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Functional networks have emerged as powerful instruments to characterize the propagation of information in complex systems, with applications ranging from neuroscience to climate and air transport. In spite of their success, reliable methods for validating the resulting structures are still missing, forcing the community to resort to expert knowledge or simplified models of the system's dynamics. We here propose the use of a real-world problem, involving the reconstruction of the structure of flights in the US air transport system from the activity of individual airports, as a way to explore the limits of such an approach. While the true connectivity is known and is, therefore, possible to provide a quantitative benchmark, this problem presents challenges commonly found in other fields, including the presence of non-stationarities and observational noise, and the limitedness of available time series. We explore the impact of elements like the specific functional metric employed, the way of detrending the time series, or the size of the reconstructed system and discuss how the conclusions here drawn could have implications for similar analyses in neuroscience.
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Rice (Oryza sativa) varieties are generated through breeding programs focused on local requirements. In Chile, the southernmost rice producer, rice productivity relies on the use and generation of temperate japonica germplasms, which need to be adapted to the intensifying effects of climate change. Advanced biotechnological tools can contribute to these breeding programs; new technologies associated with precision breeding, including gene editing, rely on procedures such as regeneration and gene transfer. In this study, the local rice varieties Platino, Cuarzo, Esmeralda, and Zafiro were evaluated for somatic embryogenesis potential using a process that involved the combined use of auxins and cytokinins. An auxin-based (2,4-D) general medium (2N6) allowed for the induction of embryogenic masses in all the genotypes. After induction, masses required culturing either in N6R (kinetin; Platino) or N6RN (BAP, kinetin, IBA, and 2,4-D; Cuarzo, Esmeralda, and Zafiro) to yield whole plants using regeneration medium (N6F, no hormone). The sprouting rates indicated Platino as the most responsive genotype; for this reason, this variety was evaluated for gene transfer. Fifteen-day-old embryo masses were assayed for Agrobacterium-mediated transformation using the bacterial strain EHA105 harboring pFLC-Myb/HPT/GFP, a modified T-DNA vector harboring a geminivirus-derived replicon. The vector included the green fluorescent protein reporter gene, allowing for continuous traceability. Reporter mRNA was produced as early as 3 d after agroinfiltration, and stable expression of the protein was observed along the complete process. These achievements enable further biotechnological steps in these and other genotypes from our breeding program.
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BACKGROUND: The SARS-CoV-2 pandemic is associated with morbidity, hospitalizations, absenteeism, and mortality among healthcare workers (HCW). AIM: To evaluate the seroconversion rate in HCW exposed to SARS-CoV-2 in the early pandemic phase in 2020 at a regional reference hospital. MATERIAL AND METHODS: One hundred seventy-nine HCW working at a regional hospital were invited to a longitudinal study performed between April-July 2020. A serological analysis by ELISA IgG for viral nucleoprotein and protein S with a secondary analysis by ELISA IgG protein S1/S2 for samples with positive or doubtful result was carried out together with a complementary online survey to inquire about occupational or community exposures to SARS-CoV-2. RESULTS: Two cases with baseline infection were detected (1.1%, one symptomatic and one asymptomatic) and no cases of seroconversion were detected. During the study period, there were 136 patients hospitalized with COVID-19, and regional weekly COVID-19 incidence ranged from 2.7 to 24.4 per 100,000 inhabitants. No SARS-CoV-2 cases were detected by PCR among 27 HCW who consulted for respiratory symptoms in the period. Online surveys confirmed direct care of COVID-19 patients and also detected a high degree of unprotected social interaction at work. CONCLUSIONS: There was no evidence of seroconversion in this group of HCW exposed to the risk of infection by SARS-CoV-2 during the onset of the COVID-19 pandemic. Personal protective equipment and other measures used by the HCW were extremely useful for their protection in the initial phase of the pandemic.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/epidemiology , Pandemics/prevention & control , Longitudinal Studies , Seroconversion , Health Personnel , Immunoglobulin GABSTRACT
Background: Histopathological analysis of tissue samples is an ancillary complementary diagnostic tool in tuberculosis (TB) with variable sensitivity and specificity according to different clinical settings. We evaluated the spectrum of histological findings, their diagnostic sensitivity, diagnostic utility, and requests over time in a sample of archival biopsies. Methods: Analysis of biopsies of confirmed TB cases between years 2011-2019 at a reference hospital in Chile. Results: The series included patients with a histological study for TB confirmed by culture (88.9%) or PCR (11.1%). In total, 34 samples were available for analysis, most of them of extrapulmonary origin (82.4%). Biopsies were taken before the start of treatment in 26 cases (76.5%) or after the start-end of treatment for different reasons in 8 cases (23.5%). Restricting the analysis to the group with pretreatment biopsies, the prevalence/diagnostic sensitivity of granulomas was 93.3%, 69.2% for caseous necrosis, 26.9% for granulomas with caseous necrosis without acid-fast bacilli (AFB), and 46.2% for AFB in any histological context. A histological score was constructed to evaluate the homogeneity of lesions, observing that 76.9% had at least four of the six components of the score. The request for biopsies was maintained over time despite the increase in the use of molecular techniques. The presence of AFB contributed to the diagnosis before microbiological results in 23.1% of the cases. Conclusions: Histological study continues to contribute to the diagnosis of TB, especially in extrapulmonary forms.
El análisis histopatológico de muestras de tejidos es una metodología antigua y auxiliar para el diagnóstico de tuberculosis (TB) con sensibilidad y especificidad variable de acuerdo al escenario clínico. Evaluamos el espectro de los hallazgos histológicos, su sensibilidad diagnóstica, su utilidad diagnóstica y cambios de solicitud en el tiempo. Métodos: Análisis de biopsias de casos de TB confirmados entre los años 2011-2019 en un hospital de referencia en Chile. Resultados: La serie incluye pacientes con estudio histológico por TB confirmados por cultivo (88,9%) o PCR (11,1%). En total se contó con 34 muestras para análisis, en su mayoría de origen extrapulmonar (82,4%). Las biopsias fueron tomadas antes del inicio del tratamiento en 26 casos (76,5%) o luego del inicio o al finalizar el tratamiento por diferentes razones en 8 casos (23,5%). Restringiendo el análisis al grupo con biopsias pretratamiento, la prevalencia/sensibilidad diagnóstica de granulomas fue de 93,3%, de necrosis caseosa 69,2%, de granulomas con necrosis caseosa sin bacilos ácido-alcohol resistentes (BAAR) de 26,9% y de BAAR en cualquier contexto histológico de 46,2%. Se construyó un score histológico para ver homogeneidad de lesiones, observando que el 76,9% tenía al menos 4 de los 6 componentes del score. La solicitud de biopsias se mantuvo en el tiempo a pesar del incremento de técnicas moleculares. La presencia de BAAR contribuyó al diagnóstico antes que los resultados microbiológicos en el 23,1% de los casos. Conclusiones: El estudio histológico sigue contribuyendo al diagnóstico, especialmente en las formas extrapulmonares de TB.
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INTRODUCCIÓN: COVID-19 cobró millones de vidas especialmente en la era pre-vacunas. Estudios preliminares mostraban eficacia promisoria del plasma de personas convalecientes anti SARS-CoV-2 (PPC). Objetivo: evaluar la eficacia del PPC en hospitalizados por COVID-19 de moderada gravedad. MATERIAL Y MÉTODOS: Estudio retrospectivo, bicéntrico, en adultos hospitalizados por COVID-19 moderado (no crítico) que requirieron oxigenoterapia. Al plasma donado por sobrevivientes de cuadros leves (600 cc) se les realizó búsqueda de IgG anti SARS-CoV-2. Se evaluó su impacto en mortalidad, estadía hospitalaria (días) y necesidad de ventilación mecánica (VMI). RESULTADOS: De los 119 pacientes incluidos, 58% eran hombres (edad mediana 60 años), 88% poseía comorbilidad y 43% tenía "CALL score" de alto riesgo. 43 pacientes (36%) recibieron PPC, sólo 15 (12,6%) precozmente (< 7 días). 22 pacientes debieron trasladarse a unidad intensiva, 18 recibieron VMI y 15 fallecieron (12,6%). El uso de PPC no se asoció a cambios en la mortalidad (p = 0,16), necesidad de VMI (p = 0,79) ni en la estadía hospitalaria (p = 0,24). Su administración en forma precoz (< 7 días de síntomas) tampoco demostró asociación significativa. La presencia de cardiopatía y el requerir posteriormente VMI fueron factores independientes asociados a mortalidad. CONCLUSIONES: El uso de PPC en pacientes hospitalizados por COVID-19 de moderada gravedad no se asoció a menor mortalidad, estadía hospitalaria ni necesidad de VMI.
INTRODUCTION: COVID-19 claimed millions of lives, mainly in the pre-vaccine era. Preliminary studies showed promising efficacy of convalescent plasma against SARS-CoV-2 (CP). Objective: To evaluate the efficacy of CP in patients hospitalized for COVID-19 with moderate severity. METHODS: Retrospective, bicentric study including adults hospitalized for moderate (non-critical) COVID-19 who required oxygen therapy. CP donated by survivors of mild cases (600 cc) were searched for IgG anti-SARS-CoV-2. Its impact on mortality, hospital stay (days), and need for mechanical ventilation (IMV) was evaluated. RESULTS: Of the 119 patients included, 58% were men (median age 60 years), 88% had comorbidity, and 43% had a high-risk CALL score. Forty-three patients (36%) received CP, only 15 (12.6%) early (< 7 days). Twenty-two patients had to be transferred to the intensive care unit; 18 received IMV, and 15 died (12.6%). The use of CP was not associated with changes in mortality (p = 0.16), need for IMV (p = 0.79), or hospital stay (p = 0.24). Its early administration (< 7 days of symptoms) did not show a significant association either. The presence of heart disease and subsequently requiring IMV were independent factors of mortality. CONCLUSIONS: The use of CP in patients hospitalized for moderately severe COVID-19 was not associated with lower mortality, hospital stay, or the need for IMV.
Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Severity of Illness Index , Immunization, Passive , SARS-CoV-2 , COVID-19/mortality , COVID-19/therapy , COVID-19 Serotherapy , Hospitalization/statistics & numerical data , Length of Stay/statistics & numerical data , Respiration, Artificial/statistics & numerical data , Retrospective Studies , Treatment OutcomeABSTRACT
OBJECTIVES: To characterize clinical aspects, evaluate the diagnostic opportunity, and identify factors associated with mortality in patients hospitalized for tuberculosis (TB). METHODS: Retrospective study of patients admitted for TB to a Regional Hospital in Chile between 2011 and 2019. RESULTS: 142 TB events required hospitalization in this period (38.2% of total cases). All risk groups were identified, with a significant increase in patients with diabetes mellitus. The pulmonary location was the most frequent (71.1%), followed by disseminated forms (16.2%). The sensitivity of microscopy smear in cases of pulmonary TB (isolated or combined) was 78.8% and lower in cases of bronchoalveolar lavage (58.3%). PCR was only occasionally applied (< 10%) with a sensitivity of 100% in sputum samples. Its use increased progressively and reached a positivity of 33% (6 out of 18 cases) in cases with negative sputum staining. The median time between symptom onset and diagnosis was prolonged (9 weeks), and 32.5% of all regional events were diagnosed at the hospital. Dose adjustments (22.1%), corticosteroid use (25%), and treatment interruptions were frequent (11%). Lethality reached 19%, and by multivariate analysis, only shock was associated with a fatal outcome. CONCLUSIONS: In this case series, the diagnosis of TB cases was delayed, scarcely diagnosed by molecular methods, highly concentrated at the hospital level, required admission in a large percentage of cases, and had a high case-fatality rate.
OBJETIVOS: Caracterizar aspectos clínicos, evaluar la oportunidad diagnóstica e identificar factores asociados a mortalidad en pacientes ingresados por tuberculosis (TB). MÉTODOS: Estudio retrospectivo de pacientes ingresados por TB a un Hospital Regional en Chile entre el 2011 y 2019. RESULTADOS: Un total de 142 eventos de TB requirieron hospitalización en el período (38,2% del total). Todos los grupos de riesgo fueron identificados con un aumento significativo de los pacientes con diabetes mellitus. La localización pulmonar fue la más frecuente (71,1%), seguida de la forma diseminada (2 o más sitios; 16,2%). La sensibilidad de la tinción de expectoración en casos de TB pulmonar (aislada o combinada) fue de 78,8% y más baja en casos de lavado broncoalveolar (58,3%). La PCR fue sólo ocasionalmente aplicada (< 10%) con una sensibilidad del 100% en muestras de expectoración. Su uso aumentó progresivamente en el período y el incremento diagnóstico de TB en casos con tinción negativa de expectoración estudiados con PCR fue de 33% (6 de 18 casos). La mediana entre inicio de síntomas y el diagnóstico fue prolongada (9 semanas) y el 32,5% de los eventos regionales fueron diagnosticados en el hospital. Los ajustes de dosis (22,1%), uso de corticoides (25%) e interrupciones del tratamiento fueron hechos frecuentes (11%). La letalidad alcanzó 19% y en el análisis multivariado sólo la aparición de shock se asoció a un desenlace fatal. CONCLUSIONES: En esta serie de casos, el diagnóstico de casos de TB fue tardío, infrecuentemente diagnosticado por métodos moleculares, concentrado en la atención terciaria, requirió hospitalización en un gran porcentaje de casos y tuvo una elevada letalidad.
Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Aged , Young Adult , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/mortality , Tuberculosis, Pulmonary/epidemiology , Sputum/microbiology , Tuberculosis/diagnosis , Tuberculosis/mortality , Tuberculosis/epidemiology , Chile/epidemiology , Retrospective Studies , Risk Factors , Hospitalization/statistics & numerical dataABSTRACT
BACKGROUND: The SARS-CoV-2 pandemic is associated with morbidity, hospitalizations, absenteeism, and mortality among healthcare workers (HCW). AIM: To evaluate the seroconversion rate in HCW exposed to SARS-CoV-2 in the early pandemic phase in 2020 at a regional reference hospital. MATERIAL AND METHODS: One hundred seventy-nine HCW working at a regional hospital were invited to a longitudinal study performed between April-July 2020. A serological analysis by ELISA IgG for viral nucleoprotein and protein S with a secondary analysis by ELISA IgG protein S1/S2 for samples with positive or doubtful result was carried out together with a complementary online survey to inquire about occupational or community exposures to SARS-CoV-2. RESULTS: Two cases with baseline infection were detected (1.1%, one symptomatic and one asymptomatic) and no cases of seroconversion were detected. During the study period, there were 136 patients hospitalized with COVID-19, and regional weekly COVID-19 incidence ranged from 2.7 to 24.4 per 100,000 inhabitants. No SARS-CoV-2 cases were detected by PCR among 27 HCW who consulted for respiratory symptoms in the period. Online surveys confirmed direct care of COVID-19 patients and also detected a high degree of unprotected social interaction at work. CONCLUSIONS: There was no evidence of seroconversion in this group of HCW exposed to the risk of infection by SARS-CoV-2 during the onset of the COVID-19 pandemic. Personal protective equipment and other measures used by the HCW were extremely useful for their protection in the initial phase of the pandemic.
ANTECEDENTES: La pandemia de SARS-CoV-2 está asociada a morbilidad, hospitalizaciones, ausentismo y mortalidad entre el personal de salud (PS). OBJETIVO: Evaluar la tasa de seroconversión en el PS expuesto al SARS-CoV-2 en la fase pandémica inicial el 2020 en un hospital regional de referencia. MATERIAL Y MÉTODOS: Ciento setenta y nueve trabajadores de la salud fueron invitados a un estudio longitudinal realizado entre abril-julio de 2020. Se efectuó un análisis serológico por ELISA IgG para nucleoproteína viral y proteína S con un análisis secundario por ELISA IgG proteína S1 / S2 para muestras con resultado positivo o dudoso junto a encuestas complementarias en línea para preguntar sobre exposiciones ocupacionales o comunitarias al SARS-CoV-2. RESULTADOS: Se detectaron dos casos con infección basal (1,1%, uno sintomático y uno asintomático) sin casos de seroconversión. Durante el período de estudio, hubo 136 pacientes hospitalizados con COVID-19, y la incidencia semanal regional de COVID-19 osciló entre 2,7 y 24,4 por 100.000 habitantes. No se detectaron casos de SARS-CoV-2 por PCR entre los 27 funcionarios que consultaron por síntomas respiratorios en este período. Las encuestas en línea confirmaron la atención directa de los pacientes con COVID-19 y también detectaron un alto grado de interacción social desprotegida en el trabajo. CONCLUSIONES: No hubo evidencia de seroconversión en un grupo de funcionarios expuestos al riesgo de infección por SARS-CoV-2 durante el inicio de la pandemia de COVID-19. Los equipos de protección personal y otras medidas utilizadas por el PS fueron de suma utilidad para su protección en la fase inicial de la pandemia.
Subject(s)
Humans , SARS-CoV-2 , COVID-19/epidemiology , Immunoglobulin G , Longitudinal Studies , Health Personnel , Pandemics/prevention & control , SeroconversionABSTRACT
INTRODUCTION: COVID-19 claimed millions of lives, mainly in the pre-vaccine era. Preliminary studies showed promising efficacy of convalescent plasma against SARS-CoV-2 (CP). OBJECTIVE: To evaluate the efficacy of CP in patients hospitalized for COVID-19 with moderate severity. METHODS: Retrospective, bicentric study including adults hospitalized for moderate (non-critical) COVID-19 who required oxygen therapy. CP donated by survivors of mild cases (600 cc) were searched for IgG anti-SARS-CoV-2. Its impact on mortality, hospital stay (days), and need for mechanical ventilation (IMV) was evaluated. RESULTS: Of the 119 patients included, 58% were men (median age 60 years), 88% had comorbidity, and 43% had a high-risk CALL score. Forty-three patients (36%) received CP, only 15 (12.6%) early (< 7 days). Twenty-two patients had to be transferred to the intensive care unit; 18 received IMV, and 15 died (12.6%). The use of CP was not associated with changes in mortality (p = 0.16), need for IMV (p = 0.79), or hospital stay (p = 0.24). Its early administration (< 7 days of symptoms) did not show a significant association either. The presence of heart disease and subsequently requiring IMV were independent factors of mortality. CONCLUSIONS: The use of CP in patients hospitalized for moderately severe COVID-19 was not associated with lower mortality, hospital stay, or the need for IMV.
Subject(s)
COVID-19 Serotherapy , COVID-19 , Hospitalization , Immunization, Passive , Length of Stay , SARS-CoV-2 , Severity of Illness Index , Humans , COVID-19/therapy , COVID-19/mortality , Male , Retrospective Studies , Middle Aged , Female , Aged , Hospitalization/statistics & numerical data , Length of Stay/statistics & numerical data , Treatment Outcome , Adult , Respiration, Artificial/statistics & numerical dataABSTRACT
BACKGROUND: Histopathological analysis of tissue samples is an ancillary complementary diagnostic tool in tuberculosis (TB) with variable sensitivity and specificity according to different clinical settings. We evaluated the spectrum of histological findings, their diagnostic sensitivity, diagnostic utility, and requests over time in a sample of archival biopsies. METHODS: Analysis of biopsies of confirmed TB cases between years 2011-2019 at a reference hospital in Chile. RESULTS: The series included patients with a histological study for TB confirmed by culture (88.9%) or PCR (11.1%). In total, 34 samples were available for analysis, most of them of extrapulmonary origin (82.4%). Biopsies were taken before the start of treatment in 26 cases (76.5%) or after the start-end of treatment for different reasons in 8 cases (23.5%). Restricting the analysis to the group with pretreatment biopsies, the prevalence/diagnostic sensitivity of granulomas was 93.3%, 69.2% for caseous necrosis, 26.9% for granulomas with caseous necrosis without acid-fast bacilli (AFB), and 46.2% for AFB in any histological context. A histological score was constructed to evaluate the homogeneity of lesions, observing that 76.9% had at least four of the six components of the score. The request for biopsies was maintained over time despite the increase in the use of molecular techniques. The presence of AFB contributed to the diagnosis before microbiological results in 23.1% of the cases. CONCLUSIONS: Histological study continues to contribute to the diagnosis of TB, especially in extrapulmonary forms.
Subject(s)
Sensitivity and Specificity , Tuberculosis , Humans , Biopsy/methods , Female , Male , Adult , Middle Aged , Tuberculosis/diagnosis , Tuberculosis/pathology , Tuberculosis/microbiology , Chile , Mycobacterium tuberculosis/isolation & purification , Mycobacterium tuberculosis/genetics , Aged , Young Adult , Retrospective Studies , Adolescent , Granuloma/pathology , Granuloma/microbiology , Granuloma/diagnosisABSTRACT
OBJECTIVES: To characterize clinical aspects, evaluate the diagnostic opportunity, and identify factors associated with mortality in patients hospitalized for tuberculosis (TB). METHODS: Retrospective study of patients admitted for TB to a Regional Hospital in Chile between 2011 and 2019. RESULTS: 142 TB events required hospitalization in this period (38.2% of total cases). All risk groups were identified, with a significant increase in patients with diabetes mellitus. The pulmonary location was the most frequent (71.1%), followed by disseminated forms (16.2%). The sensitivity of microscopy smear in cases of pulmonary TB (isolated or combined) was 78.8% and lower in cases of bronchoalveolar lavage (58.3%). PCR was only occasionally applied (< 10%) with a sensitivity of 100% in sputum samples. Its use increased progressively and reached a positivity of 33% (6 out of 18 cases) in cases with negative sputum staining. The median time between symptom onset and diagnosis was prolonged (9 weeks), and 32.5% of all regional events were diagnosed at the hospital. Dose adjustments (22.1%), corticosteroid use (25%), and treatment interruptions were frequent (11%). Lethality reached 19%, and by multivariate analysis, only shock was associated with a fatal outcome. CONCLUSIONS: In this case series, the diagnosis of TB cases was delayed, scarcely diagnosed by molecular methods, highly concentrated at the hospital level, required admission in a large percentage of cases, and had a high case-fatality rate.
Subject(s)
Tuberculosis, Pulmonary , Humans , Retrospective Studies , Male , Female , Middle Aged , Chile/epidemiology , Adult , Risk Factors , Aged , Tuberculosis, Pulmonary/epidemiology , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/mortality , Young Adult , Hospitalization/statistics & numerical data , Tuberculosis/diagnosis , Tuberculosis/epidemiology , Tuberculosis/mortality , Adolescent , Sputum/microbiologyABSTRACT
Human gait is a fundamental activity, essential for the survival of the individual, and an emergent property of the interactions between complex physical and cognitive processes. Gait is altered in many situations, due both to external constraints, as e.g. paced walk, and to physical and neurological pathologies. Its study is therefore important as a way of improving the quality of life of patients, but also as a door to understanding the inner working of the human nervous system. In this review we explore how four statistical physics concepts have been used to characterise normal and pathological gait: entropy, maximum Lyapunov exponent, multi-fractal analysis and irreversibility. Beyond some basic definitions, we present the main results that have been obtained in this field, as well as a discussion of the main limitations researchers have dealt and will have to deal with. We finally conclude with some biomedical considerations and avenues for further development.
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The main motivation of this paper is to introduce the permutation Jensen-Shannon distance, a symbolic tool able to quantify the degree of similarity between two arbitrary time series. This quantifier results from the fusion of two concepts, the Jensen-Shannon divergence and the encoding scheme based on the sequential ordering of the elements in the data series. The versatility and robustness of this ordinal symbolic distance for characterizing and discriminating different dynamics are illustrated through several numerical and experimental applications. Results obtained allow us to be optimistic about its usefulness in the field of complex time-series analysis. Moreover, thanks to its simplicity, low computational cost, wide applicability, and less susceptibility to outliers and artifacts, this ordinal measure can efficiently handle large amounts of data and help to tackle the current big data challenges.
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Resumen Introducción: La pandemia de COVID-19 ha afectado a millones de personas en todo el mundo. La identificación de sujetos infectados ha sido importante para el control. Objetivo: Evaluar el rendimiento de una reacción de polimerasa en cadena (RPC) cuantitativa en tiempo real (en inglés: RT-qPCR) para SARS-CoV-2, utilizando saliva como matriz en comparación con un hisopado nasofaríngeo (HNF). Metodología: Se reclutaron adultos en atención ambulatoria, la mayoría sintomáticos. Fueron estudiadas 530 muestras pareadas de saliva e HNF con RT-qPCR. Resultados: Fueron positivas 59 muestras de HNF y 54 de saliva. La sensibilidad con saliva fue 91%, especificidad 100%, el valor predictor positivo (VPP) 100%, valor predictor negativo (VPN) 98%. El índice Kappa fue de 0,95 y LR-0,08. En promedio, el umbral de ciclo (en inglés cycle threshold-CT) de la saliva fue 3,99 puntos más alto que los de HNF (p < 0,0001) mostrando que la carga viral (CV) es menor en saliva. La carga viral en ambas disminuyó con el tiempo después del inicio de los síntomas. El muestreo de saliva fue preferido por los sujetos en lugar de HNF. Conclusión: Este estudio demuestra que la RPC para SARS-CoV-2 utilizando saliva, es adecuada para el diagnóstico de COVID-19 en adultos ambulatorios, especialmente en la etapa temprana de los síntomas.
Abstract Background: The COVID-19 pandemic has affected millions of people around the world. Part of control strategies is testing a large proportion of the population to identify and isolate the infected subjects. Aim: To evaluate the SARS-CoV-2 detection by the performance of a reverse transcription and quantitative polymerase chain reaction (RT-qPCR) against SARS-CoV-2, using saliva as a matrix compared to a nasopharyngeal swab (NPS) to simplify obtaining a diagnostic sample. Methods: Adults in outpatient care were recruited, 95% of them symptomatic. We studied 530 paired saliva and NPS samples by SARS-CoV-2 RT-qPCR. Results: Fifty-nine individuals tested positive in NPS and 54 in saliva samples. Sensitivity for saliva sample was 91%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 98%. The Kappa index was 0.95 and LR-0.08. On average, the cycle threshold (CT) of saliva was 3.99 points higher than those of NPS (p < 0.0001) showing that viral load (VL) is lower in saliva than in NPS. Viral load in both decreased over the time after onset of symptoms. Saliva sampling was preferred by subjects instead of NPS. Conclusion: This study demonstrates that SARS-CoV-2 RT-qPCR using saliva, even with lower VL, is suitable for the diagnosis of COVID-19 in outpatient adults, especially at early stage of symptoms.
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Approximately 5% of COVID-19 patients will have a severe disease requiring invasive or non-invasive mechanical ventilation. In this conditions, sedatives and analgesics are fundamental to promote tolerance, comfort and synchrony with the mechanical ventilator. High and unusual requirements for sedation, analgesics and neuromuscular blockers have been reported in these patients, contributing to prolonged exposure, a high rate of delirium and prolongation of mechanical ventilation. These factors, added to the progressive shortage of these drugs, a high demand for care and less capacity for personalized attention, have created an adverse scenario for their proper and rational use. This paper proposes different pharmacotherapeutic optimization strategies for a rational management of sedation, analgesia and neuromuscular block in critically ill patients with COVID-19, with the therapeutic alternatives available in Chile.
Subject(s)
Analgesia , COVID-19 , Chile , Critical Illness/therapy , Humans , Hypnotics and Sedatives , Respiration, Artificial , SARS-CoV-2ABSTRACT
Approximately 5% of COVID-19 patients will have a severe disease requiring invasive or non-invasive mechanical ventilation. In this conditions, sedatives and analgesics are fundamental to promote tolerance, comfort and synchrony with the mechanical ventilator. High and unusual requirements for sedation, analgesics and neuromuscular blockers have been reported in these patients, contributing to prolonged exposure, a high rate of delirium and prolongation of mechanical ventilation. These factors, added to the progressive shortage of these drugs, a high demand for care and less capacity for personalized attention, have created an adverse scenario for their proper and rational use. This paper proposes different pharmacotherapeutic optimization strategies for a rational management of sedation, analgesia and neuromuscular block in critically ill patients with COVID-19, with the therapeutic alternatives available in Chile.
Subject(s)
Humans , COVID-19 , Analgesia , Respiration, Artificial , Chile , Critical Illness/therapy , SARS-CoV-2 , Hypnotics and SedativesABSTRACT
The woody nature of grapevine (Vitis vinifera L.) has hindered the development of efficient gene editing strategies to improve this species. The lack of highly efficient gene transfer techniques, which, furthermore, are applied in multicellular explants such as somatic embryos, are additional technical handicaps to gene editing in the vine. The inclusion of geminivirus-based replicons in regular T-DNA vectors can enhance the expression of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) elements, thus enabling the use of these multicellular explants as starting materials. In this study, we used Bean yellow dwarf virus (BeYDV)-derived replicon vectors to express the key components of CRISPR/Cas9 system in vivo and evaluate their editing capability in individuals derived from Agrobacterium-mediated gene transfer experiments of 'Thompson Seedless' somatic embryos. Preliminary assays using a BeYDV-derived vector for green fluorescent protein reporter gene expression demonstrated marker visualization in embryos for up to 33 days post-infiltration. A universal BeYDV-based vector (pGMV-U) was assembled to produce all CRISPR/Cas9 components with up to four independent guide RNA (gRNA) expression cassettes. With a focus on fungal tolerance, we used gRNA pairs to address considerably large deletions of putative grape susceptibility genes, including AUXIN INDUCED IN ROOT CULTURE 12 (VviAIR12), SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER 4 (VviSWEET4), LESION INITIATION 2 (VviLIN2), and DIMERIZATION PARTNER-E2F-LIKE 1 (VviDEL1). The editing functionality of gRNA pairs in pGMV-U was evaluated by grapevine leaf agroinfiltration assays, thus enabling longer-term embryo transformations. These experiments allowed for the establishment of greenhouse individuals exhibiting a double-cut edited status for all targeted genes under different allele-editing conditions. After approximately 18 months, the edited grapevine plants were preliminary evaluated regarding its resistance to Erysiphe necator and Botrytis cinerea. Assays have shown that a transgene-free VviDEL1 double-cut edited line exhibits over 90% reduction in symptoms triggered by powdery mildew infection. These results point to the use of geminivirus-based replicons for gene editing in grapevine and other relevant fruit species.
ABSTRACT
ABSTRACT Background: During the first pandemic wave, Covid-19 reached Latin America cities. Aim: To report clinical features and outcomes of a group of patients with Covid-19 admitted to a Chilean regional reference Center. Material and Methods: Cases were identified by a compatible clinical picture and a positive PCR or serological test. Clinical features of patients were retrieved from medical records. Results: Forty-seven adult patients (45 diagnosed by PCR, 2 by serology) were admitted between epidemiological weeks 13 to 33, corresponding to 4.4% of total regional cases. Hospitalization occurred at a median of 10 days after onset of symptoms. Fifty one percent of patients had 60 years or more. Hypertension, obesity and diabetes mellitus were present in 57, 45 and 32 % of cases, respectively. Nineteen percent of patients had no comorbid condition nor were elderly. Two cases were women in their second trimester of pregnancy. Positive IgM or IgM/IgG results obtained by rapid serological testing, had limited sensitivity during the first week (67%). Seventeen patients (36.2%) were transferred to an intensive care unit (ICU) due to respiratory failure. Chest imaging demonstrated a classical COVID-19 pattern in 87%. By univariate analysis, admission to ICU was significantly associated with tachypnea and higher CALL (comorbidity, age, lymphocyte count and lactate dehydrogenase) score. Four patients died (rendering a hospital mortality of 8.5%) and length of stay was ≥ 14 days in 46.8% of patients. By univariate analysis, mortality was associated with immunosuppression and ICU admission. Conclusions: In our regional Center, patients admitted with COVID-19 had usual risk factors and had a prolonged stay. Hospital mortality was associated with immunosuppression and ICU admission.
Antecedentes: Durante la primera ola pandémica, COVID-19 llegó a las ciudades de América Latina. Objetivos: Informar las características clínicas y los resultados asociados a COVID-19 en un grupo de pacientes ingresados en un Centro de referencia regional en el sur de Chile. Material y Métodos: Los casos fueron identificados por un cuadro clínico compatible asociado a RT-PCR positiva o prueba serológica. La información clínica de los pacientes se obtuvo de sus fichas. Resultados: Entre las semanas epidemiológicas 13 y 33 ingresaron 47 pacientes adultos (45 diagnosticados por PCR, 2 por serología), lo que representa el 4,4% del total de casos regionales. La hospitalización se produjo con una mediana de 10 días después del inicio de los síntomas. El 51% de los pacientes tenía 60 años o más. La hipertensión arterial (57,4%), la obesidad (44,7%) y la diabetes mellitus 2 (31,9%) fueron prevalentes, pero el 19% no presentaba comorbilidades ni era un adulto mayor. Dos casos ocurrieron en mujeres embarazadas en el segundo trimestre. Los resultados positivos de IgM o IgM / IgG obtenidos mediante pruebas serológicas rápidas tuvieron una sensibilidad limitada durante la primera semana (66,7%). Diecisiete pacientes (36,2%, grupo crítico) fueron trasladados a UCI por insuficiencia respiratoria. Las imágenes de tórax demostraron un patrón COVID-19 clásico en el 87% de los casos. Por análisis univariado, el ingreso en UCI se asoció significativamente con taquipnea y puntuaciones CALL (comorbidity, age, lymphocyte count and lactate dehydrogenase) elevadas. Cuatro pacientes fallecieron (mortalidad hospitalaria 8,5%) y la estadía hospitalaria fue ≥ 14 días en el 47% de los pacientes. Por análisis univariado la mortalidad se asoció a inmunodepresión y al ingreso a UCI. Conclusiones: En nuestro Centro regional, COVID-19 se asoció a factores de riesgo conocidos y tuvo una estadía prolongada. La mortalidad hospitalaria se asoció con inmunosupresión o ingreso a UCI.
Subject(s)
Adult , Aged , Female , Humans , Pregnancy , COVID-19 , Chile/epidemiology , Critical Illness , SARS-CoV-2 , Hospitalization , Intensive Care UnitsABSTRACT
ABSTRACT Background: Cytomegalovirus (CMV) is an opportunistic infection (OI) in immunosuppressed patients. However, there are no clear cut-off values available for quantitative plasmatic CMV measures (viral load [VL]) to discriminate those with CMV illness from those infected suffering a transient viral reactivation. Aim: To estimate a CMV VL cut-off point that discriminates infected patients and those with CMV related diseases, and to clinically characterize AIDS patients with this OI. Patients and Methods: Retrospective analysis of AIDS patients admitted by any reason between years 2017 and 2019 and who had a positive plasma CMV VL at any titer. Cases were categorized with illness or infected using accepted criteria and the cut-off value was obtained by receiver operating characteristic curve (ROC) analysis. Results: Twelve patients were identified as having a CMV-associated illness and seven with CMV infection. A CMV VL of 3,800 copies/mL had a sensitivity of 91.6% and 100% specificity to discriminate both states. Of the 12 patients with CMV illness, all were in AIDS stage and only five were receiving HIV therapy. Predominant clinical presentations were gastrointestinal (50%), followed by liver involvement (25%) and CMV disease (25%). All patients were treated with ganciclovir or valganciclovir. Ten patients had a favorable response (83.3%), one patient only had a laboratory improvement (8.3%) and one died during treatment (8.3%). Drug toxicity was recorded in nine patients but in only three cases, a dose adjustment was necessary. Conclusions: The predominant clinical manifestation in our series was gastrointestinal. A CMV VL cutoff level of CMV VL of 3,800 copies / mL is useful to discriminate infected patients from those with CMV related disease.
Antecedentes: Citomegalovirus (CMV) es una infección oportunista (IO) en pacientes inmunosuprimidos. Sin embargo, se requieren puntos de corte de carga viral (CV) para discriminar a aquellos con enfermedad por CMV de aquellos infectados que sufren una reactivación viral transitoria. Objetivos: Estimar un punto de corte de la CV de CMV que discrimine a los enfermos de los infectados y, además, caracterizar clínicamente a los pacientes con sida que presentan esta IO. Pacientes y Métodos: Análisis retrospectivo de pacientes con sida hospitalizados por cualquier motivo entre los años 2017 y 2019, y que presentaron un CV de CMV plasmática positiva a cualquier título. Los casos se clasificaron como enfermos utilizando criterios aceptados y el valor de corte se obtuvo mediante análisis de una curva ROC. Resultados: Durante el período de estudio, 12 pacientes fueron identificados con enfermedad asociada al CMV y siete con infección. Una CV de 3.800 copias/ml logró una sensibilidad de 91,6% y una especificidad de 100% para discriminar ambos estados. De los 12 pacientes enfermos, todos estaban en etapa de sida y solo 5 recibían terapia contra el VIH. La presentación clínica predominante fue gastrointestinal (50%) seguida del compromiso hepático (25%) y de la enfermedad por CMV (25%). Todos los pacientes fueron tratados con ganciclovir o valganciclovir. Diez pacientes tuvieron una respuesta favorable (83,3%), uno solo tuvo mejoría de laboratorio (8,3%) y otro paciente falleció durante el tratamiento (8,3%). Nueve pacientes evolucionaron con toxicidad farmacológica, pero en solo 3 casos fue necesario ajustar las dosis. Conclusiones: La forma predominante de presentación de la enfermedad fue gastrointestinal. Un punto de corte de 3.800 copias/ml discrimina pacientes infectados de aquellos con la enfermedad.
Subject(s)
Humans , Acquired Immunodeficiency Syndrome/complications , Acquired Immunodeficiency Syndrome/drug therapy , Cytomegalovirus Infections/complications , Cytomegalovirus Infections/diagnosis , Cytomegalovirus Infections/drug therapy , Antiviral Agents/therapeutic use , Ganciclovir/therapeutic use , Retrospective Studies , Viral Load , CytomegalovirusABSTRACT
BACKGROUND: During the first pandemic wave, Covid-19 reached Latin America cities. AIM: To report clinical features and outcomes of a group of patients with Covid-19 admitted to a Chilean regional reference Center. MATERIAL AND METHODS: Cases were identified by a compatible clinical picture and a positive PCR or serological test. Clinical features of patients were retrieved from medical records. RESULTS: Forty-seven adult patients (45 diagnosed by PCR, 2 by serology) were admitted between epidemiological weeks 13 to 33, corresponding to 4.4% of total regional cases. Hospitalization occurred at a median of 10 days after onset of symptoms. Fifty one percent of patients had 60 years or more. Hypertension, obesity and diabetes mellitus were present in 57, 45 and 32 % of cases, respectively. Nineteen percent of patients had no comorbid condition nor were elderly. Two cases were women in their second trimester of pregnancy. Positive IgM or IgM/IgG results obtained by rapid serological testing, had limited sensitivity during the first week (67%). Seventeen patients (36.2%) were transferred to an intensive care unit (ICU) due to respiratory failure. Chest imaging demonstrated a classical COVID-19 pattern in 87%. By univariate analysis, admission to ICU was significantly associated with tachypnea and higher CALL (comorbidity, age, lymphocyte count and lactate dehydrogenase) score. Four patients died (rendering a hospital mortality of 8.5%) and length of stay was ≥ 14 days in 46.8% of patients. By univariate analysis, mortality was associated with immunosuppression and ICU admission. CONCLUSIONS: In our regional Center, patients admitted with COVID-19 had usual risk factors and had a prolonged stay. Hospital mortality was associated with immunosuppression and ICU admission.
Subject(s)
COVID-19 , Adult , Aged , Chile/epidemiology , Critical Illness , Female , Hospitalization , Humans , Intensive Care Units , Pregnancy , SARS-CoV-2ABSTRACT
BACKGROUND: Cytomegalovirus (CMV) is an opportunistic infection (OI) in immunosuppressed patients. However, there are no clear cut-off values available for quantitative plasmatic CMV measures (viral load [VL]) to discriminate those with CMV illness from those infected suffering a transient viral reactivation. AIM: To estimate a CMV VL cut-off point that discriminates infected patients and those with CMV related diseases, and to clinically characterize AIDS patients with this OI. PATIENTS AND METHODS: Retrospective analysis of AIDS patients admitted by any reason between years 2017 and 2019 and who had a positive plasma CMV VL at any titer. Cases were categorized with illness or infected using accepted criteria and the cut-off value was obtained by receiver operating characteristic curve (ROC) analysis. RESULTS: Twelve patients were identified as having a CMV-associated illness and seven with CMV infection. A CMV VL of 3,800 copies/mL had a sensitivity of 91.6% and 100% specificity to discriminate both states. Of the 12 patients with CMV illness, all were in AIDS stage and only five were receiving HIV therapy. Predominant clinical presentations were gastrointestinal (50%), followed by liver involvement (25%) and CMV disease (25%). All patients were treated with ganciclovir or valganciclovir. Ten patients had a favorable response (83.3%), one patient only had a laboratory improvement (8.3%) and one died during treatment (8.3%). Drug toxicity was recorded in nine patients but in only three cases, a dose adjustment was necessary. CONCLUSIONS: The predominant clinical manifestation in our series was gastrointestinal. A CMV VL cutoff level of CMV VL of 3,800 copies / mL is useful to discriminate infected patients from those with CMV related disease.