Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.

BACKGROUND: Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. RESULTS: With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. CONCLUSIONS: This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.

Downhill varices: an uncommon cause of upper gastrointestinal bleeding.

BACKGROUND: Upper gastrointestinal bleeding (UGIB) is a common condition in gastroenterology, but "Downhill Varices" (DHV) or varices of the upper oesophagus are an uncommon cause of UGIB, with different aetiology from lower third oesophageal varices and different therapeutic implications. CASE REPORT: A 28-year-old male patient, with a history of chronic kidney failure secondary undergoing haemodialysis and superior vena cava syndrome (SCVS) due to multiple catheter replacements, was admitted to the Emergency Department with haematemesis secondary to a varicose vein rupture in the proximal third of oesophagus, treated initially with ethanolamine. Subsequent diagnostic studies showed the collateral circulation secondary to the SCVS. No further endoscopic or endovascular therapy could be performed and the patient will finally undergo a surgical bypass. DISCUSSION: DHVs are a very uncommon condition and endoscopic band ligation emerges as the appropriate therapeutic approach for the bleeding event. The definitive therapy continues to be that for the cause of the SVCS.

Temporal Dynamics of Airborne Concentrations of Ganoderma Basidiospores and Their Relationship with Environmental Conditions in Oil Palm (Elaeis guineensis).

Basal Stem Rot (BSR), caused by Ganoderma spp., is one of the most important emerging diseases of oil palm in Colombia and is so far restricted to only two producing areas in the country. However, despite the controls established to prevent its spread to new areas, containment has not been possible. This study aimed to understand BSR's propagation mechanisms and related environmental conditions by measuring Ganoderma basidiospores' concentrations at various heights using four 7-day Burkard volumetric samplers in a heavily affected plantation. Meteorological data, including solar radiation, temperature, humidity, precipitation, and wind speed, were also recorded. Analysis revealed higher basidiospore concentrations below 4 m, peaking at 02:00 h, with increased levels towards the study's end. Spore concentrations were not directly influenced by temperature, humidity, or precipitation, but showed higher releases during drier periods. A significant correlation was found between wind speed and spore concentration, particularly below 1.5 m/s, though higher speeds might aid long-distance pathogen spread. This study highlights the complexity of BSR propagation and the need for continued monitoring and research to manage its impact on Colombia's oil palm industry.

Prevalence of cardiovascular risk factors in a historical cohort of people living with human immunodeficiency virus during a 10-year period.

Objective: Data on the frequency of cardiovascular disease in people living with human immunodeficiency virus from low- and middle-income countries is scarce. Methods: We performed an observational study based on data from a historical cohort of people living with human immunodeficiency virus in Colombia during a 10-year follow-up to describe the prevalence of cardiovascular risk factors and their behavior according to CD4 count. Results: One thousand patients were initially included, out of which 390 had a 10-year follow-up. The mean age was 34 (standard deviation 10) years, and 90% were male. We observed an increase in the prevalence of dyslipidemia (29%-52%, p < 0.001) and obesity (1.1%-3.5%, p < 0.001). Major cardiovascular events occurred in less than 1% of patients. Patients with a CD4 count <200 cells/mm3 had a higher frequency of acute myocardial infarction and obesity. Conclusion: Over time, people living with human immunodeficiency virus present with an increasing prevalence of cardiovascular risk factors, particularly those with a lower CD4 count.

MEIS1 and MEIS2 Expression and Prostate Cancer Progression: A Role For HOXB13 Binding Partners in Metastatic Disease.

Purpose: Germline mutations within the MEIS-interaction domain of HOXB13 have implicated a critical function for MEIS-HOX interactions in prostate cancer etiology and progression. The functional and predictive role of changes in MEIS expression within prostate tumor progression, however, remain largely unexplored.Experimental Design: Here we utilize RNA expression datasets, annotated tissue microarrays, and cell-based functional assays to investigate the role of MEIS1 and MEIS2 in prostate cancer and metastatic progression.Results: These analyses demonstrate a stepwise decrease in the expression of both MEIS1 and MEIS2 from benign epithelia, to primary tumor, to metastatic tissues. Positive expression of MEIS proteins in primary tumors, however, is associated with a lower hazard of clinical metastasis (HR = 0.28) after multivariable analysis. Pathway and gene set enrichment analyses identified MEIS-associated networks involved in cMYC signaling, cellular proliferation, motility, and local tumor environment. Depletion of MEIS1 and MEIS2 resulted in increased tumor growth over time in vivo, and decreased MEIS expression in both patient-derived tumors and MEIS-depleted cell lines was associated with increased expression of the protumorigenic genes cMYC and CD142, and decreased expression of AXIN2, FN1, ROCK1, SERPINE2, SNAI2, and TGFß2.Conclusions: These data implicate a functional role for MEIS proteins in regulating cancer progression, and support a hypothesis whereby tumor expression of MEIS1 and MEIS2 expression confers a more indolent prostate cancer phenotype, with a decreased propensity for metastatic progression. Clin Cancer Res; 24(15); 3668-80. ©2018 AACR.

'Downhill varices': una causa poco frecuente de hemorragia digestiva alta / Downhill varices: an uncommon cause of upper gastrointestinal bleeding

Introducción: la hemorragia digestiva alta (HDA) es una entidad común en gastroenterología, pero las ‘Downhill varices’ (DHV) son una causa infrecuente de HDA, con diferente etiología de las varices esofágicas de tercio inferior y con diferentes implicaciones terapéuticas. Caso clínico: varón de 28 años de edad, con antecedentes de insuficiencia renal crónica sometido a hemodiálisis y síndrome de vena cava superior(SVCS) debido a múltiples sustituciones catéter, acude a urgencias por hematemesis secundaria a ruptura de una variz en tercio proximal de esófago, que inicialmente se trata con etanolamina. El estudio diagnóstico posterior demostró la circulación colateral secundaria al SVCS. No se pudo realizar terapia endoscópica o endovascular y el paciente finalmente se someterá a un bypass quirúrgico. Discusión: las DHV son una entidad infrecuente y la ligadura endoscópica con bandas se erige como el abordaje terapéutico apropiado para el evento hemorrágico. La terapia definitiva sigue siendo la de la causa del SVCS (AU)

Background: Upper gastrointestinal bleeding (UGIB) is a common condition in gastroenterology, but ‘Downhill Varices’ (DHV) or varices of the upper oesophagus are an uncommon cause of UGIB, with different aetiology from lower third oesophageal varices and different therapeutic implications. Case report: A 28-year-old male patient, with a history of chronic kidney failure secondary undergoing haemodialysis and superior vena cava syndrome (SCVS) due to multiple catheter replacements, was admitted to the Emergency Department with haematemesis secondary to a varicose vein rupture in the proximal third of oesophagus, treated initially with ethanolamine. Subsequent diagnostic studies showed the collateral circulation secondary to the SCVS. No further endoscopic or endovascular therapy could be performed and the patient will finally undergo a surgical bypass. Discussion: DHVs are a very uncommon condition and endoscopic band ligation emerges as the appropriate therapeutic approach for the bleeding event. The definitive therapy continues to be that for the cause of the SVCS (AU)

Pancreatitis aguda necrotizante posterior a quimioembolización transarterial de hepatocarcinoma: una complicación infrecuente / Acute necrotizing pancreatitis after transarterial chemoembolization of hepatocellular carcinoma: an usual complication

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Perception of Adolescent Patients on Cooperation During Orthodontic Treatment: A Qualitative Study / Percepción de los Pacientes Adolescentes sobre Cooperación Durante el Tratamiento Ortodóncico: Un Estudio Cualitativo

The objective of the present study was to identify the fundamental factors associated with patient cooperation during orthodontic treatment. A qualitative study was carried out, following a hermeneutical approach, using focus groups as the data collection instrument. Sample selection consisted of adolescent patients undergoing orthodontic treatment at CES University Dental Clinics in Medellin, Colombia. Each focus group was directed by trained psychologists. Transcriptions were carried out and afterwards analyzed. Two focus groups, each consistent of 17 patients ranging between 11 and 18 years of age, who were in active orthodontic treatment were evaluated. Five significant factors associated with patient cooperation were identified which included, knowledge, empathy, esthetics, friendly environment, and inclusion in treatment.

El objetivo del presente estudio fue identificar los factores fundamentales relacionados con la cooperación de los pacientes adolescentes durante el tratamiento de ortodoncia. Se realizó un estudio cualitativo, utilizando grupos focales como el instrumento de recolección de datos. La selección de la muestra consistió en pacientes adolescentes que reciben tratamiento de ortodoncia en la clínica de Ortodoncia de la Universidad, CES, Medellín, Colombia. Cada grupo focal fue dirigido por psicólogos entrenados y fue grabado para luego realizar la transcripción de cada uno. Fueron evaluadosos dos grupos focales, cada uno de 17 pacientes entre los 11 y 18 años de edad, que estaban en tratamiento activo de ortodoncia. Se identificaron cinco factores importantes relacionados con la cooperación del paciente, estos fueron: el conocimiento que el profesional demuestra tener frente a su paciente, la empatía entre el ortodoncista y el paciente, la estética, el ambiente clínico favorable y la inclusión de los pacientes en el tratamiento.

Bacteriemia por Streptococcus equi spp. zooepidemicus en paciente trasplantado hepático / Bacteraemia due to Streptococcus equi spp. zooepidemicus in a liver transplant recipient

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Climate factors and its influence on the expression of fungal diseases in cultivars of Heliconias / Factores climáticos y su influencia en la expresión de enfermedades fúngicas en cultivares de Heliconias / Fatores climáticos e sua inluência sobre a expressão de doenças fúngicas em cultivares de Helicônias

One of the factors limiting the production of heliconias in Colombia is fungal disease, which is influenced by climatic conditions that determine the development of the disease cycle. In order to define a possible relationship between climatic factors and the incidence or severity of the most limiting fungal, we developed a linear correlation analysis of 10 heliconia cultivars in two municipalities, in the departments of Risaralda and Valle del Cauca. We found a direct relationship between the weekly average temperature and the incidence index of Colletotrichum spp., and the severity index of Helminthosporium spp.; areas with weekly average temperatures over 25°C will likely have incidence and severity of these limiting disease exceeding 50 % and 25 % respectively. Based on these results, we propose the development and validation of a predictive model of incidence and severity of limiting diseases, using a climate forecasting system.

Uno de los factores limitantes de la producción de heliconias en Colombia son las enfermedades de origen fungoso. La determinación del desarrollo del ciclo de estas enfermedades, se encuentran influenciadas por condiciones climáticas. Con el propósito de definir posible relación entre los elementos climáticos y la incidencia y severidad de las enfermedades de origen fungoso limitantes; se desarrolló análisis de correlación lineal sobre diez cultivares del género Heliconia en el departamento de Risaralda y Valle del Cauca. Se encontró relación directa entre la temperatura media semanal frente al índice incidencia de Colletotrichum spp. y el índice de severidad de Helminthosporium spp. Se concluye que la probabilidad del índice de incidencia y de severidad de este tipo de enfermedades limitantes, donde la temperatura media semanal supera los 25°C, sobrepase el 50 y 25 % respectivamente. Basados en estos resultados se propone el desarrollo y validación de un modelo predictivo de incidencia y severidad de enfermedades limitantes, bajo un sistema de pronóstico climático.

Um dos fatores que limitam a produção de helicônias na Colômbia são as doenças fúngicas, as quais são influenciadas pelas condições climáticas que determinam o desenvolvimento do ciclo da doença. A fim de definir uma possível relação entre fatores climáticos e a incidência e gravidade das doenças, foi desenvolvida a análises de correlação linear de 10 cultivares do género Heliconia em municípios de Risaralda e Valle del Cauca. Encontrou-se uma relação direta entre a temperatura média em relação ao índice de incidência semanal de Colletotrichum spp. e índice de gravidade Helminthosporium spp. Conclui-se que a probabilidade do índice de incidência e de severidade deste tipo de doenças limitantes; nas zonas em que a temperatura média semanal exceda 25°C, excede os 50 e 25 % respectivamente. Com base nestes resultados, propomos o desenvolvimento e validação de um modelo preditivo de incidência e/ou gravidade de doenças limitantes, sob um sistema de previsão climática.