the efficiency gain (tested persons per test), and the expected upper bound of missed infections in pooled testing, all as a function of the population-wide infection levels and the false negative/positive rates of the currently used PCR tests. Assuming an infection level of 0.1% and a false negative rate of 2%, the optimal pool-size is about 34, and an efficiency gain of about 15 tested persons per test is possible. For an infection level of 1% the optimal pool-size is 11, the efficiency gain is 5.1 tested persons per test. For an infection level of 10% the optimal pool-size reduces to about 4, the efficiency gain is about 1.7 tested persons per test. For infection levels of 30% and higher there is no more benefit from pooling. To see to what extent replicates of the pooled tests improve the estimate of the maximal number of missed infections, we present results for 1 to 5 replicates.


Assuntos
Betacoronavirus/genética , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Testes Diagnósticos de Rotina/métodos , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/epidemiologia , Manejo de Espécimes/métodos , Infecções por Coronavirus/virologia , Humanos , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase/métodos , RNA Viral/genética
6.
J Breath Res ; 14(4): 042003, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-33021206

RESUMO

Diagnosis of SARS-COV-2 infection (COVID-19) is currently based on detection of the viral RNA in nasopharyngeal swab samples by reverse transcription polymerase chain reaction (RT-PCR). However, sampling via nasopharyngeal swabs frequently provokes sneezing or coughing, which results in increased risk of the viral dissemination and environmental contamination. Furthermore, the sensitivity associated with the PCR tests s limited to 60%-70%, which is mainly attributable to technical deficiency in sampling. Given that the disease is transmitted via exhaled aerosol and droplets, and that the exhaled breath condensate (EBC) is the established modality for sampling exhaled aerosol, detection of the viral RNA in EBC is a promising approach for safe and efficient diagnosis of the disease. Subjects are those patients who are diagnosed with COVID-19 by positive nasopharyngeal swab PCR test and admitted to Saitama Medical Center, Japan. EBC samples will be collected using an R-tube® or R-tubeVent® device. Collected EBC samples will be introduced into a nucleic acid purifier. The purified nucleic acids will undergo amplification through RT-PCR for detection and quantification of SARS-COV-2 RNA. To date we have collected eight samples from seven subjects. Among them, two samples from two subjects tested positive for SARS-COV-2 RNA by the RT-PCR. Reflecting the second wave of COVID-19 prevalence in Japan, new admissions of COVID-19 patients to the Saitama Medical Center are increasing, and we are expecting to collect at least 50 EBC samples from 25 patients before the end of this year.


Assuntos
Testes Respiratórios/instrumentação , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Aerossóis/análise , Betacoronavirus , Técnicas de Laboratório Clínico , Tosse , Expiração , Humanos , Japão , Pandemias , RNA Viral/análise , Projetos de Pesquisa , Manejo de Espécimes , Carga Viral
7.
Zootaxa ; 4809(3): zootaxa.4809.3.4, 2020 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-33055924

RESUMO

The identity of Nepinnotheres vicajii (Chhapgar, 1957) (described as Pinnotheres vicajii) (Pinnotheridae), a pea crab associated with the bivalve Marcia recens (Holten, 1802), is clarified. On the basis of re-diagnosis of holotype male and freshly collected female specimens from its type locality, P. vicajii is now assigned to Arcotheres Manning, 1993. A second poorly known species from India, Arcotheres casta (Antony Kuttyamma, 1971), originally collected from Meretrix casta (Gmelin, 1791) is also synonymized with A. vicajii.


Assuntos
Bivalves , Braquiúros , Animais , Feminino , Índia , Masculino , Manejo de Espécimes
8.
Biochem Med (Zagreb) ; 30(3): 030403, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33071554

RESUMO

To fight the virus SARS-CoV-2 spread to Europe from China and to give support to the collapsed public health system, the Spanish Health Authorities developed a field hospital located in the facilities of Madrid exhibition centre (IFEMA) to admit and treat patients diagnosed with SARS-CoV-2 infectious disease (COVID-19). The Department of Laboratory Medicine of La Paz University Hospital in Madrid (LMD-HULP) was designated to provide laboratory services. Due to the emergency, the IFEMA field hospital had to be prepared for patient admission in less than 1 week and the laboratory professionals had to collaborate in a multidisciplinary group to assure that resources were available to start on time. The LMD-HULP participated together with the managers in the design of the tests portfolio and the integration of the healthcare information systems (IS) (hospital IS, laboratory IS and POCT management system). Laboratorians developed a strategy to quickly train clinicians and nurses on test requests, sample collection procedures and management/handling of the POCT blood gas analyser both by written materials and training videos. The IFEMA´s preanalytical unit managed 3782 requests, and more than 11,000 samples from March 27th to April 30th. Furthermore, 1151 samples were measured by blood gas analysers. In conclusion, laboratory professionals must be resilient and have to respond timely in emergencies as this pandemic. The lab's personnel selection, design and monitoring indicators to maintain and further improve the quality and value of laboratory services is crucial to support medical decision making and provide better patient care.


Assuntos
Betacoronavirus , Infecções por Coronavirus , Unidades Móveis de Saúde/organização & administração , Pandemias , Pneumonia Viral , Cidades , Sistemas de Informação em Laboratório Clínico/organização & administração , Infecções por Coronavirus/epidemiologia , Assistência à Saúde , Necessidades e Demandas de Serviços de Saúde , Número de Leitos em Hospital , Sistemas de Informação Hospitalar/organização & administração , Hospitais Universitários/organização & administração , Humanos , Laboratórios Hospitalares/organização & administração , Recursos Humanos em Hospital/educação , Pneumonia Viral/epidemiologia , Testes Imediatos/organização & administração , Garantia da Qualidade dos Cuidados de Saúde/organização & administração , Espanha , Manejo de Espécimes
9.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1958-1961, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018386

RESUMO

Detailed extraction of retinal vessel morphology is of great significance in many clinical applications. In this paper, we propose a retinal image segmentation method, called MAU-Net, which is based on the U-net structure and takes advantages of both modulated deformable convolution and dual attention modules to realize vessels segmentation. Specifically, based on the classic U-shaped architecture, our network introduces the Modulated Deformable Convolutional (MDC) block as encoding and decoding unit to model vessels with various shapes and deformations. In addition, in order to obtain better feature presentations, we aggregate the outputs of dual attention modules: the position attention module (PAM) and channel attention module (CAM). On three publicly available datasets: DRIVE, STARE and CHASEDB1, we have achieved superior performance to other algorithms. Quantitative and qualitative experimental results show that our MAU-Net can effectively and accurately accomplish the retinal vessels segmentation task.


Assuntos
Processamento de Imagem Assistida por Computador , Vasos Retinianos , Algoritmos , Retina/diagnóstico por imagem , Vasos Retinianos/diagnóstico por imagem , Manejo de Espécimes
10.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 2019-2022, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018400

RESUMO

Echocardiography is the modality of choice for the assessment of left ventricle function. Left ventricle is responsible for pumping blood rich in oxygen to all body parts. Segmentation of this chamber from echocardiographic images is a challenging task, due to the ambiguous boundary and inhomogeneous intensity distribution. In this paper we propose a novel deep learning model named ResDUnet. The model is based on U-net incorporated with dilated convolution, where residual blocks are employed instead of the basic U-net units to ease the training process. Each block is enriched with squeeze and excitation unit for channel-wise attention and adaptive feature re-calibration. To tackle the problem of left ventricle shape and size variability, we chose to enrich the process of feature concatenation in U-net by integrating feature maps generated by cascaded dilation. Cascaded dilation broadens the receptive field size in comparison with traditional convolution, which allows the generation of multi-scale information which in turn results in a more robust segmentation. Performance measures were evaluated on a publicly available dataset of 500 patients with large variability in terms of quality and patients pathology. The proposed model shows a dice similarity increase of 8.4% when compared to deeplabv3 and 1.2% when compared to the basic U-net architecture. Experimental results demonstrate the potential use in clinical domain.


Assuntos
Ecocardiografia , Ventrículos do Coração , Ventrículos do Coração/diagnóstico por imagem , Humanos , Manejo de Espécimes
11.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 2561-2564, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-33018529

RESUMO

OBJECTIVE: We investigate an optimized non-uniform sampling strategy for blood pressure time series from the operating room (OR). Our aim is to obtain an approximate bound on the achievable reconstruction fidelity given an average sampling rate constraint. METHODS: Our data set consists of 117 hours of recordings of continuous invasive blood pressure from 28 surgery patients. We evaluate the root mean squared error (RMSE) of the zero-order hold sampling reconstruction of the blood pressure time series. We quantitatively compare the errors achieved by uniform versus optimized non-uniform sample placements for several average sample rates, ranging from 2 to 24 measurements per hour. RESULTS: An optimized non-uniform measurement schedule can lead to approximately 50% reduction of reconstruction RMSE for systolic, mean, and diastolic blood pressure time series with respect to uniform sampling, while maintaining the same average sampling rate.


Assuntos
Determinação da Pressão Arterial , Salas Cirúrgicas , Pressão Sanguínea , Humanos , Manejo de Espécimes , Sístole
13.
Bol Med Hosp Infant Mex ; 77(5): 228-233, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33064678

RESUMO

Background: Diagnostic testing for coronavirus disease (COVID)-19 is performed using nasopharyngeal swabs. This type of sampling is uncomfortable for the patient, dangerous for health workers, and its high demand has led to a global shortage of swabs. One of the alternative specimens is saliva. However, the optimal conditions for the test have not been established. Methods: Reverse transcription-polymerase chain reaction was used to detect the viral genome in saliva samples kept at room temperature, in the fridge or frozen for 2 days. In addition, the influence of brushing teeth and feeding on the detection of the virus in saliva was addressed. Finally, the efficiency of saliva in revealing the presence of the virus during the hospitalization period was determined in children. Results: The viral genome was consistently detected regardless of the storage conditions of saliva samples. Brushing teeth and feeding did not influence the sensitivity of the test. In hospitalized children, positive results were obtained only during the early days. Conclusions: These results support the idea of the use of saliva as an alternative specimen for diagnostic testing for COVID-19. The viral genome is stable and endures perturbations in the oral cavity. However, clearance of the virus from the mouth during the infection may limit the use of the test only to the early stages of the disease.


Assuntos
Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Saliva/virologia , Adolescente , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Pré-Escolar , Infecções por Coronavirus/virologia , Feminino , Genoma Viral , Hospitalização , Humanos , Masculino , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/virologia , Sensibilidade e Especificidade , Manejo de Espécimes/métodos , Temperatura , Fatores de Tempo
14.
PLoS One ; 15(10): e0241100, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33108384

RESUMO

Both polyester and foam nasal swabs were collected from convalescent COVID-19 patients at a single visit and stored in viral transport media (VTM), saline or dry. Sensitivity of each swab material and media combination were estimated, three by three tables were constructed to measure polyester and foam concordance, and cycle threshold (Ct) values were compared. 126 visits had polyester and foam swabs stored in viral transport media (VTM), 51 had swabs stored in saline, and 63 had a foam swab in VTM and a polyester swab stored in a dry tube. Polyester and foam swabs had an estimated sensitivity of 87.3% and 94.5% respectively in VTM, 87.5% and 93.8% respectively in saline, and 75.0% and 90.6% respectively for dry polyester and foam VTM. Polyester and foam Ct values were correlated, but polyester showed decreased performance for cases with a viral load near the detection threshold and higher Ct values on average.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico , Convalescença , Infecções por Coronavirus/virologia , Cavidade Nasal/virologia , Pandemias , Pneumonia Viral/virologia , Poliésteres , Poliuretanos , Manejo de Espécimes/instrumentação , Adulto , Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Meios de Cultura , Equipamentos Descartáveis/provisão & distribução , Feminino , Pessoal de Saúde , Humanos , Masculino , Pessoa de Meia-Idade , Pneumonia Viral/diagnóstico , RNA Viral/análise , Distribuição Aleatória , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Solução Salina , Sensibilidade e Especificidade , Manejo de Espécimes/métodos , Carga Viral
15.
Viruses ; 12(11)2020 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-33114233

RESUMO

Critical to facilitating SARS-CoV-2 point-of-care (POC) testing is assurance that viruses present in specimens are inactivated onsite prior to processing. Here, we conducted experiments to determine the virucidal activity of commercially available Viral Transport Mediums (VTMs) to inactivate SARS-CoV-2. Independent testing methods for viral inactivation testing were applied, including a previously described World Health Organization (WHO) protocol, in addition to a buffer exchange method where the virus is physically separated from the VTM post exposure. The latter method enables sensitive detection of viral viability at higher viral titre when incubated with VTM. We demonstrate that VTM formulations, Primestore® Molecular Transport Medium (MTM) and COPAN eNAT™ completely inactivate high-titre SARS-CoV-2 virus (>1 × 107 copies/mL) and are compatible with POC processing. Furthermore, full viral inactivation was rapidly achieved in as little as 2 min of VTM exposure. We conclude that adding certain VTM formulations as a first step post specimen collection will render SARS-CoV-2 non-infectious for transport, or for further in-field POC molecular testing using rapid turnaround GeneXpert platforms or equivalent.


Assuntos
Betacoronavirus/isolamento & purificação , Testes Imediatos , Manejo de Espécimes , Inativação de Vírus , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Meios de Cultura/análise , Meios de Cultura/farmacologia , Humanos , Testes Imediatos/normas , Manejo de Espécimes/métodos , Manejo de Espécimes/normas , Carga Viral/efeitos dos fármacos , Inativação de Vírus/efeitos dos fármacos
16.
Viruses ; 12(10)2020 10 20.
Artigo em Inglês | MEDLINE | ID: mdl-33092065

RESUMO

BACKGROUND: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral load and shedding. METHODS: Optimal assay conditions and analytical sensitivity were established for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients; 50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were also analysed. RESULTS: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection down to 1 TCID50/mL (corresponding to 4 × 103 copies (cp)/mL) was observed. No crossreaction with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771-0.891), and high correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples, respectively, collected between 60 and 100 DSO. CONCLUSIONS: Simplexa™ COVID-19 Direct assays on OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to NPS for diagnosis and monitoring SARS-CoV-2 shedding.


Assuntos
Betacoronavirus/fisiologia , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/virologia , Pneumonia Viral/virologia , Eliminação de Partículas Virais/fisiologia , Adulto , Idoso , Betacoronavirus/genética , Líquidos Corporais/virologia , Infecções por Coronavirus/diagnóstico , Testes Diagnósticos de Rotina , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/métodos , Pandemias , Faringe/virologia , Pneumonia Viral/diagnóstico , RNA Viral/análise , Sensibilidade e Especificidade , Manejo de Espécimes , Carga Viral
17.
J Breath Res ; 14(4): 047105, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-33021205

RESUMO

The influence of breath sampling on exhaled carbon monoxide (eCO) and related pulmonary gas exchange parameters is investigated in a study with 32 healthy non-smokers. Mid-infrared tunable diode laser absorption spectroscopy and well-controlled online sampling is used to precisely measure mouth- and nose-exhaled CO expirograms at exhalation flow rates (EFRs) of 250, 120 and 60 ml s-1, and for 10 s of breath-holding followed by exhalation at 120 ml s-1. A trumpet model with axial diffusion is employed to fit simulated exhalation profiles to the experimental expirograms, which provides equilibrium airway and alveolar CO concentrations and the average lung diffusing capacity in addition to end-tidal concentrations. For all breathing maneuvers, excellent agreement is found between mouth- and nose-exhaled end-tidal CO (ETCO), and the individual values for ETCO and alveolar diffusing capacity are consistent across maneuvers. The eCO parameters clearly show a dependence on EFR, where the lung diffusing capacity increases with EFR, while ETCO slightly decreases. End-tidal CO is largely independent of ambient air CO and alveolar diffusing capacity. While airway CO is slightly higher than, and correlates strongly with, ambient air CO, and there is a weak correlation with ETCO, the results point to negligible endogenous airway CO production in healthy subjects. An EFR of around 120 ml s-1 can be recommended for clinical eCO measurements. The employed method provides means to measure variations in endogenous CO, which can improve the interpretation of exhaled CO concentrations and the diagnostic value of eCO tests in clinical studies. Clinical trial registration number: 2017/306-31.


Assuntos
Testes Respiratórios/métodos , Monóxido de Carbono/análise , Expiração , Manejo de Espécimes , Adulto , Feminino , Heme/metabolismo , Humanos , Masculino , Boca , Nariz , Reologia
18.
J Breath Res ; 14(4): 046012, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-33021213

RESUMO

Breath analysis holds promise for non-invasive in vivo monitoring of disease related processes. However, physiological parameters may considerably affect profiles of exhaled volatile organic substances (VOCs). Volatile substances can be released via alveoli, bronchial mucosa or from the upper airways. The aim of this study was the systematic investigation of the influence of different sampling sites in the respiratory tract on VOC concentration profiles by means of a novel experimental setup. After ethical approval, breath samples were collected from 25 patients undergoing bronchoscopy for endobronchial ultrasound or bronchoscopic lung volume reduction from different sites in the airways. All patients had total intravenous anaesthesia under pressure-controlled ventilation. If necessary, respiratory parameters were adjusted to keep PETCO2 = 35-45 mm Hg. 30 ml gas were withdrawn at six sampling sites by means of gastight glass syringes: S1 = Room air, S2 = Inspiration, S3 = Endotracheal tube, S4 = Trachea, S5 = Right B6 segment, S6 = Left B6 segment (S4-S6 through the bronchoscope channel). 10 ml were used for VOC analysis, 20 ml for PCO2 determination. Samples were preconcentrated by solid-phase micro-extraction (SPME) and analysed by gas chromatography-mass spectrometry (GC-MS). PCO2 was determined in a conventional blood gas analyser. Statistically significant differences in substance concentrations for acetone, isoprene, 2-methyl-pentane and n-hexane could be observed between different sampling sites. Increasing substance concentrations were determined for acetone (15.3%), 2-methyl-pentane (11.4%) and n-hexane (19.3%) when passing from distal to proximal sampling sites. In contrast, isoprene concentrations decreased by 9.9% from proximal to more distal sampling sites. Blank bronchoscope measurements did not show any contaminations. Increased substance concentrations in the proximal respiratory tract may be explained through substance excretion from bronchial mucosa while decreased concentrations could result from absorption or reaction processes. Spatial mapping of VOC profiles can provide novel insights into substance specific exhalation kinetics and mechanisms.


Assuntos
Testes Respiratórios/métodos , Broncoscopia , Expiração , Manejo de Espécimes , Compostos Orgânicos Voláteis/análise , Dióxido de Carbono/química , Feminino , Humanos , Limite de Detecção , Pulmão/química , Masculino , Pessoa de Meia-Idade , Pressão Parcial
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA