Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow.

BACKGROUND: In recent years, metagenomic Next-Generation Sequencing (mNGS) has increasingly been used for an accurate assumption-free virological diagnosis. However, the systematic workflow evaluation on clinical respiratory samples and implementation of quality controls (QCs) is still lacking. METHODS: A total of 3 QCs were implemented and processed through the whole mNGS workflow: a no-template-control to evaluate contamination issues during the process; an internal and an external QC to check the integrity of the reagents, equipment, the presence of inhibitors, and to allow the validation of results for each sample. The workflow was then evaluated on 37 clinical respiratory samples from patients with acute respiratory infections previously tested for a broad panel of viruses using semi-quantitative real-time PCR assays (28 positive samples including 6 multiple viral infections; 9 negative samples). Selected specimens included nasopharyngeal swabs (n = 20), aspirates (n = 10), or sputums (n = 7). RESULTS: The optimal spiking level of the internal QC was first determined in order to be sufficiently detected without overconsumption of sequencing reads. According to QC validation criteria, mNGS results were validated for 34/37 selected samples. For valid samples, viral genotypes were accurately determined for 36/36 viruses detected with PCR (viral genome coverage ranged from 0.6 to 100%, median = 67.7%). This mNGS workflow allowed the detection of DNA and RNA viruses up to a semi-quantitative PCR Ct value of 36. The six multiple viral infections involving 2 to 4 viruses were also fully characterized. A strong correlation between results of mNGS and real-time PCR was obtained for each type of viral genome (R2 ranged from 0.72 for linear single-stranded (ss) RNA viruses to 0.98 for linear ssDNA viruses). CONCLUSIONS: Although the potential of mNGS technology is very promising, further evaluation studies are urgently needed for its routine clinical use within a reasonable timeframe. The approach described herein is crucial to bring standardization and to ensure the quality of the generated sequences in clinical setting. We provide an easy-to-use single protocol successfully evaluated for the characterization of a broad and representative panel of DNA and RNA respiratory viruses in various types of clinical samples.

Is breast ultrasound a good alternative to magnetic resonance imaging for evaluating implant integrity?

OBJECTIVE: To compare the diagnostic performance of breast ultrasound and breast magnetic resonance imaging and to correlate the findings on the two techniques that are suggestive of implant rupture. MATERIAL AND METHODS: We reviewed the images and reports of breast ultrasound and magnetic resonance imaging studies done in our diagnostic and interventional breast imaging unit to evaluate breast implants in 205 patients between January 2015 and December 2017. RESULTS: Ultrasound findings were compatible with implant rupture in 87 (42.4%) patients: intracapsular rupture in 44 (21.5%) and intracapsular and extracapsular rupture in 43 (21.0%). Ultrasound yielded 85.2% sensitivity, 89.7% specificity, 86.2% positive predictive value, and 89.0% negative predictive value. Magnetic resonance imaging findings were compatible with implant rupture in 88 (42.9%) patients: intracapsular rupture in 50 (24.4%) and intracapsular and extracapsular rupture in 38 (18.5%). The correlation between positive findings for the location of the rupture on the two imaging techniques was excellent (0.77; p < 0.0001). CONCLUSION: We found high concordance between the two techniques for the detection of intracapsular and extracapsular implant rupture. These results consolidate the use of ultrasound as the first-line imaging technique to evaluate implant integrity in our population; magnetic resonance imaging can be reserved for cases in which the ultrasound diagnosis of implant integrity is uncertain.

Epicardial pacemaker implantation and outcome in eight pet ferrets (Mustela putorius furo).

INTRODUCTION/OBJECTIVES: Minimal information exists regarding epicardial pacemaker (EP) implantation in pet ferrets (Mustela putorius furo). The objectives were to describe the indications, surgical technique, and outcome of EP implantation in ferrets for the treatment of advanced atrioventricular block (AVB). ANIMALS, MATERIALS, AND METHODS: Eight client-owned ferrets presenting to five veterinary referral centers. Signalment, physical exam findings, diagnostic tests, anesthesia protocols, surgical implantation techniques, postoperative treatment plans, and EP interrogations were reviewed. Intra- and postoperative, minor and major, and EP-related complications were established. Descriptive statistics were performed to report complication rates. Survival analyses were performed. RESULTS: All ferrets had advanced AVB: 3/8 had high-grade second-degree and 5/8 had third-degree. The primary clinical signs were collapse and weakness. Seven EP were implanted via a transdiaphragmatic approach and one via a left intercostal thoracotomy. Intraoperative complications occurred in 2/8 ferrets, both major. One ferret with severe comorbidities died during general anesthesia. Postoperative pacemaker-related complications were minor: inappropriate sinus beat sensing in 2/8 and occasional muscle fasciculations in 1/8. Two ferrets were alive at the time of manuscript submission, at 10 and 21 months postoperatively. The overall median survival time was 24 months. CONCLUSIONS: Implantation of EP was performed successfully in most ferrets for treatment of advanced AVB and was well tolerated. Ferrets with advanced AVB may experience resolution of clinical signs associated with their cardiac disease following EP implantation. Additional studies are warranted to investigate the effects of epicardial pacing on survival times in this species.

Is breast ultrasound a good alternative to magnetic resonance imaging for evaluating implant integrity? / ¿Es la ecografía mamaria una buena alternativa a la resonancia magnética en la evaluación de la integridad protésica?

OBJECTIVE: To compare the diagnostic performance of breast ultrasound and breast magnetic resonance imaging and to correlate the findings on the two techniques that are suggestive of implant rupture. MATERIAL AND METHODS: We reviewed the images and reports of breast ultrasound and magnetic resonance imaging studies done in our diagnostic and interventional breast imaging unit to evaluate breast implants in 205 patients between January 2015 and December 2017. RESULTS: Ultrasound findings were compatible with implant rupture in 87 (42.4%) patients: intracapsular rupture in 44 (21.5%) and intracapsular and extracapsular rupture in 43 (21.0%). Ultrasound yielded 85.2% sensitivity, 89.7% specificity, 86.2% positive predictive value, and 89.0% negative predictive value. Magnetic resonance imaging findings were compatible with implant rupture in 88 (42.9%) patients: intracapsular rupture in 50 (24.4%) and intracapsular and extracapsular rupture in 38 (18.5%). The correlation between positive findings for the location of the rupture on the two imaging techniques was excellent (0.77; p<0.0001). CONCLUSION: We found high concordance between the two techniques for the detection of intracapsular and extracapsular implant rupture. These results consolidate the use of ultrasound as the first-line imaging technique to evaluate implant integrity in our population; magnetic resonance imaging can be reserved for cases in which the ultrasound diagnosis of implant integrity is uncertain.

Interobserver and intraobserver variability in determining breast density according to the fifth edition of the BI-RADS® Atlas. / Estudio de la variabilidad inter- e intraobservador en la determinación de la densidad mamaria según la 5.a edición del Atlas BI-RADS®.

OBJECTIVE: To determine the level of agreement within and between observers in the categorization of breast density on mammograms in a group of professionals using the fifth edition of the American College of Radiology's BI-RADS® Atlas and to analyze the concordance between experts' categorization and automatic categorization by commercial software on digital mammograms. METHODS: Six radiologists categorized breast density on 451 mammograms on two occasions one month apart. We calculated the linear weighted kappa coefficients for inter- and intra-observer agreement for the group of radiologists and between the commercial software and the majority report. We analyzed the results for the four categories of breast density and for dichotomous classification as dense versus not dense. RESULTS: The interobserver agreement among radiologists and the majority report was between moderate and nearly perfect for the analysis by category (κ=0.64 to 0.84) and for the dichotomous classification (κ=0.63 to 0.84). The intraobserver agreement was between substantial and nearly perfect (κ=0.68 to 0.85 for 4 categories and k=0.70 to 0.87 for the dichotomous classification). The agreement between the majority report and the commercial software was moderate both for the four categories (κ=0.43) and for the dichotomous classification (κ=0.51). CONCLUSION: Agreement on breast density within and between radiologists using the criteria established in the fifth edition of the BI-RADS® Atlas was between moderate and nearly perfect. The level of agreement between the specialists and the commercial software was moderate.

[Functional immunoassays in the setting of infectious risk and immunosuppressive therapy of non-HIV immunocompromised patients]. / Place des tests immunitaires fonctionnels dans la prise en charge du risque infectieux et de la gestion des thérapies immunosuppressives chez les patients immunodéprimés non-VIH.

The holistic approach of the human immune system is based on the study of its components collectively driving a functional response to an immunogenic stimulus. To appreciate a specific immune dysfunction, a condition is mimicked ex vivo and the immune response induced is assessed. The application field of such assays are broad and expanding, from the diagnosis of primary and secondary immunodeficiencies, immunotherapy for cancer to the management of patients at-risk for infections and vaccination. These assays are immune monitoring tools that may contribute to a personalised and precision medicine. The purpose of this review is to describe immune functional assays available in the setting of non-HIV acquired immune deficiency. First, we will address the use of theses assays in the diagnosis of opportunistic infections such as viral reactivation. Secondly, we will report the usefulness of these assays to assess vaccine efficacy and to manage immunosuppressive therapies.

Diagnosing in art. / Diagnosticar en el arte.

The aim of this article is to present an appealing tool for teaching breast imaging that uses the muses of Renaissance and Baroque artists. The examples described here show how medicine and art can be combined to arouse interest in newcomers to breast imaging.

Metastases to the breast, an uncommon diagnosis: what do radiologists need to know? / Metástasis en la mama, un diagnóstico infrecuente. ¿Qué deben saber los radiólogos?

OBJECTIVE: To analyze the imaging characteristics of histologically diagnosed metastases to the breast. MATERIAL AND METHODS: We selected patients histologically diagnosed with metastases to the breast in our diagnostic and interventional breast imaging unit between March 2010 and September 2018. RESULTS: A total of 9 patients (all women; mean age, 60 y; age range, 28-89 y) were diagnosed with metastases to the breast. In 1 (11.11%) case, the primary disease was diagnosed from the breast lesion. The primary tumors were melanoma (n=5), neuroendocrine tumor (n=2, one from the small bowel and one from the cervix), lung adenocarcinoma (n=1), and ovarian cancer (n=1). The clinical and imaging manifestations depend on the type of dissemination of disease and can simulate benign and malignant primary breast lesions. CONCLUSION: There is no specific imaging pattern for metastases to the breast that would help to orient the diagnosis. It is important to consider this etiological possibility if the patient has a history of a primary tumor in another organ.

Serologic and genetic characterization of HIV type 1 subtypes on Reunion Island.

The aim of this study was to determine the HIV subtypes present on Reunion Island, a French island located in the Indian Ocean, where the first case of AIDS was diagnosed in 1987. Paired sera and blood samples were collected between September 1996 and September 1997 from 53 HIV-1-positive patients. Subtyping was performed by serotyping with a previously described subtype-specific enzyme immunoassay (SSEIA) and by genotyping with the heteroduplex mobility assay (HMA). When samples gave uninterpretable results with either of the methods, or discordant results, the V3 env region was sequenced and genetic subtypes were determined by phylogenetic analysis. Genetic subtyping showed that 48 of 53 patients were infected with HIV-1 subtype B (90.5%). This high prevalence of subtype B on Reunion Island is probably due to the regular exchanges with metropolitan France. The other five patients were infected with subtype A (9.5%); they had been directly linked to African populations. Of the 48 subtype B samples, 44 (91.7%) were correctly subtyped by SSEIA and 43 (89.6%) by HMA. However, the SSEIA did not allow the subtyping of A strains in three of five patients. Thus, the SSEIA could be an alternative routine technique for screening subtype B versus nonsubtype B HIV-1 strains.

Skin cancer screening: A growing need.

Skin cancer is the most frequently diagnosed cancer in the United States. Melanoma is the major cause of deaths due to skin cancer, however, squamous cell carcinoma and basal cell carcinoma account for considerable morbidity also. All three types are potentially curable if diagnosed at an early stage. Visual examination of the skin by a trained observer is a simple and effective screening tool which may be utilized in a multitude of settings. Patient education and self-examination augment the impact of office-based screening and mass screening programs.

Nutritional status of institutionalized children and adolescents with developmental disabilities.

The relationship was explored between anomalies associated with developmental disabilities and nutritional status of institutionalized children and adolescents who received comprehensive interdisciplinary services. Variables included dietary intake, serum laboratory values, anthropometric measurements, feeding skills assessment, and clinical assessment. Mean intakes of nutrients were greater than 67% of Recommended Daily Allowances. Laboratory values were within normal ranges with the exceptions of serum ferritin, which was borderline or below normal in 46% of the males and 55% of the females, and alkaline phosphatase, which was elevated in 70% of residents receiving anticonvulsants. Energy intake was highest in residents with adequate feeding skills, followed by nonfeeders and feeders requiring behavior management. Subjects had greater triceps skinfold and lower mid-arm muscle circumference and weight measurements as compared to reference data. Findings of this study suggest that these developmentally disabled children and adolescents who received comprehensive interdisciplinary nutritional services, in general, are adequately nourished and have nutrient intakes that meet the RDA requirements.

Estudio de la variabilidad inter - e intraobservador en la determinación de la densidad mamaria según la 5ª edición del Atlas BI-RADS(R) / Interobserver and intraobserver variability in determining breast density according to the fifth edition of the BI-RADS(R) Atlas

OBJETIVO: Determinar el acuerdo intra- e interobservador en la categorización de la densidad mamográfica entre un grupo de profesionales según la 5.a edición del Atlas BI-RADS® - ACR y analizar la concordancia entre la categorización de los expertos y un software comercial de un mamógrafo digital para categorización automática. MÉTODOS: 6 médicos categorizaron la densidad mamográfica de 451 mamografías en dos oportunidades con un intervalo de 1 mes. Calculamos los coeficientes kappa ponderados lineales de acuerdo inter- e intraobservador para el grupo médico y la concordancia entre el software comercial y el reporte de la mayoría. Analizamos los resultados para las cuatro categorías de densidad mamaria y para el resultado dicotómico de mama densa/no densa. RESULTADOS: El acuerdo interobservador entre especialistas y el reporte de la mayoría fue moderado y casi perfecto para el análisis por categoría (kappa = 0,64 a 0,84) y de manera dicotómica (kappa = 0,63 a 0,84). El acuerdo intraobservador fue sustancial y casi perfecto (kappa = 0,68 a 0,85 para 4 categorías y k=0,70 a 0,87 para el análisis dicotómico). El acuerdo entre el reporte de la mayoría y el software comercial fue moderado tanto por categoría (kappa = 0,43) como en el análisis dicotómico (kappa = 0,51). CONCLUSIÓN: Hemos observado un acuerdo entre moderado y casi perfecto inter- e intraobservador entre los radiólogos, según los criterios establecidos en la 5.ª edición del Atlas BI-RADS®. El nivel de acuerdo entre el reporte de los especialistas y un software disponible comercialmente fue moderado

OBJECTIVE: To determine the level of agreement within and between observers in the categorization of breast density on mammograms in a group of professionals using the fifth edition of the American College of Radiology's BI-RADS® Atlas and to analyze the concordance between experts' categorization and automatic categorization by commercial software on digital mammograms. METHODS: Six radiologists categorized breast density on 451 mammograms on two occasions one month apart. We calculated the linear weighted kappa coefficients for inter- and intra-observer agreement for the group of radiologists and between the commercial software and the majority report. We analyzed the results for the four categories of breast density and for dichotomous classification as dense versus not dense. RESULTS: The interobserver agreement among radiologists and the majority report was between moderate and nearly perfect for the analysis by category (Kappa = 0.64 to 0.84) and for the dichotomous classification (Kappa = 0.63 to 0.84). The intraobserver agreement was between substantial and nearly perfect (Kappa = 0.68 to 0.85 for 4 categories and k=0.70 to 0.87 for the dichotomous classification). The agreement between the majority report and the commercial software was moderate both for the four categories (Kappa = 0.43) and for the dichotomous classification (Kappa = 0.51). CONCLUSION: Agreement on breast density within and between radiologists using the criteria established in the fifth edition of the BI-RADS® Atlas was between moderate and nearly perfect. The level of agreement between the specialists and the commercial software was moderate

Diagnosticar en el arte / Diagnosing in art

El objetivo de este artículo es presentar una atractiva herramienta de enseñanza en la imagenología mamaria, utilizando las musas de los artistas del Renacimiento y el Barroco. Los ejemplos aquí descritos ilustran cómo se puede conjugar la medicina y el arte para despertar el interés de quien se introduce en el aprendizaje de la lectura mamográfica

The aim of this article is to present an appealing tool for teaching breast imaging that uses the muses of Renaissance and Baroque artists. The examples described here show how medicine and art can be combined to arouse interest in newcomers to breast imaging

Metástasis en la mama, un diagnóstico infrecuente. ¿Qué deben saber los radiólogos? / Metastases to the breast, an uncommon diagnosis: what do radiologists need to know?

Objetivo: El objetivo de este trabajo es analizar las características radiológicas de lesiones con diagnóstico histológico de metástasis en la mama. Material y métodos: En la Sección de Diagnóstico e Intervencionismo mamario, en el período comprendido entre marzo de 2010 y septiembre de 2018 se seleccionaron 9 pacientes que presentaban diagnóstico anatomopatológico de metástasis en la mama. Resultado: En total se registraron 9 pacientes de sexo femenino con diagnóstico de metástasis en la mama. La media de edad fue de 60 años (rango: 28-89 años). En 1 caso (11,11%), el diagnóstico de la enfermedad primaria se realizó a partir de la lesión mamaria. Se diagnosticaron cinco metástasis de melanoma, dos metástasis de carcinomas neuroendocrinos (uno de origen en intestino delgado y otro de origen en cérvix uterino), una metástasis de adenocarcinoma de pulmón y una metástasis de ovario. Las manifestaciones clínicas y de imagen dependen de la forma de diseminación de la enfermedad y pueden simular lesiones benignas y malignas primarias de la mama. Conclusión: Las metástasis en la mama no presentan un patrón imagenológico específico que nos oriente a este diagnóstico. Es importante pensar en esta posibilidad etiológica si el paciente presenta el antecedente del diagnóstico de un tumor primario en otro órgano

Objective: To analyze the imaging characteristics of histologically diagnosed metastases to the breast. Material and methods: We selected patients histologically diagnosed with metastases to the breast in our diagnostic and interventional breast imaging unit between March 2010 and September 2018. Results: A total of 9 patients (all women; mean age, 60 y; age range, 28-89 y) were diagnosed with metastases to the breast. In 1 (11.11%) case, the primary disease was diagnosed from the breast lesion. The primary tumors were melanoma (n=5), neuroendocrine tumor (n=2, one from the small bowel and one from the cervix), lung adenocarcinoma (n=1), and ovarian cancer (n=1). The clinical and imaging manifestations depend on the type of dissemination of disease and can simulate benign and malignant primary breast lesions. Conclusion: There is no specific imaging pattern for metastases to the breast that would help to orient the diagnosis. It is important to consider this etiological possibility if the patient has a history of a primary tumor in another organ

DNA arrays, electronic noses and tongues, biosensors and receptors for rapid detection of toxigenic fungi and mycotoxins: a review.

This paper presents an overview of how microsystem technology tools can be applied to the development of rapid, out-of-laboratory measurement capabilities for the determinations of toxigenic fungi and mycotoxins in foodstuffs. Most of the topics discussed are all under investigation within the European Commission-sponsored project Good-Food (FP6-IST). These are DNA arrays, electronic noses and electronic tongues for the detection of fungal contaminants in feed, and biosensors and chemical sensors based on microfabricated electrode systems, antibodies and novel synthetic receptors for the detection of specific mycotoxins. The approach to resolution of these difficult measurement problems in real matrices requires a multidisciplinary approach. The technology tools discussed can provide a route to the rapid, on-site generation of data that can aid the safe production of high-quality foodstuffs.