First Report of Heterodera zeae Koshy, Swarup & Sethi, 1971 (corn cyst Nematode) Infecting Corn (Zea mays) in Spain.

Heterodera zeae Koshy, Swarup & Sethi, 1971 (corn cyst nematode) is an important disease of corn in several areas of the world, including India, Nepal, Pakistan, Egypt, USA, Greece and Portugal (Subbotin et al., 2010). It is a sedentary semi-endoparasite feeding on corn roots and other Poaceae plants and has been associated with significant yield losses in corn (Subbotin et al., 2010). During autumn 2022 a plant-parasitic nematode survey performed in corn at central-western area of Spain (Talavera de la Reina, Toledo), revealed a commercial field with stunted plants. Nematodes were extracted from soil by centrifugal-flotation method (Coolen, 1979). Corn roots inspection detected infections by immature and mature cysts, and soil revealed also mature live cysts and second-stage juveniles (J2s) with a population density of 1010 eggs and J2s/500 cm3 soil (including eggs from cysts). J2s and cysts were processed to pure glycerine using De Grisse's (1969) method. DNA was isolated from single live fresh J2s specimens for amplifying and sequencing of cytochrome c oxidase subunit II (COII) mitochondrial region using the primer pair species-specific H.Gly-COIIF_inFOR/P116F-1R (Riepsamen et al., 2011); D2 and D3 expansion domains of the 28S rRNA were amplified using the D2A/D3B primers (De Ley et al. 1999); internal transcribed spacer (ITS) region using primers TW81/AB28 (Subbotin et al., 2001); and cytochrome c oxidase subunit 1 (COI) gene was amplified using the primers JB3/JB5 (Bowles et al., 1992). Brown cysts were lemon-shaped with a protruding vulval cone with fenestra ambifenestrate, bullae prominent below underbridge and characteristically arranged in finger-like bullae (Fig. 1). J2 with slightly offset lip region (3-5 annuli), stylet strong with rounded stylet knobs, lateral field with four lines, and tail short and tapering conically. Measurements of cysts (n=10) included body length 559 (432-688) µm, body width 450 (340-522) µm, fenestral length 40 (36-43) µm, semifenestral width 19 (17-21) µm, and vulval slit 40 (35-44) µm. J2 measurements (n=10) included body length 477 (420-536) µm, stylet length 21 (20-22) µm, tail length 51 (47-56) µm, and tail hyaline region 23 (20-26) µm. Morphology and morphometrics of cysts and J2, fit with original description and others from several countries (Subbotin et al., 2010). Two J2s individuals were sequenced for COII region (OQ509010-OQ509011) showing 97.1-98.1% similarity with H. zeae from USA (HM462012). Six almost identical 28S rRNA sequences from J2s (OQ449649-OQ449654) were 99.2-99.4% similar to 28S rRNA sequences of H. zeae from Greece, Afghanistan and USA (GU145612, JN583885, DQ328695). Four identical ITS DNA fragments from J2s (OQ449655-OQ449658) were 97.0-97.8% similar to ITS sequences of H. zeae from Greece, and China (GU145616, MW785771, OP692770). Finally, six COI sequences of 400 bp obtained for J2s (OQ449699-OQ449704) were under 87% similarity to several COI sequences of Heterodera spp. in NCBI, being a new molecular barcoding for identifying this species. On the basis of these results, the cyst nematodes isolated from the corn plants from the central-western area of Spain (Talavera de la Reina, Toledo) were confirmed as H. zeae and up to our knowledge it is the first report in Spain. This is a well-known pest of corn, causing important losses in this crop (Subbotin et al., 2010) and it was previously regulated as a quarantine nematode in the Mediterranean region (EPPO).

On the feasibility of the computational modelling of the endoluminal vacuum-assisted closure of an oesophageal anastomotic leakage.

Endoluminal vacuum-assisted closure (E-VAC) is a promising therapy to treat anastomotic leakages of the oesophagus and bowel which are associated with high morbidity and mortality rates. An open-pore polyurethane foam is introduced into the leakage cavity and connected to a device that applies a suction pressure to accelerate the closure of the defect. Computational analysis of this healing process can advance our understanding of the biomechanical mechanisms at play. To this aim, we use a dual-stage finite-element analysis in which (i) the structural problem addresses the cavity reduction caused by the suction and (ii) a new constitutive formulation models tissue healing via permanent deformations coupled to a stiffness increase. The numerical implementation in an in-house code is described and a qualitative example illustrates the basic characteristics of the model. The computational model successfully reproduces the generic closure of an anastomotic leakage cavity, supporting the hypothesis that suction pressure promotes healing by means of the aforementioned mechanisms. However, the current framework needs to be enriched with empirical data to help advance device designs and treatment guidelines. Nonetheless, this conceptual study confirms that computational analysis can reproduce E-VAC of anastomotic leakages and establishes the bases for better understanding the mechanobiology of anastomotic defect healing.

GITIRBio: A Semantic and Distributed Service Oriented-Architecture for Bioinformatics Pipeline.

The need to process large quantities of data generated from genomic sequencing has resulted in a difficult task for life scientists who are not familiar with the use of command-line operations or developments in high performance computing and parallelization. This knowledge gap, along with unfamiliarity with necessary processes, can hinder the execution of data processing tasks. Furthermore, many of the commonly used bioinformatics tools for the scientific community are presented as isolated, unrelated entities that do not provide an integrated, guided, and assisted interaction with the scheduling facilities of computational resources or distribution, processing and mapping with runtime analysis. This paper presents the first approximation of a Web Services platform-based architecture (GITIRBio) that acts as a distributed front-end system for autonomous and assisted processing of parallel bioinformatics pipelines that has been validated using multiple sequences. Additionally, this platform allows integration with semantic repositories of genes for search annotations. GITIRBio is available at: http://c-head.ucaldas.edu.co:8080/gitirbio.

Diffusion and Monod kinetics model to determine in vivo human corneal oxygen-consumption rate during soft contact lens wear / Modelo de difusión y cinética Monod para la determinación 'in vivo' de la tasa de consumo de oxígeno de la córnea en pacientes con lentes de contacto blandas

Purpose: We present an analysis of the corneal oxygen consumption Qc from non-linear models, using data of oxygen partial pressure or tension (pO2 ) obtained from in vivo estimation previously reported by other authors.1 Methods: Assuming that the cornea is a single homogeneous layer, the oxygen permeability through the cornea will be the same regardless of the type of lens that is available on it. The obtention of the real value of the maximum oxygen consumption rate Qc,max is very important because this parameter is directly related with the gradient pressure profile into the cornea and moreover, the real corneal oxygen consumption is influenced by both anterior and posterior oxygen fluxes. Results: Our calculations give different values for the maximum oxygen consumption rate Qc,max, when different oxygen pressure values (high and low pO2 ) are considered at the interface cornea-tears film (AU)

Objetivo: Presentamos un análisis del consumo de oxígeno de la córnea Qc a partir de modelos no lineales, utilizando los datos de presión parcial del oxígeno (pO2) obtenidos de la estimación in vivo obtenidas previamente por otros autores.1 Métodos: Asumiendo que la córnea es una capa homogénea única, la permeabilidad del oxígeno a través de la misma será la misma, independientemente del tipo de lentes que se utilicen sobre ella. La obtención del valor real de la tasa máxima de consumo de oxígeno Qc,max, es muy importante porque este parámetro está directamente relacionado con el perfil del gradiente de presión dentro de la córnea y, además, el consumo real de oxígeno de la córnea está influenciado tanto por los flujos de oxígeno anterior como posterior. Resultados: Nuestros cálculos aportan diferentes valores para la tasa de consumo máximo de oxígeno Qc,max, al considerar diferentes valores de la presión del oxígeno (pO2 elevado y bajo) en la interfase entre la córnea y la película lagrimal. Conclusión: Estos resultados son relevantes para calcular la presión parcial del oxígeno, que se encuentra en diferentes profundidades dentro del tejido de la córnea por detrás de las lentes de contacto con diferente transmisibilidad al oxígeno (AU)

Diffusion and Monod kinetics model to determine in vivo human corneal oxygen-consumption rate during soft contact lens wear.

PURPOSE: We present an analysis of the corneal oxygen consumption Qc from non-linear models, using data of oxygen partial pressure or tension (P(O2) ) obtained from in vivo estimation previously reported by other authors. (1) METHODS: Assuming that the cornea is a single homogeneous layer, the oxygen permeability through the cornea will be the same regardless of the type of lens that is available on it. The obtention of the real value of the maximum oxygen consumption rate Qc,max is very important because this parameter is directly related with the gradient pressure profile into the cornea and moreover, the real corneal oxygen consumption is influenced by both anterior and posterior oxygen fluxes. RESULTS: Our calculations give different values for the maximum oxygen consumption rate Qc,max, when different oxygen pressure values (high and low P(O2)) are considered at the interface cornea-tears film. CONCLUSION: Present results are relevant for the calculation on the partial pressure of oxygen, available at different depths into the corneal tissue behind contact lenses of different oxygen transmissibility.

Construction of coffee transcriptome networks based on gene annotation semantics.

Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST) and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF) using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

[Prevalence of severe sepsis in intensive care units. A national multicentric study]. / Prevalencia de sepsis grave en las Unidades de Cuidado Intensivo. Primer estudio nacional multicéntrico.

BACKGROUND: Severe sepsis (SS) is the leading cause of death in the Intensive Care Units (ICU). AIM: To study the prevalence of SS in Chilean ICUs. MATERIAL AND METHODS: An observational, cross-sectional study using a predesigned written survey was done in all ICUs of Chile on April 21st, 2004. General hospital and ICU data and the number of hospitalized patients in the hospital and in the ICU at the survey day, were recorded. Patients were followed for 28 days. RESULTS: Ninety four percent of ICUs participated in the survey. The ICU occupation index was 66%. Mean age of patients was 57.7+/-18 years and 59% were male, APACHE II score was 15+/-7.5 and SOFA score was 6+/-4. SS was the admission diagnosis of 94 of the 283 patients (33%) and 38 patients presented SS after admission. On the survey day, 112 patients fulfilled SS criteria (40%). APACHE II and SOFA scores were significantly higher in SS patients than in non SS patients. Global case-fatality ratio at 28 days was 15.9% (45/283). Case-fatality ratio in patients with or without SS at the moment of the survey was 26.7% (30/112) and 8.7% (17/171), respectively p <0.05. Thirteen percent of patients who developed SS after admission, died. Case-fatality ratios for patients with SS from Santiago and the other cities were similar, but APACHE II score was significantly higher in patients from Santiago. In SS patients, the independent predictors of mortality were SS as cause of hospital admission, APACHE II and SOFA scores. Ninety nine percent of SS patients had a known sepsis focus (48% respiratory and 30% abdominal). Eighty five patients that presented SS after admission, had a respiratory focus. CONCLUSIONS: SS is highly prevalent in Chilean ICUs and represents the leading diagnosis at admission. SS as cause of hospitalization, APACHE II and SOFA scores were independent predictors of mortality.