Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Farmers’ knowledge and perceptions of potato pests and their management in Uganda

As we initiate entomological research on potato (Solanum tuberosum L.) in Uganda, there is need to understand farmers’ knowledge of existing insect pest problems and their management practices. Such information is important for designing a suitable intervention and successful integrated pest management (IPM) strategy. A farm household survey using a structured questionnaire was conducted among 204 potato farmers in six districts of Uganda (i.e., Kabale, Kisoro, Mbale, Kapchorwa, Mubende, and Kyegegwa) during August and September 2013. Diseases, insect pests, price fluctuations, and low market prices were the four highest ranked constraints in potato production, in order of decreasing importance. Cutworms (Agrotis spp.), aphids (Myzus persicae (Sulzer)), and potato tuber moth (Phthorimaea operculella (Zeller)) were the three most severe insect pests. Ants (Dorylis orantalis Westwood), whiteflies (Bemisia tabaci (Gennadius)), and leafminer flies (Liriomyza huidobrensis (Blanchard)) were pests of moderate importance. Major yield losses are predominantly due to late blight (Phytophthora infestans (Mont.) de Bary) and reached 100% without chemical control in the districts of Kabale, Kisoro, Mbale, and Kapchorwa. On average, farmers had little to moderate knowledge about pest characteristics. The predominant control methods were use of fungicides (72% of respondents) and insecticides (62% of respondents). On average, only 5% of the 204 farmers knew about insect pests and their natural enemies. This lack of knowledge calls for training of both farmers and extension workers in insect pest identification, their biology, and control. Empowering farmers with knowledge about insect pests is essential for the reduction of pesticide misuse and uptake of more environmentally friendly approaches like IPM. Field surveys would need follow-up in order to assess the actual field infestation rates and intensities of each insect pest and compare the results with the responses received from farmers.

The Individual is Nothing, the Class Everything: Psychophysics and Modeling of Recognition in Obect Classes

Most psychophysical studies of object recognition have focussed on the recognition and representation of individual objects subjects had previously explicitely been trained on. Correspondingly, modeling studies have often employed a 'grandmother'-type representation where the objects to be recognized were represented by individual units. However, objects in the natural world are commonly members of a class containing a number of visually similar objects, such as faces, for which physiology studies have provided support for a representation based on a sparse population code, which permits generalization from the learned exemplars to novel objects of that class. In this paper, we present results from psychophysical and modeling studies intended to investigate object recognition in natural ('continuous') object classes. In two experiments, subjects were trained to perform subordinate level discrimination in a continuous object class - images of computer-rendered cars - created using a 3D morphing system. By comparing the recognition performance of trained and untrained subjects we could estimate the effects of viewpoint-specific training and infer properties of the object class-specific representation learned as a result of training. We then compared the experimental findings to simulations, building on our recently presented HMAX model of object recognition in cortex, to investigate the computational properties of a population-based object class representation as outlined above. We find experimental evidence, supported by modeling results, that training builds a viewpoint- and class-specific representation that supplements a pre-existing repre-sentation with lower shape discriminability but possibly greater viewpoint invariance.

Nanoscale heat transfer and information technology

The summary from Goodson’s group on their recent work on heat transfer issues in the microelectronics and data storage industries illustrate the critical role of heat transfer for some areas of information technology. In this article, we build on their work and discuss some directions worthy of further research.

Description and analysis of pulmonary rehabilitation care programs current state in four cities of Colombia

Purpose: there are many studies reporting the benefits of pulmonary rehabilitation, but few of them exhibit the behavior and activities of these services. This article presents the characteristics of services, parts management and training level of team members, in addition to the variables or instruments used to measure the effectiveness and impact in these programs. Method: it was made a cross sectional convenience sample which included seven pulmonary rehabilitation services in four Colombian cities (Bogotá, Medellín, Manizales and Cali), selected by the coverage, for having at least one year of experience and for being formally established and recognized nationwide. The interdisciplinary team of each service answered a survey that was validated through a pilot test and expert consensus. Participation was voluntary. Results: labor onset pulmonary rehabilitation services correspond to an average of a decade, with COPD and asthma pathologies of attention. The programs are characterized by an outpatient treatment with an average duration of eight to twelve weeks, with a frequency of an hour three times a week. Also, the director of the service is regularly a pulmonologist and the coordinator a physiotherapist (57.14%). The posgradual training of these professionals is notable, and they report to have procedural, administrative and communicative skills, but qualify regular there research skills. The physical and technological resources are well tested. 71.42% have done impact studies, but only 28.57% have been published. All have in common training in upper limbs, lower limbs, respiratory muscles, counseling, functional assessment and quality of life. The effectiveness and impact of programs is measured by the walking test, quality of life questionnaires and activities of daily living.

Synthesis, structure and reactivity of novel CuI, CuII and CuIII complexes containing triaza and hexaaza macrocyclic ligands

El treball de tesi s'emmarca dins del camp de la bioinorgànica, disciplina que estudia les propietats estructurals i de reactivitat dels centres actius dels enzims, servint-se de models síntètics de baix pes molecular per tal d'intentar reproduïr la reactivitat presentada per l'enzim i conèixer els mecanismes de reacció a nivell molecular que tenen lloc en els processos biològics.1 Més concretament el treball posa especial èmfasi en els processos d'activació d'oxigen molecular que tenen lloc en les metaloproteïnes de Coure del Tipus 3, com són l'hemocianina i la tirosinasa, ambdues presentant un complex dinuclear de Cu(I)) en el centre actiu de la forma reduïda, capaç d'activar l'O2 cap a espècies de tipus peròxid.2 Un altre camp d'interès ha estat l'estudi dels processos d'activació d'enllaços C-H no activats en hidrocarburs, tant per la seva importàcia a nivell industrial com per comprendre els mecanismes intrínsecs d'aquesta activació a través de metalls de trancisió.3,4 Durant el treball de tesi presentat s'ha desenvolupat la síntesi de nous complexes de Coure(I), Coure(II) y Cu(III) utilitzant lligands macrocíclics de tipus triaza i hexaaza, i s'han estudiat la seves propietats estructurals així com la seva reactivitat. La reacció dels lligands triazacíclics H32m, H2Me33m i H33m amb sals de coure(II) dóna lloc a una reacció de desproporció de Cu(II) per obtenir-se en quantitats equimolars un complex organometàl·lic de Cu(III) i un complex de Cu(I). La caracterizació estructural exhaustiva dels complexes del tipus aryl-Cu(III) evidencia la formació d'un enllaç organometàl·lic entre l'àtom de Cu(III) i el carboni més próxim de l'anell aromàtic del lligand. Aquesta reacció, a més de representar una nova forma de desproporció en la química del Cu, suposa l'activació d'un enllaç C-H aromàtic a temperatura ambient que, mitjançant l'estudi cinètic d'aquesta desproporció per espectroscòpia UV-Vis, dels càlcul de l'efecte cinètic isotòpic utilitzant el lligand deuterat en el C-H de l'anell, juntament amb el recolzament teòrics dels càlculs DFT per a la optimització de geometries d'intermedis de reacció, ens permeten proposar un mecanisme de reacció pel nostre sistema, on l'activació de l'enllaç C-H aromàtic transcorre per la formació d'un enllaç de tipus agòstic C-H ? Cu(II),5 seguit de la desprotonació del C-H aromàtic per acció d'una base i posterior transferència electrònica per obtenir el complex organometàlic de Cu(III) i el complex de de Cu(I). En quant a la reactivitat d'aquests complexes organometàl·lics aryl-Cu(III) s'ha observat que una base en medi aquós causa la inestabilitat d'aquests compostos, evolucionant cap a la inserció d'un àtom d'oxigen sobre la posició activada de l'anell aromàtic, per a donar lloc a un complex dinuclear de Cu(II) amb dos grups fenoxo actuant de pont entre els àtoms metàl·lics. La reacció transcorre per un intermedi colorejat, caracteritzat com el complex ayl-Cu(III) monodesprotonat en una de les seves amines benzíliques, els quals s'observen igualment en la reacció dels correponents complexos de Cu(I) amb oxigen molecular (O2). És en els nostres sistemes en els quals es descriu per primera vegada la participació d'intermedis organometàl·lics Cu(III)-C en processos d'hidroxilació aromàtica, tals com el desenvolupat per l'enzim tirosinasa o per alguns dels seus models químics de síntesi.6,7,8 S'han estudiat les propietats magnètiques dels quatre bis(fenoxo)complexes de Cu(II) descrits, obtenint-se uns acoplaments de tipus antiferromagnètic o ferromagnètic de diversa magnitud, depenent del solapament orbitalari a l'enllaç Cu-O, a través del qual es produeix el superintercanvi. Nous complexos de Cu(I) sintetitzats amb lligands hexaazamacrocíclics han estat estudiats, i posant especial èmfasi a la seva reactivitat respecta a l'activació d'oxigen molecular (O2). S'ha observat una reactivitat diferenciada segons la concentració de complex de Cu(I) utilitzada, de manera que a altes concentracions s'obté un carbonato complex tetranuclear de Cu(II) per fixació de CO2 atmosfèric, mentre que a baixes concentracions s'observa la hidroxilació aromàtica intramolecular d'un dels anells benzílics del lligand, reacció que presumiblement transcorre per atac electrofílic d'un peroxo complex intermedi sobre el sistema ? de l'anell.6 Els resultats obtinguts en aquest treball ens mostren la facilitat per activar enllaços C-H aromàtics per metalls de transició de la primera sèrie (Cu, Ni) quan aquests estan suficientment pròxims a l'enllaç C-H, en unes condicions de reacció molt suaus (1atm., temperatura ambient). Els nous complexos organometàl·lics Aryl-Cu(III) són el producte d'una nova reacció de desproporció de Cu(II), així com un posició aromàtica activada que podria ser el punt de partida per l'estudi de funcionalització selectiva d'aquests grups aromàtics.

Dynamic management and restoration of virtual paths in broadband networks based on distributed software agents

La gestió de xarxes és un camp molt ampli i inclou molts aspectes diferents. Aquesta tesi doctoral està centrada en la gestió dels recursos en les xarxes de banda ampla que disposin de mecanismes per fer reserves de recursos, com per exemple Asynchronous Transfer Mode (ATM) o Multi-Protocol Label Switching (MPLS). Es poden establir xarxes lògiques utilitzant els Virtual Paths (VP) d'ATM o els Label Switched Paths (LSP) de MPLS, als que anomenem genèricament camins lògics. Els usuaris de la xarxa utilitzen doncs aquests camins lògics, que poden tenir recursos assignats, per establir les seves comunicacions. A més, els camins lògics són molt flexibles i les seves característiques es poden canviar dinàmicament. Aquest treball, se centra, en particular, en la gestió dinàmica d'aquesta xarxa lògica per tal de maximitzar-ne el rendiment i adaptar-la a les connexions ofertes. En aquest escenari, hi ha diversos mecanismes que poden afectar i modificar les característiques dels camins lògics (ample de banda, ruta, etc.). Aquests mecanismes inclouen els de balanceig de la càrrega (reassignació d'ample de banda i reencaminament) i els de restauració de fallades (ús de camins lògics de backup). Aquests dos mecanismes poden modificar la xarxa lògica i gestionar els recursos (ample de banda) dels enllaços físics. Per tant, existeix la necessitat de coordinar aquests mecanismes per evitar possibles interferències. La gestió de recursos convencional que fa ús de la xarxa lògica, recalcula periòdicament (per exemple cada hora o cada dia) tota la xarxa lògica d'una forma centralitzada. Això introdueix el problema que els reajustaments de la xarxa lògica no es realitzen en el moment en què realment hi ha problemes. D'altra banda també introdueix la necessitat de mantenir una visió centralitzada de tota la xarxa. En aquesta tesi, es proposa una arquitectura distribuïda basada en un sistema multi agent. L'objectiu principal d'aquesta arquitectura és realitzar de forma conjunta i coordinada la gestió de recursos a nivell de xarxa lògica, integrant els mecanismes de reajustament d'ample de banda amb els mecanismes de restauració preplanejada, inclosa la gestió de l'ample de banda reservada per a la restauració. Es proposa que aquesta gestió es porti a terme d'una forma contínua, no periòdica, actuant quan es detecta el problema (quan un camí lògic està congestionat, o sigui, quan està rebutjant peticions de connexió dels usuaris perquè està saturat) i d'una forma completament distribuïda, o sigui, sense mantenir una visió global de la xarxa. Així doncs, l'arquitectura proposada realitza petits rearranjaments a la xarxa lògica adaptant-la d'una forma contínua a la demanda dels usuaris. L'arquitectura proposada també té en consideració altres objectius com l'escalabilitat, la modularitat, la robustesa, la flexibilitat i la simplicitat. El sistema multi agent proposat està estructurat en dues capes d'agents: els agents de monitorització (M) i els de rendiment (P). Aquests agents estan situats en els diferents nodes de la xarxa: hi ha un agent P i diversos agents M a cada node; aquests últims subordinats als P. Per tant l'arquitectura proposada es pot veure com una jerarquia d'agents. Cada agent és responsable de monitoritzar i controlar els recursos als que està assignat. S'han realitzat diferents experiments utilitzant un simulador distribuït a nivell de connexió proposat per nosaltres mateixos. Els resultats mostren que l'arquitectura proposada és capaç de realitzar les tasques assignades de detecció de la congestió, reassignació dinàmica d'ample de banda i reencaminament d'una forma coordinada amb els mecanismes de restauració preplanejada i gestió de l'ample de banda reservat per la restauració. L'arquitectura distribuïda ofereix una escalabilitat i robustesa acceptables gràcies a la seva flexibilitat i modularitat.

The inclusive process of training in social museology: alternative museology in action in Carapateira, Portugal

Pierre Mayrand is a long-time member of ICTOP and founder of MINOM. He did graduate studies in Montreal and overseas, studying art history with a specialization in architecture and urban planning. In 1970, when the Université du Québec was founded, Pierre entered the teaching profession, participating (as director, professor, and researcher) in the setting up of programs in national heritage, museology and cultural development. He is still active in teaching and project development now as a altermuseologist.

The effects of training in the tracking procedure on the speechreading ability of two profoundly hearing-impaired children

This paper discusses a study to determine whether training employing in the tracking procedure would prove beneficial to profoundly hearing-impaired children in comprehension of spoken language.

Distribution and mobility of trace elements in soils and vegetation around the mining and smelting areas of Tharsis, Riotinto and Huelva, Iberian Pyrite Belt, SW Spain

Trace elements may present an environmental hazard in the vicinity of mining and smelting activities. However, the factors controlling their distribution and transfer within the soil and vegetation systems are not always well defined. Total concentrations of up to 15,195 mg center dot kg (-1) As, 6,690 mg center dot kg(-1) Cu, 24,820 mg center dot kg(-1) Pb and 9,810 mg center dot kg(-1) Zn in soils, and 62 mg center dot kg(-1) As, 1,765 mg center dot kg(-1) Cu, 280 mg center dot kg(-1) Pb and 3,460 mg center dot kg (-1) Zn in vegetation were measured. However, unusually for smelters and mines of a similar size, the elevated trace element concentrations in soils were found to be restricted to the immediate vicinity of the mines and smelters (maximum 2-3 km). Parent material, prevailing wind direction, and soil physical and chemical characteristics were found to correlate poorly with the restricted trace element distributions in soils. Hypotheses are given for this unusual distribution: (1) the contaminated soils were removed by erosion or (2) mines and smelters released large heavy particles that could not have been transported long distances. Analyses of the accumulation of trace elements in vegetation (median ratios: As 0.06, Cu 0.19, Pb 0.54 and Zn 1.07) and the percentage of total trace elements being DTPA extractable in soils (median percentages: As 0.06%, Cu 15%, Pb 7% and Zn 4%) indicated higher relative trace element mobility in soils with low total concentrations than in soils with elevated concentrations.

Factors affecting distribution and mobility of trace elements (Cu, Pb, Zn) in a perennial grapevine (Vitis vinifera L.) in the Champagne region of France

Soil and Vitis vinifera L (coarse and fine roots, leaves, berries) concentration and geochemical partitioning of Cu, Pb and Zn were determined in a contaminated calcareous Champagne plot to assess their mobility and transfer. Accumulation ratios in roots remained low (0.1-0.4 for Cu and Zn, <0.05 for Pb). Differences between elements resulted from vegetation uptake strategy and soil partitioning. Copper, significantly associated with the oxidisable fraction (27.8%), and Zn with the acid soluble fraction (33.3%), could be mobilised by rhizosphere acidification and oxidisation, unlike Pb, essentially contained in the reducible fraction (72.4%). Roots should not be considered as a whole since the more reactive fine roots showed higher accumulation ratios than coarse ones. More sensitive response of fine roots, lack of correlation between chemical extraction results and vegetation concentrations, and very limited translocation to aerial parts showed that fine root concentrations should be used when assessing bioavailability. (C) 2008 Elsevier Ltd. All rights reserved.

Adaptation of the Integrated Nitrogen Model for Catchments (INCA) to seasonally snow-covered catchments

Testing of the Integrated Nitrogen model for Catchments (INCA) in a wide range of ecosystem types across Europe has shown that the model underestimates N transformation processes to a large extent in northern catchments of Finland and Norway in winter and spring. It is found, and generally assumed, that microbial activity in soils proceeds at low rates at northern latitudes during winter, even at sub-zero temperatures. The INCA model was modified to improve the simulation of N transformation rates in northern catchments, characterised by cold climates and extensive snow accumulation and insulation in winter, by introducing an empirical function to simulate soil temperatures below the seasonal snow pack, and a degree-day model to calculate the depth of the snow pack. The proposed snow-correction factor improved the simulation of soil temperatures at Finnish and Norwegian field sites in winter, although soil temperature was still underestimated during periods with a thin snow cover. Finally, a comparison between the modified INCA version (v. 1.7) and the former version (v. 1.6) was made at the Simojoki river basin in northern Finland and at Dalelva Brook in northern Norway. The new modules did not imply any significant changes in simulated NO3- concentration levels in the streams but improved the timing of simulated higher concentrations. The inclusion of a modified temperature response function and an empirical snow-correction factor improved the flexibility and applicability of the model for climate effect studies.

A new Snow-SVAT to simulate the accumulation and ablation of seasonal snow cover beneath a forest canopy

A new snow-soil-vegetation-atmosphere transfer (Snow-SVAT) scheme, which simulates the accumulation and ablation of the snow cover beneath a forest canopy, is presented. The model was formulated by coupling a canopy optical and thermal radiation model to a physically-based multi-layer snow model. This canopy radiation model is physically-based yet requires few parameters, so can be used when extensive in-situ field measurements are not available. Other forest effects such as the reduction of wind speed, interception of snow on the canopy and the deposition of litter were incorporated within this combined model, SNOWCAN, which was tested with data taken as part of the Boreal Ecosystem-Atmosphere Study (BOREAS) international collaborative experiment. Snow depths beneath four different canopy types and at an open site were simulated. Agreement between observed and simulated snow depths was generally good, with correlation coefficients ranging between r^2=0.94 and r^2=0.98 for all sites where automatic measurements were available. However, the simulated date of total snowpack ablation generally occurred later than the observed date. A comparison between simulated solar radiation and limited measurements of sub-canopy radiation at one site indicates that the model simulates the sub-canopy downwelling solar radiation early in the season to within measurement uncertainty.