Holocarboxylase Synthetase-dependent Biotinylation of Histone H4

Holocarboxylase synthetase (HCS) catalyzes the binding of biotin to lysine (K) residues in histones H3 and H4. Histone biotinylation marks play important roles in the repression of genes and retrotransposons. Preliminary studies suggested that K16 in histone H4 is a target for biotinylation by HCS. Here we demonstrated that H4K16bio is overrepresented in repeat regions {pericentromeric alpha satellite repeats; long terminal repeats (LTR)} compared with euchromatin promoters. H4K16bio was also enriched in the repressed interleukin-2 gene promoter. The enrichment at LTR22 and promoter 1 of the sodium-dependent multivitamin transporter (SMVT) depended on biotin supply; and was significantly lower in fibroblasts from an HCS-deficient patient compared with an HCS wild-type control. We conclude that H4K16bio is a real phenomenon and plays a role in the transcriptional repression of repeats and genes. HCS catalyzes the covalent binding of biotin to carboxylases, in addition to its role as a histone biotinyl ligase. HCS null individuals are not viable whereas HCS deficiency is linked to developmental delays and phenotypes such as short life span and low stress resistance. Here, we developed a 96-well plate assay for high-throughput analysis of HCS based on the detection of biotinylated p67 using IRDye-streptavidin and infrared spectroscopy. We demonstrated that the catalytic activity of rHCS depends on temperature and time, and proposed optimal substrate and enzyme concentrations to ensure ideal measurement of rHCS activity and its kinetics. Additionally, we demonstrated that this assay is sensitive enough to detect biotinylation of p67 by endogenous HCS from Jurkat lymphoid cells.

JVM-based Techniques for Improving Java Observability

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure, called marker tracing framework (MTF), to address the deficiencies in the existing solutions for providing better observability for VM-based languages. MTF serves as a solid foundation for implementing fine-grained low-overhead program instrumentation. Specifically, MTF allows analysis clients to: 1) define custom events with rich semantics ; 2) specify precisely the program locations where the events should trigger; and 3) adaptively enable/disable the instrumentation at runtime. In addition, MTF-based analysis clients are more powerful by having access to all information available to the VM. To demonstrate the utility and effectiveness of MTF, we present two analysis clients: 1) dynamic typestate analysis with adaptive online program analysis (AOPA); and 2) selective probabilistic calling context analysis (SPCC). In addition, we evaluate the runtime performance of MTF and the typestate client with the DaCapo benchmarks. The results show that: 1) MTF has acceptable runtime overhead when tracing moderate numbers of marker events; and 2) AOPA is highly effective in reducing the event frequency for the dynamic typestate analysis; and 3) language VMs can be exploited to offer greater observability.

Electrophysiological Responses of the Naupactus bipes Beetle to Essential Oils from Piperaceae Species

Electrophysiological responses based on electroantennographic detection (GC-EAD) and electroantennography (EAG) analysis of Naupactus bipes beetles (Germar, 1824) (Coleoptera: Curculionidae: Brachycerinae) were used to test volatile oils of Piper gaudichaudianum, P. regnellii and P. hispidum. In the EAG experiments, female and male beetles showed significant EAG response to the three volatile oils of Piper species, with the females' responses slightly higher than the males'. The experiments with GC-EAD revealed that some terpenoids (namely, alpha-pinene, beta-pinene, myrcene, alpha-copaene and germacrene) present in the leaf essential oils of the Piper species are perceptible to female and male beetles.

Differences in Evolution of Children with Non-severe Acute Lower Respiratory Tract Infection With and Without Radiographically Diagnosed Pneumonia

Objective: To identify differences in the evolution of children with non-severe acute lower respiratory tract infection between those with and without radiographically diagnosed pneumonia. Design: Prospective cohort study. Setting: A public university pediatric hospital in Salvador, Northeast Brazil. Patients: Children aged 2-59 months. Methods: By active surveillance, the pneumonia cases were prospectively identified in a 2-year period. Each case was followed-up for changes in various clinical symptoms and signs. Demographic, clinical and radiographic data were recorded in standardized forms. Exclusion was due to antibiotic use in the previous 48 hours, signs of severe disease, refusal to give informed consent, underlying chronic illness, hospitalization in the previous 7 days or amoxicillin allergy. Chest X-ray (CXR) was later read by at least 2 independent pediatric radiologists. Main Outcome Measures: Radiographic diagnosed pneumonia based on agreed detection of pulmonary infiltrate or pleural effusion in 2 assessments. Results: A total of 382 patients receiving amoxicillin were studied, of whom, 372 (97.4%) had concordant radiographic diagnosis which was pneumonia (52%), normal CXR (41%). and others (7%). By multivariate analysis, age (OR=1.03; 95% CI: 1.02-1.05), disease >= 5days (OR = 1.04; 95% CI: 1.001-1.08), reduced pulmonary expansion (OR = 3.3; 95% CI: 1.4-8.0), absence of wheezing (OR = 0.5; 95% CI: 0.3-0.9), crackles on admission (OR = 2.0; 95% CI: 1.2-3.5), inability to drink on day 1 (OR = 4.2; 95% CI: 1.05-17.3), consolidation percussion sign (OR = 7.0; 95% CI: 1.5-32.3), tachypnea (OR = 2.0; 95% CI: 1.09-3.6) and fever (OR = 3.6; 95% CI: 1.4-9.4) on day 2 were independently associated with pneumonia. The highest positive predictive value was at the 2nd day of evolution for tachypnea (71.0%) and fever (81.1%). Conclusion: Persistence of fever or tachypnea up to the second day of amoxicillin treatment is predictive of radiographically diagnosed pneumonia among children with non-severe lower respiratory tract diseases.

A fragment-based approach for ligand binding affinity and selectivity for the liver X receptor beta

Selective modulation of liver X receptor beta (LXR beta) has been recognized as an important approach to prevent or reverse the atherosclerotic process. In the present work, we have developed robust conformation-independent fragment-based quantitative structure-activity and structure-selectivity relationship models for a series of quinolines and cinnolines as potent modulators of the two LXR sub-types. The generated models were then used to predict the potency of an external test set and the predicted values were in good agreement with the experimental results, indicating the potential of the models for untested compounds. The final 2D molecular recognition patterns obtained were integrated to 3D structure-based molecular modeling studies to provide useful insights into the chemical and structural determinants for increased LXR beta binding affinity and selectivity. (C) 2011 Elsevier Inc. All rights reserved.

Longitudinal bar buckling behavior

Reinforced concrete columns might fail because of buckling of the longitudinal reinforcing bar when exposed to earthquake motions. Depending on the hoop stiffness and the length-over-diameter ratio, the instability can be local (in between two subsequent hoops) or global (the buckling length comprises several hoop spacings). To get insight into the topic, an extensive literary research of 19 existing models has been carried out including different approaches and assumptions which yield different results. Finite element fiberanalysis was carried out to study the local buckling behavior with varying length-over-diameter and initial imperfection-over-diameter ratios. The comparison of the analytical results with some experimental results shows good agreement before the post buckling behavior undergoes large deformation. Furthermore, different global buckling analysis cases were run considering the influence of different parameters; for certain hoop stiffnesses and length-over-diameter ratios local buckling was encountered. A parametric study yields an adimensional critical stress in function of a stiffness ratio characterized by the reinforcement configuration. Colonne in cemento armato possono collassare per via dell’instabilità dell’armatura longitudinale se sottoposte all’azione di un sisma. In funzione della rigidezza dei ferri trasversali e del rapporto lunghezza d’inflessione-diametro, l’instabilità può essere locale (fra due staffe adiacenti) o globale (la lunghezza d’instabilità comprende alcune staffe). Per introdurre alla materia, è proposta un’esauriente ricerca bibliografica di 19 modelli esistenti che include approcci e ipotesi differenti che portano a risultati distinti. Tramite un’analisi a fibre e elementi finiti si è studiata l’instabilità locale con vari rapporti lunghezza d’inflessione-diametro e imperfezione iniziale-diametro. Il confronto dei risultati analitici con quelli sperimentali mostra una buona coincidenza fino al raggiungimento di grandi spostamenti. Inoltre, il caso d’instabilità globale è stato simulato valutando l’influenza di vari parametri; per certe configurazioni di rigidezza delle staffe e lunghezza d’inflessione-diametro si hanno ottenuto casi di instabilità locale. Uno studio parametrico ha permesso di ottenere un carico critico adimensionale in funzione del rapporto di rigidezza dato dalle caratteristiche dell’armatura.

Corpora in the Social Sciences- How corpus-based appraches can support qualitative interview analyses

[EN]Qualitative and quantitative research approaches are often considered as incompatible, and when they are brought together in a study, the analyses often stay within the realm of the same research field. The study at hand aims at combining the two methods from the perspectives of different disciplines and tries to determine to which degree a corpus-based analysis might support the traditional content-focused approach to qualitative data and render additional results.

Processing of measured acceleration response for SHM purpose

Structural Health Monitoring (SHM) is the process of characterization for existing civil structures that proposes for damage detection and structural identification. It's based firstly on the collection of data that are inevitably affected by noise. In this work a procedure to denoise the measured acceleration signal is proposed, based on EMD-thresholding techniques. Moreover the velocity and displacement responses are estimated, starting from measured acceleration.

On land management: landowners' attitudes to land and farming in Valdera, Tuscany

This thesis aims at explaining the intersecting dynamics of structural changes in agriculture and urbanisation, which involves changes in urban-rural relationships. The research questions are: how and why do landowners differ in their attitudes to land and farming? what are the main implications on rural landscapes and the policy implications? Relationships between urbanisation and agriculture are firstly analysed through a critical literature review; the analysis focuses on the 'landowner' as the key actor who actively takes decisions on the rural landscape From the empirical study – which is based on a Tuscan area (Valdera), and addressed through qualitative methods – a great diversity of landowners' attitudes to land and farming emerge, thus contributing to the agricultural restructuring, such as: 1) the emphasis on recreational function of the countryside for urban people 2) contracting out of land management, especially when landowners live or/and have 'urban' employment 3) the active role of hobby farmers in land management 4) agricultural operations simplification and lack of investments (especially in case of property rights expropriation). The thesis is framed in three papers, with the same methods and research questions. It seems evident that rural landscapes is subjected to functional changes (e.g. residential) and structural changes (landscape polarisation), which requires the need 1) to consider that rural landscape management is increasingly less connected to agricultural production as economic activity; 2) to give a coherence to the range of policy interventions (physical planning, landscape, sectoral).

Modelli Gravitazionali per l'analisi del Commercio Internazionale

Il modello gravitazionale e' ormai diventato un "cavallo da battaglia" in economia internazionle ed e' comunemente utilizzato nella determinazione dei flussi commerciali. Recentemente, molti studi hanno mostrato l'importanza della dipendenza spaziale, che va' a considerare quegli effetti dovuti al cosiddetto "third country". Intervengono a questo scopo la modellistica e le tecniche di stima di Econometria Spaziale. Verra' fatto uso di tali tecniche allo scopo di stimare con un modello gravitazionale spaziale il commercio internazionale tra paesi dell'OCSE per un panel di 22 anni. L'obiettivo e' quindi duplice: da un lato, si andra' ad applicare le piu' moderne tecniche di Econometria Spaziale, in un campo in cui tali contributi scarseggiano. Dall'altro lato,verra' fornita una interpretazione del comportamento del commercio internazionale tra paesi dell'OCSE, approfondendo gli aspetti relativi all'effetto del"third country" e del fenomeno migratorio. Inoltre , viene proposta un'analisi che ha lo scopo di validare l'ipotesi di omissione della distanza dal modello gravitazione strutturale.

Advanced schemes for surface plasmon resonance and plasmon-enhanced fluorescence biosensors

Advanced optical biosensor platforms exploiting long range surface plasmons (LRSPs) and responsive N-isopropylacrylamide (NIPAAm) hydrogel binding matrix for the detection of protein and bacterial pathogen analytes were carried out. LRSPs are optical waves that originate from coupling of surface plasmons on the opposite sites of a thin metallic film embedded between two dielectrics with similar refractive indices. LRSPs exhibit orders of magnitude lower damping and more extended profile of field compared to regular surface plasmons (SPs). Their excitation is accompanied with narrow resonance and provides stronger enhancement of electromagnetic field intensity that can advance the sensitivity of surface plasmon resonance (SPR) and surface plasmon-enhanced fluorescence spectroscopy (SPFS) biosensors. Firstly, we investigated thin gold layers deposited on fluoropolymer surface for the excitation of LRSPs. The study indicates that the morphological, optical and electrical properties of gold film can be changed by the surface energy of fluoropolymer and affect the performance of a SPFS biosensor. A photo-crosslinkable NIPAAm hydrogel was grafted to the sensor surface in order to serve as a binding matrix. It was modified with bio-recognition elements (BREs) via amine coupling chemistry and offered the advantage of large binding capacity, stimuli responsive properties and good biocompatibility. Through experimental observations supported by numerical simulations describing diffusion mass transfer and affinity binding of target molecules in the hydrogel, the hydrogel binding matrix thickness, concentration of BREs and the profile of the probing evanescent field was optimized. Hydrogel with a up to micrometer thickness was shown to support additional hydrogel optical waveguide (HOW) mode which was employed for probing affinity binding events in the gel by means of refractometric and fluorescence measurements. These schemes allow to reach limits of detection (LODs) at picomolar and femtomolar levels, respectively. Besides hydrogel based experiments for detection of molecular analytes, long range surface plasmon-enhanced fluorescence spectroscopy (LRSP-FS) was employed for detection of bacterial pathogens. The influence of capture efficiency of bacteria on surfaces and the profile of the probing field on sensor response were investigated. The potential of LRSP-FS with extended evanescent field is demonstrated for detection of pathogenic E. coli O157:H7 on sandwich immunoassays . LOD as low as 6 cfu mL-1 with a detection time of 40 minutes was achieved.rn

Vergleich der Elastographie-gesteuerten Biopsie mit der Systembiopsie bei der Detektion von Prostatakarzinomen

Hintergrund: Die Systembiopsie gilt als Goldstandard zum Nachweis eines Prostatakarzinoms, obwohl ein relevanter Anteil an Prostatakarzinomen nicht diagnostiziert wird. Wir wollten mit unserer Arbeit die Frage beantworten, ob mittels elastographisch gezielter Biopsien die Prostatakarzinom-Detektion im Vergleich zur Goldstandard-Systembiopsie verbessert werden kann. Material und Methode: 152 Patienten wurden in einer prospektiven Studie einer 12-fachen Prostata-Systembiopsie unterzogen. In Linksseitenlagerung wurde dabei aus jedem der vordefinierten 6 Prostatasegmente je 1 laterale und 1 mediale Stanze entnommen. Elastographisch suspekte Areale wurden zusätzlich gezielt biopsiert. Als statistisch signifikant wurde p<0,05 angenommen. Ergebnisse: Bei 62 der 152 Patienten (40,8%) wurde ein Prostatakarzinom diagnostiziert. Die Detektionsrate der Systembiopsie betrug 39,5% (60/152), die Detektionsrate der Elastographie 29,6% (45/152). Somit war die Systembiopsie der elastographisch gezielten Biopsie signifikant überlegen (p=0,039).Jedoch war die Wahrscheinlichkeit mit einer Prostatastanze ein Karzinomherd zu entdecken, für die elastographischen Biopsien 3,7-fach höher als für die Systembiopsien. Die Sensitivität der Elastographie betrug 72,6% und die Spezifität 66,6%. Der positive Vorhersagewert für die Elastographie war 60%, der negative Vorhersagewert 78%. Die Kombination von Systembiopsie und elastographisch gezielten Biopsien bot die höchste Detektionsrate. In der rechten Prostatahälfte (48%) verzeichneten wir doppelt so viele elastographisch falsch-positive Befunde wie in der linken Prostatahälfte (25%). Desweiteren fanden sich am häufigsten falsch-positive Befunde im Prostata-Apex (46%) und am seltensten in der Prostata-Basis (29%). Schlussfolgerung: In unserer Studie war die elastographisch gezielte Biopsie der Systembiopsie signifikant unterlegen (p=0,039). Die Kombination von Systembiopsie mit elastographisch gezielten Biopsien bot die höchste Detektionsrate und kann daher empfohlen werden. Die Auffälligkeiten in der Segment-bezogenen Auswertung und ein möglicher Einfluss der Patienten-Lagerung müssen durch weitere Studien überprüft werden.rn

Test der Speziellen Relativitätstheorie mittels Laserspektroskopie an relativistischen 7 Li +-Ionen am ESR

Die Invarianz physikalischer Gesetze unter Lorentztransformationen ist eines der fundamentalen Postulate der modernen Physik und alle Theorien der grundlegenden Wechselwirkungen sind in kovarianter Form formuliert. Obwohl die Spezielle Relativitätstheorie (SRT) in einer Vielzahl von Experimenten mit hoher Genauigkeit überprüft und bestätigt wurde, sind aufgrund der weitreichenden Bedeutung dieses Postulats weitere verbesserte Tests von grundsätzlichem Interesse. Darüber hinaus weisen moderne Ansätze zur Vereinheitlichung der Gravitation mit den anderen Wechselwirkungen auf eine mögliche Verletzung der Lorentzinvarianz hin. In diesem Zusammenhang spielen Ives-Stilwell Experimente zum Test der Zeitdilatation in der SRT eine bedeutende Rolle. Dabei wird die hochauflösende Laserspektroskopie eingesetzt, um die Gültigkeit der relativistischen Dopplerformel – und damit des Zeitdilatationsfaktors γ – an relativistischen Teilchenstrahlen zu untersuchen. Im Rahmen dieser Arbeit wurde ein Ives-Stilwell Experiment an 7Li+-Ionen, die bei einer Geschwindigkeit von 34 % der Lichtgeschwindigkeit im Experimentierspeicherring (ESR) des GSI Helmholtzzentrums für Schwerionenforschung gespeichert waren, durchgeführt. Unter Verwendung des 1s2s3S1→ 1s2p3P2-Übergangs wurde sowohl Λ-Spektroskopie als auch Sättigungsspektroskopie betrieben. Durch die computergestützte Analyse des Fluoreszenznachweises und unter Verwendung optimierter Kantenfilter für den Nachweis konnte das Signal zu Rauschverhältnis entscheidend verbessert und unter Einsatz eines zusätzlichen Pumplasers erstmals ein Sättigungssignal beobachtet werden. Die Frequenzstabilität der beiden verwendeten Lasersysteme wurde mit Hilfe eines Frequenzkamms spezifiziert, um eine möglichst hohe Genauigkeit zu erreichen. Die aus den Strahlzeiten gewonnen Daten wurden im Rahmen der Robertson-Mansouri-Sexl-Testtheorie (RMS) und der Standard Model Extension (SME) interpretiert und entsprechende Obergrenzen für die relevanten Testparameter der jeweiligen Theorie bestimmt. Die Obergrenze für den Testparameter α der RMS-Theorie konnte gegenüber den früheren Messungen bei 6,4 % der Lichtgeschwindigkeit am Testspeicherring (TSR) des Max-Planck-Instituts für Kernphysik in Heidelberg um einen Faktor 4 verbessert werden.

Multivariate analysis methods in the search for the Higgs boson produced in association with top pairs at the ATLAS experiment at LHC.

The Large Hadron Collider, located at the CERN laboratories in Geneva, is the largest particle accelerator in the world. One of the main research fields at LHC is the study of the Higgs boson, the latest particle discovered at the ATLAS and CMS experiments. Due to the small production cross section for the Higgs boson, only a substantial statistics can offer the chance to study this particle properties. In order to perform these searches it is desirable to avoid the contamination of the signal signature by the number and variety of the background processes produced in pp collisions at LHC. Much account assumes the study of multivariate methods which, compared to the standard cut-based analysis, can enhance the signal selection of a Higgs boson produced in association with a top quark pair through a dileptonic final state (ttH channel). The statistics collected up to 2012 is not sufficient to supply a significant number of ttH events; however, the methods applied in this thesis will provide a powerful tool for the increasing statistics that will be collected during the next LHC data taking.

Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.