Molecular Characterization by Multilocus Sequence Typing and Diversity Analysis of Rickettsia asembonensis in Peru.

Despite several reports worldwide documenting the presence of Rickettsia asembonensis in samples derived from ectoparasites, animals and more recently humans, genomic information of these specimens remains scarce, and when available, is usually limited to small genomic fragments of limited value. We generated complete sequences for two conserved (17-kDa antigen gene and gltA) and three variable (sca4, ompB and ompA) genes in five R. asembonensis DNA samples detected in cat and dog fleas in Peru. Complete gene sequences were used to conduct multi-locus sequence typing and phylogenetic analyses to assess diversity and infer relationships among strains and other reference sequences. The 17-kDa antigen gene was highly conserved across Rickettsia species. Of the variable genes ompB was the most variable, but this diversity was not captured through phylogenetics alone even when efforts were made to maximize potential diversity in terms of flea species, animal host and location. Through a combination of de novo and reference-based genome assembly we identified a 75 bp insertion in ompA that encodes a 25 aa repetitive motif found in other Rickettsia species, but not present in the original prototype strain from Kenya. R. asembonensis has only recently been shown to be a bona-fide human pathogen. As such, and compounded by a lack of available genomic information, it remains understudied. Our work directly addresses the lack of genomic information available worldwide for the study of these novel Rickettsia species and specifically contributes to our understanding of the diversity and molecular epidemiology of R. asembonensis in Peru.

Cementerios y cadáveres durante las crisis epidémicas en Guadalajara, Jalisco. México / Cemeteries and bodies in epidemic crisis in Guadalajara, Jalisco. México

Resumen Objetivo: Describir las características de los cementerios y el tratamiento higiénico de cadáveres durante las pandemias a través de la historia. Materiales y método: Es un estudio histórico que parte de la heurística y se combina con el criticismo para evaluar las fuentes utilizadas y responder al objetivo. El universo de trabajo se construyó con documentos del Archivo Histórico Municipal de Guadalajara sobre los panteones de esta ciudad y la revisión bibliográfica en bibliotecas y medios electrónicos relacionados con el tema. Resultados: Las inhumaciones estuvieron a cargo de la iglesia al principio, por razones médico-sanitarias, se trasladaron a orillas de las ciudades en el siglo XIX, y durante el siglo XX se construyeron otros más, quedando algunos dentro de la zona urbana. En 1785-1786, dejaban los cadáveres desnudos y amontonados a las puertas de las iglesias. Se pedía dejarlos en puntos específicos debido a su riesgo para la salud pública. Los cadáveres eran trasladados en cajas de madera cerradas para evitar más contagios. Actualmente, durante la pandemia en México, cada estado ha tomado estrategias para el control de contagios. El gobierno de Jalisco ha conformado la Comisión Interinstitucional de Manejo de Cadáveres por COVID-19, y la aplicación de normas de bioseguridad tanto en hospitales como fuera de ellos. Conclusiones: La evolución de los panteones de Guadalajara, ha dependido de asuntos sociales y de salud, vinculado a intereses económicos, políticos y religiosos. A pesar de las normas establecidas, los panteones han quedado dentro de la zona urbana en consecuencia al crecimiento poblacional, su ubicación geográfica representa una situación crítica, de ahí la importancia del control sanitario y normas de bioseguridad en el manejo de cadáveres.

Abstract Objective. To describe the characteristics of cemeteries and the hygienic treatment of corpses during pandemics throughout history. Materials and method. It is a historical study that starts from Heuristics and it is combined with Criticism to evaluate the sources used and respond to the objective. The universe of work was done with documents from the Guadalajara Municipal Historical Archive on the pantheons of this city and the bibliographic review in libraries and electronic media related to the subject. Results The burials were in charge of the church at first, for medical-sanitary reasons, they moved to the cities' borders in the 19th century, and during the 20th century others were built, some remained within the urban area.1785-1786 The bodies were left naked and piled up at the churches doors. They were asked to leave them at specific points due to their risk to public health. The bodies were transported in closed wooden boxes to avoid further contagion. Currently, during the pandemic in Mexico, each state has adopted strategies for contagion control. Jalisco's government has formed the Inter- institutional Commission for the Management of Dead Bodies by COVID-19, and the application of biosafety regulations both in and outside hospitals. Conclusions. The evolution of the pantheons of Guadalajara has depended on social and health issues, linked to economic, political and religious interests. Despite the established norms, the pantheons have remained within the urban area due to population growth, their geographical location represents a critical situation, hence the importance of sanitary control and biosafety standards in the management of corpses.

Isolation of Complete Equine Encephalitis Virus Genome from Human Swab Specimen, Peru.

While studying respiratory infections in Peru, we identified Venezuelan equine encephalitis virus (VEEV) in a nasopharyngeal swab, indicating that this alphavirus can be present in human respiratory secretions. Because VEEV may be infectious when aerosolized, our finding is relevant for the management of VEEV-infected patients and for VEEV transmission studies.

Rickettsia asembonensis Characterization by Multilocus Sequence Typing of Complete Genes, Peru.

While studying rickettsial infections in Peru, we detected Rickettsia asembonensis in fleas from domestic animals. We characterized 5 complete genomic regions (17kDa, gltA, ompA, ompB, and sca4) and conducted multilocus sequence typing and phylogenetic analyses. The molecular isolate from Peru is distinct from the original R. asembonensis strain from Kenya.

The microRNA landscape of cutaneous squamous cell carcinoma.

Cutaneous squamous cell carcinoma (cSCC) is a keratinocyte-derived skin tumor. It is the second-most-common cancer affecting the Caucasian population and is responsible for >20% of all skin-cancer-related deaths. The estimated incidence of non-melanoma skin cancer in the USA is >1000000 cases per year, of which roughly 20-30% are squamous cell carcinoma. To better understand and treat this challenging cancer, current research focuses on development of novel strategies to improve the understanding of tumor biogenesis on an individual basis. microRNAs are becoming important biomarkers in the diagnosis, prognosis and treatment of cSCC. This review describes the current knowledge on miRNA expression in cSCC and its role as a biomarker for personalized medicine.

Full-genome amplification and sequencing of Zika viruses using a targeted amplification approach.

We have developed methods for full-genome sequencing of Zika viruses (ZIKVs) based on a targeted amplification approach. We used alignments of publicly available complete genome data to design a primer set that selectively amplifies ZIKVs. The approach includes amplification strategies for templates present at both high- and low-copy number, and PCR cycling conditions that have been normalized across genome fragments in order to streamline laboratory handling. Abundant templates can be amplified using a strategy that uses 6 overlapping amplicons to cover the complete viral genome, whereas scarce templates can be amplified using a strategy that uses 11 overlapping amplicons of smaller size. The workflow is sequencing platform agnostic, and thus, can be used in low resource settings where access to traditional Sanger sequencing is the only option available. Given the scarcity of tools for ZIKV, this approach should facilitate epidemiological surveillance and other studies that require the generation of complete viral genomic information quickly and cost-effectively.

Efficient modification of λ-DNA substrates for single-molecule studies.

Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.

Competencia clínica de médicos de seguridad social guatemaltecos para manejar hepatitis virales en atención primaria / Clinical competences for human viral hepatitis treatment of primary healthcare physicians from the Guatemalan social security system

RESUMEN Objetivo Medir la competencia clínica para el diagnóstico y manejo de hepatitis virales en médicos de primer nivel de atención a la salud. Metodología Se efectuó un estudio transversal en el que usando un instrumento previamente validado se midió la competencia y posteriormente se comparó entre médicos adscritos a diversas unidades médicas de atención primaria a la salud (UMAPS) del Instituto Guatemalteco de Seguridad Social (IGSS). La información fue analizada mediante estadística descriptiva e inferencial no paramétrica. Se evaluaron 104 médicos de 5 UMAPS del IGSS. Resultados Se encontró un nivel muy bajo de competencia clínica para el diagnóstico y tratamiento de las hepatitis virales, dentro de un intervalo de 9 a 62 puntos obtenidos en el instrumento que tiene un valor máximo teórico de 88, sin encontrar diferencias estadísticamente significativas entre UMAPS. Conclusiones: Se requiere educación continua en los médicos de las UMAPS del IGSS para mejorar sus competencias en hepatitis virales.(AU)

ABSTRACT Objective To measure the clinical competence for diagnosis and treatment of human viral hepatitis in primary health care physicians. Methodology Cross-sectional study in which a previously validated instrument to measure competences was used, and subsequent comparison between physicians at various primary health care units (PHCT) from the Guatemalan Institute of Social Security (GISS). This information was analyzed using descriptive and non-parametrical statistics. 104 physicians, from 5 PHCT ascribed to GISS were analyzed. Results A low level of clinical competence for diagnosis and treatment of human viral hepatitis in this physicians group was found, within a range of 9 to 62 points obtained through an instrument with a maximum theoretical value of 88; no significant statistical difference between PHCT was found. Conclusions PHCT physicians from require continuing education to improve their clinical competence on human viral hepatitis.(AU)

[Clinical competences for human viral hepatitis treatment of primary healthcare physicians from the Guatemalan social security system]. / Competencia clínica de médicos de seguridad social guatemaltecos para manejar hepatitis virales en atención primaria.

OBJECTIVE: To measure the clinical competence for diagnosis and treatment of human viral hepatitis in primary health care physicians. METHODOLOGY: Cross-sectional study in which a previously validated instrument to measure competences was used, and subsequent comparison between physicians at various primary health care units (PHCT) from the Guatemalan Institute of Social Security (GISS). This information was analyzed using descriptive and non-parametrical statistics. 104 physicians, from 5 PHCT ascribed to GISS were analyzed. RESULTS: A low level of clinical competence for diagnosis and treatment of human viral hepatitis in this physicians group was found, within a range of 9 to 62 points obtained through an instrument with a maximum theoretical value of 88; no significant statistical difference between PHCT was found. CONCLUSIONS: PHCT physicians from require continuing education to improve their clinical competence on human viral hepatitis.

OBJETIVO: Medir la competencia clínica para el diagnóstico y manejo de hepatitis virales en médicos de primer nivel de atención a la salud. METODOLOGÍA: Se efectuó un estudio transversal en el que usando un instrumento previamente validado se midió la competencia y posteriormente se comparó entre médicos adscritos a diversas unidades médicas de atención primaria a la salud (UMAPS) del Instituto Guatemalteco de Seguridad Social (IGSS). La información fue analizada mediante estadística descriptiva e inferencial no paramétrica. Se evaluaron 104 médicos de 5 UMAPS del IGSS. RESULTADOS: Se encontró un nivel muy bajo de competencia clínica para el diagnóstico y tratamiento de las hepatitis virales, dentro de un intervalo de 9 a 62 puntos obtenidos en el instrumento que tiene un valor máximo teórico de 88, sin encontrar diferencias estadísticamente significativas entre UMAPS. Conclusiones: Se requiere educación continua en los médicos de las UMAPS del IGSS para mejorar sus competencias en hepatitis virales.

Targeted full-genome amplification and sequencing of dengue virus types 1-4 from South America.

We report optimized workflows for full-genome sequencing of dengue viruses (DENVs) 1-4. Based on alignments of publicly available complete genomes we modified and expanded existing primers sets to amplify DENV genotypes that were previously difficult or impossible to sequence. We also report improvements to streamline laboratory handling, including a dual amplification strategy for easy and difficult to sequence "high-copy" and "low-copy" templates, respectively, and normalization of PCR cycling conditions across serotypes. High-copy templates can be sequenced following amplification of as few as 5 overlapping segments covering the complete viral genome, whereas low-copy templates can be sequenced following amplification of no more than 10 overlapping segments of smaller size. These changes have been validated using a balanced set of wild-type DENV genomes (11 of DENV1, 14 of DENV2, 13 of DENV3 and 7 of DENV4) derived from human serum samples collected throughout South America over the past 15 years. The changes described enable generation of complete DENV genomes from wild-type samples without the need for viral enrichment via passaging through laboratory cell lines. This should facilitate quick and cost-effective generation of DENV full-genome sequences of the type needed for accurate epidemiological surveillance and thorough evolutionary studies of wild-type DENVs.

Assessing the impact of public health interventions on the transmission of pandemic H1N1 influenza a virus aboard a Peruvian navy ship.

BACKGROUND: Limited data exist on transmission dynamics and effectiveness of control measures for influenza in confined settings. OBJECTIVES: To investigate the transmission dynamics of a 2009 pandemic H1N1 influenza A outbreak aboard a Peruvian Navy ship and quantify the effectiveness of the implemented control measures. METHODS: We used surveillance data and a simple stochastic epidemic model to characterize and evaluate the effectiveness of control interventions implemented during an outbreak of 2009 pandemic H1N1 influenza A aboard a Peruvian Navy ship. RESULTS: The serological attack rate for the outbreak was 49·1%, with younger cadets and low-ranking officers at greater risk of infection than older, higher-ranking officers. Our transmission model yielded a good fit to the daily time series of new influenza cases by date of symptom onset. We estimated a reduction of 54·4% in the reproduction number during the period of intense control interventions. CONCLUSION: Our results indicate that the patient isolation strategy and other control measures put in place during the outbreak reduced the infectiousness of isolated individuals by 86·7%. Our findings support that early implementation of control interventions can limit the spread of influenza epidemics in confined settings.

Mortalidad por homicidios en México: tendencias, variaciones socio-geográficas y factores asociados / Deaths by homicide in Mexico: trends, socio-geographical variations and associated factors

Este estudio analiza la tendencia de las tasas de homicidio (total y por arma de fuego) en México entre 1990 y 2009 e identifica las variables que mejor explican las variaciones geográficas de las tasas en el bienio 2008-2009. Se calcularon tasas de homicidios, ajustadas por edad, para ambos sexos entre 1990 y 2009, y para cada estado en 2008-2009. El análisis de regresión lineal múltiple fue usado para identificar factores asociados a las variaciones interestatales de las tasas de homicidio. Los resultados muestran que la tasa de homicidio disminuyó entre 1992 y 2007, pero se ha duplicado en los últimos dos años (de 7.6 a 16.6 por 100,000). En 2009, la tasa de homicidio masculina fue cerca de 9 veces mayor que la tasa femenina y casi dos tercios de los homicidios fueron por arma de fuego. El análisis multivariado revela que la impunidad, el narcotráfico, el consumo de alcohol y drogas y la deserción escolar -por ese orden- son factores claves para entender las variaciones geográficas de las tasas de homicidio en México en 2008-2009. Así, para reducir los homicidios y las variaciones espaciales de la tasa, se necesita no solo combatir a los cárteles de la droga sino sobre todo implementar reformas estructurales en el sistema de procuración de justicia y disminuir las disparidades socioeconómicas entre los estados.

This study seeks to analyze the trend of homicide rates (total and by firearm) in Mexico between 1990 and 2009 and identify the variables that best explain the geographical variations of these rates in the 2008-2009 two-year period. Homicide rates, adjusted for age, were calculated for both sexes between 1990 and 2009 and for each state in 2008-2009. Factors associated with the interstate variations in the homicide rates were identified using multiple linear regression analysis. Results show that the homicide rate in Mexico decreased between 1990 and 2007, but doubled over the last two years (from 7.6 to 16.6 per 100,000). In 2009, the male homicide rate was almost 9 times higher than the female rate and about two-thirds of homicides involved firearms. Multivariate analysis reveals that impunity, drug trafficking, alcohol and drug consumption and school dropout in basic education - in that order - are key factors for understanding the geographical variations in homicide rates in Mexico in 2008-2009. Findings suggest that to reduce the number of homicide victims and spatial variations in the rate, it is necessary not only to fight the drug cartels, but above all to implement structural reforms in the criminal justice system and reduce the socioeconomic disparities among states.

[Deaths by homicide in Mexico: trends, socio-geographical variations and associated factors]. / Mortalidad por homicidios en México: tendencias, variaciones socio-geográficas y factores asociados.

This study seeks to analyze the trend of homicide rates (total and by firearm) in Mexico between 1990 and 2009 and identify the variables that best explain the geographical variations of these rates in the 2008-2009 two-year period. Homicide rates, adjusted for age, were calculated for both sexes between 1990 and 2009 and for each state in 2008-2009. Factors associated with the interstate variations in the homicide rates were identified using multiple linear regression analysis. Results show that the homicide rate in Mexico decreased between 1990 and 2007, but doubled over the last two years (from 7.6 to 16.6 per 100,000). In 2009, the male homicide rate was almost 9 times higher than the female rate and about two-thirds of homicides involved firearms. Multivariate analysis reveals that impunity, drug trafficking, alcohol and drug consumption and school dropout in basic education - in that order - are key factors for understanding the geographical variations in homicide rates in Mexico in 2008-2009. Findings suggest that to reduce the number of homicide victims and spatial variations in the rate, it is necessary not only to fight the drug cartels, but above all to implement structural reforms in the criminal justice system and reduce the socioeconomic disparities among states.

Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.

Transcription by sigma54 RNA polymerase depends on activators that contain ATPase domains of the AAA+ class. These activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. Here, we report the first crystal structures of the ATPase domain of an activator, the NtrC1 protein from the extreme thermophile Aquifex aeolicus. This domain alone, which is active, crystallized as a ring-shaped heptamer. The protein carrying both the ATPase and adjacent receiver domains, which is inactive, crystallized as a dimer. In the inactive dimer, one residue needed for catalysis is far from the active site, and extensive contacts among the domains prevent oligomerization of the ATPase domain. Oligomerization, which completes the active site, depends on surfaces that are buried in the dimer, and hence, on a rearrangement of the receiver domains upon phosphorylation. A motif in the ATPase domain known to be critical for coupling energy to remodeling of polymerase forms a novel loop that projects from the middle of an alpha helix. The extended, structured loops from the subunits of the heptamer localize to a pore in the center of the ring and form a surface that could contact sigma54.

[Regional variations in homicide mortality in Jalisco, Mexico]. / Variaciones regionales de la mortalidad por homicidios en Jalisco, México.

The present study describes regional variations in homicide rates in Jalisco State, Mexico, in 1989-1991, 1994-1996, and 1999-2000, analyzing the trends by gender and socioeconomic stratum. Using mortality data generated by the National Institute for Statistics, Geography, and Information Technology, homicide rates adjusted by age and gender were calculated, along with rate/female rate ratios; rate ratios by socioeconomic stratum and 95% confidence intervals were also calculated. According to the results, the homicide rate showed: a downward trend in the 1990s; a regional homicide mortality pattern, with the highest rates in peripheral regions, considered among the poorest areas in the State; municipalities with the lowest socioeconomic conditions also presenting a statistically significant excess homicide mortality; and an evident over-mortality from homicide among males. The results point to tasks and challenges for public health and law enforcement institutions, including the need to implement different inter-institutional policies that take into consideration the characteristics of homicide and violent crime in Jalisco.

Variaciones regionales de la mortalidad por homicidios en Jalisco, México / Regional variations in homicide mortality in Jalisco, Mexico

El presente estudio busca describir las variaciones regionales de la mortalidad por homicidios en el estado de Jalisco, México, en 1989-1991, 1994-1996 y 1999-2000, analizando a su vez el comportamiento de la tasa de homicidios según género y estratos de bienestar socioeconómico. A partir de la información sobre mortalidad generada por el Instituto Nacional de Estadística, Geografía y Informática, se calcularon tasas ajustadas por edad y género e índices de sobremortalidad masculina. Además, se calcularon razones de tasa y su intervalo de confianza (95 por ciento). Los resultados reflejan que la tasa de homicidios presenta una tendencia decreciente en los años 90; que existe un patrón regional de la mortalidad por homicidios, observándose las tasas más altas en regiones periféricas del estado consideradas entre las más pobres; que los municipios ubicados en el estrato de bienestar más bajo presentan un exceso de mortalidad por homicidios estadísticamente significativo, y que hay una evidente sobremortalidad masculina por esta causa. Aspectos como los antes descritos implican tareas y desafíos para la salud pública y para los organismos encargados de preservar la ley y el orden, entre ellos la necesidad de implementar políticas intersectoriales diferenciadas, que tomen en consideración las particularidades que rodean al homicidio y al crimen violento en Jalisco

Cementerios y salud pública en Guadalajara / Cementeries and public health in Guadalajara

Introducción: el presente estudio tiene el objetivo de dar cuenta de la institucionalización de la muerte a través del tiempo en los cementerios de la ciudad de Guadalajara.Diseño: descriptivo.Material y método: revisión de escritos y documentos localizados referentes a Campos Santos y Cementerios, en los archivos públicos y eclesiásticos de la ciudad de Guadalajara. Jalisco. México.Resultados: la influencia religiosa y familiar en la disposición de los cadáveres durante la colonia, se ve sustituida por la intervención del Estado en forma de control de los cuerpos muertos a través de una legislación influenciada por los conocimientos de la época.Discusión: en los cementerios en la ciudad de Guadalajara, hasta mediados del siglo XX, las representaciones y la legislación, cambiaron poco en términos de controlar, organizar y secuenciar la vida y la muerte de los ciudadanos. Sin embargo, a inicios del actual siglo XXI, la modernidad con sus contradicciones, se revierte al Estado controlador de los cuerpos muertos, en cuanto otros procesos, como el de urbanización-industrialización, que reclaman espacios para los cuerpos de los vivos.Actualmente las estrategias del Estado para disponer los cadáveres, se orientan hacia la minimización del cuerpo, sin perder el control.

Cementerios y salud pública en Guadalajara / Cementeries and public health in Guadalajara

Introducción: el presente estudio tiene el objetivo de dar cuenta de la institucionalización de la muerte a través del tiempo en los cementerios de la ciudad de Guadalajara.Diseño: descriptivo.Material y método: revisión de escritos y documentos localizados referentes a Campos Santos y Cementerios, en los archivos públicos y eclesiásticos de la ciudad de Guadalajara. Jalisco. México.Resultados: la influencia religiosa y familiar en la disposición de los cadáveres durante la colonia, se ve sustituida por la intervención del Estado en forma de control de los cuerpos muertos a través de una legislación influenciada por los conocimientos de la época.Discusión: en los cementerios en la ciudad de Guadalajara, hasta mediados del siglo XX, las representaciones y la legislación, cambiaron poco en términos de controlar, organizar y secuenciar la vida y la muerte de los ciudadanos. Sin embargo, a inicios del actual siglo XXI, la modernidad con sus contradicciones, se revierte al Estado controlador de los cuerpos muertos, en cuanto otros procesos, como el de urbanización-industrialización, que reclaman espacios para los cuerpos de los vivos.Actualmente las estrategias del Estado para disponer los cadáveres, se orientan hacia la minimización del cuerpo, sin perder el control. (AU)

Defunciones masculinas de 1786, en el Hospital Real de San Miguel Belén de la ciudad de Guadalajara / Male deaths in 1786 at the Royal Hospital of San Miguel of Guadalajara city, Jalisco, Mexico

Se presentan los registros sobre defunciones masculinas acaecidas en 1786, durante el periodo de hambruna que sufrió el país, en el Hospital Real de San Miguel de Belén de la ciudad de Guadalajara, México. Éstas se calcularon en razón de 50 por 1000 habitantes, de ellas ocurrieron en 41 por ciento en indios, 25 por ciento españoles, 17 por ciento de mulatos y 7 por ciento de mestizos. El grupo de edad mayoritariamente afectado fue el de 25 a 34 años. Se discute su paralelismo con otros reportes del centro del país, así como la importancia de dicha epidemia para fundar el actual Hospital Civil de Guadalajara.