Blind docking of 260 protein-ligand complexes with EADock 2.0.

Molecular docking softwares are one of the important tools of modern drug development pipelines. The promising achievements of the last 10 years emphasize the need for further improvement, as reflected by several recent publications (Leach et al., J Med Chem 2006, 49, 5851; Warren et al., J Med Chem 2006, 49, 5912). Our initial approach, EADock, showed a good performance in reproducing the experimental binding modes for a set of 37 different ligand-protein complexes (Grosdidier et al., Proteins 2007, 67, 1010). This article presents recent improvements regarding the scoring and sampling aspects over the initial implementation, as well as a new seeding procedure based on the detection of cavities, opening the door to blind docking with EADock. These enhancements were validated on 260 complexes taken from the high quality Ligand Protein Database [LPDB, (Roche et al., J Med Chem 2001, 44, 3592)]. Two issues were identified: first, the quality of the initial structures cannot be assumed and a manual inspection and/or a search in the literature are likely to be required to achieve the best performance. Second the description of interactions involving metal ions still has to be improved. Nonetheless, a remarkable success rate of 65% was achieved for a large scale blind docking assay, when considering only the top ranked binding mode and a success threshold of 2 A RMSD to the crystal structure. When looking at the five-top ranked binding modes, the success rate increases up to 76%. In a standard local docking assay, success rates of 75 and 83% were obtained, considering only the top ranked binding mode, or the five top binding modes, respectively.

Palvelutoimittajan kyvykkyyden arviointimalli CAT- Palvelutoimittajan kehittäminen osana hankintamenetelmää

Suorituskyvyn mittaamista on tehty jo kauan yrityksissä. Nyt tämä suuntaus on löytämässä tiensä myös julkiselle sektorille, jossa palvelutoimittajien kyvykkyyden ja suorituskyvyn mittaamista on alettu suunnittelemaan ja laajamittaisemminkin. Toistaiseksi julkisella sektorilla ei ole tutkittu palvelutoimittajankyvykkyyden mittaamista. Tämän tutkimuksen tavoitteena oli antaa Tiehallinnolletoimittajavalinnan ja toimittajan kehittämisen työkalu, kyvykkyyden arviointimalli. Tavoitteena oli antaa myös kattava teoriakatsaus toimittajavalinnasta ja - kehittämisestä. Tutkimuksen teoreettinen osa keskittyy toimittajavalintaan infra-alalla, julkiseen hankintalainsäädäntöön ja toimittajan kehittämiseen. Empiirisessä osassa keskityttiin palvelutoimittajan kyvykkyyden arviointimalliin, CAT:iin, sen kykytekijöihin ja indikaattoreihin sekä mallin modifiointiin. Tiehallinnon malli on pitkälti samansisältöinen kuin Highways Agencyn malli, joskin selkeämpi ja lyhempi. Yksi kykytekijä, toiminnan laatu, lisättiin tässä työssä olevaan arviointimalliin.

Strategic investment appraisal; extended real options approach

Tutkielma keskittyy lisäämään investointiarviointiprosessien rationaalisuutta strategisten investointien arvioinnissa duopoli- / oligopolimarkkinoilla. Tutkielman päätavoitteena on selvittää kuinka peliteorialla laajennettu reaalioptioperusteinen investointien arviointimenetelmä, laajennettu reaalioptiokehikko, voisi mahdollisesti parantaa analyysien tarkkuutta. Tutkimus lähestyy ongelmaa investoinnin ajoituksen sekä todellisten investoinnin arvoattribuuttien riippuvuuksien kautta. Laajennettu reaalioptiokehikko on investointien analysointi- ja johtamistyökalu, joka tarjoaa osittain rajoitetun (sisältää tällä hetkellä ainoastaan parametrisen ja peliteoreettisen epävarmuuden) optimaalisen arvovälin investoinnin todellisesta arvosta. Kehikossa, ROA kartoittaa mahdolliset strategiset hyödyt tunnistamalla investointiinliittyvät eri optiot ja epävarmuudet, peliteoria korostaa ympäristön luomia paineita investointiin liittyvän epävarmuuden hallitsemisessa. Laajennettu reaalioptiokehikko tarjoaa rationaalisemman arvion strategisen investoinnin arvosta, koska se yhdistää johdonmukaisemmin option toteutuksen ja siten myös optioiden aika-arvon, yrityksen todellisiin rajoitettuihin (rajoituksena muiden markkinatoimijoiden toimet) polkuriippuvaisiin kyvykkyyksiin.

Effect of aminoethoxyvinilglycine (AVG) on preharvest fruit drop and maturity of apples

Apple trees cultivars Gala and Fuji were sprayed four weeks before commercial harvest with aminoethoxyvinilglycine (AVG), at doses of 0, 125, or 250 mg L-1, and assessed for preharvest fruit drop, fruit growth, and maturation on tree. In 'Gala', 64 days after AVG spraying, fruit drop for control treatment was 85%, and AVG (at 125 and 250 mg L-1) reduced it to 10%. In 'Fuji', 64 days after AVG spraying, fruit drop for control was 6%, while treatments with AVG (at 125 and 250 mg L-1) increased fruit drop to 10%. AVG was a powerful retardant of fruit maturation for 'Gala' but not for 'Fuji'. In 'Gala', the most affected attribute was the skin background color, followed, in decreasing order, by soluble solids content, the starch index, skin red color, the flesh firmness, and titratable acidity. In 'Gala', only flesh firmness retention was improved by increasing AVG dose from 125 mg L-1 to 250 mg L-1. The AVG at 250 mg L-1 inhibited "Gala" late fruit growth but not 'Fuji'.

Measuring irregularities and surface defects from printed patterns

Quality inspection and assurance is a veryimportant step when today's products are sold to markets. As products are produced in vast quantities, the interest to automate quality inspection tasks has increased correspondingly. Quality inspection tasks usuallyrequire the detection of deficiencies, defined as irregularities in this thesis. Objects containing regular patterns appear quite frequently on certain industries and science, e.g. half-tone raster patterns in the printing industry, crystal lattice structures in solid state physics and solder joints and components in the electronics industry. In this thesis, the problem of regular patterns and irregularities is described in analytical form and three different detection methods are proposed. All the methods are based on characteristics of Fourier transform to represent regular information compactly. Fourier transform enables the separation of regular and irregular parts of an image but the three methods presented are shown to differ in generality and computational complexity. Need to detect fine and sparse details is common in quality inspection tasks, e.g., locating smallfractures in components in the electronics industry or detecting tearing from paper samples in the printing industry. In this thesis, a general definition of such details is given by defining sufficient statistical properties in the histogram domain. The analytical definition allowsa quantitative comparison of methods designed for detail detection. Based on the definition, the utilisation of existing thresholding methodsis shown to be well motivated. Comparison of thresholding methods shows that minimum error thresholding outperforms other standard methods. The results are successfully applied to a paper printability and runnability inspection setup. Missing dots from a repeating raster pattern are detected from Heliotest strips and small surface defects from IGT picking papers.

Sink limitations to yield in wheat : how could it be reduced?

Further genetic gains in wheat yield are required to match expected increases in demand. This may require the identification of physiological attributes able to produce such improvement, as well as the genetic bases controlling those traits in order to facilitate their manipulation. In the present paper, a theoretical framework of source and sink limitation to wheat yield is presented and the fine-tuning of crop development as an alternative for increasing yield potential is discussed. Following a top-down approach, most crop physiologists have agreed that the main attribute explaining past genetic gains in yield was harvest index (HI). By virtue of previous success, no further gains may be expected in HI and an alternative must be found. Using a bottom-up approach, the present paper firstly provides evidence on the generalized sink-limited condition of grain growth, determining that for further increases in yield potential, sink strength during grain filling has to be increased. The focus should be on further increasing grain number per m2, through fine-tuning pre-anthesis developmental patterns. The phase of rapid spike growth period (RSGP) is critical for grain number determination and increasing spike growth during pre-anthesis would result in an increased number of grains. This might be achieved by lengthening the duration of the phase (though without altering flowering time), as there is genotypic variation in the proportion of pre-anthesis time elapsed either before or after the onset of the stem elongation phase. Photoperiod sensitivity during RSGP could be then used as a genetic tool to further increase grain number, since slower development results in smoother floret development and more floret primordia achieve the fertile floret stage, able to produce a grain. Far less progress has been achieved on the genetic control of this attribute. None of the well-known major Ppd alleles seems to be consistently responsible for RSGP sensitivity. Alternatives for identifying the genetic factors responsible for this sensitivity (e.g. quantitative trait locus (QTL) identification in mapping populations) are being considered.

Medidas preventivas para evitar los vertidos de crudo: un enfoque desde la economía

En este artículo analizamos el poder disuasorio de los sistemas de inspección y vigilancia puestos en funcionamiento en los Estados Unidos y en la Unión Europea con el objetivo de asegurar que los buques que transportan hidrocarburos cumplan con los requisitos de navegabilidad y mantenimiento exigibles bajo la legislación correspondiente. En particular analizamos las características disuasorias de la legislación norteamericana e internacional a la luz de las enseñanzas de la teoría económica; discutimos las características de los sistemas de inspección y vigilancia implantados tanto en los Estados Unidos como en la Unión Europea; y concluimos recomendando medidas que incrementarían la efectividad de estas prácticas.

Post-market environmental monitoring of Bt maize in Spain: Non-target effects of varieties derived from the event MON810 on predatory fauna

The Spanish Government has established post-market environmental monitoring (PMEM) as mandatory for genetically modified (GM) crop varieties cultivated in Spain. In order to comply with this regulation, effects of Bt maize varieties derived from the event MON810 on the predatory fauna were monitored for two years in northeast and central Spain. The study was carried out with a randomized block design in maize fields of 3-4 ha on which the abundance of plant-dwelling predators and the activity-density of soil-dwelling predators in Bt vs. non-Bt near-isogenic varieties were compared. To this end, the plots were sampled by visual inspection of a certain number of plants and pitfall traps 6 or 7 times throughout two seasons. No significant differences in predator densities on plants were found between Bt and non-Bt varieties. In the pitfall traps, significant differences between the two types of maize were found only in Staphylinidae, in which trap catches in non-Bt maize were higher than in Bt maize in central Spain. Based on the statistical power of the assays, surrogate arthropods for PMEM purposes are proposed; Orius spp. and Araneae for visual sampling and Carabidae, Araneae, and Staphylinidae for pitfall trapping. The other predator groups recorded in the study, Nabis sp. and Coccinellidae in visual sampling and Dermaptera in pitfall trapping, gave very poor power results. To help to establish a standardized protocol for PMEM of genetically modified crops, the effect-detecting capacity with a power of 0.8 of each predator group is given.