Predicting drug metabolism: experiment and/or computation?

Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.

Conservação pós-colheita de manga 'Tommy Atkins' orgânica sob recobrimentos bio-orgânicos

O objetivo deste trabalho foi avaliar a conservação pós-colheita de manga 'Tommy Atkins' orgânica destinada à exportação, colhida com Boas Práticas Agrícolas (CBP) e sem Boas Práticas Agrícolas (SBP), sob recobrimentos bio-orgânicos. Manga colhida na maturidade comercial foi recoberta com extrato de erva-doce a 1,5% (CBP+ED, SBP+ED), com extrato de erva-doce adicionada à fécula de mandioca a 3,0% (CBP+ED+F, SBP+ED+F) e Controle (sem recobrimento, CBP e SBP), armazenada a 10±0,5 ºC e 85±2% UR. O uso de BPA manteve a qualidade. O recobrimento com ED comprometeu a aparência da manga pela incidência de manchas na casca; recobrimento associando F + ED manteve a qualidade e retardou o amadurecimento.

Kuiva-, bio-, hyöty- ja ongelmajätteiden keskitetysti kilpailutettu kuljetusjärjestelmä Etelä-Karjalassa

Tutkimuksen tarkoituksena oli tuottaa tietoa kuiva-, bio-, hyöty- ja ongelmajätteiden keskitetysti kilpailutetun kuljetusjärjestelmän eduista ja haitoista Etelä-Karjalan Jätehuolto Oy:n alueella. Tutkimuksessa esitellään jätteenkuljetusjärjestelmien ominaisuudet ja niiden suunnittelu sekä jätehuoltoa ja jätteenkuljetuksia koskeva lainsäädäntö. Keskitetysti kilpailutettu jätteenkuljetusjärjestelmä mitoitettiin järjestelmän nykytilan kuvauksen sekä muualla Suomessa kilpailutuksesta saatujen kokemusten avulla. Järjestelmää arvioitiin vertaamalla kaluston tarvetta, kuormapainoja sekä kuljetuskustannuksia nykyiseen tilanteeseen. Lopuksi arvioitiin jatkokehitystarpeita ja tarvittavia toimenpiteitä, kun keskitettyyn kilpailuttamiseen siirrytään. Jätteenkuljetusten keskitetyllä kilpailuttamisella voidaan saavuttaa etuja nykyiseen kuntakohtaiseen jätteenkuljetukseen verrattuna. Edut syntyvät kun päällekkäiset ajot sekä siirtoajot vähenevät ja kuormakoot kasvavat. Kuljetukset voidaan hoitaa pienemmällä kalustomäärällä, jolloin myös kuljetuskustannukset laskevat.

Aspectos bio y cronoestratigraficos del Mioceno de Bera (Tarragona )

Se estudian los Moluscos, Foraminíferos, Palinología, Nanoplancton calcáreo de unos nuevos niveles arcilloso-limosos descubiertos en la excavación de un pozo en las proximidades de la Ermita de Berà (Tarragona); la excelente conservación de los restos paleontológicos permite un estudio más exahustivo. En conjunto, la mayoría de las características indican que se trataría de una sedimentación en condiciones neríticas alrededor de los 30 metros de profundidad con ciertas influencias de carácter estuarino. La presencia de abundantes Orbulina, T. mayeri, junto con G. praemenardii y ausencia de G. fohsi peripheroronda (presente en otras secciones próximas) permite atribuir los niveles a la biozona de G. mayeri, de edad Serravalliense; los datos de Nanoplancton son acordes con dicha edad.

Potential of local bio-geoengineering to mitigate dangerous temperature increases in a global warming scenario

Crops and forests are already responding to rising atmospheric carbon dioxide and air temperatures. Increasing atmospheric CO2 concentrations are expected to enhance plant photosynthesis. Nevertheless, after long-term exposure, plants acclimate and show a reduction in photosynthetic activity (i.e. down-regulation). If in the future the Earth"s temperature is allowed to rise further, plant ecosystems and food security will both face significant threats. The scientific community has recognized that an increase in global temperatures should remain below 2°C in order to combat climate change. All this evidence suggests that, in parallel with reductions in CO2 emissions, a more direct approach to mitigate global warming should be considered. We propose here that global warming could be partially mitigated directly through local bio-geoengineering approaches. For example, this could be done through the management of solar radiation at surface level, i.e. by increasing global albedo. Such an effect has been documented in the south-eastern part of Spain, where a significant surface air temperature trend of -0.3°C per decade has been observed due to a dramatic expansion of greenhouse horticulture.

Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity.

The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras.

Reliable computation of robust response tori on the verge of breakdown

We prove the existence and local uniqueness of invariant tori on the verge of breakdown for two systems: the quasi-periodically driven logistic map and the quasi-periodically forced standard map. These systems exemplify two scenarios: the Heagy-Hammel route for the creation of strange non- chaotic attractors and the nonsmooth bifurcation of saddle invariant tori. Our proofs are computer- assisted and are based on a tailored version of the Newton-Kantorovich theorem. The proofs cannot be performed using classical perturbation theory because the two scenarios are very far from the perturbative regime, and fundamental hypotheses such as reducibility or hyperbolicity either do not hold or are very close to failing. Our proofs are based on a reliable computation of the invariant tori and a careful study of their dynamical properties, leading to the rigorous validation of the numerical results with our novel computational techniques.

Computer-aided system for morphometric mandibular index computation (Using dental panoramic radiographs)

Objective: We propose and validate a computer aided system to measure three different mandibular indexes: cortical width, panoramic mandibular index and, mandibular alveolar bone resorption index. Study Design: Repeatability and reproducibility of the measurements are analyzed and compared to the manual estimation of the same indexes. Results: The proposed computerized system exhibits superior repeatability and reproducibility rates compared to standard manual methods. Moreover, the time required to perform the measurements using the proposed method is negligible compared to perform the measurements manually. Conclusions: We have proposed a very user friendly computerized method to measure three different morphometric mandibular indexes. From the results we can conclude that the system provides a practical manner to perform these measurements. It does not require an expert examiner and does not take more than 16 seconds per analysis. Thus, it may be suitable to diagnose osteoporosis using dental panoramic radiographs

On the computation of reducible invariant tori on a parallel computer

We present an algorithm for the computation of reducible invariant tori of discrete dynamical systems that is suitable for tori of dimensions larger than 1. It is based on a quadratically convergent scheme that approximates, at the same time, the Fourier series of the torus, its Floquet transformation, and its Floquet matrix. The Floquet matrix describes the linearization of the dynamics around the torus and, hence, its linear stability. The algorithm presents a high degree of parallelism, and the computational effort grows linearly with the number of Fourier modes needed to represent the solution. For these reasons it is a very good option to compute quasi-periodic solutions with several basic frequencies. The paper includes some examples (flows) to show the efficiency of the method in a parallel computer. In these flows we compute invariant tori of dimensions up to 5, by taking suitable sections.

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries.

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Abstract Objective: Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods: Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL) of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results: Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion: The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography.

Shout and Act: an Algorithm for Digital Objects Preservation Inspired from Rescue Robots

We adapt the Shout and Act algorithm to Digital Objects Preservation where agents explore file systems looking for digital objects to be preserved (victims). When they find something they “shout” so that agent mates can hear it. The louder the shout, the urgent or most important the finding is. Louder shouts can also refer to closeness. We perform several experiments to show that this system works very scalably, showing that heterogeneous teams of agents outperform homogeneous ones over a wide range of tasks complexity. The target at-risk documents are MS Office documents (including an RTF file) with Excel content or in Excel format. Thus, an interesting conclusion from the experiments is that fewer heterogeneous (varying skills) agents can equal the performance of many homogeneous (combined super-skilled) agents, implying significant performance increases with lower overall cost growth. Our results impact the design of Digital Objects Preservation teams: a properly designed combination of heterogeneous teams is cheaper and more scalable when confronted with uncertain maps of digital objects that need to be preserved. A cost pyramid is proposed for engineers to use for modeling the most effective agent combinations