Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 47
Filtrar
2.
Open Forum Infect Dis ; 8(7): ofab144, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34316498

RESUMO

The coronavirus disease 2019 pandemic has upended life throughout the globe. Appropriate emphasis has been placed on developing effective therapies and vaccines to curb the pandemic. While awaiting such countermeasures, mitigation efforts coupled with robust testing remain essential to controlling spread of the disease. In particular, serological testing plays a critical role in providing important diagnostic, prognostic, and therapeutic information. However, this information is only useful if the results can be accurately interpreted. This pandemic placed clinical testing laboratories and requesting physicians in a precarious position because we are actively learning about the disease and how to interpret serological results. Having developed robust assays to detect antibodies generated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and serving the hardest-hit areas within the New York City epicenter, we found 3 types of discordances in SARS-CoV-2 test results that challenge interpretation. Using representative clinical vignettes, these interpretation dilemmas are highlighted, along with suggested approaches to resolve such cases.

3.
Acad Pathol ; 8: 23742895211015347, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34046523

RESUMO

In February of 2020, New York City was unprepared for the COVID-19 pandemic. Cases of SARS-CoV-2 infection appeared and spread rapidly. Hospitals had to repurpose staff and establish diagnostic testing for this new viral infection. In the background of the usual respiratory pathogen testing performed in the clinical laboratory, SARS-CoV-2 testing at the Montefiore Medical System grew exponentially, from none to hundreds per day within the first week of testing. The job of appropriately routing SARS-CoV-2 viral specimens became overwhelming. Additional staff was required to triage these specimens to multiple in-house testing platforms as well as external reference laboratories. Since medical school classes and many research laboratories shut down at the Albert Einstein College of Medicine and students were eager to help fight the pandemic, we seized the opportunity to engage and train senior MD-PhD students to assist in triaging specimens. This volunteer force enabled us to establish the "Pathology Command Center," staffed by these students as well as residents and furloughed dental associates. The Pathology Command Center staff were tasked with the accessioning and routing of specimens, answering questions from clinical teams, and updating ever evolving protocols developed in collaboration with a team of Infectious Disease clinicians. Many lessons were learned during this process, including how best to restructure an accessioning department and how to properly onboard students and repurpose staff while establishing safeguards for their well-being during these unprecedented times. In this article, we share some of our challenges, successes, and what we ultimately learned as an organization.

4.
Acad Pathol ; 8: 23742895211006818, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34013020

RESUMO

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, created an unprecedented need for comprehensive laboratory testing of populations, in order to meet the needs of medical practice and to guide the management and functioning of our society. With the greater New York metropolitan area as an epicenter of this pandemic beginning in March 2020, a consortium of laboratory leaders from the assembled New York academic medical institutions was formed to help identify and solve the challenges of deploying testing. This report brings forward the experience of this consortium, based on the real-world challenges which we encountered in testing patients and in supporting the recovery effort to reestablish the health care workplace. In coordination with the Greater New York Hospital Association and with the public health laboratory of New York State, this consortium communicated with state leadership to help inform public decision-making addressing the crisis. Through the length of the pandemic, the consortium has been a critical mechanism for sharing experience and best practices in dealing with issues including the following: instrument platforms, sample sources, test performance, pre- and post-analytical issues, supply chain, institutional testing capacity, pooled testing, biospecimen science, and research. The consortium also has been a mechanism for staying abreast of state and municipal policies and initiatives, and their impact on institutional and laboratory operations. The experience of this consortium may be of value to current and future laboratory professionals and policy-makers alike, in dealing with major events that impact regional laboratory services.

5.
JMIR Dermatol ; 4(1): e25999, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34028471

RESUMO

Background: As teledermatology has been widely adopted during the COVID-19 pandemic, it is essential to examine patients' experiences and satisfaction with teledermatology. Objective: We aimed to assess the teledermatology experiences of new and existing clinic patients in the context of the rapid shift toward teledermatology practices during the COVID-19 pandemic. Methods: We conducted a cross-sectional study of 184 teledermatology patients who were assessed during the COVID-19 pandemic at a major southeastern medical center from May 13 to June 5, 2020. The primary outcome was patient satisfaction levels among new and existing patients. The secondary outcome was patients' willingness to use teledermatology in the future. Results: Of the 288 teledermatology patients who were assessed during the study period, 184 (63.9%) completed the survey. Patients reported high overall satisfaction with teledermatology, with 86.4% (159/184) of participants reporting positive overall satisfaction and experiences with teledermatology. New patients had significantly higher Likert scores for overall satisfaction with teledermatology than those of follow-up patients (new patients: mean 4.70; existing patients: mean 4.43; P=.03). Overall, patients' satisfaction with teledermatology did not significantly differ based on age (P=.36), race and ethnicity (P=.46), education level (P=.11), residence (P=.74), or insurance status (P=.74). There were no significant differences in overall satisfaction between patients with and without prior telehealth experience (P=.53), between the video and telephone visit types (P=.17), and among platform types (P=.22). Prior telehealth experience was associated with higher odds of being willing to use telehealth in the future (odds ratio 2.39, 95% CI 1.31-4.35; P=.004). Conclusions: This cross-sectional survey study demonstrates that during the rapid expansion of teledermatology, new clinic patients had significantly higher scores for overall satisfaction with their teledermatology experience compared to those of established clinic patients (P=.03). Prior telehealth experience was associated with higher odds of being willing to use teledermatology in the future. Overall, teledermatology expansion was met with high levels of patient satisfaction during the COVID-19 pandemic.

6.
Vaccines (Basel) ; 9(4)2021 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-33916180

RESUMO

The COVID-19 pandemic has generated intense interest in the rapid development and evaluation of vaccine candidates for this disease and other emerging diseases. Several novel methods for preparing vaccine candidates are currently undergoing clinical evaluation in response to the urgent need to prevent the spread of COVID-19. In many cases, these methods rely on new approaches for vaccine production and immune stimulation. We report on the use of a novel method (SolaVAX) for production of an inactivated vaccine candidate and the testing of that candidate in a hamster animal model for its ability to prevent infection upon challenge with SARS-CoV-2 virus. The studies employed in this work included an evaluation of the levels of neutralizing antibody produced post-vaccination, levels of specific antibody sub-types to RBD and spike protein that were generated, evaluation of viral shedding post-challenge, flow cytometric and single cell sequencing data on cellular fractions and histopathological evaluation of tissues post-challenge. The results from this preliminary evaluation provide insight into the immunological responses occurring as a result of vaccination with the proposed vaccine candidate and the impact that adjuvant formulations, specifically developed to promote Th1 type immune responses, have on vaccine efficacy and protection against infection following challenge with live SARS-CoV-2. This data may have utility in the development of effective vaccine candidates broadly. Furthermore, the results of this preliminary evaluation suggest that preparation of a whole virion vaccine for COVID-19 using this specific photochemical method may have potential utility in the preparation of one such vaccine candidate.

7.
Arch Pathol Lab Med ; 145(8): 929-936, 2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-33821952

RESUMO

CONTEXT.­: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) testing is used for serosurveillance and will be important to evaluate vaccination status. Given the urgency to release coronavirus disease 2019 (COVID-19) serology tests, most manufacturers have developed qualitative tests. OBJECTIVE.­: To evaluate clinical performance of 6 different SARS-CoV-2 IgG assays and their quantitative results to better elucidate the clinical role of serology testing in COVID-19. DESIGN.­: Six SARS-CoV-2 IgG assays were tested using remnant specimens from 190 patients. Sensitivity and specificity were evaluated for each assay with the current manufacturer's cutoff and a lower cutoff. A numeric result analysis and discrepancy analysis were performed. RESULTS.­: Specificity was higher than 93% for all assays, and sensitivity was higher than 80% for all assays (≥7 days post-polymerase chain reaction testing). Inpatients with more severe disease had higher numeric values compared with health care workers with mild or moderate disease. Several discrepant serology results were those just below the manufacturers' cutoff. CONCLUSIONS.­: Severe acute respiratory syndrome coronavirus 2 IgG antibody testing can aid in the diagnosis of COVID-19, especially with negative polymerase chain reaction. Quantitative COVID-19 IgG results are important to better understand the immunologic response and disease course of this novel virus and to assess immunity as part of future vaccination programs.


Assuntos
Anticorpos Antivirais/sangue , Teste Sorológico para COVID-19/métodos , COVID-19/imunologia , Imunoglobulina G/sangue , SARS-CoV-2/imunologia , COVID-19/diagnóstico , COVID-19/epidemiologia , Teste de Ácido Nucleico para COVID-19/estatística & dados numéricos , Teste Sorológico para COVID-19/estatística & dados numéricos , Estudos de Coortes , Humanos , Cidade de Nova Iorque/epidemiologia , Pandemias , Sensibilidade e Especificidade , Índice de Gravidade de Doença
8.
mSphere ; 6(2)2021 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-33883259

RESUMO

The coronavirus disease 2019 (COVID-19) global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to place an immense burden on societies and health care systems. A key component of COVID-19 control efforts is serological testing to determine the community prevalence of SARS-CoV-2 exposure and quantify individual immune responses to prior SARS-CoV-2 infection or vaccination. Here, we describe a laboratory-developed antibody test that uses readily available research-grade reagents to detect SARS-CoV-2 exposure in patient blood samples with high sensitivity and specificity. We further show that this sensitive test affords the estimation of viral spike-specific IgG titers from a single sample measurement, thereby providing a simple and scalable method to measure the strength of an individual's immune response. The accuracy, adaptability, and cost-effectiveness of this test make it an excellent option for clinical deployment in the ongoing COVID-19 pandemic.IMPORTANCE Serological surveillance has become an important public health tool during the COVID-19 pandemic. Detection of protective antibodies and seroconversion after SARS-CoV-2 infection or vaccination can help guide patient care plans and public health policies. Serology tests can detect antibodies against past infections; consequently, they can help overcome the shortcomings of molecular tests, which can detect only active infections. This is important, especially when considering that many COVID-19 patients are asymptomatic. In this study, we describe an enzyme-linked immunosorbent assay (ELISA)-based qualitative and quantitative serology test developed to measure IgG and IgA antibodies against the SARS-CoV-2 spike glycoprotein. The test can be deployed using commonly available laboratory reagents and equipment and displays high specificity and sensitivity. Furthermore, we demonstrate that IgG titers in patient samples can be estimated from a single measurement, enabling the assay's use in high-throughput clinical environments.


Assuntos
Anticorpos Antivirais/sangue , Teste Sorológico para COVID-19/métodos , COVID-19/diagnóstico , COVID-19/imunologia , SARS-CoV-2/imunologia , Adolescente , Adulto , Idoso , Especificidade de Anticorpos , COVID-19/epidemiologia , Teste Sorológico para COVID-19/estatística & dados numéricos , Estudos de Casos e Controles , Estudos de Coortes , Ensaio de Imunoadsorção Enzimática/métodos , Ensaio de Imunoadsorção Enzimática/estatística & dados numéricos , Monitoramento Epidemiológico , Feminino , Humanos , Imunoglobulina A/sangue , Imunoglobulina G/sangue , Masculino , Pessoa de Meia-Idade , Pandemias , Estudos Soroepidemiológicos , Glicoproteína da Espícula de Coronavírus/imunologia , Adulto Jovem
9.
medRxiv ; 2021 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-33594384

RESUMO

The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS- CoV-2 genomic diversity. Mapping the trajectories of variants, we found that while some have become 'endemic' to the Bronx, other, novel variants rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between a case of reinfection and a case of persistent infection. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.

10.
Diagn Microbiol Infect Dis ; 99(4): 115300, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33388575

RESUMO

The clinical and public health utility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic testing requires a better understanding of the dynamics of the humoral response to infection. To track seroconversion of IgG and IgM antibodies in patients with SARS-CoV-2 infection and its association with patient and clinical factors and outcomes. Residual patient specimens were analyzed on the Abbott ARCHITECT i2000 instrument using the Abbott SARS-CoV-2 IgG assay and prototype SARS-CoV-2 IgM assay. Age, sex, comorbidities, symptom onset date, mortality, and specimen collection date were obtained from electronic medical records. Three hundred fifty-nine longitudinal samples were collected from 89 hospitalized patients 0 to 82 days postsymptom onset. Of all, 51.7% of the patients developed IgG and IgM antibodies simultaneously; 32.8% seroconverted for IgM before IgG. On average, patients seroconverted for IgG by 8 days and for IgM by 7 days postsymptom onset. All patients achieved IgG seropositivity by 19 days and IgM seropositivity by 17 days. Median time to IgG and IgM seroconversion was prolonged and initial levels of IgG were lower in immunocompromised patients and patients <65 years of age compared to immune competent patients and those ≥65 years of age. Immunocompromised patients also had persistently lower levels of IgM that peaked on day 17.6 and decreased thereafter compared to immune competent patients. IgM seroconversion in patients who died reached significantly higher levels later after symptom onset than in those who recovered. SARS-CoV-2 infected patients have similar time to seroconversion for IgG and IgM. However, differences in immune status and age alter time to seroconversion. These results may help guide serologic testing application in COVID-19 management.


Assuntos
Anticorpos Antivirais/sangue , Imunoglobulina G/sangue , Imunoglobulina M/sangue , SARS-CoV-2/imunologia , Soroconversão , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/diagnóstico , Teste Sorológico para COVID-19/métodos , Feminino , Hospitalização , Humanos , Imunidade Humoral/imunologia , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Sensibilidade e Especificidade , Estados Unidos , Adulto Jovem
11.
Transpl Infect Dis ; 23(1): e13449, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32810315

RESUMO

INTRODUCTION: The advent of direct-acting antivirals (DAAs) has created an avenue for transplantation of hepatitis C virus (HCV)-infected donors into uninfected recipients (D+/R-). The donor transmission of HCV is then countered by DAA administration during the post-operative period. However, initiation of DAA treatment is ultimately dictated by insurance companies. METHODS: A retrospective chart review of 52 D+/R- kidney recipients who underwent DAA treatment post-transplant was performed. Patients were grouped according to their prescription coverage plans, managed by either commercial or government pharmacy benefit managers (PBMs). RESULTS: Thirty-nine patients had government PBMs and 13 had commercial PBMs. Demographics were similar between the two groups. All patients developed HCV viremia, but cleared the virus after treatment with DAA. Patients with government PBMs were treated earlier compared to those with commercial PBMs (11 days vs 26 days, P = .01). Longer time to DAA initiation resulted in higher peak viral loads (ß = 0.39, R2  = .15, P = .01) and longer time to HCV viral load clearance (ß = 0.41, R2  = .17, P = .01). CONCLUSIONS: D+/R- transplantation offers patients an alternative strategy to increase access. However, treatment can be profoundly delayed by a third-party payer authorization process that may be subjecting patients to unnecessary risks and worsened outcomes.


Assuntos
Hepatite C Crônica , Transplante de Rim , Antivirais/uso terapêutico , Hepacivirus , Hepatite C Crônica/tratamento farmacológico , Humanos , Seguro Saúde , Estudos Retrospectivos
12.
J Clin Pathol ; 2020 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144357

RESUMO

With the global outbreak of COVID-19, the demand for testing rapidly increased and quickly exceeded the testing capacities of many laboratories. Clinical tests which receive CE (Conformité Européenne) and Food and Drug Administration (FDA) authorisations cannot always be tested thoroughly in a real-world environment. Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the US FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time reverse transcriptase-PCR testing.

13.
Vaccine ; 38(45): 7156-7165, 2020 10 21.
Artigo em Inglês | MEDLINE | ID: mdl-32978002

RESUMO

Although vaccination with BCG prevents disseminated forms of childhood tuberculosis (TB), it does not protect against pulmonary infection or Mycobacterium tuberculosis (Mtb) transmission. In this study, we generated a complete deletion mutant of the Mtb Esx-5 type VII secretion system (Mtb Δesx-5). Mtb Δesx-5 was highly attenuated and safe in immunocompromised mice. When tested as a vaccine candidate to boost BCG-primed immunity, Mtb Δesx-5 improved protection against highly virulent Mtb strains in the murine and guinea pig models of TB. Enhanced protection provided by heterologous BCG-prime plus Mtb Δesx-5 boost regimen was associated with increased pulmonary influx of central memory T cells (TCM), follicular helper T cells (TFH) and activated monocytes. Conversely, lower numbers of T cells expressing exhaustion markers were observed in vaccinated animals. Our results suggest that boosting BCG-primed immunity with Mtb Δesx-5 is a potential approach to improve protective immunity against Mtb. Further insight into the mechanism of action of this novel prime-boost approach is warranted.


Assuntos
Mycobacterium bovis , Mycobacterium tuberculosis , Tuberculose , Sistemas de Secreção Tipo VII , Animais , Antígenos de Bactérias , Vacina BCG , Cobaias , Imunização Secundária , Camundongos , Mycobacterium tuberculosis/genética , Tuberculose/prevenção & controle , Vacinação
14.
medRxiv ; 2020 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-32935116

RESUMO

The COVID-19 global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to place an immense burden on societies and healthcare systems. A key component of COVID-19 control efforts is serologic testing to determine the community prevalence of SARS-CoV-2 exposure and quantify individual immune responses to prior infection or vaccination. Here, we describe a laboratory-developed antibody test that uses readily available research-grade reagents to detect SARS-CoV-2 exposure in patient blood samples with high sensitivity and specificity. We further show that this test affords the estimation of viral spike-specific IgG titers from a single sample measurement, thereby providing a simple and scalable method to measure the strength of an individual's immune response. The accuracy, adaptability, and cost-effectiveness of this test makes it an excellent option for clinical deployment in the ongoing COVID-19 pandemic.

15.
J Clin Microbiol ; 58(9)2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32611796

RESUMO

The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either were nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% confidence interval [CI]: 81.1% to 98.2%), and negative percent agreement was 96% (95% CI: 89% to 0.99%). Four discrepant specimens (Cepheid positive only, n = 2; Hologic positive only, n = 2) exhibited average cycle threshold (CT ) values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR-positive, nasopharyngeal/oropharyngeal PCR-negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract.


Assuntos
Betacoronavirus/genética , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Fezes/virologia , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase , COVID-19 , Teste para COVID-19 , Vacinas contra COVID-19 , Técnicas de Laboratório Clínico/métodos , Técnicas de Laboratório Clínico/normas , Técnicas de Laboratório Clínico/estatística & dados numéricos , Humanos , Limite de Detecção , Pandemias , Reação em Cadeia da Polimerase/métodos , Reação em Cadeia da Polimerase/normas , Reação em Cadeia da Polimerase/estatística & dados numéricos , RNA Viral/análise , RNA Viral/genética , Reprodutibilidade dos Testes , SARS-CoV-2
16.
J Clin Microbiol ; 58(10)2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32727828

RESUMO

The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID50)/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Diagnóstico Molecular , Técnicas de Amplificação de Ácido Nucleico , Automação Laboratorial , Betacoronavirus/genética , Teste para COVID-19 , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Humanos , Nasofaringe/virologia , RNA Viral/genética , Reprodutibilidade dos Testes , SARS-CoV-2 , Sensibilidade e Especificidade , Proteínas Virais/genética
17.
Sci Rep ; 10(1): 7651, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32377001

RESUMO

Flow cytometers can now analyze up to 50 parameters per cell and millions of cells per sample; however, conventional methods to analyze data are subjective and time-consuming. To address these issues, we have developed a novel flow cytometry analysis pipeline to identify a plethora of cell populations efficiently. Coupled with feature engineering and immunological context, researchers can immediately extrapolate novel discoveries through easy-to-understand plots. The R-based pipeline uses Fluorescence Minus One (FMO) controls or distinct population differences to develop thresholds for positive/negative marker expression. The continuous data is transformed into binary data, capturing a positive/negative biological dichotomy often of interest in characterizing cells. Next, a filtering step refines the data from all identified cell phenotypes to populations of interest. The data can be partitioned by immune lineages and statistically correlated to other experimental measurements. The pipeline's modularity allows customization of statistical testing, adoption of alternative initial gating steps, and incorporation of other datasets. Validation of this pipeline through manual gating of two datasets (murine splenocytes and human whole blood) confirmed its accuracy in identifying even rare subsets. Lastly, this pipeline can be applied in all disciplines utilizing flow cytometry regardless of cytometer or panel design. The code is available at https://github.com/aef1004/cyto-feature_engineering.


Assuntos
Citodiagnóstico/métodos , Suscetibilidade a Doenças/imunologia , Citometria de Fluxo , Animais , Biomarcadores , Células Sanguíneas/metabolismo , Citometria de Fluxo/métodos , Humanos , Imunofenotipagem , Camundongos , Mycobacterium tuberculosis/imunologia , Fenótipo , Tuberculose/diagnóstico , Tuberculose/imunologia , Tuberculose/microbiologia
18.
Curr Protoc Cytom ; 93(1): e74, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32421215

RESUMO

Flow cytometry allows the visualization of physical, functional, and/or biological properties of cells including antigens, cytokines, size, and complexity. With increasingly large flow cytometry panels able to analyze up to 50 parameters, there is a need to standardize flow cytometry protocols to achieve high-quality data that can be input into analysis algorithms. Without this clean data, algorithms may incorrectly categorize the cell populations present in the samples. In this protocol, we outline a comprehensive methodology to prepare samples for polychromatic flow cytometry. The use of multiple washing steps and rigorous controls creates high-quality data with good separation between cell populations. Experimental data acquired using this protocol can be analyzed via computational algorithms that perform end-to-end analysis. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Preparation of single-cell suspension for flow cytometry Support Protocol 1: Lung preparation Support Protocol 2: Counting cells on a flow cytometer Basic Protocol 2: Surface and intracellular flow cytometry staining Support Protocol 3: Single-color bead controls.


Assuntos
Citometria de Fluxo/métodos , Citometria de Fluxo/normas , Animais , Contagem de Células , Espaço Intracelular/metabolismo , Pulmão/citologia , Camundongos Endogâmicos C57BL , Análise de Célula Única , Baço/citologia , Linfócitos T/imunologia
19.
Clin Transplant ; 34(4): e13833, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32072689

RESUMO

The advent of direct-acting antivirals (DAAs) has provided the impetus to transplant kidneys from hepatitis C virus-positive donors into uninfected recipients (D+/R-). Thirty D+/R- patients received DAA treatment. Sustained virologic response (SVR12) was defined as an undetectable viral load in 12 weeks after treatment. An age-matched cohort of uninfected donor and recipient pairs (D-/R-) transplanted during same time period was used for comparison. The median day of viral detection was postoperative day (POD) 2. The detection of viremia in D+/R- patients was 100%. The initial median viral load was 531 copies/µL (range: 10-1 × 108 copies/µL) with a median peak viral load of 3.4 × 105 copies/µL (range: 804-1.0 × 108 copies/µL). DAAs were initiated on median POD 9 (range: 5-41 days). All 30 patients had confirmed SVR12. During a median follow-up of 10 months, patient and graft survival was 100%, and acute rejection was 6.6% with no major adverse events related to DAA treatment. Delayed graft function was significantly decreased in D+/R- patients as compared to the age-matched cohort (27% vs 60%; P = .01). D+/R- transplantation offers patients an alternative strategy to increase access.


Assuntos
Hepatite C Crônica , Hepatite C , Transplante de Rim , Antivirais/uso terapêutico , Hepacivirus , Hepatite C/tratamento farmacológico , Hepatite C Crônica/tratamento farmacológico , Humanos , Rim
20.
Acad Pathol ; 6: 2374289519884711, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31799380

RESUMO

Medical school curricula limit students' exposure to pathology practice while pathology subspecialty training programs require residents to apply for fellowships as early as the end of their first year of training. Thus, limited exposure to pathology practice creates significant confusion and anxiety, often making the fellowship application process premature. Additionally, early focus on subspecialty training in order to acquire a fellowship adds to the initial lack of emphasis on general pathology training. We prepared a voluntary online survey with questions developed through focus groups and advice from an expert in survey design to determine which fellowships are desired and how successful residents are in their pursuit of these fellowships. The survey was distributed through the Pathology Residency Program Directors' (PRODS) listserv. Answers were solicited from pathology trainees throughout the entire training cycle. There were 141 (4.6% response rate) total respondents with each postgraduate year represented. One hundred twenty-two (95%) of 129 residents plan on completing 1 or 2 fellowships after residency training. Encouragingly, 94 (75%) of 126 pathology residents attained their desired specialty fellowship. However, 32 (32%) of 99 residents who acquired at least one fellowship chose a general surgical pathology fellowship. Furthermore, 33 (24%) respondents had already decided to pursue a specific specialty while still in medical school. An additional 32 (23%) came to their decision during postgraduate year 1. Therefore, although most residents are successful in attaining their desired fellowship, further research is needed to understand the effect of early commitment to a subspecialty and its impact on pathology education.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...