An optimization model for metabolic pathways

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp441/DC1)

Características generales de las subcuencas del margen peninsular meditarráneo ("Rift" del Surco de Valencia)

This paper describes the general characteristics, namely the geometry and the sedimentary infill, of several troughs of Tertiary age present in the off-shore eastem Mediterranean margin of Spain. Al1 of them are included within the Valencia Trough, a rift basin developed during Paleogene and early Miocene times between the Balearic archipelago and mainland Spain. Although some authors (Soler et al., 1983; Fontboté et al., 1990; Roca and Desegaulx, 1992; Watts and Torné, 1992; Martínez del Olmo, 1994) have recently described the Valencia Trough as a foredeep basin of the Betics, we think that the referred foredeep does not extend as far as to the westernmost area of the Mediterranean. This is based on the evidence provided by the interpretation of numerous seismic surveys and nearly two hundred wells drilled without finding a single repetition or a clear evidence of compression in the area of this study. This rift is tbe southemmost branch of the European rift, which crosses most of western Europe from the Rhine graben through the westem Alps southwards into Morocco along the eastem coast of Spain (Sanz de Galdeano, 1990; Fontboté et al., 1990). The substratum of the basin is basically formed by Mesozoic (mainly carbonates) and pre-Mesozoic sediments (mainly clastics and metamorphics), folded and deformed during the Pyrenean orogeny and later fractured as horsts and grabens during the rift stage. The carbonates were severely fractured and intensively karsted during subaerial exposure following the deformation of the region. These processes have enhanced tbeir reservoir cbaracteristics (porosity and permeability) thus allowing the accumulation of hydrocarbons. Aborted during middle Miocene times, this rift started its development in the north during Paleogene times (Rosas and Barcelona troughs) and the sediments of this age constitute the bulk of the infill. On the contrary, in the southern sub-basins (Tarragona and Castellón troughs) the formation of the rift was younger, dunng early middle Miocene times, and the bulk of sediments infilling the troughs are of this age. This change in the age of the sedimentary infill, younger towards the south paralells the southwards development of the main rift. The sediments were filling the rift troughs, and by middle Miocene times al1 reliefs (horsts and grahens) had been leveled off. During early Miocene times the sedimentation in the troughs (mainly starved basins) took place under restricted marine conditions that favored the accumulation and preservation of the organic matter and the subsequent development of hydrocarhon source beds in some of them (Demaison and Bourgeois, 1984). The high thermal gradient, typical of rift hasins, favored the early maturation of the organic matter. The migration of the newly generated hydrocarbons into the neighbour paleoreliefs, mostly formed by karsted carbonates (Martínez del Olmo and Esteban, 1983), brought about severa1 oil fields that have been actively explored and exploited. So far only in the Tarragona trough commercial accumulations have been found (Amposta, Casablanca, Dorada and Tarraco) but other troughs (namely Rosas and Barcelona) have had good shows and the geocheniical analysis have also demonstrated the existence of good source rocks. Frorn the middle Miocene on, the sedimentation changed dramatically to a prograding continental shelf of passive margin type. Two megasequences are distinguished: the first one during the rniddle-late Miocene and the second one during Plio-Quatemary times, separated by the Messinian unconformity that locally produced important erosional canyons in the underlying sediments

Observational epidemiological study to identify the clinical profile of naïve patients starting antiretroviral (ARV) therapy in Spain

Purpose of the study: To identify the proportion of patients starting ARV treatment with NNRTIs or with a PI/r and to explore and compare their clinical profile establishing different factors whereby physicians select the initial ARV treatment in a Spanish clinical setting. Methods: An observational study was conducted in two different phases. In Phase I a cross-sectional registration was conducted for patients who initiated ARV treatment in a 6-month period in 65 Spanish hospitals. In Phase II clinical and social-demographic features were collected retrospectively of patients who visited HIV clinics between August and November 2010 who had started ARV treatment containing an NNRTIs or a PI/r in Phase I. Summary of results: In Phase I, 1,687 subjects who initiated ARV treatment were registered, of which 53% started with an NNRTI-based regimen whereas 42% started with a PI/r-based regimen. Two percent of the treatment initiations occurred in a clinical trial. In Phase II, 642 patients were paired consecutively and retrospectively. The group of patients was composed of predominantly male subjects (81% vs 19%). The median time between diagnosis and the start of ARV treatment was 3.6±5.3 years. At the initiation of treatment, 72% of patients had a CD4 count below 350 cells/µl. Although treatment based on NNRTIs in naïve patients is the most frequent option in Spain, the analysis of clinical profiles shows that PI/r-based therapy is more often used than NNRTIs with statistical significance in patients with high viral load, Fig. A (≥100.000 copies/ml) (58% vs 42%; OR:1,75; 95% CI: 1,26–2,43; p<0,01), with CD4 cell counts <200 cells/µl, Fig. B (68% vs 31%; OR: 2,92; 95% CI: 1,99–4,27; p<0,01), and in patients at CDC stage C (65% vs 35%; OR: 2,05; CI: 1,27–3,31; p<0,01). Conclusions: In Spain, HIV is still diagnosed late (as measured by CD4 count<350 cells/µl). Treatment based on NNRTIs are more frequently used in naïve patients, although PIs/r-based regimens play an important role being the preferred option in patients with high viral load (≥100.000 copies/ml) and low CD4 cell count (<200 cells/µl)

Tasa de éxito subjetivo y objetivo en pacientes operados con cinta suburetral transobturatriz: ocho años de seguimiento

Indexación: Scopus; Scielo.Antecedentes: La Incontinencia Urinaria de Esfuerzo (IOE) representa el 50% de las incontinencias urinarias en la mujer, produciendo un gran impacto en su calidad de vida. Actualmente el TOT es una de las técnicas quirúrgicas más utilizadas para su tratamiento. Objetivos: Determinar la tasa de éxito objetiva y subjetiva de las pacientes operadas por IOE e incontinencia de orina mixta (IOM) mediante TOT, y determinar la tasa de complicaciones perioperatorias. Métodos: Se realizó un estudio retrospectivo de cohorte de 8 años de seguimiento, en el que se evaluó mediante anamnesis, examen físico y protocolos quirúrgicos la tasa de éxito objetivo y subjetivo del TOT. Resultados: La tasa de éxito objetivo y subjetivo fue 92% y 76% respectivamente. El 8,3% de las pacientes presentó alguna complicación y la tasa de exposición de malla fue de 1,2%. Conclusiones: El TOT es una excelente alternativa para el tratamiento de la IOE en el Hospital de Quilpué.http://ref.scielo.org/6tnxn

Reliability and validity of an instrument that uses photographs to measure the ability for differential diagnosis of injuries caused by pressure and/or incontinence

Indexación: Scopus; Scielo.Objetivo: Evaluar la fiabilidad y validez de un instrumento que permite medir la habilidad visual para identificar y clasificar Dermatitis Asociada a Incontinencia (DAI), Ulceras por Presión (UPP) y lesiones mixtas, por parte de profesionales de enfermería. Material y método: Se aplicó un instrumento autoadministrado conformado por 14 fotografías a una muestra por conveniencia de 28 profesionales de enfermería, donde se debía identificar la lesión y luego clasificar su estado de avance. A modo exploratorio se calculó la fiabilidad anidada con Alpha de Cronbach y la validez con Análisis de Componentes Principales (ACP). Resultados: La fiabilidad inicial de las 14 fotografías (Alpha de Cronbach= 0,174) fue baja y tras eliminar 7 la fiabilidad fue aceptable (Alpha de Cronbach= 0,709). Se estableció la presencia de dos dimensiones: por un lado, la habilidad de diagnosticar DAI que explica un 35% de la varianza y, por otro, la habilidad de diagnosticar UPP, que explica el 22% de la varianza, ya sea que se encuentren separadas o juntas en un mismo paciente. Las lesiones DAI son diagnosticadas en mayor proporción que las lesiones mixtas. Conclusión: El estudio aportó 6 fotografías fiables y válidas que pueden ser utilizadas en futuros trabajos para construir un instrumento más robusto que pueda ser utilizado en Chile para la capacitación en el área. La muestra estudiada tiene fortalezas en el diagnóstico de DAI y dificultades en el diagnóstico de lesiones mixtas.Aim: To evaluate the reliability and validity of an instrument that allows to measure the visual ability to identify and classify Incontinence Associated Dermatitis (IAD), Pressure Ulcers (PU) and mixed lesions, by nursing professionals. Material and method: A self-administered instrument consisting of 14 photographs was applied to a convenience sample of 28 nurses. A set of 14 photographs were shown in which they were asked to identify and then classify the state of the lesion. In an exploratory manner, the nested reliability was calculated with Cronbach’s Alpha and the validity with Principal Component Analysis (PCA). Results: The initial reliability of the 14 photographs was low (Cronbach Alpha = 0.174), after removing 7 photographs the reliability became acceptable (Cronbach Alpha = 0.709). The presence of two dimensions was established: on the one hand the ability to diagnose IAD, which explains 35% of the variance, and secondly, the ability to diagnose PU, which explains 22% of the variance, whether they are separated or together in the same patient. IAD is better diagnosed than mixed lesions. Conclusion: The study provided 6 reliable and valid photos that can be used in future work to build a more robust instrument that can be used in Chile for training in the area. The studied sample shows strengths when diagnosing IAD and difficulties when diagnosing mixed lesions. © 2017, Universidad de Concepcion. All rights reserved.https://scielo.conicyt.cl/scielo.php?script=sci_arttext&pid=S0717-95532017000300059&lng=en&nrm=iso&tlng=e

Tratamiento quirúrgico en las cifosis congénitas: Revisión de 14 pacientes

Los autores efectúan una revisión de 14 pacientes con cifosis congénita, intervenidos entre los años 1979-1989, con un seguimiento medio de 7 años. La edad media preoperatoria fue de 11 años (todos ellos mayores de 5 años), con una cifosis media de 7 9 . En 6 casos se realizó una artrodesis posterior y en 8 una anterior combinada con una fusión posterior. Inicialmente obtuvieron una corrección media de la curva de 18° con la artrodesis posterior y 20° con la artrodesis combinada. La pérdida postoperatoria final fue de 10° y 8° respectivamente. En un caso, se produjo una pseudoartrosis por fusión corta. Como complicaciones postoperatorias en 5 pacientes, una radiculopatía, una infección superficial y cuatro protusiones de material que requirieron su extracción. Los autores analizan los factores que han podido influir en los resultados obtenidos, comparándolos posteriormente con los conseguidos por otros centros hospitalarios importantes.Fourteen patients with congenital kyphosis treated surgically between 1979- 1989 were reviewed. All had a follow-up of 2 years or more, with an average follow-up of 7 years. The average age at surgery was 11 and the average kyphosis was 79°. Six cases had posterior fusion only and eigth had combined anterior and posterior fusion. The results showed an average correction of the curve at surgery of 18° with posterior arthrodesis and 20° with combined arthrodesis. There was thus an average loss of 10° and 8° respectively from the time of surgery in both types of treatment. Pseudoarthrosis by short fusion ocurred in one case. Other complications after surgery were 1 radiculopathy, one wound infection and four rod protusion (six patients). The factors that have influence in this results were analysed. A comparison from the results of treatment at other medical centers was also carried out

Changes in Salivary Analytes of Horses Due to Circadian Rhythm and Season: A Pilot Study.

This study aims to evaluate the circadian and circannual variations in a panel of analytes in horse saliva that have been previously described as biomarkers related to stress and disease, in order to interpret them correctly when they are measured in this species. This panel of analytes integrated cortisol, salivary alpha-amylase (sAA), lipase (Lip), total esterase (TEA), butyrylcholinesterase (BChE), adenosine deaminase (ADA), γ-glutamyl transferase (gGT), creatine kinase (CK), urea, total bilirubin, total protein (TP), and phosphorus. These analytes were measured in saliva obtained from a population of five clinically healthy mares from 06:30 to 20:30, every 2 h over two consecutive days in two different photoperiod seasons, winter and spring. The temperature and relative humidity did not change between the two consecutive days sampled in each sampled season, and no thermal discomfort was observed. Changes throughout the course of the day were observed for cortisol, sAA, TEA, BChE, ADA, and CK. However, a circadian pattern was only observed for cortisol, TEA, BChE, ADA, and CK. Moreover, the values obtained for sAA, Lip, and BChE were significantly different between seasons, with different daily rhythms for cortisol, TEA, BChE, and ADA depending on the season. In conclusion, this pilot study indicates that the time of the day and the season influence salivary analytes in horses, showing a rhythmic pattern for cortisol, TEA, BChE, ADA, and CK. These factors should thus be taken into consideration for the interpretation of analytes in horse saliv