Interrogating eleven fast-evolving genes for signatures of recent positive selection in worldwide human populations

Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs inchimpanzee, mouse, rat and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes were then further explored for signatures of recent positive selection using SNP data. We genotyped 223 SNPs in 39 worldwide populations from the HGDP Diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each gene. After exploring the allele frequency spectrum, population differentiation and the maintainance of long unbroken haplotypes, we found signals of recent adaptative phenomena in only one of the 11 candidate gene regions. However, the signal ofrecent selection in this region may come from a different, neighbouring gene (CD5) ratherthan from the candidate gene itself (VPS37C). For this set of positively-selected genes in thehuman lineage, we find no indication that these genes maintained their rapid evolutionarypace among human populations. Based on these data, it therefore appears that adaptation forhuman-specific and for population-specific traits may have involved different genes.

Forecasting the Earth"s radiation belts and modeling solar energetic particle events: Recent results from SPACECAST

High-energy charged particles in the van Allen radiation belts and in solar energetic particle events can damage satellites on orbit leading to malfunctions and loss of satellite service. Here we describe some recent results from the SPACECAST project on modelling and forecasting the radiation belts, and modelling solar energetic particle events. We describe the SPACECAST forecasting system that uses physical models that include wave-particle interactions to forecast the electron radiation belts up to 3 h ahead. We show that the forecasts were able to reproduce the >2 MeV electron flux at GOES 13 during the moderate storm of 7-8 October 2012, and the period following a fast solar wind stream on 25-26 October 2012 to within a factor of 5 or so. At lower energies of 10- a few 100 keV we show that the electron flux at geostationary orbit depends sensitively on the high-energy tail of the source distribution near 10 RE on the nightside of the Earth, and that the source is best represented by a kappa distribution. We present a new model of whistler mode chorus determined from multiple satellite measurements which shows that the effects of wave-particle interactions beyond geostationary orbit are likely to be very significant. We also present radial diffusion coefficients calculated from satellite data at geostationary orbit which vary with Kp by over four orders of magnitude. We describe a new automated method to determine the position at the shock that is magnetically connected to the Earth for modelling solar energetic particle events and which takes into account entropy, and predict the form of the mean free path in the foreshock, and particle injection efficiency at the shock from analytical theory which can be tested in simulations.

Multiplex targeted high-throughput sequencing for Mendelian cardiac disorders.

Mendelian cardiomyopathies and arrhythmias are characterized by an important genetic heterogeneity, rendering Sanger sequencing very laborious and expensive. As a proof of concept, we explored multiplex targeted high-throughput sequencing (HTS) as a fast and cost-efficient diagnostic method for individuals suffering from Mendelian cardiac disorders. We designed a DNA capture assay including all exons from 130 genes involved in cardiovascular Mendelian disorders and analysed simultaneously four samples by multiplexing. Two patients had familial hypertrophic cardiomyopathy (HCM) and two patients suffered from long QT syndrome (LQTS). In patient 1 with HCM, we identified two known pathogenic missense variants in the two most frequently mutated sarcomeric genes MYH7 and MYBPC. In patient 2 with HCM, a known acceptor splice site variant in MYBPC3 was found. In patient 3 with LQTS, two missense variants in the genes SCN5A and KCNQ were identified. Finally, in patient 4 with LQTS a known missense variant was found in MYBPC3, which is usually mutated in patients with cardiomyopathy. Our results showed that multiplex targeted HTS works as an efficient and cost-effective tool for molecular diagnosis of heterogeneous disorders in clinical practice and offers new insights in the pathogenesis of these complex diseases.

Mixed spectral-structural classification of very high resolution images with summation kernels

In this paper, mixed spectral-structural kernel machines are proposed for the classification of very-high resolution images. The simultaneous use of multispectral and structural features (computed using morphological filters) allows a significant increase in classification accuracy of remote sensing images. Subsequently, weighted summation kernel support vector machines are proposed and applied in order to take into account the multiscale nature of the scene considered. Such classifiers use the Mercer property of kernel matrices to compute a new kernel matrix accounting simultaneously for two scale parameters. Tests on a Zurich QuickBird image show the relevance of the proposed method : using the mixed spectral-structural features, the classification accuracy increases of about 5%, achieving a Kappa index of 0.97. The multikernel approach proposed provide an overall accuracy of 98.90% with related Kappa index of 0.985.

Effect of maternal clinical chorioamnionitis on neonatal morbidity in very-low birthweight infants: a case control study

Aims: To assess the relationship between maternal clinical chorioamnionitis and neonatal outcome in preterm very-low birthweight (VLBW) infants. Methods: An observational case-control study was conducted in the Neonatology Services of 12 acute-care teaching hospitals in Spain. Between January 2004 and December 2006, all consecutive VLBW (F1500 g) infants born to a mother with clinical chorioamnionitis were enrolled. Controls were infants without chorioamnionitis matched by gestational age who were born immediately after each index case. Results: There were 165 cases and 163 controls. A significantly higher percentage of cases than controls required intubation (53% vs. 35.8%), had normal intrauterine growth (98.1% vs. 84.7%), were born in a tertiary center (inborn) (95.1% vs. 89.1%), from single gestations (76.4% vs. 65.6%) and vaginal delivery (47.3% vs. 33.3%), showed a lowerApgar score at 5 min, and presented a higher rate of earlyonset sepsis (10.4% vs. 1.2%). Older maternal age (32.5 vs. 30.8 years), premature labor (67.3% vs. 25.8%), premature rupture of membranes (61.3% vs. 25.8%), and antibiotic treatment (88.5% vs. 52.3%) were significantly more frequent among cases than controls. Conclusions: After controlling by gestational age, maternal chorioamnionitis was associated with neonatal depression and early sepsis but not with other prematurity-related complications.

Effect of maternal clinical chorioamnionitis on neonatal morbidity in very-low birthweight infants: a case control study

Aims: To assess the relationship between maternal clinical chorioamnionitis and neonatal outcome in preterm very-low birthweight (VLBW) infants. Methods: An observational case-control study was conducted in the Neonatology Services of 12 acute-care teaching hospitals in Spain. Between January 2004 and December 2006, all consecutive VLBW (F1500 g) infants born to a mother with clinical chorioamnionitis were enrolled. Controls were infants without chorioamnionitis matched by gestational age who were born immediately after each index case. Results: There were 165 cases and 163 controls. A significantly higher percentage of cases than controls required intubation (53% vs. 35.8%), had normal intrauterine growth (98.1% vs. 84.7%), were born in a tertiary center (inborn) (95.1% vs. 89.1%), from single gestations (76.4% vs. 65.6%) and vaginal delivery (47.3% vs. 33.3%), showed a lowerApgar score at 5 min, and presented a higher rate of earlyonset sepsis (10.4% vs. 1.2%). Older maternal age (32.5 vs. 30.8 years), premature labor (67.3% vs. 25.8%), premature rupture of membranes (61.3% vs. 25.8%), and antibiotic treatment (88.5% vs. 52.3%) were significantly more frequent among cases than controls. Conclusions: After controlling by gestational age, maternal chorioamnionitis was associated with neonatal depression and early sepsis but not with other prematurity-related complications.

Prognostic value of cortically induced motor evoked activity by TMS in chronic stroke: caveats from a very revealing single clinical case

Background: We report the case of a chronic stroke patient (62 months after injury) showing total absence of motor activity evoked by transcranial magnetic stimulation (TMS) of spared regions of the left motor cortex, but near-to-complete recovery of motor abilities in the affected hand. Case presentation: Multimodal investigations included detailed TMS based motor mapping, motor evoked potentials (MEP), and Cortical Silent period (CSP) as well as functional magnetic resonance imaging (fMRI) of motor activity, MRI based lesion analysis and Diffusion Tensor Imaging (DTI) Tractography of corticospinal tract (CST). Anatomical analysis revealed a left hemisphere subinsular lesion interrupting the descending left CST at the level of the internal capsule. The absence of MEPs after intense TMS pulses to the ipsilesional M1, and the reversible suppression of ongoing electromyographic (EMG) activity (indexed by CSP) demonstrate a weak modulation of subcortical systems by the ipsilesional left frontal cortex, but an inability to induce efficient descending volleys from those cortical locations to right hand and forearm muscles. Functional MRI recordings under grasping and finger tapping patterns involving the affected hand showed slight signs of subcortical recruitment, as compared to the unaffected hand and hemisphere, as well as the expected cortical activations. Conclusions: The potential sources of motor voluntary activity for the affected hand in absence of MEPs are discussed. We conclude that multimodal analysis may contribute to a more accurate prognosis of stroke patients.

Fast Bias Field Correction for 9.4 Tesla Magnetic Resonance Imaging

In this paper the problem of intensity inhomogeneity athigh magnetic field on magnetic resonance images isaddressed. Specifically, rat brain images at 9.4Tacquired with a surface coil are bias corrected. Wepropose a low- pass frequency model that takes intoaccount not only background-object contours but alsoother important contours inside the image. Twopre-processing filters are proposed: first, to create avolume of interest without contours, and second, toextrapolate the image values of such masked area to thewhole image. Results are assessed quantitatively andvisually in comparison to standard low pass filterapproach, and they show as expected better accuracy inenhancing image intensity.

Computational and Experimental Analysis of Flow Field in the Diffusers of Centrifugal Compressors

Centrifugal compressors are widely used for example in process industry, oil and gas industry, in small gas turbines and turbochargers. In order to achieve lower consumption of energy and operation costs the efficiency of the compressor needs to be improve. In the present work different pinches and low solidity vaned diffusers were utilized in order to improve the efficiency of a medium size centrifugal compressor. In this study, pinch means the decrement of the diffuser flow passage height. First different geometries were analyzed using computational fluid dynamics. The flow solver Finflo was used to solve the flow field. Finflo is a Navier-Stokes solver. The solver is capable to solve compressible, incompressible, steady and unsteady flow fields. Chien's k-e turbulence model was used. One of the numerically investigated pinched diffuser and one low solidity vaned diffuser were studied experimentally. The overall performance of the compressor and the static pressure distribution before and after the diffuser were measured. The flow entering and leaving the diffuser was measured using a three-hole Cobra-probe and Kiel-probes. The pinch and the low solidity vaned diffuser increased the efficiency of the compressor. Highest isentropic efficiency increment obtained was 3\% of the design isentropic efficiency of the original geometry. It was noticed in the numerical results that the pinch made to the hub and the shroud wall was most beneficial to the operation of the compressor. Also the pinch made to the hub was better than the pinchmade to the shroud. The pinch did not affect the operation range of the compressor, but the low solidity vaned diffuser slightly decreased the operation range.The unsteady phenomena in the vaneless diffuser were studied experimentally andnumerically. The unsteady static pressure was measured at the diffuser inlet and outlet, and time-accurate numerical simulation was conducted. The unsteady static pressure showed that most of the pressure variations lay at the passing frequency of every second blade. The pressure variations did not vanish in the diffuser and were visible at the diffuser outlet. However, the amplitude of the pressure variations decreased in the diffuser. The time-accurate calculations showed quite a good agreement with the measured data. Agreement was very good at the design operation point, even though the computational grid was not dense enough inthe volute and in the exit cone. The time-accurate calculation over-predicted the amplitude of the pressure variations at high flow.

Voltage fluctuations in IC power supply distribution

The supply voltage decrease and powerconsumption increase of modern ICs made the requirements for low voltage fluctuation caused by packaging and on-chip parasitic impedances more difficult to achieve. Most of the research works on the area assume that all the nodes of the chip are fed at thesame voltage, in such a way that the main cause of disturbance or fluctuation is the parasitic impedance of packaging. In the paper an approach to analyze the effect of high and fast current demands on the on-chip power supply network. First an approach to model the entire network by considering a homogeneous conductive foil is presented. The modification of the timing parameters of flipflops caused by spatial voltage drops through the IC surface are also investigated.

Whole body protein synthesis and energy expenditure in very low birth weight infants.

The aim of the present work was to study whole body protein synthesis and breakdown, as well as energy metabolism, in very low birth weight premature infants (less than 1500 g) during their rapid growth phase. Ten very low birth weight infants were studied during their first and second months of life. They received a mean energy intake of 114 kcal/kg X day and 3 g protein/kg X day as breast milk or milk formula. The average weight gain was 15 g/kg X day. The apparent energy digestibility was 88%, i.e. 99 kcal/kg X day. Their resting postprandial energy expenditure was 58 kcal/kg X day, indicating that 41 kcal/kg X day was retained. The apparent protein digestibility was 89%, i.e. 2.65 g/kg X day. Their rate of protein oxidation was 0.88 g/kg X day so that protein retention was 1.76 g/kg X day. There was a linear relationship between N retention and N intake (r = 0.78, p less than 0.001). The slope of the regression line indicates a net efficiency of N utilization of 67%. Estimates of body composition from the energy balance, coupled with N balance method, showed that 25% of the gain was fat and 75% was lean tissue. Whole body protein synthesis and breakdown were determined using repeated oral administration of 15N glycine for 60-72 h, and 15N enrichment in urinary urea was measured. Protein synthesis averaged 11.2 g/kg X day and protein breakdown 9.4 g/kg X day. Muscular protein breakdown, as estimated by 3-methylhistidine excretion, contributed to 12% of the total protein breakdown.(ABSTRACT TRUNCATED AT 250 WORDS)

Ennakoivan Bluetooth -verkon hyödyntäminen paikkatietoon pohjautuvan opastusjärjestelmän toteutuksessa

Tekniikan kehitys ja elämänrytmin kiihtyminen ajaa eteenpäin sekä tarvetta että mahdollisuuksia toteuttaahenkilökohtaisia opastusjärjestelmiä. Lyhyen kantaman langattomat kommunikaatioteknologiat mahdollistavat erilaisten paikkasidonnaisten palveluiden, kuten opastusjärjestelmien toteuttamisen kohtuullisilla kustannuksilla. Markkinoilla olevista järjestelmistä sisätiloihin sijoittuvaan reaaliaikaiseen opastukseen soveltuvaa järjestelmää on vaikea löytää ja useimmat niistä hyödyntävät WLAN -tekniikkaa, joka ei ole kovin laajasti tuettuna matkapuhelimen kaltaisissa kannettavissa päätelaitteissa. Tässä työssä tuodaan esille Bluetooth -tekniikalla toteutettavien reaaliaikaisten järjestelmien ongelmia ja esitellään yksi ratkaisumalli. Toimintaa vaikeuttaa lähinnä pitkä yhteyden muodostumisaika, joka koostuu verkon laitteiden hakemiseen kuluvasta pitkästä vaikeasti kestoltaan arvioitavasta ajasta ja valittuun kohteeseen yhteyden muodostamiseen kuluneesta ajasta. Toteutetussa Bluetooth -opastusjärjestelmässä opastettavien laitteiden hakeminen liityntäpistettä vaihdettaessa on voitu jättää pois, koska yhteyden muodostamiseen vaaditut tiedot välitetään liityntäpisteille kiinteän Ethernet -verkon välityksellä. Työntuloksena syntyneen opastusjärjestelmän käyttökokemukset osoittavat opastusverkon suunnittelun olevan haastava tehtävä, mutta verkon toimintakuntoon saattamisen jälkeen järjestelmän suorituskykyyn saadaan huomattava parannus. Demonstraatiototeutus rajoittaa käytettävän laitteiston Linux-pohjaisiin järjestelmiin, vaikka laajemman käyttöönoton varmistamiseksi järjestelmä tulisi tehdä siirrettäväksiesimerkiksi Symbian -alustalle.

Highlight Removal in Spectral Images

Monissasovelluksissa on hyvin tärkeää vähentää valolähteen vaikutusta kohteen oikean värin havainnoimiseksi. Tämä on tarpeen mm. virtuaalisissa museoissa, telelääketieteessä, verkkokaupassa ja verkkorahassa. Tässä tutkielmassa on kehitetty tekniikkaa kirkkaiden heijastusten poistoon spektrikuvista. Työ sisältää katsauksen yleisen värillisen kuvan ymmärtämiseen, mihin perustuen analysoitiin erilaisia kirkkaiden heijastusten poistO'tekniikoita. Työssä kehitettiin uusi kirkkaiden heijastusten poistO'menetelmä, joka perustuu dikromaattiseen heijastus-malliin, joka kuvaa spektrisen datan objektin omaan väriin ja valaisevan valon väriin perustuen. Ehdotettu kirkkaiden heijastusten poistO'menetelmä hyödyntää erilaisia olemassaolevia menetelmiä, kuten pääkomponenttimenetelmää ja tiedon luokittelu-menetelmää. Yritys kehittää nopeasti toimiva algoritmi, joka myös suoriutuu tehtävästä hyvin, on onnistunut. Kokeet toteutettiin ehdotetun menetelmän mukaisesti ja toimivalla algoritmilla saatiin halutut lopputulokset. Edelleentyö sisältää ehdotuksia esitetyn algoritmin parantamiseksi.