Isolation and characterization of a monoclonal anti-quadruplex DNA antibody from autoimmune "viable motheaten" mice

A cell line that produces an autoantibody specific for DNA quadruplex structures has been isolated and cloned from a hybridoma library derived from 3-month-old nonimmunized autoimmune, immunodeficient "viable motheaten" mice. This antibody has been tested extensively in vitro and found to bind specifically to DNA quadruplex structures formed by two biologically relevant sequence motifs. Scatchard and nonlinear regression analyses using both one- and two-site models were used to derive association constants for the antibody-DNA binding reactions. In both cases, quadruplexes had higher association constants than triplex and duplex molecules. The anti-quadruplex antibody binds to the quadruplex formed by the promoter-region-derived oligonucleotide d(CGCG4GCG) (Ka = 3.3 x 10(6) M-1), and has enhanced affinity for telomere-derived quadruplexes formed by the oligonucleotides d(TG4) and d(T2G4T2G4T2G4T2G4) (Ka = 5.38 x 10(6) and 1.66 x 10(7) M-1, respectively). The antibody binds both types of quadruplexes but has preferential affinity for the parallel four-stranded structure. In vitro radioimmunofilter binding experiments demonstrated that purified anti-DNA quadruplex antibodies from anti-quadruplex antibody-producing tissue culture supernatants have at least 10-fold higher affinity for quadruplexes than for triplex and duplex DNA structures of similar base composition and length. The antibody binds intramolecular DNA triplexes formed by d(G4T3G4T3C4) and d(C4T3G4T3G4), and the duplex d(CGCGCGCGCG)2 with an affinities of 6. 76 x 10(5), 5.59 x 10(5), and 8.26 x 10(5) M-1, respectively. Competition experiments showed that melted quadruplexes are not effective competitors for antibody binding when compared to native structures, confirming that the quadruplex is bound structure-specifically. To our knowledge, this is the first immunological reagent known to specifically recognize quadruplex structures. Subsequent sequence analysis demonstrates homologies between the antibody complementarity determining regions and sequences from Myb family telomere binding proteins, which are hypothesized to control cell aging via telomeric DNA interactions. The presence of this antibody in the autoimmune repertoire suggests a possible linkage between autoimmunity, telomeric DNA binding proteins, and aging.     

Hand gesture recognition from depth and infrared Kinect data for CAVE applications interaction

This paper presents a real-time framework that combines depth data and infrared laser speckle pattern (ILSP) images, captured from a Kinect device, for static hand gesture recognition to interact with CAVE applications. At the startup of the system, background removal and hand position detection are performed using only the depth map. After that, tracking is started using the hand positions of the previous frames in order to seek for the hand centroid of the current one. The obtained point is used as a seed for a region growing algorithm to perform hand segmentation in the depth map. The result is a mask that will be used for hand segmentation in the ILSP frame sequence. Next, we apply motion restrictions for gesture spotting in order to mark each image as a ‘Gesture’ or ‘Non-Gesture’. The ILSP counterparts of the frames labeled as “Gesture” are enhanced by using mask subtraction, contrast stretching, median filter, and histogram equalization. The result is used as the input for the feature extraction using a scale invariant feature transform algorithm (SIFT), bag-of-visual-words construction and classification through a multi-class support vector machine (SVM) classifier. Finally, we build a grammar based on the hand gesture classes to convert the classification results in control commands for the CAVE application. The performed tests and comparisons show that the implemented plugin is an efficient solution. We achieve state-of-the-art recognition accuracy as well as efficient object manipulation in a virtual scene visualized in the CAVE.     

3D porosity prediction from seismic inversion and neural networks

In this work, we address the problem of transforming seismic reflection data into an intrinsic rock property model. Specifically, we present an application of a methodology that allows interpreters to obtain effective porosity 3D maps from post-stack 3D seismic amplitude data, using measured density and sonic well log data as constraints. In this methodology, a 3D acoustic impedance model is calculated from seismic reflection amplitudes by applying an L₁-norm sparse-spike inversion algorithm in the time domain, followed by a recursive inversion performed in the frequency domain. A 3D low-frequency impedance model is estimated by kriging interpolation of impedance values calculated from well log data. This low-frequency model is added to the inversion result which otherwise provides only a relative numerical scale. To convert acoustic impedance into a single reservoir property, a feed-forward Neural Network (NN) is trained, validated and tested using gamma-ray and acoustic impedance values observed at the well log positions as input and effective porosity values as target. The trained NN is then applied for the whole reservoir volume in order to obtain a 3D effective porosity model. While the particular conclusions drawn from the results obtained in this work cannot be generalized, such results suggest that this workflow can be applied successfully as an aid in reservoir characterization, especially when there is a strong non-linear relationship between effective porosity and acoustic impedance.     

A Framework for Integrating Non-Functional Requirements into Conceptual Models

The development of complex information systems calls for conceptual models that describe aspects beyond entities and activities. In particular, recent research has pointed out that conceptual models need to model goals, in order to capture the intentions which underlie complex situations within an organisational context. This paper focuses on one class of goals, namely non-functional requirements (NFR), which need to be captured and analysed from the very early phases of the software development process. The paper presents a framework for integrating NFRs into the ER and OO models. This framework has been validated by two case studies, one of which is very large. The results of the case studies suggest that goal modelling during early phases can lead to a more productive and complete modelling activity.       

H] Tryptamine and 3H-water as diffusible internal standards for measuring brain extraction of radio-labeled substances following carotid injection

Urinary amino acid excretion was determined in 31 leukemic patients and 29 normal individuals by rapid gas chromatographic analysis of 16 amino acids as their N-acetyl-n-propyl esters. The leukemic patients were concurrently undergoing, or had recently completed, chemotherapy. It was found that aspartic acid, threonine, and serine were of significance in distinguishing between patients "on" therapy and those "off" therapy. Patients with advanced disease have the greatest aminoaciduria, although both the normal and leukemic populations have wide individual ranges. Within both populations, men excrete a greater variety and quantity of amino acids than women. It is concluded that analysis of urinary amino acids represents a history of complex metabolic events, which is potentially useful for evaluating patient response to chemotherapy in leukemia.     

Spin Polarization by Tilted Magnetic Field in Wide Ga1?xAlxAs Parabolic Quantum Wells

Wide parabolic wells can be created by properly controlling the Al content during the growth of successive Ga_1–xAl_xAs thin layers. Under a tilted magnetic field these systems present interesting transport properties, which are associated to their composition dependent g-factor. We present an exact solution for the eigenstates of an electron gas inside such a quantum well. We calculate the renormalized cyclotron frequencies as functions of the angle of tilt, as well as the density of states, and the Fermi level. We discuss the conditions for the existence of spin-polarized charge.     

Damage Model and Progressive Failure Analyses for Filament Wound Composite Laminates

Recent improvements in manufacturing processes and materials properties associated with excellent mechanical characteristics and low weight have made composite materials very attractive for application on civil aircraft structures. However, even new designs are still very conservative, because the composite failure phenomenon is very complex. Several failure criteria and theories have been developed to describe the damage process and how it evolves, but the solution of the problem is still open. Moreover, modern filament winding techniques have been used to produce a wide variety of structural shapes not only cylindrical parts, but also “flat” laminates. Therefore, this work presents the development of a damage model and its application to simulate the progressive failure of flat composite laminates made using a filament winding process. The damage model was implemented as a UMAT (User Material Subroutine), in ABAQUS^TM Finite Element (FE) framework. Progressive failure analyses were carried out using FE simulation in order to simulate the failure of flat filament wound composite structures under different loading conditions. In addition, experimental tests were performed in order to identify parameters related to the material model, as well as to evaluate both the potential and the limitations of the model. The difference between numerical and the average experimental results in a four point bending set-up is only 1.6 % at maximum load amplitude. Another important issue is that the model parameters are not so complicated to be identified. This characteristic makes this model very attractive to be applied in an industrial environment.     

Photoluminescence study of GaAs thin films and nanowires grown on Si(111)

Mg-doped GaAs nanowires have been grown by molecular beam epitaxy on a partially Au-coated Si(111) substrate by the vapor–liquid–solid mechanism. Outside the coated areas, a thin film of GaAs was grown epitaxially at the same time. The optical properties in both parts of the sample were investigated by photoluminescence spectroscopy, as a function of temperature. A structured emission in the range ～1.25–1.55 eV was observed at 10 K and the resemblances in both cases were identified. The radiative transitions are discussed with relevance to known defect centers in the GaAs thin films and to their possible relation with the zinc-blende and wurtzite phases in the nanowires. The presence of both crystalline phases in the nanowires was confirmed by μ-Raman spectroscopy.