Exchange Effects and CIDEP

Väitöskirjassa on tutkittu tilastollisen koesuunnittelun teoriaa. Koesuunnittelua tarvitaan, kun tilastollisiin mittauksiin on käytettävissä vain rajallinen määrä resursseja mutta samalla kuitenkin halutaan luotettavaa tietoa. Tutkimuksen kolmessa ensimmäisessä artikkelissa on kehitetty koesuunnitelmia satunnaiskertoimisille regressiomalleille. Malleja voidaan soveltaa, kun tehdään usealle yksilölle peräkkäisiä mittauksia, esimerkiksi eri aikapisteissä. Väitöskirjan artikkeleissa sovelluskohteena ovat olleet puiden rungot, joista on mitattu läpimittoja eri korkeuksilla. Kutakin yksilöä, tässä tapauksessa puunrunkoa, vastaavat omat regressiomallin kertoimet. Koesuunnitelma käsittää tiedon siitä, miten mittausten määrä jakaantuu eri yksilöiden välillä ja yksilöiden sisäisesti. Tavoitteena on joko arvioida mallin keskimääräiset parametrit mahdollisimman tarkasti tai ennustaa uusia havaintoarvoja. Ensimmäisessä artikkelissa on ennustealue on sama kuin havaintoväli ja toisessa se on havaintovälin ulkopuolella. Kolmannessa artikkelissa on esillä käänteisennusteongelma, kun halutaan arvioida pistettä, jossa vastemuuttuja, esim. puun läpimitta, saavuttaa tietyn tason. Koesuunnitelmia vertaillaan keskenään käyttämällä erilaisia optimaalisuuskriteereitä. Kolmannessa ja neljännessä väitöskirjan artikkelissa tarkastellaan DS-kriteeriä, jota on tutkittu vain vähän tähän mennessä. DS-kriteeri on siinä mielessä yleinen, että koesuunnitelman ollessa DS-optimaalinen se on optimaalinen myös monen perinteisen optimaalisuuskriteerin suhteen. Yleensä DS-optimaalista suunnitelmaa ei ole olemassa, mutta suunnitelmia voidaan parantaa DS-kriteerin suhteen. Tutkimuksessa on rajoituttu yksinkertaisiin polynomimalleihin, joten lisätutkimus on tarpeen DS-kriteerin käytöstä laajemmissa yhteyksissä.The thesis consists of five papers and a summary. It has two main themes in the area of experimental design. Firstly, optimal designs for estimation, prediction and inverse prediction are developed in random coefficient linear regression models. Mainly first-degree models are dealt with. The results can be applied in repeated measurements situations. Secondly, a relatively new design criterion, the distance optimality criterion, is introduced. Its properties are studied and some results in estimation and prediction problems deduced. The criterion can be used to find optimal designs or to improve designs in polynomial regression models. It has interesting relations to traditional D- and E-optimality criteria

Infrared spectroscopy of small-molecule endofullerenes

Hydrogen is one of the few molecules which has been incarcerated in the molecular cage of C$_{60}$ and forms endohedral supramolecular complex H$_2$@C$_{60}$. In this confinement hydrogen acquires new properties. Its translational motion becomes quantized and is correlated with its rotations. We applied infrared spectroscopy to study the dynamics of hydrogen isotopologs H$_2$, D$_2$ and HD incarcerated in C$_{60}$. The translational and rotational modes appear as side bands to the hydrogen vibrational mode in the mid infrared part of the absorption spectrum. Because of the large mass difference of hydrogen and C$_{60}$ and the high symmetry of C$_{60}$ the problem is identical to a problem of a vibrating rotor moving in a three-dimensional spherical potential. The translational motion within the C$_{60}$ cavity breaks the inversion symmetry and induces optical activity of H$_2$. We derive potential, rotational, vibrational and dipole moment parameters from the analysis of the infrared absorption spectra. Our results were used to derive the parameters of a pairwise additive five-dimensional potential energy surface for H$_2$@C$_{60}$. The same parameters were used to predict H$_2$ energies inside C$_{70}$[Xu et al., J. Chem. Phys., {\bf 130}, 224306 (2009)]. We compare the predicted energies and the low temperature infrared absorption spectra of H$_2$@C$_{70}$.Comment: Updated author lis

Photochemistry of ketones adsorbed on size/shape selective zeolites. A supramolecular approach to persistent carbon centered radicals

2H NMR, EPR, computational and product analyses of the photolysis of 2,4-diphenylpentan-3-one (DPP) adsorbed on MFI size/shape selective zeolites are consistent with supramolecular structural changes as a function of surface coverage that provide a novel method for the generation of persistent diffusing organic free radicals

Dynamic properties and optical phase conjugation of two-photon pumped ultrashort blue stimulated emission in a chromophore solution

The dynamic properties of two-photon pumped blue lasing (~470 nm) in the solution of an organic chromophore [2-acetyl-6-(dimethylamino)naphthalene], excited by ~160-fs laser pulses at ~775 nm, have been studied. Both the forward and backward stimulated emission are enhanced by feedback from the reflection at the two optical windows of the solution filled cuvette. Under current experimental conditions, the lasing wavelengths in the forward and backward directions were almost the same, but both blueshifted compared to the fluorescence peak wavelength of the sample solution. The temporal behavior of the lasing output was recorded by a high-speed streak camera system. The multipulse structure and spectral properties of the output lasing are semiquantitatively explained. In addition, excellent optical phase-conjugation properties of the backward stimulated emission were observed; the aberration influences from an aberrator on the backward lasing beam were automatically removed

Innovation through R&D activities in the European context: Antecedents and consequences

Despite the fact that the determinants and the consequences of R&D activities have been extensively studied in previous research, further efforts to integrate disparate streams of literature might bring new insights into innovation decision-making by firms. In particular, this article studies the simultaneous effects that a set of factors (at both company and environmental levels of analysis) have on R&D activity, which explain firm growth. A two-stage probit least squares (2SPLS) estimation is applied to data from the EU-EFIGE/Bruegel-UniCredit dataset for seven European countries for the years 2007-2009. The main findings show that not all the R&D determinants lead to firm growth. In particular, R&D activities are affected by the employment of a significant number of foreign executives, a higher percentage of employees with fixed-term contracts, appropriate labour regulations and access to employees who have received external training, all of which are positively related to firm growth. Based on these results, policy and practical implications to improve firms’ performances are discussed

Defects in TRPM7 channel function deregulate thrombopoiesis through altered cellular Mg2+ homeostasis and cytoskeletal architecture

Mg2+ plays a vital role in platelet function, but despite implications for life-threatening conditions such as stroke or myocardial infarction, the mechanisms controlling [Mg2+](i) in megakaryocytes (MKs) and platelets are largely unknown. Transient receptor potential melastatin-like 7 channel (TRPM7) is a ubiquitous, constitutively active cation channel with a cytosolic alpha-kinase domain that is critical for embryonic development and cell survival. Here we report that impaired channel function of TRPM7 in MKs causes macrothrombocytopenia in mice (Trpm7(fl/fl-Pf4Cre)) and likely in several members of a human pedigree that, in addition, suffer from atrial fibrillation. The defect in platelet biogenesis is mainly caused by cytoskeletal alterations resulting in impaired proplatelet formation by Trpm7(fl/fl-Pf4Cre) MKs, which is rescued by Mg2+ supplementation or chemical inhibition of non-muscle myosin IIA heavy chain activity. Collectively, our findings reveal that TRPM7 dysfunction may cause macrothrombocytopenia in humans and mice

Symmetry-breaking in the endofullerene H2O@C60 revealed in the quantum dynamics of ortho and para-water: a neutron scattering investigation

Inelastic neutron scattering (INS) has been employed to investigate the quantum dynamics of water molecules permanently entrapped inside the cages of C60 fullerene molecules. This study of the supramolecular complex, H2O@C60, provides the unique opportunity to study isolated water molecules in a highly symmetric environment. Free from strong interactions, the water molecule has a high degree of rotational freedom enabling its nuclear spin isomers, ortho-H2O and para-H2O to be separately identified and studied. The INS technique mediates transitions between the ortho and para spin isomers and using three INS spectrometers, the rotational levels of H2O have been investigated, correlating well with the known levels in gaseous water. The slow process of nuclear spin conversion between ortho-H2O and para-H2O is revealed in the time dependence of the INS peak intensities over periods of many hours. Of particular interest to this study is the observed splitting of the ground state of ortho-H2O, raising the three-fold degeneracy into two states with degeneracy 2 and 1 respectively. This is attributed to a symmetry-breaking interaction of the water environment

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde