Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2×2×3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

Functional error modeling for uncertainty quantification in hydrogeology

Approximate models (proxies) can be employed to reduce the computational costs of estimating uncertainty. The price to pay is that the approximations introduced by the proxy model can lead to a biased estimation. To avoid this problem and ensure a reliable uncertainty quantification, we propose to combine functional data analysis and machine learning to build error models that allow us to obtain an accurate prediction of the exact response without solving the exact model for all realizations. We build the relationship between proxy and exact model on a learning set of geostatistical realizations for which both exact and approximate solvers are run. Functional principal components analysis (FPCA) is used to investigate the variability in the two sets of curves and reduce the dimensionality of the problem while maximizing the retained information. Once obtained, the error model can be used to predict the exact response of any realization on the basis of the sole proxy response. This methodology is purpose-oriented as the error model is constructed directly for the quantity of interest, rather than for the state of the system. Also, the dimensionality reduction performed by FPCA allows a diagnostic of the quality of the error model to assess the informativeness of the learning set and the fidelity of the proxy to the exact model. The possibility of obtaining a prediction of the exact response for any newly generated realization suggests that the methodology can be effectively used beyond the context of uncertainty quantification, in particular for Bayesian inference and optimization.

The UlaG protein familly defines novel structural and functional motifs grafted on an ancient RNase fold

Background: Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-b-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent)metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides. Results: Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gramnegative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation. Conclusions: Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.

Functional testing in TETRA system

Terrestrial Trunked Radio (TETRA) on moderni digitaalinen matkapuhelinjärjestelmän standardi, joka on suunniteltu täyttämään erityisesti viranomaisten vaativat tarpeet turvallisuuden ja luotettavuuden suhteen. Ohjelmiston testaus on tärkeä osa sen laadun takaamiseksi. Testaus on jaettu useisiin vaiheisiin ja se kattaa koko ohjelmiston elinkaaren: ohjelmiston kehittelystä alkaen asiakkaalle lähetettyyn valmiiseen tuotteeseen saakka. Toiminnallisuustestauksen suorittaa joko ohjelmiston suunnittelijat tai erillinen testausryhmä käyttäen Nokia TETRA-järjestelmän testauslaboratoriota. Testauksen tarkoituksena on varmistaa, että ohjelmisto, sen aliohjelmat ja ominaisuudet täyttävät niille annetut toiminnalliset ja laadulliset vaatimukset. Tämä diplomityö antaa yleiskuvan toiminnallisuustestausprosessista Nokia TETRA järjestelmän laboratoriossa. Se tarjoaa esimerkkitestitapauksen avulla kokonaiskuvan siitä, kuinka toiminnallisuustestausprosessi suoritetaan alusta loppuun.

Characteristics of Flowing Film

Työssä tutkittiin uutta teknologiaa pigmenttipäällystykseen. Tämä tekniikka on yleisesti tunnettua eräillä muilla teollisuudenaloilla. Kirjallisuustutkimuksessa on esitelty prosessia ja sen eri osatekijöitä sekä muilla aloilla tunnettuja prosessimuuttujia. Päällystyspastojen ja päällystettävien pintojen teoriaa on selvitetty uuden tekniikan ja pigmenttipäällystyksen valossa. Uuden tekniikan perusmekanismeja tutkittiin kokeellisessa osassa. Valuvan nestefilmin stabiilisuutta tutkittiin minimivirtauksen avulla. Stabiilisuustutkimuksen suorittamiseen käytettiin apuna Taguchi-matriisia DOE-ohjelmalla (Design of Experiments). Kokeiden perusteella minimivirtauksen kannalta päällystyspastalle edullisempi koostumus on kalsiumkarbonaatti- kuin kaoliinipasta. Sideaineella on pienempi osuus lateksia ja polyvinyylialkoholia parempi. Suurempi osuus pinta-aktiivista ainetta ja matala pastan kuiva-ainepitoisuus ovat suositeltuja. Tehokas ilmanpoisto päällystyspastasta on myös tärkeää lopullisen tuloksen kannalta. Koekoneella ajetuissa päällystyskokeissa havaittiin valuvan filmin ominaisuuksien tärkeys. Pienetkin kaasumäärät päällystyspastassa häiritsivät lopullisen päällysteen laatua. Päällystyspastan ilmanpoisto on avainasemassa erityisesti kun päällystetään suurella nopeudella pieniä päällystemääriä. Koeajoissa havaittiin kaikki kirjallisuudessa esitellyt rajoittavat tekijät. Kokeissa päällystettiin 400-1600 m/min nopeudella 5-20 g/m² päällystemääriä. Olosuhteet stabiilille nestefilmille vaativat edelleen kehitystä suurella nopeudella päällystettäessä. Päällysteen eroavaisuuksia verrattiin teräpäällystysmenetelmiin. Terä-päällystyksellä saadaan sileä mutta epätasaisesti peittävä pinta kun taas uuden tekniikan päällyste mukailee päällystettävän alustan topografiaa. Tasapaksun päällysteen etuna on hyvä peittävyys jo pienellä päällystemäärällä.

Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis.

Pneumocystis species are fungal parasites colonizing mammal lungs with strict host specificity. Pneumocystis jirovecii is the human-specific species and can turn into an opportunistic pathogen causing severe pneumonia in immunocompromised individuals. This disease is currently the second most frequent life-threatening invasive fungal infection worldwide. The most efficient drug, cotrimoxazole, presents serious side effects, and resistance to this drug is emerging. The search for new targets for the development of new drugs is thus of utmost importance. The recent release of the P. jirovecii genome sequence opens a new era for this task. It can now be carried out on the actual targets to be inhibited instead of on those of the relatively distant model Pneumocystis carinii, the species infecting rats. We focused on the folic acid biosynthesis pathway because (i) it is widely used for efficient therapeutic intervention, and (ii) it involves several enzymes that are essential for the pathogen and have no human counterparts. In this study, we report the identification of two such potential targets within the genome of P. jirovecii, the dihydrofolate synthase (dhfs) and the aminodeoxychorismate lyase (abz2). The function of these enzymes was demonstrated by the rescue of the null allele of the orthologous gene of Saccharomyces cerevisiae.

Brain functional abnormality in schizo-affective disorder: an fMRI study.

Background.Schizo-affective disorder has not been studied to any significant extent using functional imaging. The aim of this study was to examine patterns of brain activation and deactivation in patients meeting strict diagnostic criteria for the disorder. METHOD: Thirty-two patients meeting research diagnostic criteria (RDC) for schizo-affective disorder (16 schizomanic and 16 schizodepressive) and 32 matched healthy controls underwent functional magnetic resonance imaging (fMRI) during performance of the n-back task. Linear models were used to obtain maps of activations and deactivations in the groups. RESULTS: Controls showed activation in a network of frontal and other areas and also deactivation in the medial frontal cortex, the precuneus and the parietal cortex. Schizo-affective patients activated significantly less in prefrontal, parietal and temporal regions than the controls, and also showed failure of deactivation in the medial frontal cortex. When task performance was controlled for, the reduced activation in the dorsolateral prefrontal cortex (DLPFC) and the failure of deactivation of the medial frontal cortex remained significant. CONCLUSIONS: Schizo-affective disorder shows a similar pattern of reduced frontal activation to schizophrenia. The disorder is also characterized by failure of deactivation suggestive of default mode network dysfunction.

Refractory intraretinal or subretinal fluid in neovascular age-related macular degeneration treated with intravitreal ranizubimab: Functional and Structural Outcome.

PURPOSE: To investigate the visual acuity results of eyes with neovascular age-related macular degeneration and refractory fluid despite monthly treatment with ranibizumab, and to investigate differences between refractory subretinal fluid and intraretinal cystic changes. METHODS: Retrospective chart review of consecutive treatment-refractory neovascular age-related macular degeneration, defined as persistent intraretinal or subretinal fluid despite monthly ranibizumab injections during 12 months or more. Data were evaluated for baseline characteristics, type and location of the refractory fluid, mean visual acuity change, number of injections, and the time point of first complete disappearance of all fluid on spectral domain optical coherence tomography. RESULTS: Seventy-six eyes (74 patients, mean age, 76.8 years) were identified. The mean follow-up was 33.6 months (range, 12-73 months). The mean number of injections was 11.4 in the first year and 27.7 over follow-up. The refractory fluid was located subfoveally in 61.8%. In 27 eyes (35.5%), the fluid resolved after a mean of 21.8 months (range, 13-49 months). Mean visual acuity increased by 9.0, 7.9, and 7.9 letters by Month 12, Month 24, and Month 36, respectively. Subgroup analysis revealed a higher risk for fibrosis (odds ratio, 3.30) or atrophy (odds ratio, 3.34) in patients with refractory cysts as compared with refractory subretinal fluid. Furthermore, refractory cysts showed a higher risk for a 10-letter visual acuity loss (P = 0.018). CONCLUSION: Fluid refractory to monthly treatment with ranibizumab for neovascular age-related macular degeneration still allowed for well-maintained visual improvement, even in subfoveal location. Late fluid resolution may occur. However, refractory cysts were associated with poorer anatomical and functional outcome than subretinal fluid.

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses.

BACKGROUND: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction factors, we performed genome-wide scans for human genes sharing molecular and evolutionary signatures of known restriction factors and tested the anti-HIV-1 activity of the most promising candidates. RESULTS: Our analyses identified 30 human genes that share characteristics of known restriction factors. Functional analyses of 27 of these candidates showed that over-expression of a strikingly high proportion of them significantly inhibited HIV-1 without causing cytotoxic effects. Five factors (APOL1, APOL6, CD164, TNFRSF10A, TNFRSF10D) suppressed infectious HIV-1 production in transfected 293T cells by >90% and six additional candidates (FCGR3A, CD3E, OAS1, GBP5, SPN, IFI16) achieved this when the virus was lacking intact accessory vpr, vpu and nef genes. Unexpectedly, over-expression of two factors (IL1A, SP110) significantly increased infectious HIV-1 production. Mechanistic studies suggest that the newly identified potential restriction factors act at different steps of the viral replication cycle, including proviral transcription and production of viral proteins. Finally, we confirmed that mRNA expression of most of these candidate restriction factors in primary CD4+ T cells is significantly increased by type I interferons. CONCLUSIONS: A limited number of human genes share multiple characteristics of genes encoding for known restriction factors. Most of them display anti-retroviral activity in transient transfection assays and are expressed in primary CD4+ T cells.

An Optimum Coating Colour Formula for CSWO-printing

Pigmenttipäällystyksen tarkoituksena on parantaa painopapereiden pintaominaisuuksia. Tämän työn tarkoituksena oli löytää sopiva päällystyspasta päällystetylle coldset-paperille. Kirjallisuusosassa on käsitelty coldset-painatusta ja sen ongelmia. Päällystysmenetelmän perusteita, pastan ominaisuuksia ja niiden vaikutusta päällystystulokseen on myös käsitelty. Lisäksi on esitelty joitakin päällystetyn paperin pinnantutkimusmenetelmiä. Kokeellisessa osassa on tutkittu erilaisten pastakoostumusten ja päällystemäärien sekä kalanteroinnin vaikutusta paperin painettavuuteen. Paperit on päällystetty Helicoaterilla ja joitakin pastoja on testattu myös pilot-mittakaavaisessa päällystyksessä. Selitystä paperin käyttäytymiseen painatuksessa on etsitty päällystetyn paperin pintarakenteesta. Paras painettavuus saavutetaan päällysteellä, jossa pigmenttinä on vain karbonaatti. Painojälkeä voidaan parantaa käyttämällä kalsinoitua kaoliinia yhdessä karbonaatin kanssa, mutta tämän päällysteen pintalujuus ei ole riittävä CSWO-painatukseen. Tärkkipigmentti parantaa veden ja painovärin absorptiota ja siten tekee painetun tuotteen kuivemmaksi ja miellyttävämmän tuntuiseksi, mutta aiheuttaa smearingia. Tämä johtuu liian nopeasta musteen asettuvuudesta. "Pehmeä" SB-lateksi soveltuu paremmin offset-painatukseen kuin "kova" lateksi, joka sisältää myös PVAc:ta. "Pehmeällä" lateksilla saadaan parempi pintalujuus ja painojälki kuin "kovalla" lateksilla. Paperin pölyävyyttä painatuksessa voidaan vähentää nostamalla päällystemäärää ja laskemalla pastan kuiva-ainepitoisuutta. Kalanteroinnilla ei pintalujuutta tai painojälkeä voida parantaa. Selitys tutkimuksessa käsiteltyjen papereiden painojäljelle ja painettavuudelle löydetään tutkimalla päällysteen pintarakennetta. Painojälkeen vaikuttaa eniten päällysteen peittoaste. Huonoa peittävyyttä voidaan parantaa nostamalla päällystemäärää. Pölyäminen painatuksessa johtuu pigmenteistä, jotka eivät ole sidottuja paperin pintaan. Tämä taas johtuu pastan huonosta vesiretentiosta. Hyödyllisintä tietoa näiden papereiden pintarakenteesta saadaan tutkimalla pintaa pyyhkäisyelektonimikroskoopilla (SEM), atomivoimamikroskoopilla (AFM) ja laserindusoidulla plasmaspektrometrilla (LIPS). LIPSin etuna on se, että päällystemääräjaukauma voidaan määrittää sekä x-y- että z-suunnassa samanaikaisesti samasta kohdasta. LIPSissä myös näytteen preparointitarve on hyvin vähäinen.