Reconstructing native American migrations from whole-genome and whole-exome data.

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

Single centre experience of the application of self navigated 3D whole heart cardiovascular magnetic resonance for the assessment of cardiac anatomy in congenital heart disease.

BACKGROUND: For free-breathing cardiovascular magnetic resonance (CMR), the self-navigation technique recently emerged, which is expected to deliver high-quality data with a high success rate. The purpose of this study was to test the hypothesis that self-navigated 3D-CMR enables the reliable assessment of cardiovascular anatomy in patients with congenital heart disease (CHD) and to define factors that affect image quality. METHODS: CHD patients ≥2 years-old and referred for CMR for initial assessment or for a follow-up study were included to undergo a free-breathing self-navigated 3D CMR at 1.5T. Performance criteria were: correct description of cardiac segmental anatomy, overall image quality, coronary artery visibility, and reproducibility of great vessels diameter measurements. Factors associated with insufficient image quality were identified using multivariate logistic regression. RESULTS: Self-navigated CMR was performed in 105 patients (55% male, 23 ± 12y). Correct segmental description was achieved in 93% and 96% for observer 1 and 2, respectively. Diagnostic quality was obtained in 90% of examinations, and it increased to 94% if contrast-enhanced. Left anterior descending, circumflex, and right coronary arteries were visualized in 93%, 87% and 98%, respectively. Younger age, higher heart rate, lower ejection fraction, and lack of contrast medium were independently associated with reduced image quality. However, a similar rate of diagnostic image quality was obtained in children and adults. CONCLUSION: In patients with CHD, self-navigated free-breathing CMR provides high-resolution 3D visualization of the heart and great vessels with excellent robustness.

A Feedfordward Adaptive Controller to Reduce the Imaging Time of Large-Sized Biological Samples with a SPM-Based Multiprobe Station

The time required to image large samples is an important limiting factor in SPM-based systems. In multiprobe setups, especially when working with biological samples, this drawback can make impossible to conduct certain experiments. In this work, we present a feedfordward controller based on bang-bang and adaptive controls. The controls are based in the difference between the maximum speeds that can be used for imaging depending on the flatness of the sample zone. Topographic images of Escherichia coli bacteria samples were acquired using the implemented controllers. Results show that to go faster in the flat zones, rather than using a constant scanning speed for the whole image, speeds up the imaging process of large samples by up to a 4x factor.

MgO/Ag(001) interface structure and STM images from first principles

The interface of MgO/Ag(001) has been studied with density functional theory applied to slabs. We have found that regular MgO films show a small adhesion to the silver substrate, the binding can be increased in off-stoichiometric regimes, either by the presence of O vacancies at the oxide film or by a small excess of O atoms at the interface between the ceramic to the metal. By means of theoretical methods, the scanning tunneling microscopy signatures of these films is also analyzed in some detail. For defect free deposits containing 1 or 2 ML and at low voltages, tunnelling takes place from the surface Ag substrate, and at large positive voltages Mg atoms are imaged. If defects, oxygen vacancies, are present on the surface of the oxide they introduce much easier channels for tunnelling resulting in big protrusions and controlling the shape of the image, the extra O stored at the interface can also be detected for very thin films.

Images as Proof. Photographic portrayal of Catastrophes in Helsingin Sanomat, 1969-1979

Tutkielman aiheena ovat Helsingin Sanomissa 1969 – 1979 uutisoitujen onnettomuuksien kuvallisen esittämisen tavat. Aihetta lähestytään analysoimalla V. K. Hietasen ottamia uutisartikkelien yhteydessä julkaistuja katastrofivalokuvia. Analyysi tapahtuu vertailemalla negatiiveja julkaistuihin kuviin, syventymällä kuvavalintoihin, sekä siihen, miten ne mahdollisesti vaikuttavat lukijoiden käsitykseen todellisuudesta. Tutkielmassa valokuvat toimivat itsenäisinä historian lähteinä, niiden arvo ja luotettavuus punnitaan omassa kontekstissaan. Vaikkakin lehtikuvat ovat pääasiallisena lähteenä, niiden suhde artikkeleihin ja kuvateksteihin on merkityksellinen. Katastrofi-termi viittaa tutkimuksessa onnettomuus- ja rikoskuviin, niiden yhdistäviä tekijöitä ovat draamallisuus ja dramaattisuus. Toisaalta kuvat ovat todisteita dramaattisesta tapahtumasta, toisaalta ne on rakennettu kertomaan tapahtuman tarina joko yksittäisessä kuvassa tai monesta kuvasta koostuvassa kuvasarjassa. Todistaminen ja kuvien rakentaminen tapahtuu pitkälti henkilöiden kautta. Personifikaation avulla uutisartikkelit ja niiden kuvat tuodaan lähemmäksi lukijoita. Valokuvien todistus- ja totuusarvot vaihtelevat julkaisuyhteydestä riippuen, vaikka kuvien alkuperäinen tarkoitus on todistaa tapahtumien todenperäisyydestä. Samoin vaatimus niiden autenttisuudesta on artikkelityypille alisteinen. Kuvavalinnoissa tasapainoillaan todellisuuden näyttämisen ja peittämisen välillä. Lukijoille luodaan kuvavalinnoin mediatapahtumia, joissa onnettomuuksien dramaattisuus korostuu, mutta samalla heille kuitenkin luodaan kuva harmonisesta yhteiskunnasta, jossa auktoriteetit ja yhteisöt liittävät voimansa yhteen taistelussa pahaa vastaan.