Packet flow analysis in IP networks using data-flow analysis

Static analysis (aka offline analysis) of a model of an IP network is useful for understanding, debugging, and verifying packet flow properties of the network. Data-flow analysis is a method that has typically been applied to static analysis of programs. We propose a new, data-flow based approach for static analysis of packet flows in networks. We also investigate an application of our analysis to the problem of inferring a high-level policy from the network, which has been addressed in the past only for a single router.

Pattern-growth based frequent serial episode discovery

Frequent episode discovery is a popular framework for pattern discovery from sequential data. It has found many applications in domains like alarm management in telecommunication networks, fault analysis in the manufacturing plants, predicting user behavior in web click streams and so on. In this paper, we address the discovery of serial episodes. In the episodes context, there have been multiple ways to quantify the frequency of an episode. Most of the current algorithms for episode discovery under various frequencies are apriori-based level-wise methods. These methods essentially perform a breadth-first search of the pattern space. However currently there are no depth-first based methods of pattern discovery in the frequent episode framework under many of the frequency definitions. In this paper, we try to bridge this gap. We provide new depth-first based algorithms for serial episode discovery under non-overlapped and total frequencies. Under non-overlapped frequency, we present algorithms that can take care of span constraint and gap constraint on episode occurrences. Under total frequency we present an algorithm that can handle span constraint. We provide proofs of correctness for the proposed algorithms. We demonstrate the effectiveness of the proposed algorithms by extensive simulations. We also give detailed run-time comparisons with the existing apriori-based methods and illustrate scenarios under which the proposed pattern-growth algorithms perform better than their apriori counterparts. (C) 2013 Elsevier B.V. All rights reserved.

Ring opening of activated cyclopropanes with NIS/NaN3: synthesis of C-1 linked pseudodisaccharides

NIS/NaN3 mediated ring opening of various donor-acceptor cyclopropanes has been investigated. The study shows the necessity of the donor oxygen lone pair in such ring opening reactions. This methodology has been utilized in the synthesis of C-1 linked pseudodisaccharides through the use of click chemistry. (C) 2013 Elsevier Ltd. All rights reserved.

量纲分析

量纲分析是一门非常值得研究和学习的知识，它是探讨科学规律，解决科学和工程的一个有效的工具。熟练掌握量纲分析应当是科学和技术工作者应有的基本训练。
本书内容包括：量纲分析的基本概念；量纲分析在熟知的力学现象中的应用；量纲分析在某些经典的力学问题中的应用以及郑哲敏先生的研究集体近三四十年中在爆炸力学诸多的应用实例等几个部分。 

水动力学讲义手稿

水动力学讲义手稿》是1958年钱学森先生在清华大学给第一届力学研究班学员讲授《水动力学》课程用的备课笔记。钱先生选材简赅精切，遴的内容具有基础性、经典性，整个手稿清晰耐读，详略得体，推演细腻，覆盖全面。
《水动力学讲义手稿》可供科技人员、教研人员及广大师生研究和学习之用。

Ortsbezogene Informationen in Internet-Datenbanken - das Beispiel "Baltic SeaWeb"

Whoever in future will need information about a location or an area, either literature, measurement data, photos or administrative information, might only click on that spot on a screen map in the internet. A search programme started thereby will offer all available information in databanks. A step forward to such a solution, to the retrieval of location related literature and measurement data from different kinds of databanks, is presented by the project “Baltic Sea Web” (http://www.baltic.vtt.fi/ demonstrator/index.html). The basic idea was to make the available information about a certain location accessible via a link of their geographical coordinates, longitude and latitude, to a map in a web browser

Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

A cocktail of thermally stable, chemically synthesized capture agents for the efficient detection of anti-gp41 antibodies from human sera and techniques

This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60°C.

Development of protein-catalyzed capture (PCC) agents with application to the specific targeting of the E17K Point mutation of Akt1

This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.

These technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Efficacy and safety of autologous platelet rich plasma for the treatment of vascular ulcers in primary care: Phase III study

Background: Vascular ulcers are commonly seen in daily practice at all levels of care and have great impact at personal, professional and social levels with a high cost in terms of human and material resources. Given that the application of autologous platelet rich plasma has been shown to decrease healing times in various different studies in the hospital setting, we considered that it would be interesting to assess the efficacy and feasibility of this treatment in primary care. The objectives of this study are to assess the potential efficacy and safety of autologous platelet rich plasma for the treatment of venous ulcers compared to the conventional treatment (moist wound care) in primary care patients with chronic venous insufficiency (C, clinical class, E, aetiology, A, anatomy and P, pathophysiology classification C6). Design: We will conduct a phase III, open-label, parallel-group, multicentre, randomized study. The subjects will be 150 patients aged between 40 and 100 years of age with an at least 2-month history of a vascular venous ulcer assigned to ten primary care centres. For the treatment with autologous platelet rich plasma, all the following tasks will be performed in the primary care setting: blood collection, centrifugation, separation of platelet rich plasma, activation of coagulation adding calcium chloride and application of the PRP topically after gelification. The control group will receive standard moist wound care. The outcome variables to be measured at baseline, and at weeks 5 and 9 later include: reduction in the ulcer area, Chronic Venous Insufficiency Quality of Life Questionnaire score, and percentage of patients who require wound care only once a week. Discussion: The results of this study will be useful to improve the protocol for using platelet rich plasma in chronic vascular ulcers and to favour wider use of this treatment in primary care.

El pintor navarro Juan Ochoa de Arín (1600-1652) y su producción en Gipuzkoa

Investigación realizada dentro del Programa de Formación y Perfeccionamiento de Personal Investigador del Gobierno Vasco (2010-2013).

Centro de gestión de contenido en RDF

La primera idea de la realización de este proyecto, fue concebida por la necesidad de tener un sistema por el cual se pudieran cambiar datos de una aplicación, en un sistema móvil, a través de una página web. Sin embargo al conocer la potencia que tiene RDF para ser muy escalable terminó siendo un sistema de gestión de contenido general en RDF. Este sistema de gestión se ha realizado para ser lo más simple posible para un usuario, de tal manera que con solo 2 click en la página web y rellenando un formulario simple, pudiera tener una base de datos sin muchos conocimientos sobre la gestión de las mismas. Aunque claramente no es un sistema potente como si fuera una base de datos en Oracle, por citar un ejemplo, sirve para poder agregar, modificar y eliminar datos con sencillez. Así este sistema de gestión da una posibilidad muy sencilla de realizar tus propias bases de datos. Además aunque tiene un motor SQL para la gestión interna de almacenamiento, la salida de los datos es en RDF/XML con lo que podría ser compatible con un sistema más amplio como Oracle Database Semantic Technologies. Este CMS también tendrá un sistema de seguridad basado en usuario y contraseña. Para que la edición del contenido sea accesible solo a usuarios con acceso, mientras que la exportación de los datos será pública, y podrá ser accesible por cualquier usuario mediante una URI.

Modificação química do poli(cloreto de vinila) com nucleófilos nitrogenados assistida por micro-ondas

Nesse trabalho foram realizadas reações de substituição nucleofílica (SN2), utilizando aquecimento térmico convencional e por irradiação de micro-ondas (MO), de alguns átomos cloro em amostras comerciais de poli(cloreto de vinila) (PVC), por grupos nitrila e também por grupos azida. Os grupos nitrila e azida foram substituidos na matriz em diferentes teores (10% e 20%). As reações do PVC com azida foram eficazes, apresentado percentuais de derivatização muito próximos dos valores desejados. Já no estudo com a nitrila não foi obtido o resultado esperado. Os copolímeros PVC azido substituídos foram modificados com propargilato de etila, sob catálise de iodeto de cuproso (CuI), para a obtenção de heterocíclicos do tipo triazólicos. Todos os copolímeros obtidos foram caracterizados por espectroscopia na região do infravermelho (FTIR) e os teores de nitrogênio incorporado foram determinados por análise elementar (AE). Através da análise dos dados obtidos, foi comprovado que a utilização da irradiação micro-ondas, quando comparada ao aquecimento convencional, é um processo mais seletivo e diminui, significativamente, os tempos de reação