cvlr: finding heterogeneously methylated genomic regions using ONT reads.

Summary: Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous methylation. Our software can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads. Availability and implementation: https://github.com/EmanueleRaineri/cvlr. Contact: simon.heath@cnag.crg.eu. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Repercusión de la pandemia COVID-19 en la actividad pediátrica en Atención Primaria / Impact of the COVID-19 pandemic on the pediatric activity in Primary Care

Introducción. La pandemia por COVID-19 ha supuesto un cambio en nuestras vidas y deseamos conocer su influencia en las consultas de pediatría en Atención Primaria. Pacientes y métodos. Estudio observacional retrospectivo de la actividad en un Centro de Salud urbano entre enero 2019 y marzo 2021. Se realiza aleatorización estratificada para elegir semana y día y se incluyen todos los pacientes. La información se extrae del programa Medora. Se recogen las variables: fecha de consulta, fecha de nacimiento, profesional, sexo, patología crónica, tipo y motivo de consulta, hospitalización reciente y afectación por COVID-19. Se realiza un análisis de regresión logística binaria y análisis de regresión de joinpoint. Resultados. La muestra es de 1.802 consultas. La tendencia de las tasas de consultas es estable de forma global y en la atención de enfermería, pero hay cambios estacionales en la atención de los pediatras. Durante la pandemia el tipo de consulta a la demanda/urgencia ha sido inferior que la programada (Odds Ratio = 0,19, IC al 95%: 0,1 a 0,3) y la atención telefónica/no presencial superior a la programada (Odds Ratio = 4,01: IC95% 2,3 a 6,95). El comportamiento de las consultas por tipo de patologías, consulta de revisión, vacunaciones o aspectos administrativos ha sido similar antes y durante la pandemia. Conclusión. El volumen de atenciones en nuestro Centro de Salud ha sido similar durante el periodo estudiado. La atención telefónica/no presencial ha sido cuatro veces superior a la consulta programada. Existen diferencias estacionales con descenso estival (AU)

Introduction. Our aim is to know the impact of the pandemic on pediatric activity in Primary Care.Patients and methods. Retrospective observational study of pediatric activity in an urban Health Center between January 2019 and March 2021. Stratified randomization is performed to choose the week and day. All patients are included. The information collected is extracted from the Medora program. Date of consultation, date of birth, professional, sex, chronic pathology, type and reason for consultation, recent hospitalization and involvement by COVID-19 are collected. Binary logistic regression analysis and regression analysis of joinpoint are performed.Results. The sample is made up of 1802 consultations. Trend in consultation rates is stable globally and in nursing care, but there are seasonal changes in pediatric care. During the pandemic, the demand/urgent consultation was lower than scheduled (Odds Ratio = 0.19, 95% CI 0.1 to 0.3) and telephone/non-face-to-face consultations were higher than scheduled (Odds Ratio = 4.01: 95% CI 2.3 to 6.95). The behavior of consultations by type of pathology, review consultation, vaccinations or administrative aspects has been similar before and during the pandemic.Conclusion. The number of consultations in our Health Center has been similar along the studied period. Telephone/non-face-to-face assistance has been four times higher thanscheduled consultation. There are seasonal differences in pediatric care with a summer decline (AU)

[Recurrent and alternating peripheral facial palsy in a Rehabilitation department]. / Parálisis facial periférica recurrente y alternante en un servicio de Rehabilitación.

Peripheral facial palsy is a relatively frequent condition in rehabilitation departments. The most common aetiology is idiopathic, known as Bell's palsy, which usually has a good prognosis and resolves without sequels. The presence of uncommon symptoms with the facial palsy should lead to suspicion of another possible aetiology, as occurred in the case presented here. Melkersson-Rosenthal's syndrome is one of the entities to keep in mind in the diagnosis of atypical facial palsies. This is an underdiagnosed disease due to the variability of its clinical manifestations. Classically, it manifests as a recurrent and alternating facial edema with peripheral facial palsy and fissured tongue.

Oxidation mechanisms of amoxicillin and paracetamol in the photo-Fenton solar process.

The present study shows the results of solar photo-Fenton oxidation of paracetamol (PCT) and amoxicillin (AMX). Fe2(SO4)3 was used as the source of iron and EDDS as the iron complexing agent, employing different doses of hydrogen peroxide. Two aqueous matrices, a synthetic wastewater and real wastewater from El Ejido WWTP effluent (Almeria) were used. In all cases, the process was operated under conditions of natural sunlight. Results showed that the degradation of both drugs is favoured when the aqueous matrix presents low concentration of carbonates. Under the conditions studied here, degradation percentages above 90% were obtained in the synthetic wastewater and 80% in the actual effluent. The degradation products were determined using liquid chromatography coupled to high-resolution mass spectrometry with hybrid quadrupole time-of-flight analyser. The intermediates detected throughout the oxidative process for both micro-contaminants were mainly products of hydroxylation reactions. The toxicity of the samples was determined using the bacterium Vibrio fischeri. In the acute toxicity test, it was observed that the bacteria did not undergo inhibition in any of the cases. However, chronic toxicity studies showed that the higher the Hydraulic Retention Time (HRT) employed in the assays, the higher the bacterial inhibition.

Parálisis facial periférica recurrente y alternante en un servicio de Rehabilitación / Recurrent and alternating peripheral facial palsy in a Rehabilitation department

La parálisis facial periférica es un cuadro relativamente frecuente en las consultas de los servicios de Rehabilitación. Con gran diferencia, la etiología más frecuente es idiopática, la denominada parálisis de Bell, que suele tener buen pronóstico y desaparecer sin secuelas. La presencia de sintomatología atípica acompañante a la parálisis debe hacernos sospechar otras posibles etiologías, como en el caso que presentamos a continuación. El síndrome de Melkersson-Rosenthal es una de esas enfermedades que deben de ser tenidas en cuenta a la hora de realizar un diagnóstico diferencial ante parálisis faciales de evolución atípica. Se trata de una entidad infradiagnosticada por la variabilidad de su expresión clínica. Característicamente, puede presentarse como un edema facial recurrente y alternante, acompañado de parálisis facial y lengua plicata

Peripheral facial palsy is a relatively frequent condition in rehabilitation departments. The most common aetiology is idiopathic, known as Bell's palsy, which usually has a good prognosis and resolves without sequels. The presence of uncommon symptoms with the facial palsy should lead to suspicion of another possible aetiology, as occurred in the case presented here. Melkersson-Rosenthal's syndrome is one of the entities to keep in mind in the diagnosis of atypical facial palsies. This is an underdiagnosed disease due to the variability of its clinical manifestations. Classically, it manifests as a recurrent and alternating facial edema with peripheral facial palsy and fissured tongue

Secondary serological response of patients with chronic hepatosplenic suppurative brucellosis.

Chronic hepatosplenic suppurative brucellosis (CHSB) is a local reactivation of a previous brucellosis, coursing with an immunoglobulin G (IgG) and IgA secondary immunological response. The observation of two cases of CHSB with an apparent IgM response gave rise to a detailed serological study of three of our patients. We studied the first sample from all three patients and successive samples from two of them. In cases 1 and 2, we found samples with positive IgM lateral flow and IgM enzyme-linked immunosorbent assay results concomitantly with rheumatoid factor (RF); after absorption with anti-RF serum, these results were rendered negative. In patients 2 and 3 the diagnosis of brucellosis was delayed, because none of the test results were initially very significant. However, a clear seroconversion of IgG antibodies was observed in subsequent months; titers of the Brucellacapt and Coombs tests increased in similar ways, although Brucellacapt decreased more rapidly than Coombs, which persisted at high titers for years. In patient 3 a relapse was observed in the fourth year of follow-up, detected by Coombs and also by IgG lateral flow and counterimmunoelectrophoresis (CIEP), although not by the rose bengal, agglutination, or Brucellacapt tests. Serological changes in CHSB may sometimes be mild and are detected mainly by the Coombs test. Brucellacapt does not offer additional information, although IgG lateral flow and CIEP may be of some use. Careful surveillance of titer changes in the Coombs test is the best marker of infection activity. As the disease progresses, an intense IgG response may develop and RF sometimes appears, simulating an IgM response.

Treatment of chlorinated solvents by TiO2 photocatalysis and photo-Fenton: influence of operating conditions in a solar pilot plant.

Titanium dioxide photocatalysis (using 20 0mg l(-1) of TiO2), under aerobic and anaerobic conditions, and photo-Fenton (2 and 56 mg l(-1) iron) were applied to the treatment of different NBCS (non-biodegradable chlorinated solvents), such as dichloroethane, dichloromethane and trichloromethane dissolved in water at 50 mg l(-1). All the tests were performed in a 35-l solar pilot plant with compound parabolic collectors (CPCs) under natural illumination. The two solar treatments were compared with attention to chloride release and TOC mineralisation, as the main parameters. Photo-Fenton was found to be the more appropriate treatment for these compounds, assuming volatilisation as a drawback of photocatalytic degradation of NBCS dissolved in water. In this context, several operating parameters related to NBCS degradation, e.g., treatment time, temperature, hydrogen peroxide consumption and volatility of parent compounds are discussed. The correct choice of operating conditions can very often diminish the problem of volatilisation during treatment.

Supervivencia al año de los pacientes VIH positivos ingresados en UCI en el período previo a la terapia antirretroviral combinada / One-year survival of hiv-positive patients admittes to the intensive care unit before the era of combined antirretrovital therapy (pre-haart)

Fundamento. En este estudio histórico hemos querido conocer la supervivencia al año de los pacientes infectados por el VIH ingresados en UCI, durante el período previo a la introducción de la terapia antirretroviral combinada, para que sirvan de referencia a estudios posteriores donde los enfermos se beneficien de las terapéuticas combinadas y de otros futuros tratamientos. Métodos. Estudio longitudinal. Variable dependiente: supervivencia en días desde el ingreso. Período: enero 1985 a enero 1997.Resultados. Se estudiaron 102 enfermos VIH positivos, la mayoría varones jóvenes que ingresaron por insuficiencia respiratoria. El 60,8 por ciento cumplía criterios de sida-1987 y el 65,7 los ampliados de 1993. El 77,5 por ciento se había infectado por el uso de drogas por vía parenteral (ADVP). Se consiguió el seguimiento al año en el 95,1 por ciento (97 de 102) de los pacientes. De éstos, el 63,9 por ciento fallecieron en los primeros 3 meses tras el ingreso, el 5,15 por ciento entre los 3 y 6 meses, el 4,12 por ciento entre los 6 y 12 meses y el 26,8 por ciento vivieron más de un año. Los factores que se asociaron con una disminución significativa de la supervivencia al año (p < 0,05) fueron: sexo femenino, mecanismo de transmisión del VIH diferente a la ADVP, cumplir criterios de sida, procedencia desde una planta de medicina o cirugía (ningún superviviente al año), necesidad de intubación, e ingreso en UCI sin el diagnóstico del cuadro que motivó el ingreso. La presencia de hipotensión, hipoxia, anemia, número de linfocitos totales < 1.000 µl y CD4 < 100 µl disminuyeron de forma significativa la supervivencia al año. Conclusiones. La introducción de la terapia retroviral combinada y de nuevas terapéuticas, hacen necesario la realización de nuevos estudios y el seguimiento continuado de este grupo de pacientes (AU)

Open, randomized therapeutic trial of six antimicrobial regimens in the treatment of human brucellosis.

This report describes the results of six antimicrobial regimens used for the treatment of brucellosis in an open, randomized study performed over two periods (1980-1983 and 1984-1987). In the first period, rifampicin and doxycycline were used for 4 weeks, trimethoprim-sulfamethoxazole for 6 months, and doxycycline for 6 weeks. During the second period, we used streptomycin for 2 or 3 weeks together with doxycycline for 6 weeks and rifampicin with doxycycline for 6 weeks. Comparison of the results showed the following: (1) no statistically significant findings were revealed when the different regimens were compared and (2) the regimens containing streptomycin yielded statistically more favorable results than those consisting of rifampicin and monotherapy when the patients treated with rifampicin were compared with those taking streptomycin and those receiving single-agent therapy. No significant differences were observed between monotherapeutic regimens and those including rifampicin.