Reliability of the Greulich & Pyle method for bone estimation in a Spanish sample

As an indicator of growth rate, bone age is used to determine the level of development and to predict chronological age when this is not known. The repeatability of the measurement (intra-and inter-observer) and the systematic error inherent to Bone Age (BA) estimation using the Greulich & Pyle (GPA) method has been estimated using a sample from the Spanish population. The inter-observer Lin's concordance correlation coefficient was ρc=0.98, with a value of 0.05±0.52 for girls and 0.06±0.44 for boys (difference between observations in years), whereas the intra-observer Lin's concordance correlation coefficient was ρc=0.99 (0.05±0.27 for girls and 0.10±0.36 for boys). The mean difference between the bone and chronological ages was 0.51±1.13 years in girls and 0.32±1.11 years in boys. Given the systematic errors with regard to the reference population, we propose the adjustment required to apply the ages calculated according to the atlas and indicate the limitations inherent to predicting chronological age when only information from the bones in the hand and wrist is used

An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment

Background: In integrative bioinformatic analyses, it is of great interest to stablish the equivalence between gene or (more in general) feature lists, up to a given level and in terms of their annotations in the Gene Ontology. The aim of this article is to present an equivalence test based on the proportion of GO terms which are declared as enriched in both lists simultaneously. Results: On the basis of these data, the dissimilarity between gene lists is measured by means of the Sorensen-Dice index. We present two flavours of the same test: One of them based on the asymptotic normality of the test statistic and the other based on the bootstrap method. Conclusions: The accuracy of these tests is studied by means of simulation and their possible interest is illustrated by using them over two real datasets: A collection of gene lists related to cancer and a collection of gene lists related to kidney rejection after transplantation

Non-chemical weed management for sustainable rice production in the Ebro Delta

Weed control is one of the major challenges in rice cultivation, and the use of agrochemicals in this crop is severely restricted under the new European agricultural policy. Therefore, new effective non-chemical weed control agents are the key to sustain European rice production. We investigated four non-chemical weed management strategies in the Ebro Delta in north-eastern Spain, two in dry-seeded rice fields and two in water-seeded rice fields. In addition, two controls per sowing conditions were included; a positive control consisting in chemical herbicides treatment and a negative control consisting in no weeding and no seeding. In all tests but negative controls, the rice variety Argila was employed. "Simple dry seeding" was the best treatment for dry seeding, while "false seeding" (stale seed bed) and planting was the best performing under water seeding conditions. Both mentioned treatments were as effective as chemical control in reducing the density of weeds and the weeding time for those species more abundant in Ebro Delta rice fields (i.e. Echinochloa oryzoides, Echinochloa crus-galli, Scirpus maritimus and Heteranthera reniformis). Our results indicated that some of the non-chemical weed control methods can reduce weed pressure to levels similar to standard chemical herbicide treatments under certain seeding conditions

An equivalence approach to the integrative analysis of feature lists

Background Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting lists of genes into predefined levels of the Gene Ontology, in such a way that a multinomial model can be used for estimation and testing. Of particular interest is the fact that it may be used for proving equivalence (in the sense of 'enough similarity') between two lists, instead of proving differences between them, which seems conceptually better suited to the end goal of establishing similarity among gene lists. An equivalence method has been derived that uses a distance-based approach and the confidence interval inclusion principle. Equivalence is declared if the upper limit of a one-sided confidence interval for the distance between two profiles is below a pre-established equivalence limit. Results In this work, this method is extended to establish the equivalence of any number of gene lists. Additionally, an algorithm to obtain the smallest equivalence limit that would allow equivalence between two or more lists to be declared is presented. This algorithm is at the base of an iterative method of graphic visualization to represent the most to least equivalent gene lists. These methods deal adequately with the problem of adjusting for multiple testing. The applicability of these techniques is illustrated in two typical situations: (i) a collection of cancer-related gene lists, suggesting which of them are more reasonable to combine -as claimed by the authors- and (ii) a collection of pathogenesis-based transcript sets, showing which of these are more closely related. The methods developed are available in the goProfiles Bioconductor package. Conclusions The method provides a simple yet powerful and statistically well-grounded way to classify a set of genes or other feature lists by establishing their equivalence at a given equivalence threshold. The classification results can be viewed using standard visualization methods. This may be applied to a variety of problems, from deciding whether a series of datasets generating the lists can be combined to the simplification of groups of lists

Medidas de divergencia en análisis de datos

Un problema interesante que se plantea en análisis de datos es la elección adecuada de medidas que cuantifiquen las analogías y diferencias entre individuos, poblaciones o grupos de poblaciones. De forma general, han sido desarrolladas distintas formas de elección de tales medidas, siendo destacables las medidas que provienen de diferencias intrínsecas entre individuos, las medidas que provienen de consideraciones sobre funciones, de entropía, y las medidas que provienen exclusivamente de consideraciones teóricas. En esta memoria, hemos estudiado estas medidas a partir de la clasificación de medidas de distanciación realizada por Burbea y Rao (1982). En la primera parte (cap. 1, 2 y 3), se presentan las distintas divergencias, se estudian inter-relaciones y se analiza la convexidad. En la segunda parte (cap. 4) se estudian las métricas diferenciales asociadas a divergencias invariantes frente a cambios no singulares de parámetros y variables aleatorias. En la tercera parte (cap. 5 y 6) se analizan las relaciones entre la J-divergencia y las entropías comúnmente utilizadas. Finalmente, en los anexos I y II se presentan los programas utilizados en el cap. 6

BECCS-Hub i Stockholm: Integration av biogas i BECCS värdekedja

Bioenergi med avskiljning och lagring av koldioxid (BECCS) håller på att utvecklas till en viktig teknik för negativa utsläpp och planeras spela en avgörande roll för Sveriges mål om noll nettoutsläpp av koldioxid till 2045. Stora BECCS-anläggningar förväntas, till exempel den som planeras i Värtahamnen av Stockholm Exergi. Mindre punktkällor för koldioxidutsläpp, som avloppsreningsverket i Käppala, en biogasproducent, skulle också kunna bidra till negativa utsläpp genom BECCS, dvs. genom att fånga upp biogen koldioxid från anaerob jäsning. Ekonomiska faktorer begränsar dock implementeringen av hela BECCS-värdekedjan i mindre skala. Genom att använda en närliggande större BECCS-anläggning kan dessa kostnadsbarriärer övervinnas genom att skapa nav för BECCS och utnyttja synergier.  I detta arbete undersöks de tekniska och ekonomiska utmaningarna med att integrera en CO2-ström från Käppala WWTP med Stockholm Exergis anläggning. Olika scenarier för CO2-integrering identifierades, med beaktande av flera faktorer, inklusive CO2-koncentration och renhetsbegränsningar för kondensering, kortdistanstransport och affärsmodell bakom biogasproducenten.  Käppala reningsverk släpper för närvarande ut biogen CO2 i form av en CO2/luftblandning till atmosfären. Detta arbete visade att CO2 kan tas emot av Stockholm Exergi i form av en CO2/luftblandning, CO2-gas eller kondenserad CO2. Käppala reningsverk skulle antingen kunna behålla sin nuvarande vattenreningsprocess, som ger CO2/luftblandningen, eller modernisera sin biogasuppgraderingsprocess för att producera koncentrerad CO2. Vidare konstaterades att en rörledning är det mest ekonomiska alternativet för kortdistanstransport av CO2, antingen i en blandning eller i koncentrerad form, men långa ledtider kräver långsiktig planering. Om transporten istället sker med lastbilar krävs en ombyggnad och ett förvätskningssteg vid Käppalaverket.  En litteraturgenomgång av tillgängliga tekniker för Käppala reningsverk identifierade en membranprocess som den mest lämpliga tekniken för en modernisering av biogasuppgraderingsprocessen. Modellering och simuleringar med MATLAB/Aspen Plus utvärderade hålfibermembranmoduler och två material, 6FDA-durene och Matrimid® 5218. Den förstnämnda presterade bättre för CH4/CO2-separation men uppnådde inte renhetskraven för biometan under de fastställda antagandena.  Framtida arbete bör fokusera på rigorös ekonomisk genomförbarhet, utforskning av alternativa integrationsscenarier och identifiering av problematiska föroreningar och dess inverkan på kondensering och BECCS-värdekedjan. Bio-energy with carbon capture and storage (BECCS) is emerging as a major negative emission technology and is scheduled to play a crucial role to Sweden’s net-zero goal by 2045. Large BECCS facilities are anticipated, such as the one planned in Värtahamnen by Stockholm Exergi. Smaller CO2 point sources like Käppala wastewater treatment plant (WWTP), a biogas producer, could also contribute to negative emissions through BECCS, i.e., by capturing the biogenic CO2 from anaerobic fermentation. However, economic constraints limit the implementation of the entire BECCS value chain on a smaller scale. Utilizing a nearby larger BECCS facility can help overcome these cost barriers by creating hubs for BECCS, leveraging synergies.  This work explores the technical and economic challenges of integrating a CO2 stream from Käppala WWTP with Stockholm Exergi’s facility. Various scenarios for CO2 integration were identified, considering multiple factors, including CO2 concentration and purity constraints for liquefaction, short-distance transport, and business model behind the biogas producer.  Käppala WWTP currently releases biogenic CO2 in the form of a CO2/air mixture to the atmosphere. This work found that CO2 can be received by Stockholm Exergi in the form of a CO2/air mixture, CO2 gas, or liquefied CO2. Whereas Käppala WWTP could either keep their current water scrubbing process, yielding the CO2/air mixture, or perform a revamp of their biogas upgrading process to produce concentrated CO2. Moreover, it was found that a pipeline is the most economical option for short-distance transport of CO2, either in a mixture or concentrated form, but long lead times make necessary long-term planning. If instead transport is carried out by trucks, a revamp and a liquefaction stage at Käppala WWTP are necessary.  A literature review on the available technologies targeted at Käppala WWTP identified a membrane process as the most appropriate technology for a revamp of the biogas upgrading process. Modeling and simulations using MATLAB/Aspen Plus evaluated hollow fiber membrane modules and two materials, 6FDA-durene and Matrimid® 5218. The former performed better for CH4/CO2 separation but did not achieve bio-methane purity requirements under the established assumptions. Future work should focus on rigorous economic feasibility, exploring alternative integration scenarios, and identification of problematic impurities and its impact on liquefaction and BECCS value chain.

Convexidad y simetría de la J-divergencia generalizada

En este trabajo se caracteriza la simetría de la J-divergencia generalizada en términos del parámetro y de la función que la determina. Se plantea seguidamente la convexidad y la simetrización en función del parámetro, atendiendo a la forma de la función f(t) que la determina. Finalmente, se revisa la convexidad en función de las variables atendiendo a la concavidad y convexidad de las funciones f(t) y 1/f''(t)

Medidas de incertidumbre asociadas a J-divergencias

In this paper we show a family of uncertainty measures, related with the J-divergences. They are obtained through a distance between a distribution and the distribution with equiprobable events. We study some theoretical properties of the family, taking into account the loss of uncertainty, the concavity and the condition to be a decisive measure. Finally, we compare some sample characteristics of the uncertainty measures defined by the function f(t) = -t log t, with the entropy measures most commonly usedEn este trabajo se presenta la familia de medidas de incertidumbre asociadas a J-divergencias, que resultan de la distancia entre una distribución y la distribución en la que todos los procesos son equiprobables. Se estudian propiedades teóricas de la familia atendiendo a la pérdida de incertidumbre, a la concavidad y a la condición de medida decisiva. Finalmente se compara a nivel muestral la medida de incertidumbre definida por la función f(t) = -t log t con las medidas de entropía comúnmente usada

Operation of transit corridors served by two routes: Physical design, synchronization, and control strategies

Many transit network layouts require the operation of multiple routes along a common transit segment in the busiest area of the city. At some points, these routes branch out to provide spatial coverage to the city periphery. These schemes allow more efficient deployment of resources at the expense of introducing more complexity into the system operation. This study aims to determine the effect of the branched layout of a corridor, demand distribution and traffic lights on the total cost of the system as well as its service regularity. The transit corridor is operated by buses, although it can be generalized for other transit modes. An operational model to estimate the travel and waiting time of users and the performance of buses on each route segment is developed. The model considers the stochastic effect of the passenger arrivals at stops and vehicle acceleration–deceleration rates. An optimization procedure to determine the optimal headway and relative synchronization of routes, which minimizes the total cost incurred by transit agencies and users or the headway variations in the common route segment, is introduced. Furthermore, a performance evaluation of bus control strategies based on a combination of holding points and green extensions at traffic signals in the H10 cross-town corridor of Barcelona’s new bus network is presented