Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

Historia natural de la piuria y microhematuria después de la cirugía de próstata / Natural History of Pyuria and Microhematuria After Prostate Surgery

Objetivo: Las alteraciones del examen general de orina (EGO) son comunes después de la cirugía prostática. Sin embargo, el tiempo de normalización no ha sido establecido. La presencia de estas alteraciones puede propiciar abordajes diagnósticos innecesarios. El objetivo de este estudio es determinar el tiempo de normalización para ambos parámetros. Material y métodos: Estudiamos pacientes sometidos a cirugía prostática sin complicaciones infecciosas durante su seguimiento. Incluimos pacientes sometidos a resección transuretral de próstata (RTUP) con energía monopolar y bipolar y a prostatectomía abierta (PA). Se utilizaron curvas de Kaplan-Meier para determinar el tiempo de persistencia. Se utilizó ANOVA para comparar los 3 grupos de acuerdo a la cirugía. Analizamos el impacto del uso preoperatorio de inhibidores de la 5-alfa reductasa y correlacionamos el peso del tejido resecado con la persistencia de ambos parámetros. Resultados: Analizamos 85 pacientes: 44 sometidos a RTUP monopolar, 27 a RTUP bipolar y 14 a PA. El tiempo de persistencia de piuria fue significativamente mayor que el de microhematuria, con una mediana de 274 vs 176 días. Estos resultados no se vieron afectados por el tipo de energía utilizada, ni por el uso de inhibidores de la 5-alfa reductasa. Encontramos una correlación entre el peso del tejido resecado y la persistencia de piuria posterior a cirugía endoscópica: 23 g (fue el mejor punto de corte). Conclusiones: La piuria persiste más que la microhematuria independientemente del tipo de cirugía. Existe una correlación entre el tejido resecado y la persistencia de piuria. La presencia de estas alteraciones después de la cirugía prostática no siempre es un hallazgo patológico (AU)

Objective: Urinalysis alterations are common after prostatic surgery. However, time to normalization has not been established. Presence of pyuria and microhematuria can lead to unnecessary diagnostic procedures. The objective of this study is to determine the time to normalization for both parameters. Materials and methods: We reviewed medical records of patients who underwent prostatic surgery without infectious complications during follow-up. We included patients who underwent transurethral resection of the prostate (TURP) with either monopolar or bipolar energy, or open prostatectomy (OP). Kaplan–Meier curves were used to determine the time of persistence of both parameters. ANOVA was used to compare the 3 groups according to the type of surgery. We analyzed the impact of preoperative use of 5-α-reductase inhibitors, and searched for a correlation between the weight of resected tissue and persistence of both parameters. Results: 85 patients were analyzed: 44 underwent monopolar TURP, 27 bipolar TURP, and 14 OP. Persistence of pyuria was significantly longer than microhematuria with a median of 274 days vs. 176 days. Neither the use of monopolar or bipolar energy, nor the use of preoperative 5α-reductase inhibitors affected the persistence time. We found a positive correlation between the resected tissue weight and the persistence of leukocyturia after endoscopic surgery: 23 g was the best cut-off point. Conclusions: Pyuria persists longer than microhematuria regardless of the type of surgery. There is a correlation between the resected tissue weight and the persistence of this feature. The presence of pyuria and microhematuria after prostatic surgery is not always a pathological finding (AU)

Natural history of pyuria and microhematuria after prostate surgery.

OBJECTIVE: Urinalysis alterations are common after prostatic surgery. However, time to normalization has not been established. Presence of pyuria and microhematuria can lead to unnecessary diagnostic procedures. The objective of this study is to determine the time to normalization for both parameters. MATERIAL AND METHODS: We reviewed medical records of patients who underwent prostatic surgery without infectious complications during follow-up. We included patients who underwent transurethral resection of the prostate (TURP) with either monopolar or bipolar energy, or open prostatectomy (OP). Kaplan-Meier curves were used to determine the time of persistence of both parameters. ANOVA was used to compare the 3 groups according to the type of surgery. We analyzed the impact of preoperative use of 5-α-reductase inhibitors, and searched for a correlation between the weight of resected tissue and persistence of both parameters. RESULTS: 85 patients were analyzed: 44 underwent monopolar TURP, 27 bipolar TURP, and 14 OP. Persistence of pyuria was significantly longer than microhematuria with a median of 274 days vs. 176 days. Neither the use of monopolar or bipolar energy, nor the use of preoperative 5α-reductase inhibitors affected the persistence time. We found a positive correlation between the resected tissue weight and the persistence of leukocyturia after endoscopic surgery: 23 g was the best cut-off point. CONCLUSIONS: Pyuria persists longer than microhematuria regardless of the type of surgery. There is a correlation between the resected tissue weight and the persistence of pyuria. The presence of pyuria and microhematuria after prostatic surgery is not always a pathological finding.

Factores pronósticos en pielonefritis enfisematosa / Prognostic Factors in Emphysematous Pyelonephritis

Objetivos: Analizar nuestra experiencia con 18 casos de pielonefritis enfisematosa (PE) en un centro de tercer nivel. Material y métodos: De 262 pacientes hospitalizados por pielonefritis aguda, 18 mostraron hallazgos radiológicos de PE. Utilizamos la clasificación de Wan y Huang. Analizamos las características clínicas, radiológicas y terapéuticas de los pacientes. Buscamos factores pronósticos de mortalidad. Resultados: De 2005 a 2010 17 mujeres y un hombre recibieron tratamiento por PE. La media de edad fue de 52,4 años. El 72% de los pacientes padecían hipertensión y el 66% diabetes tipo 2. Los hallazgos clínicos más comunes fueron: taquicardia (11), fiebre (11) y dolor en flanco (9). Doce pacientes presentaron sepsis grave y 2 choque séptico. El 61% de los pacientes tuvo insuficiencia renal aguda a su ingreso. Nueve sujetos recibieron manejo conservador; se colocó catéter doble J a 5 pacientes y drenaje percutáneo a 3. Solo realizamos una nefrectomía después de un manejo conservador no exitoso. La mortalidad fue del 11%. Las alteraciones en el estado de conciencia (p=0,0001), disfunción orgánica múltiple (p=0.0004), hiperglucemia (p=0,003) y leucocitosis (> 20.000 K) (p=0,01) fueron más comunes en aquellos pacientes que no sobrevivieron. No hubo diferencias en mortalidad entre los pacientes tratados de forma conservadora (solo manejo médico) y aquellos que recibieron tratamiento invasivo. Conclusiones: La PE debe sospecharse en pacientes con múltiples comorbilidades que se presentan con sepsis grave. La alteración en el estado de alerta, la disfunción orgánica múltiple, la hiperglucemia y la leucocitosis son factores de mal pronóstico. El tratamiento invasivo debe utilizarse de forma juiciosa, y el tratamiento conservador puede ser una estrategia segura en casos seleccionados (AU)

Objectives: The purpose of this study is to analyze our experience with 18 cases of Emphysematous pyelonephritis (EPN) in a tertiary care center and describe our treatment strategy. Material and methods: Of 262 patients admitted with acute pyelonephritis, 18 had CT findings of EPN. The Wan and Huang classifications were used. We assessed the clinical, radiological, and therapeutic characteristics of these patients and investigated potential prognostic factors of mortality. Results: Between 2005 and 2010, 17 women and 1 man with EPN were treated. Mean age was 52.4 years. Diabetes was found in 66% and hypertension in 72%. The most common clinical findings were tachycardia (11), fever (11) and flank pain (9); 66% (12) presented with severe sepsis and 2 had septic shock. Acute renal injury developed in 61%. Nine patients were treated exclusively with conservative management; 5 had double J stenting, 3 had CT-guided PCD and 1 required nephrectomy after unsuccessful medical management. Mortality was 11%. Altered consciousness (P=0.0001), multiple organ failure (P=.0004), hyperglycemia (P=0.003) and elevated leukocyte count (> 20000 K) (P=0.01) were more frequent among patients dying from EPN. No difference in mortality was found between patients managed conservatively and those undergoing invasive therapy. Conclusions: Although rare, EPN should be suspected in patients with multiple comorbidities presenting with severe sepsis. Altered consciousness, multiple organ failure, hyperglycemia and elevated leukocyte count are poor prognosis indicators. Invasive management should be used judiciously and medical treatment can be a safe strategy in selected cases (AU)

[Prognostic factors in emphysematous pyelonephritis]. / Factores pronósticos en pielonefritis enfisematosa.

OBJECTIVES: The purpose of this study is to analyze our experience with 18 cases of Emphysematous pyelonephritis (EPN) in a tertiary care center and describe our treatment strategy. MATERIAL AND METHODS: Of 262 patients admitted with acute pyelonephritis, 18 had CT findings of EPN. The Wan and Huang classifications were used. We assessed the clinical, radiological, and therapeutic characteristics of these patients and investigated potential prognostic factors of mortality. RESULTS: Between 2005 and 2010, 17 women and 1 man with EPN were treated. Mean age was 52.4 years. Diabetes was found in 66% and hypertension in 72%. The most common clinical findings were tachycardia (11), fever (11) and flank pain (9); 66% (12) presented with severe sepsis and 2 had septic shock. Acute renal injury developed in 61%. Nine patients were treated exclusively with conservative management; 5 had double J stenting, 3 had CT-guided PCD and 1 required nephrectomy after unsuccessful medical management. Mortality was 11%. Altered consciousness (P=.0001), multiple organ failure (P=.0004), hyperglycemia (P=.003) and elevated leukocyte count (> 20000 K) (P=.01) were more frequent among patients dying from EPN. No difference in mortality was found between patients managed conservatively and those undergoing invasive therapy. CONCLUSIONS: Although rare, EPN should be suspected in patients with multiple comorbidities presenting with severe sepsis. Altered consciousness, multiple organ failure, hyperglycemia and elevated leukocyte count are poor prognosis indicators. Invasive management should be used judiciously and medical treatment can be a safe strategy in selected cases.

Selección y evaluación de un estabilizante integrado de gomas sobre las propiedades de calidad en mezclas para helado duro / Selection and evaluation of a stabilizer composed of rubbers on quality properties in mixtures for hard ice cream

Antecedentes: El mercado actual demanda helados con excelentes características de textura y cuerpo, las cuales, en conjunto con el sabor, determinan en gran medida la aceptabilidad de estos. En esta industria es marcada la tendencia hacia el uso de estabilizantes integrados, que potencializan sinergismos entre componentes, obteniendo productos finales de mejor calidad. Objetivos: En el presente trabajo se evalúa el efecto de la adición de una mezcla de goma de algarrobo, goma guar y goma karaya como agentes estabilizantes sobre algunas características de calidad (bromatológicas, sensoriales y de estabilidad) de helados de crema duros. Métodos: La investigación se desarrolla en dos etapas; en la primera de ellas se evalúa el efecto de las gomas individualmente (100%), en mezclas binarias (50:50 %) y en mezclas ternarias (33.3: 33.3: 33.3 %), aplicadas en un nivel del 0.3% (p/p) en el sistema mezcla de helado duro. En la segunda etapa, se evalúa el efecto del nivel de aplicación en la mezcla de helado duro, ensayando niveles de 0,3, 0,35 y 0,4% (p/p) de la mezcla 50% goma de algarrobo y 50% de goma guar, comparándola contra un testigo que tuvo un estabilizante comercial aplicado al 0,3% (p/p), lo cual originó cuatro tratamientos. Resultados: Con los resultados de la primera fase se realiza la determinación de la tixotropía, lo cual permitió establecer como mejores mezclas las correspondientes a la proporción 50% goma de algarrobo / 50% goma guar y la mezcla 100% de goma guar, de acuerdo con la metodología de superficie de respuesta. La relación final de precios permitió seleccionar la mezcla goma guar: goma de algarrobo para aplicación, sumado a que dicha combinación posibilitó evaluar comportamientos e interacciones como mezcla. En la segunda etapa los resultados arrojan que el helado formado por la mezcla 50% goma de algarrobo y 50% goma guar, presenta un menor porcentaje de derretimiento y un menor tiempo en la caída de la primera gota frente al testigo.

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity.

The carpet shell clam (Ruditapes decussatus) and Manila clam (Ruditapes philippinarum), which are cultured bivalve species with important commercial value, are affected by diseases that result in large economic losses. Because the molecular mechanism of the immune response of bivalves, especially clams, is scarce and fragmentary, we have examined all Expressed Sequence Tags (EST) resources available in public databases for these two species in order to increase our knowledge on genes related with the immune function in these animals. After automatic annotation and classification of the 3784 not-annotated ESTs of R. decussatus and 4607 of R. philippinarum found in GenBank, 424 ESTs of R. decussatus and 464 of R. philippinarum were found to be putatively involved in immune response. These were carefully reviewed and reannotated. As a result, 13 immune-related ESTs were selected and studied to compare the immune response of R. decussatus and R. philippinarum following a Vibrio alginolyticus challenge. Quantitative PCR was performed, and the expression of each EST was determined. The results showed that, in R. philippinarum, the immune response seems to be faster than that in R. decussatus. Additionally, expression of NF-κB activating genes in R. decussatus did not seem to be sufficient to promote an immune response after Vibrio infection. R. philippinarum, however, was able to trigger and efficiently regulate the transcriptional activity of NF-κB, even when low expression values were reported.

Conocimientos y actitudes frente a los documentos de voluntades anticipadas en pacientes atendidos por el PADES (Plan de Atención Domiciliaria Equipos de Soporte) / No disponible

Objetivo: explorar conocimientos y actitudes de los pacientes en fase terminal sobre las voluntades anticipadas. Método: Diseño: cualitativo de carácter fenomenológico, de corte transversal, a través de entrevista semiestructurada de final abierto. Emplazamiento: pacientes en fase terminal atendidos en 2007 por un PADES de Barcelona, Participantes: selección intencional por muestreo no probabilístico, entre los pacientes que cumplían los criterios de inclusión/exclusión, Se estableció una muestra de 10 pacientes, Cinco fueron excluidos por empeoramiento clínico y uno por negativa a participar. Intervenciones: entrevista semiestructurada en formato de final abierto. Mediciones: la metodología del estudio no aporta resultados generalizables a nivel estadístico, sino que ayudan a obtener tendencias de la actuación de las personas. Resultados: participaron 4 pacientes, ninguno había realizado un documento de voluntades anticipadas (DVA), el grado de conocimientos sobre este era bastante limitado. Por otra parte, la actitud frente a los DVA y frente al proceso de toma de decisiones al final de la vida fue diferente en cada participante. Conclusiones: el derecho a realizar un DVA es desconocido para los pacientes. Ni la certeza de un diagnóstico letal, ni la proximidad de la muerte les ha hecho preocuparse de las posibles decisiones sanitarias que tendrán que tomarse en el futuro. Los pacientes que confían en su grupo familiar, y/o que confían en su médico y que han expresado sus valores y que saben que estos le serán respetados, no encuentran en un DVA una respuesta a una necesidad, sencillamente porque no consideran tenerla (AU)

Objective: to explore the knowledge and attitudes of terminally ill patients about advanced living will. Method: Design: a cross-sectional, qualitative, phenomenological study using a semistructured interview with open-ended questions to terminally ill patients attended by a Home Palliative Care Service in Barcelona during 2007. Patients were recruited using non-intentional, non-probabilistic sampling among those meeting inclusion criteria. Ten patients were selected but five were excluded because of clinical deterioration and one refused to participate. Results: none of the four patients had made a living will, and their knowledge about it was very limited. Different attitudes about living wills and end-of-life decision-making were observed in all participants. Conclusions: the right to make an advanced living will document is still unknown by patients. It seems that, for these patients, awareness of the prognosis or nearing death does not constitute a major concern about potential difficulties in the future decision-making process. Those who trust their families or their physicians, and had shared their values with others in the past, do not seem to find an answer to a problem in a living will, simply because they do not consider that they have a problem at all (AU)

Evolución y resultados de la consulta externa de Cuidados Paliativos en el Institut Català d’Oncologia: 2001-2005 / No disponible

Objetivo: describir el proceso de citación en la consulta externa y sus principales resultados clínicos del Servicio de Cuidados Paliativos del Institut Català d’Oncologia, para el periodo 2001-2005. Pacientes y métodos: pacientes consecutivos por los que se consultó y se visitaron en las consultas externas durante el periodo de estudio. Cada paciente por el que se consultó fue evaluado y programado para visita siguiendo un protocolo claramente definido. En cada visita se registraron variables demográficas y clínicas y se evaluaron el dolor, anorexia, estreñimiento, insomnio, debilidad, ansiedad y depresión. La eficacia en el control sintomático se analizó para aquellos pacientes que fueron capaces de hacer tres visitas consecutivas. Resultados: referente al proceso de citación fueron evaluables 2.385 pacientes. El 80% de los pacientes programados vinieron a visita y la mediana de tiempo entre la demanda y la visita fue de 10 días. La evaluación del control sintomático fue posible para 553 pacientes, mostrando un significativo buen control de todos los síntomas con excepción de la astenia. El 55% de los pacientes requirieron opioides para el dolor, observándose un cambio en el patrón pasando de morfina a fentanilo TTS. Conclusiones: la carga asistencial, en nuestro centro, en la consulta externa de cuidados paliativos es alta. Los resultados del proceso de citación muestran un alto cumplimiento con un mínimo tiempo de espera entre la petición y la visita. Los resultados clínicos muestran un buen control global de los síntomas con excepción de la astenia. También se observa un cambio en el patrón de la prescripción de opioides. Este estudio ha de ser considerado como la línea basal para futuros estudios en nuestro centro o en otros de características similares (AU)

Objective: to describe the appointment scheduling process in the outpatient clinic, and the main clinical results of the palliative care service at Institut Català d’Oncologia for the period 2001-2005. Patients and methods: patients consecutively visited in the outpatient clinic during the study period. Each patient was evaluated and scheduled following a clearly defined appointment protocol. Demographic and clinical variables, and symptom control for pain, anorexia, constipation, insomnia, weakness, anxiety, and depression were recorded for each visit. Symptom control efficacy was analyzed for patients able to pay three consecutive visits. Results: regarding the appointment process, 2,385 patients were evaluable. Eigthy percent of patients scheduled were able to attend the visit, and the median time between request and visit was 10 days. Symptom control was evaluable for 553 patients, with a significantly good control for all symptoms but weakness. Opioids for pain were used by 55% of patients, with a progressive change in the pattern of prescription from morphine to fentanil-TTS. Conclusion: in our center palliative care outpatient activity has a high workload. The results of our appointment process show high compliance with a minimum delay between request and visit. Overall, clinical outcomes demonstrate a good control for a set of paradigmatic symptoms in advanced cancer patients, except fort weakness. Also, a change was found in the pattern of opioid prescription. This study should be considered a baseline report that may be of help for further analyses, both in our Institute and other cancer centers (AU)

Hialuronidasa en el manejo de la obstrucción de las sondas vesicales en pacientes con cáncer / No disponible

La retención aguda de orina, secundaria a obstrucción de la sonda vesical por detritus celulares, en pacientes con invasión vesical tumoral por patología oncológica avanzada en fase terminal, plantea serias dificultades de manejo, gran deterioro de la calidad de vida y un importante sufrimiento para el paciente, la familia y el equipo asistencial cuando las medidas paliativas convencionales fracasan y otros tratamientos más «agresivos» o «invasivos» no están indicados dentro del contexto global del enfermo. En teoría, un tratamiento que «disolviera» estos detritus celulares, resolvería el problema mecánico obstructivo y por tanto los episodios de retención urinaria. El ácido hialurónico es un componente importante de la matriz intercelular y su hidrolización por la enzima hialuronidasa, produce una disminución de la viscosidad y de la acción de barrera de esta. Bajo la hipótesis de que la hialuronidasa contribuyera a «disolver» estos detritus celulares, presentamos en esta nota clínica nuestra experiencia con dos casos clínicos de retención aguda de orina refractarios, que al ser tratados con hialuronidasa intravesical presentaron una excelente respuesta en el control de los síntomas obstructivos urinarios previos (AU)

Acute urinary retention secondary to the obstruction of urinary in dwelling catheters by cellular debris in patients with neoplastic bladder invasion entails serious management difficulties in end-stage malignancies.This situation greatly deteriorates quality of life, and has a significant impact on the suffering of patients, their families, and the multidisciplinary team, becoming a problem when standard palliative care treatment shave failed and more aggressive or invasive measures are not indicated because of the patient's overall status.Theoretically, a treatment that «dissolves» this cellular debris may be a satisfactory palliative solution to this obstructive mechanical problem, and there fore to the acute urinary retention episodes. Hyaluronic acid is an important component of the extracellular matrix. It is hydrolyzed by hyaluronidase, an enzyme that may reduce the viscosity and barrier action of this matrix. Under the hypothesis that, by using hyaluronidase, we may «dissolve» cellular debris, we present in this paper our experience with two cases of previously refractory acute urinary retention that finally achieved excellent symptom control after using intravesical hylauronidase infusions (AU)

Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hosts.

Marteilia refringens is a protozoan parasite causing a disease notifiable to the Office International des Epizooties (OIE) and its distribution has implications for the transfer of live animals. The internal transcribed spacer-1 (ITS-1) from Marteilia clones contains polymorphism. Digestion with HhaI reveals two different restriction profiles, previously referred as 'O' (Marteilia from oyster or Marteilia refringens) and 'M' (Marteilia from mussels or Marteilia maurini). The aim of the present work was to determine whether the two previously described Marteilia molecular types (O and M) exist in the Iberian Peninsula and the strictness of the association with their bivalve host species. The sequence variability in the ITS-1 of Marteilia species was studied in mussels, Mytilus galloprovincialis, and flat oysters, Ostrea edulis, from different geographical locations in Spain, to establish the existence and the distribution of different species or molecular types. Although there were two distinct evolutionary lineages that corresponded more or less strictly with the 'M' and 'O' types, it was evident from the estimated phylogeny that some 'O' types have switched to 'M' type, and vice versa. Moreover, 'O' types were found in mussels and 'M' types were found in oysters, which suggests that there have been several cross-species transmissions of Marteilia between mussels and oysters.

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.

We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant reference sequences. The algorithm is fast and includes a Bonferroni corrected statistical test of recombination to circumvent the multiple testing problems encountered when using the BOOTSCAN method to explore alignments for evidence of recombination. Using both simulated and real datasets we demonstrate that the modified algorithm is more powerful than other phylogenetic recombination detection methods and performs almost as well as one of the best substitution distribution recombination detection methods.

Widespread recombination in published animal mtDNA sequences.

Mitochondrial DNA (mtDNA) recombination has been observed in several animal species, but there are doubts as to whether it is common or only occurs under special circumstances. Animal mtDNA sequences retrieved from public databases were unambiguously aligned and rigorously tested for evidence of recombination. At least 30 recombination events were detected among 186 alignments examined. Recombinant sequences were found in invertebrates and vertebrates, including primates. It appears that mtDNA recombination may occur regularly in the animal cell but rarely produces new haplotypes because of homoplasmy. Common animal mtDNA recombination would necessitate a reexamination of phylogenetic and biohistorical inference based on the assumption of clonal mtDNA transmission. Recombination may also have an important role in producing and purging mtDNA mutations and thus in mtDNA-based diseases and senescence.

RDP2: recombination detection and analysis from sequence alignments.

UNLABELLED: RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM chi(2), CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: darren@science.uct.ac.za SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.

Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster.

Variation in pigmentation is common in marine invertebrates, although few studies have shown the existence of genetic differentiation of chromatic forms in these organisms. We studied the genetic structure of a colonial ascidian with populations of different colour morphs in the northwestern Mediterranean. A fragment of the c oxidase subunit 1 (COI) mitochondrial gene was sequenced in seven populations of Pseudodistoma crucigaster belonging to three different colour morphs (orange, yellow and grey). Maximum likelihood analyses showed two well-supported clades separating the orange morph from the yellow-grey morphotypes. Genetic divergence between these clades was 2.12%, and gamma(ST) values between populations of the two clades were high (average 0.936), pointing to genetic isolation. Nested clade and coalescence analyses suggest that a past fragmentation event may explain the phylogeographical origin of these two clades. Non-neutral mtDNA evolution is observed in our data when comparing the two clades, showing a significant excess of nonsynonymous polymorphism within the yellow-grey morphotype using the McDonald-Kreitman test, which is interpreted as further support of reproductive isolation. We conclude that the two clades might represent separate species. We compare the population genetic differentiation found with that estimated for other colonial and solitary ascidian species, and relate it to larval dispersal capabilities and other life-history traits.

Colonización por especies de Candida en orofaringe y tracto gastrointestinal en niños con neutropenia febril / Oropharingeal and gastrointestinal Candida sp. colonization in children with febrile neutropenia

Objetivo: determinar la relación existente entre la colonización por especies de Candida en tracto gastrointestinal y orofaringe y el desarrollo de fungemia en pacientes oncológicos con neutropenia febril (NF). Diseño: estudio descriptivo. Lugar: Centro Hemato-oncológico Infantil U de Antioquia / Hospital Universitario San Vicente de Paúl – Medellín (enero 99-noviembre 2000). Población: niños con cáncer y NF. Mediciones: hisopado orofaríngeo, materia fecal (MF) y orina los días 0, 7, 14, 21 y 28 de hospitalización para recuento de levaduras; hemocultivos día 0, y otros de acuerdo a la clínica. Se utilizó Sabouraud, CHROMagar Candida- R®,BACTEC (PEDS PLUS/ F® y Mycosis IC/F®) y MinitekTM®. Resultados: se estudiaron 60 episodiosde NF en 45 pacientes, entre 2 y 13 años, promedio días neutropenia 6,3; promedio hospitalización 13,6 días. Al ingreso 14/60 estaban colonizados en orofarínge y 28/60 en MF. Predominó C. albicans; C. tropicalis y C. parapsilosis aumentaron posteriormente; se encontró una tendencia al aumento de la colonización, no significativo, con los días de hospitalización. No se presentaron fungemias. Conclusiones: no se pudo relacionar los recuentos con diseminación, posiblemente por NF de corta duración. Las especies diferentes a C. albicans son importantes, se requieren estudios para determinar el origen intra o extrahospitalario y su sensibilidad

[The conceptual revolutions about nature as imposed by 20th century physics]. / Las revoluciones conceptuales acerca de la naturaleza impuestas por la física del siglo XX.

A catalogue is offered of the thirteen conceptual--and observational--revolutions which took place in twentieth century Physics, those which should be considered the most revelant for their significance in the scientific and philosophical thought about Nature as established along that century. The are organized in the three areas where they were originated: Relativity, Quantum Physics and Cosmology. Several of these conceptual revolutions appeared in Physics explicitly, while the rest only happened to arise in a latent way. The ones and the others are remarked in this contribution with philosophical expressions and through the world horizon, a perspective which opens in a general manner each revolution to the whole of the scientific and philosophical of the past century.

Evaluation of methods for detecting recombination from DNA sequences: computer simulations.

Recombination is a key evolutionary process that shapes the architecture of genomes and the genetic structure of populations. Although many statistical methods are available for the detection of recombination from DNA sequences, their absolute and relative performance is still unknown. Here we evaluated the performance of 14 different recombination detection algorithms. We used the coalescent with recombination to simulate DNA sequences with different levels of recombination, genetic diversity, and rate variation among sites. Recombination detection methods were applied to these data sets, and whether they detected or not recombination was recorded. Different recombination methods showed distinct performance depending on the amount of recombination, genetic diversity, and rate variation among sites. The model of nucleotide substitution under which the data were generated did not seem to have a significant effect. Most methods increase power with more sequence divergence. In general, recombination detection methods seem to capture the presence of recombination, but they are not very powerful. Methods that use substitution patterns or incompatibility among sites were more powerful than methods based on phylogenetic incongruence. Most methods do not seem to infer more false positives than expected by chance. Especially depending on the amount of diversity in the data, different methods could be used to attain maximum power while minimizing false positives. Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand.