The performance of four molecular methods for the laboratory diagnosis of congenital toxoplasmosis in amniotic fluid samples

Introduction Toxoplasmosis may be life-threatening in fetuses and in immune-deficient patients. Conventional laboratory diagnosis of toxoplasmosis is based on the presence of IgM and IgG anti-Toxoplasma gondii antibodies; however, molecular techniques have emerged as alternative tools due to their increased sensitivity. The aim of this study was to compare the performance of 4 PCR-based methods for the laboratory diagnosis of toxoplasmosis. One hundred pregnant women who seroconverted during pregnancy were included in the study. The definition of cases was based on a 12-month follow-up of the infants. Methods Amniotic fluid samples were submitted to DNA extraction and amplification by the following 4 Toxoplasma techniques performed with parasite B1 gene primers: conventional PCR, nested-PCR, multiplex-nested-PCR, and real-time PCR. Seven parameters were analyzed, sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), negative likelihood ratio (NLR) and efficiency (Ef). Results Fifty-nine of the 100 infants had toxoplasmosis; 42 (71.2%) had IgM antibodies at birth but were asymptomatic, and the remaining 17 cases had non-detectable IgM antibodies but high IgG antibody titers that were associated with retinochoroiditis in 8 (13.5%) cases, abnormal cranial ultrasound in 5 (8.5%) cases, and signs/symptoms suggestive of infection in 4 (6.8%) cases. The conventional PCR assay detected 50 cases (9 false-negatives), nested-PCR detected 58 cases (1 false-negative and 4 false-positives), multiplex-nested-PCR detected 57 cases (2 false-negatives), and real-time-PCR detected 58 cases (1 false-negative). Conclusions The real-time PCR assay was the best-performing technique based on the parameters of Se (98.3%), Sp (100%), PPV (100%), NPV (97.6%), PLR (â^ž), NLR (0.017), and Ef (99%).

Effect of a polymeric protective coating on optical and electrical properties of poly (p-phenylene vinylene) derivatives

The resistance to photodegradation of poly [(2-methoxy-5-n-hexyloxy)-p-phenylene vinylene] (OC1OC6-PPV) films was significantly enhanced by the use of poly(vinyl alcohol) 99% hydrolyzed as protective coating. The deposition of poly(vinyl alcohol) onto OC1OC6-PPV films did not affect the absorption and the emission spectra of the luminescent polymer. The protected film showed 5% drop on the absorbance at 500nm after 270 hours of light exposure while the unprotected film completely degraded in the same conditions. The conductivity of the protected film remained stable (around 7 × 10-10 S/m) while the value for the unprotected one dropped around two orders of magnitude after 100 hours of light exposure.

Ruolo dell'elastometria pulsata monodimensionale ad ultrasuoni (fibroscan) nella stadiazione della fibrosi epatica in pazienti sottoposti a trapianto ortotopico di fegato con recidiva di epatite C

PREMESSA: La progressione della recidiva d’epatite C è accelerata nei pazienti sottoposti a trapianto di fegato e ciò ha portato alla necessità di sviluppare nuove e validate metodiche non invasive per la quantificazione e la misura della fibrosi epatica. SCOPI: Stabilire l’efficacia dell’elastometria epatica (Fibroscan®) e dei parametri sierici di fibrosi, attualmente disponibili nella pratica clinica, per predire il grado di fibrosi nei pazienti sottoposti a trapianto epatico. METODI: La correlazione fra fibrosi epatica, determinata mediante biopsia epatica ed esame istologico, e Fibroscan® o indici clinico-sierologici di fibrosi (Benlloch, Apri, Forns, Fibrotest and Doppler resistance index), è stata studiata in pazienti che avevano ricevuto un trapianto ortotopico di fegato con evidenza di recidiva d’epatite da HCV. Un totale di 36 pazienti, con la seguente classificazione istologica: fibrosi secondom METAVIR F1=24, F2=8, F3=3, F4=1, sono stati arruolati nella popolazione oggetto di studio. Un totale di 29 individui volontari sani sono serviti come controllo. Le differenze fra gli stadi di fibrosi sono state calcolate mediante analisi statistica non parametrica. Il miglior cut-off per la differenziazione di fibrosi significativa (F2-F4) è stato identificato mediante l’analisi delle curve ROC. RISULTATI: La rigidità epatica ha presentato valori di 4.4 KPa (2.7-6.9) nei controlli (mediane e ranges), con valori in tutti i soggeti <7.0 KPa; 7.75 KPa (4.2-28.0) negli F1; 16.95 KPa (10.2-31.6) negli F2; 21.10 KPa nell’unico paziente F4 cirrotico. Le differenze sono state statisticamente significative per i soggetti controllo versus F1 e F2 (p<0.0001) e per F1 versus F2 (p<0.0001). Un cut-off elastografico di 11.2 KPagarantisce 88% di Sensibilità, 90% di Specificità, 79% di PPV e 95% di NPV nel differenziare i soggetti F1 dagli F2-F4. Le AUROC, relativamente alla capacità di discriminare fra i differenti gradi di fibrosi, evidenziavano un netto vantaggio per il Fibroscan® rispetto ad ognuno degli indici non invasivi di fibrosi. CONCLUSIONI: L’elastometria epatica presenta una buona accuratezza diagnostica nell’identificare pazienti con fibrosi epatica di grado significativo, superiore a quella di tutti gli altri test non invasivi al momento disponibili nella clinica, nei pazienti portatori di trapianto epatico ortotopico da cadavere con recidiva di HCV.

Parapoxvirus: basi genomiche della patogenesi

Parapoxvirus (PPV) are member of a genus in the family poxviridae which currently encompasses four species: the prototype orf virus (OV), bovine papular stomatitis virus (BPSV), pseudocowpox virus (PCPV) and parapoxvirus of New Zealand red deer (PVNZ). PPVs cause widespread, but localized diseases of small and large ruminants and they can also be transmitted to man. Knowledge of the molecular biology of PPV is still limited as compared to orthopoxviruses, especially vaccinia virus (VACV). The PPV genome displays a high G+C content and relatively small size for poxvirus. Coventional electron microscopy displays PPV virions with ovoid shape and slightly smaller in size than the brickshaped orthopoxviruses. The most striking feature, which readily enables identification of PPV, is a tubule-like structure that surrounds the particle in a spiral fashion. PPV genome organization and content is very similar to that of other poxviruses, the central region contain 88 genes which are present in all poxviruse, in contrast the terminal regions are variable and contain a set of genes unique to the genus PPV. Genes in the near-terminal regions of the genome are frequently not essential for growth in cultured cells encoding factors with important roles in virushost interactions including modulating host immune responses and determining host range. Recently it was suggested that the open reading frames (ORFs) 109 and 110 of the OV genome have a major role in determining species specificity during natural infection in sheep and goats. This hypothesis is based on the analysis of a few number of sequences of different sheep and goats viral isolates. PPV replicate into the cytoplasm of infected cells and produce three structurally different infectious particles: the intracellular mature virions (IMV), intracellular enveloped virions (IEV) and the extracellular enveloped virions (EEV). The vaccinia A33R and A34R hotologue proteins encoded by the ORFS 109 and 110 are expressed in the envelope of the IEV and EEV. The F1L immunodominant protein of orf virus is the major component of the surface tubule structure of the IMV and can post-translationaly insert into membranes via Cterminal, hydrofobic anchor sequence like its orthologue VACV H3L protein. Moreover the F1L protein binds to glycosaminoglycans on the cell surface and has an important role in IMV adsorption to mammalian cells. In this study we investigated the morphogenesis of the PPV through the construction of a mutant virus deleted of the F1L protein. A study of the deleted virus life cycle was conducted in different type of cells and its morphology was observed with electron microscopy. It was demonstared that F1L protein have important role in morphogenesis and infectivity. Moreover it is essential to determine the spiral fashion of the tubule like structure of the virion surface. Some pathogenetic aspects of the PPV infection were studied, in particular the protein implicated in the host range were analysed in detail. An experimental infection with OV and PCPV was conducted in goats and sheep. After infection, the severity of the lesions were comparable in both the animal species. The OV did not result in severe disease neither in sheep nor in goats, suggesting that host factors, rather than virus strain characteristics, may play an important role in the pathogenesis of the Parapoxvirus infections. The PCPV failed to produce any lesion in both sheep and goats, ruling out the possibility of any recombination between PCPV and OV during natural infection in these animal species. The phylogenetic analysis of the ORFs 109 and 110 from several goats and sheep viral isolates showed a clustering based on the antigenic content of the protein that was independent from species and geographic origin.

Meccanismi evolutivi dei parapoxvirus: caratterizzazione genomica di pseudocowpoxvirus e messa a punto di sistemi per lo studio delle ricombinazioni

The Poxviruses are a family of double stranded DNA (dsDNA) viruses that cause disease in many species, both vertebrate and invertebrate. Their genomes range in size from 135 to 365 kbp and show conservation in both organization and content. In particular, the central genomic regions of the chordopoxvirus subfamily (those capable of infecting vertebrates) contain 88 genes which are present in all the virus species characterised to date and which mostly occur in the same order and orientation. In contrast, however, the terminal regions of the genomes frequently contain genes that are species or genera-specific and that are not essential for the growth of the virus in vitro but instead often encode factors with important roles in vivo including modulation of the host immune response to infection and determination of the host range of the virus. The Parapoxviruses (PPV), of which Orf virus is the prototypic species, represent a genus within the chordopoxvirus subfamily of Poxviridae and are characterised by their ability to infect ruminants and humans. The genus currently contains four recognised species of virus, bovine papular stomatitis virus (BPSV) and pseudocowpox virus (PCPV) both of which infect cattle, orf virus (OV) that infects sheep and goats, and parapoxvirus of red deer in New Zealand (PVNZ). The ORFV genome has been fully sequenced, as has that of BPSV, and is ~138 kb in length encoding ~132 genes. The vast majority of these genes allow the virus to replicate in the cytoplasm of the infected host cell and therefore encode proteins involved in replication, transcription and metabolism of nucleic acids. These genes are well conserved between all known genera of poxviruses. There is however another class of genes, located at either end of the linear dsDNA genome, that encode proteins which are non-essential for replication and generally dictate host range and virulence of the virus. The non-essential genes are often the most variable within and between species of virus and therefore are potentially useful for diagnostic purposes. Given their role in subverting the host-immune response to infection they are also targets for novel therapeutics. The function of only a relatively small number of these proteins has been elucidated and there are several genes whose function still remains obscure principally because there is little similarity between them and proteins of known function in current sequence databases. It is thought that by selectively removing some of the virulence genes, or at least neutralising the proteins in some way, current vaccines could be improved. The evolution of poxviruses has been proposed to be an adaptive process involving frequent events of gene gain and loss, such that the virus co-evolves with its specific host. Gene capture or horizontal gene transfer from the host to the virus is considered an important source of new viral genes including those likely to be involved in host range and those enabling the virus to interfere with the host immune response to infection. Given the low rate of nucleotide substitution, recombination can be seen as an essential evolutionary driving force although it is likely underestimated. Recombination in poxviruses is intimately linked to DNA replication with both viral and cellular proteins participate in this recombination-dependent replication. It has been shown, in other poxvirus genera, that recombination between isolates and perhaps even between species does occur, thereby providing another mechanism for the acquisition of new genes and for the rapid evolution of viruses. Such events may result in viruses that have a selective advantage over others, for example in re-infections (a characteristic of the PPV), or in viruses that are able to jump the species barrier and infect new hosts. Sequence data related to viral strains isolated from goats suggest that possible recombination events may have occurred between OV and PCPV (Ueda et al. 2003). The recombination events are frequent during poxvirus replication and comparative genomic analysis of several poxvirus species has revealed that recombinations occur frequently on the right terminal region. Intraspecific recombination can occur between strains of the same PPV species, but also interspecific recombination can happen depending on enough sequence similarity to enable recombination between distinct PPV species. The most important pre-requisite for a successful recombination is the coinfection of the individual host by different virus strains or species. Consequently, the following factors affecting the distribution of different viruses to shared target cells need to be considered: dose of inoculated virus, time interval between inoculation of the first and the second virus, distance between the marker mutations, genetic homology. At present there are no available data on the replication dynamics of PPV in permissive and non permissive hosts and reguarding co-infetions there are no information on the interference mechanisms occurring during the simultaneous replication of viruses of different species. This work has been carried out to set up permissive substrates allowing the replication of different PPV species, in particular keratinocytes monolayers and organotypic skin cultures. Furthermore a method to isolate and expand ovine skin stem cells was has been set up to indeep further aspects of viral cellular tropism during natural infection. The study produced important data to elucidate the replication dynamics of OV and PCPV virus in vitro as well as the mechanisms of interference that can arise during co-infection with different viral species. Moreover, the analysis carried on the genomic right terminal region of PCPV 1303/05 contributed to a better knowledge of the viral genes involved in host interaction and pathogenesis as well as to locate recombination breakpoints and genetic homologies between PPV species. Taken together these data filled several crucial gaps for the study of interspecific recombinations of PPVs which are thought to be important for a better understanding of the viral evolution and to improve the biosafety of antiviral therapy and PPV-based vectors.

Schichtpräparation und Charakterisierung von Wellenleitern aus Polymeren

In der vorliegenden Arbeit wurde die Bedeutung verschiedener Präparationsparameter auf die Schichtpräparation von Polymerfilmen durch Schleuderbeschichtung untersucht. Insbesondere war der Einfluß der Konzentration bzw. Viskosität der Polymerlösungen, der Umdrehungszahl und der Präparationstemperatur auf die Schichtdicke und Schichtrauhigkeit von Interesse. Eine systematische Variation der Präparationsparameter wurde an Polystyrol/Toluol-, Polycarbonat/DMF- und Polycarbonat/Cyclohexanon-Lösungen vorgenommen. Es stellte sich heraus, daß eine Schichtpräparation beim Gebrauch des Lösungsmittels DMF erst bei Temperaturen oberhalb der Raumtemperatur möglich wurde. Das Auftreten von Defekten in den aus höherkonzentrierten Lösungen hergestellten Schichten ist möglicherweise auf die Bildung von Gelpartikeln in den Lösungen zurückzuführen. Die Lösungsmittelauswahl spielt daher eine Schlüsselrolle bei der Präparation defektfreier Schichten. Es sollte ein Lösungsmittel verwendet werden, dessen Löslichkeitsparameter mit dem zu lösenden Polymeren idealerweise übereinstimmt und das einen hohen Siedepunkt besitzt. Falls die Schichtdicke auf einen bestimmten Wert festgelegt ist, so folgen aus den Polystyrol- und Polycarbonatergebnissen unterschiedliche Schlußfolgerungen zur Reduzierung der Rauhigkeit, die sich jedoch auf einen gemeinsamen Nenner bringen lassen. Betrachtet man die an Polystyrol- und Polycarbonatschichten gewonnenen Resultate gemeinsam, so erscheint es zur Reduzierung der Rauhigkeit bei vorgegebener Schichtdicke sinnvoller, die Präparation bei großer Umdrehungszahl und hoher Konzentration durchzuführen als bei kleiner Umdrehungszahl aus niederkonzentrierten Lösungen. Eine Variation der Präparationstemperatur erweist sich als außerordentlich hilfreich zur Optimierung der Schichtqualität. Dies zeigt sich insbesondere bei der Präparation von Polycarbonat-, D/A-PPV- und Polyvinylkarbazol-Schichten, wenn DMF als Lösungsmittel verwendet wird. Durch eine Temperaturerhöhung ist zudem eine größere Schichtdicke erreichbar. Dies kann sich unter Umständen bei schwerlöslichen Substanzen als vorteilhaft erweisen, um die für Wellenleiteranwendungen erforderliche Mindestschichtdicke zu erreichen. Aus den Abhängigkeiten der Schichtdicke von den Präparationsparametern Konzentration und Umdrehungszahl lassen dich Potenzgesetze der Form ? ableiten. Der Exponent ? hängt vom speziellen Polymer/Lösungsmittelsystem und von der Temperatur ab; für ? wurde meistens ein Wert von -0.5 gefunden. Zur Bestimmung der Exponenten sind nur vier verschiedene Parametersätze (?,?) notwendig. Bei Kenntnis von ? und ? kann die Schichtdicke für eine beliebige (?,?)-Kombination im voraus in guter Näherung bestimmt werden, was in der Praxis häufig nützlich ist. Durch Beachtung dieser Präparationsregeln konnten neben dämpfungsarmen Polystyrol- und Polycarbonatschichten auch filme aus konjugierten Polymeren hergestellt werden, deren Dämpfungskoeffizienten teilweise deutlich unter 1 dB/cm lagen. Hier sind besonders die Resultate an DPOP-PPV und CNE-PPV Schichten hervorzuheben. Die erreichten Dämpfungswerte sind besser bzw. vergleichbar mit den geringsten Werten, die bisher in der Literatur zu konjugierten Polymerfilmen veröffentlicht wurden. Bei einigen Substanzen scheiterte die Präparation ausreichend dicker Filme bzw. Dämpfungsmessungen an einer zu geringen Löslichkeit oder an der Bildung polykristalliner Domänen bzw. sonstiger Defekte. Dies macht deutlich, daß eine erfolgreiche Schichtpräparation wesentlich von der chemischen struktur abhängt. Die Abschätzung des Güteparameters (Figure Of Merit) ergab mit den gemessenen nichtlinear-optischen Suszeptibilitäten ?

Synthese und Reaktivität styrylsubstituierter p-Benzochinone

Synthese und Reaktivität styrylsubstituierter p-Benzochinone Oligo- und Poly(1,4-phenylenvinylene) (OPV, PPV) stellen eine für die Materialwissenschaft äußerst interessante Verbindungsklasse dar, die in Form von Halbleitern, Photoleitern, elektrolumineszierenden Systemen und negativen Photoresists breitgefächerte Anwendung findet. Allerdings stellt die Alterung dieser Materialien in Gegenwart von Sauerstoff und anderen Oxidationsmitteln ein signifikantes Problem dar. So wird z. B. die technische Anwendung von Leuchtdioden auf Polymerbasis durch ihre geringe Betriebsdauer eingeschränkt. Als Beitrag zur Untersuchung des oxidativen Abbaus von Poly- bzw. Oligo(p-phenylenvinylenen) [PPV, OPV] wurden verschiedene 2-Styryl-1,4-benzochinone - sowie höhere Oligomere - synthetisiert, die das Strukturelement einer hoch oxidierten Form von OPV's aufweisen. Durch Einführung einer Cyanogruppe an der olefinischen Doppelbindung wurde die Reaktivität der Modellsysteme gezielt beeinflußt. Die 2-Styryl-1,4-benzochinone mit unsubstituierter Doppelbindung dimerisieren in Lösung quantitativ im Sinne von Diels-Alder-Reaktionen zu den entsprechenden Cycloaddukten. Die Dimerisierungen verlaufen chemo-, regio- und stereoselektiv, was sich anhand von Grenzorbital-Betrachtungen erklären läßt.An der Oberfläche von Kieselgel erfolgt eine vollständige Umwandlung der Dimere, deren zwei Hauptprodukte identifiziert werden konnten: Neben Verbindungen, die durch eine intramolekulare [4+2]-Cycloaddition nach erfolgter Dehydrierung / Oxidation gebildet werden, entstehen verschiedene Additionsprodukte der Dimere mit Nucleophilen (Wasser, Ethanol). Cyanosubstitution führt bereits bei den als Vorstufe dienenden Stilbenen zu einer erleichterten (E/Z)-Photoisomerisierung in Lösung, die zu einem photostationären Gleichgewicht führt, welches sich durch einen hohen Anteil der (E)-Konfiguration auszeichnet. Nach erfolgter Oxidation kann ebenfalls eine Dimerisierung beobachtet werden. Bei direkter Nachbarschaft der Cyanogruppe zum Chinonring erfolgt stattdessen ein intramolekularer Ringschluß unter Ausbildung eines Benzofuranderivats.Die beobachtete Reaktivität der synthetisierten Chinonsysteme steht in Einklang mit einem möglichen sekundären Abbaumechanismus, der nach primärer Oxidation zu der Alterung von PPV's beitragen kann.

Metodi biochimici e biomolecolari applicati alla medicina clinica: rendimento della real-time TaqMan PCR per la valutazione della resistenza alla claritromicina in H.pylori e tests fecali nella diagnorstica del carcinoma colo-rettale: M2PK, calprotectina e FOBT

1) Background: The most common methods to evaluate clarithromycin resistance is the E-Test, but is time consuming. Resistance of Hp to clarithromycin is due to point mutations in the 23S rRNA. Eight different point mutations have been related to CH resistance, but the large majority of the clarithromycin resistance depends on three point mutations (A2142C, A2142G and A2143G). A novel PCR-based clarithromycin resistance assays, even on paraffin-embedded biopsy specimens, have been proposed. Aims: to assess clarithromycin resistance detecting these point mutation (E-Test as a reference method);secondly, to investigate relation with MIC values. Methods: Paraffin-embedded biopsies of patients Hp-positive were retrieved. The A2142C, A2142G and A2143G point mutations were detected by molecular analysis after DNA extraction by using a TaqMan real-time PCR. Results: The study enrolled 86 patients: 46 resistant and 40 sensible to CH. The Hp status was evaluated at endoscopy, by rapid urease test (RUT), histology and hp culture. According to real-time PCR, 37 specimens were susceptible to clarithromycin (wild type dna) whilst the remaining 49 specimens (57%) were resistant. A2143G is the most frequent mutation. A2142C always express a resistant phenotype and A2142G leads to a resitant phenotype only if homozigous. 2) Background: Colonoscopy work-load for endoscopy services is increasing due to colorectal cancer prevention. We tested a combination of faecal tests to improve accuracy and prioritize the access to colonoscopy. Methods: we tested a combination of fecal tests (FOBT, M2-PK and calprotectin) in a group of 280 patients requiring colonoscopy. Results: 47 patients had CRC and 85 had advanced adenoma/s at colonoscopy/histology. In case of single test, for CRC detection FOBT was the test with the highest specificity and PPV, M2-PK had the highest sensitivity and higher NPV. Combination was more interesting in term of PPV. And the best combination of tests was i-FOBT + M2-PK.

Conjugated semiconducting organic materials for electronic applications

Since conjugated polymers, i.e. polymers with spatially extended pi-bonding system have offered unique physical properties, unobtainable for conventional polymers, significant research efforts directed to better understanding of their chemistry, physics and engineering have been undertaken in the past two and half decades. In this thesis we discuss the synthesis, characterisation and investigation of conjugated semiconducting organic materials for electronic applications. Owing to the versatile properties of metal-organic hybrid materials, there is significant promise that these materials can find use in optical or electronic devices in the future. In addressing this issue, the synthesis of bisthiazol-2-yl-amine (BTA) based polymers is attempted and their metallation is investigated. The focus of this work has been to examine whether the introduction of coordinating metal ions onto the polymer backbone can enhance the conductivity of the material. These studies can provide a basis for understanding the photophysical properties of metal-organic polymers based on BTA. In their neutral (undoped) form conjugated polymers are semiconductors and can be used as active components of plastics electronics such as polymer light-emitting diodes, polymer lasers, photovoltaic cells, field-effect transistors, etc. Toward this goal, it is an objective of the study to synthesize and characterize new classes of luminescent polymeric materials based on anthracene and phenanthrene moieties. A series of materials based on polyphenylenes and poly(phenyleneethynylene)s with 9,10-anthrylene subunits are not only presented but the synthesis and characterization of step-ladder and ladder poly(p-phenylene-alt-anthrylene)s containing 9,10-anthrylene building groups within the main chain are also explored. In a separate work, a series of soluble poly-2,7- and 3,6-phenanthrylenes are synthesized. This can enable us to do a systematic investigation into the optical and electronic properties of PPP-like versus PPV-like. Besides, the self-organization of 3,6-linked macrocyclic triphenanthrylene has been investigated by 2D wide-angle X-ray scattering experiments performed on extruded filaments in solution and in the bulk. Additionally, from the concept that donor-acceptor materials can induce efficient electron transfer, the covalent incorporation of perylene tetracarboxydiimide (PDI) into one block of a poly(2,7-carbazole) (PCz)-based diblock copolymer and 2,5-pyrrole based on push-pull type material are achieved respectively.

Modeling of complex chemical reactions and macromolecular orientation phenomena in confined geometries

The cooperative motion algorithm was applied on the molecular simulation of complex chemical reactions and macromolecular orientation phenomena in confined geometries. First, we investigated the case of equilibrium step-growth polymerization in lamellae, pores and droplets. In such systems, confinement was quantified as the area/volume ratio. Results showed that, as confinement increases, polymerization becomes slower and the average molecular weight (MW) at equilibrium decreases. This is caused by the sterical hindrance imposed by the walls since chain growth reactions in their close vicinity have less realization possibilities. For reactions inside droplets at surfaces, contact angles usually increased after polymerization to compensate conformation restrictions imposed by confinement upon growing chains. In a second investigation, we considered monodisperse and chemically inert chains and focused on the effect of confinement on chain orientation. Simulations of thin polymer films showed that chains are preferably oriented parallel to the surface. Orientation increases as MW increases or as film thickness d decreases, in qualitative agreement with experiments with low MW polystyrene. It is demonstrated that the orientation of simulated chains results from a size effect, being a function of the ratio between chain end-to-end distance and d. This study was complemented by experiments with thin films of pi-conjugated polymers like MEH-PPV. Anisotropic refractive index measurements were used to analyze chain orientation. With increasing MW, orientation is enhanced. However, for MEH-PPV, orientation does not depend on d even at thicknesses much larger than the chain contour length. This contradiction with simulations was discussed by considering additional causes for orientation, for instance the appearance of nematic-like ordering in polymer films. In another investigation, we simulated droplet evaporation at soluble surfaces and reproduced the formation of wells surrounded by ringlike deposits at the surface, as observed experimentally. In our simulations, swollen substrate particles migrate to the border of the droplet to minimize the contact between solvent and vacuum, which costs the most energy. Deposit formation in the beginning of evaporation results in pinning of the droplet. When polymer chains at the substrate surface have strong uniaxial orientation, the resulting pattern is no longer similar to a ring but to a pair of half-moons. In a final stage, as an extension for the model developed for polymerization in nanoreactors, we studied the effect of geometrical confinement on a hypothetical oscillating reaction following the mechanism of the so called periodically forced Brusselator. It was shown that a reaction which is chaotic in the bulk may be driven to periodicity by confinement and vice-versa, opening new perspectives for chaos control.

Machine-learning methods for structure prediction of β-barrel membrane proteins

Different types of proteins exist with diverse functions that are essential for living organisms. An important class of proteins is represented by transmembrane proteins which are specifically designed to be inserted into biological membranes and devised to perform very important functions in the cell such as cell communication and active transport across the membrane. Transmembrane β-barrels (TMBBs) are a sub-class of membrane proteins largely under-represented in structure databases because of the extreme difficulty in experimental structure determination. For this reason, computational tools that are able to predict the structure of TMBBs are needed. In this thesis, two computational problems related to TMBBs were addressed: the detection of TMBBs in large datasets of proteins and the prediction of the topology of TMBB proteins. Firstly, a method for TMBB detection was presented based on a novel neural network framework for variable-length sequence classification. The proposed approach was validated on a non-redundant dataset of proteins. Furthermore, we carried-out genome-wide detection using the entire Escherichia coli proteome. In both experiments, the method significantly outperformed other existing state-of-the-art approaches, reaching very high PPV (92%) and MCC (0.82). Secondly, a method was also introduced for TMBB topology prediction. The proposed approach is based on grammatical modelling and probabilistic discriminative models for sequence data labeling. The method was evaluated using a newly generated dataset of 38 TMBB proteins obtained from high-resolution data in the PDB. Results have shown that the model is able to correctly predict topologies of 25 out of 38 protein chains in the dataset. When tested on previously released datasets, the performances of the proposed approach were measured as comparable or superior to the current state-of-the-art of TMBB topology prediction.

Thin films of polythiophene: Linear and nonlinear optical characterization

Wir haben die linearen und nichtlinearen optischen Eigenschaften von dünnen Schichten und planaren Wellenleitern aus mehreren konjugierten Polymeren (MEH-PPV und P3AT) und Polymeren mit -Elektronen Systemen in der Seitenkette (PVK und PS) untersucht und verglichen. PVK und PS haben relativ kleine Werte des nichtlinearen Brechungsindex n2 bei 532 nm, nämlich (1,2 ± 0,5)10-14 cm2/W und (2,6 ± 0,5) 10-14 cm2/W.rnWir haben die linearen optischen Konstanten von mehreren P3ATs untersucht, insbesondere den Einfluss der Regioregularität und Kettenlänge der Alkylsubstituenten. Wir haben das am besten geeignete Polymere für Wellenleiter Anwendungen identifiziert, welches P3BT-ra genannt ist. Wir haben die linearen optischen Eigenschaften dünner Schichten des P3BT-ra untersucht, die mit Spincoating aus verschiedenen Lösungsmitteln mit unterschiedlichen Siedetemperaturen präparieret wurden. Wir haben festgestellt, dass P3BT-ra Filme aus Toluol-Lösungen die am besten geeigneten Wellenleiter für die intensitätsabhängigen Prismen-Kopplungs Experimente sind, weil diese geringe Wellenleiterdämpfungsverluste bei = 1064 nm haben. rnWir haben die Dispersionen des Wellenleiterdämfungsverlustes gw, des nichtlinearen Brechungsindex n2 und des nichtlinearen Absorptionskoeffizienten 2 von Wellenleitern aus P3BT-ra im Bereich von 700 - 1500 nm gemessen. Wir haben große Werte des nichtlinearen Brechungsindex bis 1,5x10-13 cm2/W bei 1150 nm beobachtet. Wir haben gefunden, dass die Gütenkriterien (“figures of merit“) für rein optische Schalter im Wellenlängebereich 1050 - 1200 nm erfüllt sind. Dieser Bereich entspricht dem niederenergetischen Ausläufer der Zwei-Photonen-Absorption. Die Gütekriterien von P3BT-ra gehören zu den besten der bisher bekannten Werte von konjugierten Polymeren.rnWir haben gefunden, dass P3BT-ra ein vielversprechender Kandidat für integriert-optische Schalter ist, weil es eine gute Kombination aus großer Nichtlinearität dritter Ordnung, geringen Wellenleiterdämpfungverlusten und ausreichender Photostabilität zeigt. rnWir haben einen Vergleich der gemessenen Dispersion von gw, n2 und 2 mit der Theorie durchgeführt. Durch Kurvenanpassung der Dispersion von gw haben wir gefunden, dass Rayleigh-Streuung der dominierende Dämpfungsmechanismus in MEH-PPV und P3BT-ra Wellenleitern ist. Ein quantenmechanischer Ansatz wurde zur Berechnung der nichtlinearen Suszeptibilität dritter Ordnung (3) verwendet, um die gemessenen Spektren von n2 und 2 von P3BT-ra und MEH-PPV zu simulieren. Dies kann erklären, dass sättigbare Absorption und Zwei-Photonen Absorption die hauptsächlichen Effekte sind, welche die Dispersion von n2 und 2 verursachen. rn

Untersuchungen zur Photophysik einzelner konjugierter Polymerketten bei tiefen Temperaturen

Die spektroskopische Untersuchung einzelner konjugierter Polymermoleküle, welche multichromophore Systeme darstellen, bei 1,2K eröffnete den Zugang zu den unterschiedlichen Chromophoren. In Fluoreszenzemissions- wie -anregungsspektren des Poly(2-methoxy-5-(2’-ethylhexyloxy)-rnp-phenylenvinylen) (MEH-PPV) konnten Nullphononenlinien (rein elektronische (0-0)-Übergänge) emittierender Chromophore beobachtet werden, deren Breiten durch das experimentelle Auflösungsvermögen limitiert waren. Dadurch konnte eine obere Grenze für die homogene Linienbreite festgelegt werden. Infolge starker linearer Elektron-Phonon-Kopplung und spektraler Diffusion war die Beobachtung von Nullphononenlinien jedoch auf eine Minderheit der Chromophorernbeschränkt. In geeigneten Probesystemen konnten in Anregungsspektren auch Nullphononenlinien solcher Chromophore identifiziert werden, die als Donoren im intramolekularen Energietransfer fungieren. Aufgrund der dadurch verkürzten Fluoreszenzlebensdauer und der damit verbundenen Linienverbreiterung erlaubte ihre Untersuchung die Ermittlung von Energietransferraten. Eine bei Proben höherer Molmasse auftretenden niederenergetische Subpopulation an Emittern wurde auf Grundlage ihres Fluoreszenzemissions-, -anregungs- und -abklingverhaltens und unter Berücksichtigung theoretischer Arbeiten auf längere chromophore Einheiten zurückgeführt, die sich infolge von Packungseffekten in geordneten Regionen der Polymerkette ausbilden. Die schwächere lineare Elektron-Phonon-Kopplung des leiterartig verknüpften Polypentaphenylen (LPPentP) äußerte sich in einer erhöhten Wahrscheinlichkeit des Auftretens von Nullphononenlinien. Die genaue Bestimmung von Energietransferraten litt allerdings unter einem weiteren signifikanten Beitrag zur Linienbreite neben der Lebensdauer des angeregten Zustandes (möglicherweisernspektrale Diffusion oder schnelle Dephasierungsprozesse).

Management of submacular hemorrhage with intravitreal versus subretinal injection of recombinant tissue plasminogen activator

To compare the efficacy of pars plana vitrectomy (ppV) with intravitreal injection of recombinant tissue plasminogen activator (rtPA) and gas versus ppV with subretinal injection of rtPA and intravitreal injection of gas.

Computed tomographic coronary angiography in patients with surgically treated type A aortic dissection: preliminary results

Acute type A aortic dissection is a serious emergency with a mortality rate of up to 40% within the first 24 h when left untreated. Surgical therapy needs to be initiated promptly. Due to this urgent situation, preoperative evaluation of the coronary arteries is not routinely performed in these patients. The aim of this study was to evaluate the accuracy of 64-slice computed tomography angiography (CTA) for postoperative coronary artery assessment in these patients. Ten consecutive patients with two or more cardiovascular risk factors were prospectively enrolled. Patients had type A aortic dissection treated surgically with a supracoronary graft of the ascending aorta. Performance of CTA to exclude significant stenosis (>50% lumen narrowing) and/or coronary artery dissection was compared with quantitative coronary angiography. A total of 147 segments were evaluated. Three segments (2%) were excluded from analysis. CTA correctly assessed one of three significant stenoses in three patients and correctly excluded coronary artery disease (CAD) in six of ten patients. One patient was rated false positive. Overall accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of CT for identifying coronary artery disease by segment was 98%, 33%, 99%, 50%, and 99%, respectively (P<0.05). By patient, it was 70%, 33%, 86%, 50%, and 75%, respectively. No coronary artery dissection was found. Noninvasive CTA may be a viable alternative to conventional angiography for postoperative coronary artery evaluation in patients with surgically treated type A aortic dissection and cardiovascular risk factors. An NPV of 99% should allow for reliable exclusion of CAD. Further studies with higher patient numbers are warranted.