Design and performance evaluation of switching architectures for high-speed Internet

The motivation for this thesis is the desire to build faster and scalable routers that efficiently handle the exponential traffic growth in the Internet. The Internet forwards information through a mesh of routers and switches, which has to keep up with the increasing demands of traffic. Shared-memory based switches are known to provide the best throughput-delay performance for a given memory size. In this thesis performance of commonly used memory-sharing schemes for the shared memory switches are evaluated under balanced and unbalanced bursty traffic. The scalability of shared-memory switches has been a research issue for quite sometime. One approach is to employ multiple memory modules and use them in parallel to enhance the capacity. The two well-known architectures in this category are (i) shared-multibuffer (SMB) switch architecture invented by Yamanaka et al. of Mitsubishi Electric Corporation, Japan; and (ii) the sliding-window (SW) switch architecture invented by Dr. Kumar of UTPA, Texas, USA. In this thesis, performance of these two architectures are evaluated and compared. Furthermore, in this thesis, the SW switch architecture is extended to enable priority switching to provide differentiated Quality of Service (QoS) for different traffic classes

Sequence-specific DNA binders for nucleotide resolution analysis genomic 5-methylcytosine by cell imaging

5-methylcytosine (5mC) is a fundamental epigenetic modification in mammalian genomes involved in development, cell differentiation and genomic imprinting. In addition, aberrant DNA methylation patterns are responsible for the pathogenesis of many diseases including neurodegenerative disorders, cardiovascular affections and cancer. In this thesis, we describe the development of a novel method for image-based analysis of 5mC using pairs of fluorescent Transcription Activator Like-Effectors (TALEs). These DNA binding proteins can recognize specific sequences of canonical or epigenetically modified DNA via modular repeats that interact with nucleobases in a one-to-one correspondence. We employed fluorescent TALE pairs that differ only in the repeat responsible for recognizing cytosine (C) at CpG dinucleotides and the fluorophore fused to them (either eGFP or mCherry). By using the 5mC selective repeat HD in one of the TALEs, we can detect differences in methylation level, while the universal binder repeat G* in the other TALE is not responsive to 5mC and allows to detect local changes in chromatin compaction. This way it is possible to analyze 5mC independently of potential differences in target accessibility. We applied our method using recombinantly expressed and purified TALE pairs in cellular stains to image SatIII DNA. This pericentromeric DNA is the origin of nuclear stress bodies (nSBs), exhibits aberrant methylation in several cancers and remains challenging to study by conventional methods due to its highly repetitive nature. We proved the applicability of our method to study 5mC differences in user-defined repetitive sequences with single nucleotide and strand resolution. Furthermore, we correlated the methylation status of SatIII with the presence of heat shock factor 1 (HSF1) at its recognition sequence after stress, revealing a role for 5mC in HSF1 recruitment as initial step of nSB formation in a subpopulation of cells. Finally, we constructed and screened a library of size-reduced TALE repeats to identify potential 5mC binders. We found that RVD NH* binds selectively to 5mC, but not C and its application in combination with HD TALEs allows for improved imaging with higher dynamic range. These studies offer a promising imaging tool for studying 5mC function in repetitive sequences and its interplay with other imageable chromatin-interacting proteins with nucleotide, strand, locus and cell resolution

A Passivity-Based High-Bandwidth Voltage Control for Grid-Forming Inverters

The increasing number of power electronic devices connected to the power system is leading it to new stability challenges. The uncertainty of the grid-model may complicate the controller design and compromise stability. As a countermeasure, LQR and pole-placement techniques can be re-oriented to design for passivity, which is leading to new controller design paradigms. Nevertheless, as a general rule, all the variables of the system are considered in the full bandwidth, which may become unfeasible or costly in the industrial scenario. An original controller design technique for LC or LCL filter which accomplishes passivity in a wide range of frequency is proposed. Besides, it reduces the voltage sensor needs, even controlling it, being suitable for Grid-Forming. As consequence, the complexity of the software, hardware and price are reduced. Experimental verification is provided: impedance of the converter from the grid side and response against a changes in the reference/load

Programmable Protein-DNA Crosslinking for the Direct Capture and Quantification of 5-Formylcytosine

5-Formylcytosine (5fC) is an epigenetic nucleobase of mammalian genomes that occurs as intermediate of active DNA demethylation. 5fC uniquely interacts and reacts with key nuclear proteins, indicating functions in genome regulation. Transcription-activator-like effectors (TALEs) are repeat-based DNA binding proteins that can serve as probes for the direct, programmable recognition and analysis of epigenetic nucleobases. However, no TALE repeats for the selective recognition of 5fC are available, and the typically low genomic levels of 5fC represent a particular sensitivity challenge. We here advance TALE-based nucleobase targeting from recognition to covalent cross-linking. We report TALE repeats bearing the ketone-amino acid p-acetylphenylalanine (pAcF) that universally bind all mammalian cytosine nucleobases, but selectively form diaminooxy-linker-mediated dioxime cross-links to 5fC. We identify repeat-linker combinations enabling single CpG resolution, and demonstrate the direct quantification of 5fC levels in a human genome background by covalent enrichment. This strategy provides a new avenue to expand the application scope of programmable probes with selectivity beyond A, G, T and C for epigenetic studies

Programmable protein-DNA crosslinking for the direct capture and quantification of 5-formylcytosine

5-Formylcytosine (5fC) is an epigenetic nucleobase of mammalian genomes that occurs as intermediate of active DNA demethylation. 5fC uniquely interacts and reacts with key nuclear proteins, indicating functions in genome regulation. Transcription-activator-like effectors (TALEs) are repeat-based DNA binding proteins that can serve as probes for the direct, programmable recognition and analysis of epigenetic nucleobases. However, no TALE repeats for the selective recognition of 5fC are available, and the typically low genomic levels of 5fC represent a particular sensitivity challenge. We here advance TALEbased nucleobase targeting from recognition to covalent crosslinking. We report TALE repeats bearing the ketoneamino acid p-acetylphenylalanine (pAcF) that universally bind all mammalian cytosine nucleobases, but selectively form diaminooxy-linker-mediated dioxime crosslinks to 5fC. We identify repeat-linker combinations enabling single CpG resolution, and demonstrate the direct quantification of 5fC levels in a human genome background by covalent enrichment. This strategy provides a new avenue to expand the application scope of programmable probes with selectivity beyond A, G, T and C for epigenetic studies

Experimental artifact in MOKE measurements when using paramagnetic sample holders

We describe here an artifact that may affect to magneto-optical Kerr measurements. When paramagnetic sample holders (SH) with non-negligible susceptibilities are used, the inhomogeneity of the applied magnetic field can induce forces and torques on it, shifting the reflected beam, and altering its intensity at the photodetector. The effect is even and can be avoided using low susceptibility paramagnetic or diamagnetic SH We also present a detailed analytical description of the magnetic forces involved and provide some estimated values of the SH shifting, showing that they might distort the magneto-optical Kerr effect signal. Moreover, in this paper we show how the artifact can be removed from the experimental curves with an appropriated data analysis.Fil: Munoz-Noval, Alvaro. Comunidad de Madrid; EspañaFil: Bonin, Claudio Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Física del Litoral. Universidad Nacional del Litoral. Instituto de Física del Litoral; ArgentinaFil: Bonetto, Fernando Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Física del Litoral. Universidad Nacional del Litoral. Instituto de Física del Litoral; ArgentinaFil: Garcia, Miguel Angel. Institute For Ceramic And Glass; Españ

Removal of urothelium affects bladder contractility and release of ATP but not release of NO in rat urinary bladder

<p>Abstract</p> <p>Background</p> <p>The objective of our work was to investigate both the contractile function and the release of ATP and NO from strips of bladder tissue after removal of the urothelium.</p> <p>Methods</p> <p>The method of removal was a gentle swabbing motion rather than a sharp surgical cutting to separate the urothelium from the smooth muscle. The contractile response and ATP and NO release were measured in intact as well as on swabbed preparations. The removal of the urothelial layer was affirmed microscopically.</p> <p>Results</p> <p>After the swabbing, the smaller contractions were evoked by electrical as well as by chemical stimulation (50 μM carbachol or 50 μM α, β meATP). Electrical stimulation, carbachol and substance P (5 μM) evoked lower release of ATP in the swabbed strips than in intact strips. Although release of NO evoked by electrical stimulation or substance P was not changed, release of NO evoked by carbachol was significantly less in the swabbed preparations.</p> <p>Conclusion</p> <p>Since swabbing removes only the urothelium, the presence of the suburothelial layer may explain the difference between our findings and those of others who found an increase in contractility. Evoked release of ATP is reduced in swabbed strips, indicating that ATP derives solely from the urothelium. On the other hand, electrical stimulation and substance P evoke identical degrees of NO release in both intact and swabbed preparations, suggesting that NO can be released from the suburothelium. Conversely, carbachol-induced release of NO is lower in swabbed strips, implying that the cholinergic receptors (muscarinic or nicotinic) are located in the upper layer of the urothelium.</p

Internet-based training of coronary artery patients: the Heart Cycle Trial

© 2016, Springer Japan. Low adherence to cardiac rehabilitation (CR) might be improved by remote monitoring systems that can be used to motivate and supervise patients and tailor CR safely and effectively to their needs. The main objective of this study was to evaluate the feasibility of a smartphone-guided training system (GEX) and whether it could improve exercise capacity compared to CR delivered by conventional methods for patients with coronary artery disease (CAD). A prospective, randomized, international, multi-center study comparing CR delivered by conventional means (CG) or by remote monitoring (IG) using a new training steering/feedback tool (GEx System). This consisted of a sensor monitoring breathing rate and the electrocardiogram that transmitted information on training intensity, arrhythmias and adherence to training prescriptions, wirelessly via the internet, to a medical team that provided feedback and adjusted training prescriptions. Exercise capacity was evaluated prior to and 6 months after intervention. 118 patients (58 ± 10 years, 105 men) with CAD referred for CR were randomized (IG: n = 55, CG: n = 63). However, 15 patients (27 %) in the IG and 18 (29 %) in the CG withdrew participation and technical problems prevented a further 21 patients (38 %) in the IG from participating. No training-related complications occurred. For those who completed the study, peak VO 2 improved more (p = 0.005) in the IG (1.76 ± 4.1 ml/min/kg) compared to CG (−0.4 ± 2.7 ml/min/kg). A newly designed system for home-based CR appears feasible, safe and improves exercise capacity compared to national CR. Technical problems reflected the complexity of applying remote monitoring solutions at an international level

Core-electron contributions to the molecular magnetic response

Orbital contributions to the magnetic response depend on the method used to compute them. Here, we show that dissecting nuclear magnetic shielding tensors using natural localized molecular orbitals (NLMOs) leads to anomalous core contributions. The arbitrariness of the assignment might significantly affect the interpretation of the magnetic response of nonplanar molecules such as C-60 or [14]helicene and the assessment of their aromatic character. We solve this problem by computing the core- and sigma-components of the induced magnetic field (and NICS) and the magnetically induced current density by removing the valence electrons (RVE). We estimate the core contributions to the magnetic response by performing calculations on the corresponding highly charged molecules, such as C6H630+ for benzene, using gauge-including atomic orbitals and canonical molecular orbitals (CMOs). The orbital contributions to nuclear magnetic shielding tensors are usually estimated by employing a natural chemical shielding (NCS) analysis in NLMO or CMO bases. The RVE approach shows that the core contribution to the magnetic response is small and localized at the nuclei, contrary to what NCS calculations suggest. This may lead to a completely incorrect interpretation of the magnetic sigma-orbital response of nonplanar structures, which may play a major role in the overall magnetic shielding of the system. The RVE approach is thus a simple and inexpensive way to determine the magnetic response of the core- and sigma-electrons.Peer reviewe