gebhart/patrepeval huggingface dataset:
Delivery of AAV2/9-Microdystrophin Genes Incorporating Helix 1 of the Coiled-Coil Motif in the C-Terminal Domain of Dystrophin Improves Muscle Pathology and Restores the Level of α1-Syntrophin and α-Dystrobrevin in Skeletal Muscles of <i>mdx</i> Mice (2011)

Duchenne muscular dystrophy is a severe X-linked inherited muscle wasting disorder caused by mutations in the dystrophin gene. Adeno-associated virus (AAV) vectors have been extensively used to deliver genes efficiently for dystrophin expression in skeletal muscles. To overcome limited packaging capacity of AAV vectors (<5 kb), truncated recombinant microdystrophin genes with deletions of most of rod and carboxyl-terminal (CT) domains of dystrophin have been developed. We have previously shown the efficiency of mRNA sequence-optimized microdystrophin (ΔR4-23/ΔCT, called MD1) with deletion of spectrin-like repeat domain 4 to 23 and CT domain in ameliorating the pathology of dystrophic mdx mice. However, the CT domain of dystrophin is thought to recruit part of the dystrophin-associated protein complex, which acts as a mediator of signaling between extracellular matrix and cytoskeleton in muscle fibers. In this study, we extended the ΔR4-23/ΔCT microdystrophin by incorporating helix 1 of the coiled-coil motif in the CT domain of dystrophin (MD2), which contains the α1-syntrophin and α-dystrobrevin binding sites. Intramuscular injection of AAV2/9 expressing CT domain-extended microdystrophin showed efficient dystrophin expression in tibialis anterior muscles of mdx mice. The presence of the CT domain of dystrophin in MD2 increased the recruitment of α1-syntrophin and α-dystrobrevin at the sarcolemma and significantly improved the muscle resistance to lengthening contraction-induced muscle damage in the mdx mice compared with MD1. These results suggest that the incorporation of helix 1 of the coiled-coil motif in the CT domain of dystrophin to the microdystrophins will substantially improve their efficiency in restoring muscle function in patients with Duchenne muscular dystrophy.
Ray-by-ray noise weighting in a Filtered Backprojection (FBP) algorithm (2012)

This paper is an extension of our recently developed FBP-MAP (Filtered Backprojection Maximum a Posteriori) algorithm, which has view-by-view noise weighting and a quadratic smoothing prior. The current method has ray-by-ray noise weighting and can encourage edge-preserving smoothing. An objective function is set up for the image reconstruction problem. The projection data are weighted according to their noise variances. An edge-preserving strategy is used to regulate the image noise while maintaining the sharp edges. The objective function leads to an iterative algorithm, and an FBP-type algorithm is developed in an ad hoc manner to emulate the iterative algorithm. The proposed algorithm has been implemented for the circular-orbit cone-beam geometry based on Feldkamp's algorithm. Image reconstructions with computer simulations and real cadaver data are presented to illustrate the effectiveness and feasibility of the proposed algorithm. The new FBP-type algorithm is able to significantly reduce or remove the noise texture, which the conventional FBP is unable to do. A ray-based noise weighting scheme is introduced to the FBP algorithm for the first time. The new FBP algorithm is also able to incorporate an edge-reserving prior. This new FBP-type algorithm significantly reduces or removes the streaking artifacts in low-dose CT.
Hyper Text Coffee Pot Control Protocol (HTCPCP/1.0) (1998)

This document describes HTCPCP, a protocol for controlling, monitoring, and diagnosing coffee pots.
The two α subunits of <i>Escherichia coli</i> RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element (1997)

RNA polymerase core enzyme of Escherichia coli is composed of two alpha subunits and one each of the beta and beta' subunits. The C-terminal domain of the RNA polymerase alpha subunit plays a key role in molecular communications with class I transcription factors and upstream (UP) elements of promoter DNA, using the same protein surface. To identify possible differences in the functional roles of the two alpha subunits, we have developed a reconstitution method for hybrid RNA polymerases containing two distinct alpha subunit derivatives in a defined orientation ("oriented alpha-heterodimer"). The binding sites of two alpha C-terminal domains on the UP element DNA were determined by hydroxyl radical-based DNA cleavage mediated by (p-bromoacetamidobenzyl)-EDTA x Fe, which was bound at Cys-269 on the UP recognition surface of one or both alpha subunits. The results clearly indicated that the two alpha subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the beta'-associated alpha subunit is bound to the promoter-distal region.
Subband processing of finite length signals without border distortions (1992)

New equations are derived for the perfect reconstruction of the boundary regions of a subband processed image. These equations are valid for filter banks with an arbitrary number of filters, having arbitrary nonlinear phase, and allowing any border extension method in the analysis section. The filter bank is maximally decimated in a wide sense, i.e., the sum of samples among the subbands is equal to the sum of the image samples, without having to store extended subband signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Event Based Sampling with Application to Spectral Estimation (2002)

In this thesis event based sampling, estimation of a single resonance frequency and the application indirect tire pressure monitoring system are studied.Event based sampling is an alternative to tr ...
A Semantic Graph Query Language (2006)

Semantic graphs can be used to organize large amounts of information from a number of sources into one unified structure. A semantic query language provides a foundation for extracting information from the semantic graph. The graph query language described here provides a simple, powerful method for querying semantic graphs.
Ants Of The Genus Tetramorium In The United States With The Description Of A New Species. (1943)

xBio:D Automated Upload
Efficient and Highly Selective Oxidation of Primary Alcohols to Aldehydes by <i>N</i>-Chlorosuccinimide Mediated by Oxoammonium Salts (1996)

2,2,6,6-Tetramethyl-1-piperidinyloxy catalyzes efficient oxidation of primary alcohols to aldehydes by N-chlorosuccinimide, in a biphasic dichloromethane-aqueous pH 8.6 buffer system in the presence of tetrabutylammonium chloride. Aliphatic, benzylic, and allylic alcohols are readily oxidized with no overoxidation to carboxylic acids. Secondary alcohols are oxidized to ketones with a much lower efficiency. Very high chemoselectivities are observed when primary alcohols are oxidized in the presence of secondary ones. Primary-secondary diols are selectively transformed into hydroxy aldehydes, with, in some cases, no detectable formation of the isomeric keto alcohols.
Managing SOX compliance in the age of SOA. (2006)

Freeze-drying achieved suitable conservation and may improve bank functioning, by protecting nutritional properties, polyphenol-related functionality, and oxidative integrity of human milk through a 1-day treatment with easy maintenance.
Neurological manifestations of HIV infection in adults - an overview : neurology (2001)

HIV is a neutrophic virus. It is therefore not surprising that neurological symptoms are widely prevalent following infection, Peripheral and central nervous system (CNS) symptoms are common, frequently debilitating, and often life-threatening. These occur throughout the natural history of HIV-related illness, from seroconversion through to full-blown immunodeficiency disease. It is estimated that between 40% and 70% of persons infected with the HIV virus develop symptomatic neurological disturbances. In autopsy neuropathological studies. CNS abnormalities are found to occur in up to 90% of patients with advanced AIDS. Most of the information available to clinicians in South Africa comes from literature from the USA or Europe, despite the fact that we see a vast amount of HIV-related neurology. The aim of this article is to give an overview of the clinical neurological manifestations of HIV, to provide more detail on a few conditions that we see commonly, and to highlight South African neuro-HIV research.
The treatment strategies of autoimmune disease may need a different approach from conventional protocol: A review (2012)

Autoimmune disease (AD) is one of the emerging noncommunicable diseases. Remission is a possibility in AD, but current treatment strategies are not able to achieve this. We have well-established protocols for infections, oncology, metabolic diseases, and transplantation which are often used as models for the management of AD. Studies and observations suggest that in contrast to diseases used as a role model, AD has wide variability, different causative and pathogenic process, which is highly dynamic, making the current treatment strategies to fall short of expected complete remission. In this brief review, it is attempted to highlight the current understanding of AD and the probable gaps in the treatment strategies. Few hypothetical suggestions to modify the treatment protocols are presented.
[Concepts of the mechanisms of action of cyclosporin in psoriasis. A review with guidelines on therapy]. (1993)

For severe forms of psoriasis ciclosporin has now been proven to be a clinically effective therapeutic regimen. Beside inhibiting T-cell activation, ciclosporin exerts various effects on other cells of the immune system, e.g. Langerhans cells, mast cells and endothelial cells. The influence of ciclosporin on these cells may be relevant to an understanding of its beneficial effect in psoriasis treatment. New information about the molecular mechanism of action regarding calcineurin-regulated signal transduction pathways provide further insight into the pharmacological effects. On the basis of new findings concerning the mode of action of ciclosporin and the results of recent multicentre studies in psoriasis, new guidelines for therapy are given.
Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy (2010)

We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.
Optical wireless underwater communication for AUV: Preliminary simulation and experimental results (2011)

An optical wireless underwater communication simulation model is proposed, which serves as the theoretical model of the underwater optical wireless communication simulator for AUVs. Various parameters that will influence the light distribution and optical communication performance are explored. As a preliminary result, this paper focuses on the light distribution and propagation in water, and the communication channel characteristics. Given the parameters of the transmitter and water turbidity, the model provides the received light power in every position. With the calculation of the noise power in the receiver, an estimation of data rate capacity is provided. This research aims at building the simulator, which eventually will help the underwater optical wireless communication system design.
Optimized Oxygen Plasma Etching of Polyurethane‐Based Electro‐optic Polymer for Low Loss Optical Waveguide Fabrication (1996)

Oxygen plasma etching of thermosetting polyurethane electro‐optic polymers containing disperse red 19 side groups was characterized in detail for making low loss optical waveguides and modulators. The effect of varying parameters such as the RF power, oxygen pressure, and flow rate on optical loss, etching rate, and etching selectivity to photoresist etch mask was studied. These parameters were optimized to minimize the surface roughness in etched areas. By properly choosing the etching conditions, scattering loss due to the surface roughness can be reduced from 0.9 dB/cm to less than 0.1 dB/cm at the wavelength of 1.3 μm, which is much smaller than the absorption loss of the polymer.
Synthesis of current-mode pass transistor networks (2002)

The basic properties of the MOS current-mode circuits are considered, and the network synthesis for realization of unary multivalued functions is discussed. The main concern is the minimization of hardware realization. Functional blocks to compose a current-mode circuit from the viewpoint of a design cost are considered. Some decomposition methods of unary functions are proposed and their circuit realizations with MOS pass transistor networks are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structure and phosphodiesterase activity of Bis-Tris coordinated lanthanide(III) complexes (1998)

A commonly used buffer, 2,2-bis(hydroxymethyl)-2,2′,2″-nitrilotriethanol (Bis-Tris) coordinates lanthanide(III) ion strongly in water to form molecular species that are highly active for the hydrolysis of a phosphate diester, bis(4-nitrophenyl) phosphate.
Lithiation of Some 3[2-(2'-Bromophenyl)ethyl]thiophenes and Intramolecular Transmetalation (1981)

The r e a c t i o n of some halo-1-(thienyll-2-phenylethanes such as 3-(2-phenylethyl)th~ophene ( l ) , 3-[2-(2'-bromophenyl ) e t h y l l t h i o p h e n e ( 2 ) , 4-[2-(2'-bromo-4'-chloropheny1)ethyl I -2 -e t h y l t h i o p h e n e ( 3 ) and 4 -[ 2 -( 2 'bromophenyl)ethyl I-2-chlorothiophene (i) w i t h b u t y l l i t h i u m and l i t h i u mdiisopropylarnide (LDA) under v a r i o u s c o n d i t i o n s has been i n v e s t i g a t e d .C o m p e t i t ~o n between halogen-metal exchange i n t h e benzene r i n g and m e t a l a t ~o n o f t h e thiophene r i n g was observed and an i n t r a m o l e c u l a r t r a n s m e t a l a t i o n r e a c t i o n was found.
A General Approach for Generating Fluorescent Probes to Visualize Piconewton Forces at the Cell Surface (2016)

Mechanical forces between cells and their extracellular matrix (ECM) are mediated by dozens of different receptors. These biophysical interactions play fundamental roles in processes ranging from cellular development to tumor progression. However, mapping the spatial and temporal dynamics of tension among various receptor-ligand pairs remains a significant challenge. To address this issue, we have developed a synthetic strategy to generate modular tension probes combining the native chemical ligation (NCL) reaction with solid phase peptide synthesis (SPPS). In principle, this approach accommodates virtually any peptide or expressed protein amenable to NCL. We generated a small library of tension probes displaying different ligands, flexible linkers, and fluorescent reporters, enabling the mapping of integrin and cadherin tension, and demonstrating the first example of long-term (∼3 days) molecular tension imaging. This approach provides a toolset to better understand mechanotransduction events fundamental to cell biology.
The combining DAG: a technique for parallel data flow analysis (1994)

As the number of available multiprocessors increases, so does the importance of providing software support for these systems, including parallel compilers. Data flow analysis, an important component of software tools, may be computed many times during the compilation of a program, especially when compiling for a multiprocessor. Although converting a sequential data flow algorithm to a parallel algorithm can present some opportunities for computing data flow in parallel, more parallelism can be exposed by the development of new parallel data flow algorithms. We present a technique that computes rapid data flow problems in parallel and thus is applicable for commonly used classical data flow problems, including reaching definitions, reachable uses, available expressions, and very busy expressions. Unlike previous techniques, our technique exploits the inherent parallelism in the data flow computation that occurs across independent paths, within linear paths, and in paths through loops of a control flow graph. The technique first changes cyclic structures in a control flow graph to acyclic structures and then builds a combining directed acyclic graph (DAG) that represents the paths through the control flow graph needed to compute data flow. Data flow is then computed using two passes over the DAG by computing the data flow for the nodes on each level of the DAG in parallel. We also present experimental results comparing the performance of our algorithm with a sequential algorithm and a parallelized sequential algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Transformer between a thin post-wall waveguide to a standard metal waveguide (2003)

The authors propose a transformer between a thin post-wall waveguide and a standard metal waveguide. The transformer is used to connect an RF circuit fed by a planar line with a waveguide planar antenna fed through an aperture. In the feed of a planar line, such as a triplate line, via an aperture, some posts are often placed around the line to prevent undesired leakage into the dielectric substrate. The post-wall waveguide consists of densely arrayed posts in the walls and the connection to a microstrip line with the same height is expected to be easy. However direct connection between a post-wall waveguide and a standard waveguide may be difficult because the post-wall waveguide is much thinner than the standard one. A piece of dielectric substrate with two gaps is inserted in a standard waveguide for matching to the post-wall. We analyze the transformer and manufacture a model for operation in the 22 GHz band. We also investigate the dimensions of the transformer for various heights of the postwall waveguide.
Reactive direct current magnetron sputtering of aluminum oxide coatings (1995)

Aluminum oxide coatings were reactively direct current magnetron sputtered using an arc suppression unit to stop arcing on the cathode. The process was very controllable when the arc suppression unit was used, and it did not produce any debilitating arcing as is commonly found with conventional reactive direct current magnetron sputtering. Arc suppression is a major advancement in reactive dc magnetron sputtering technology. With the automatic feedback partial pressure control of the reactive gas, all compositions of AlOx, where 0≤x≤1.5, are possible. There are no forbidden compositions as there are with flow control of the reactive gas. All coatings were deposited with a floating substrate bias, and the color of the AlOx films ranged from metallic when there was no or a small partial pressure of oxygen during deposition to a very clear film when the oxygen partial pressure was 0.08 mTorr. The clear film was amorphous, and its average index of refraction, n, was 1.6. The Vickers hardness of the clear film was only 830 kgf mm−2 due to its amorphous structure, and the scratch test critical load for a 1.9 μm thick film on an M2 steel substrate, was only 0.4 kgf. It is believed that substrate bias will improve the mechanical and optical properties of the films.
Green Biofactories: Recombinant Protein Production in Plants (2010)

Until recently, low accumulation levels have been the major bottleneck for plant-made recombinant protein production. However, several breakthroughs have been described in the past few years allowing for very high accumulation levels, mainly through chloroplast transformation and transient expression, coupled with subcellular targeting and protein fusions. Another important factor influencing our ability to use plants for the production of recombinant proteins is the availability of quick and simple purification strategies. Recent developments using oleosin, zein, ELP and hydrophobin fusion tags have shown promise as efficient and cost-effective methods for non-chromatographic separation. Furthermore, plant glycosylation is a major barrier to the parenteral administration of plant-made biopharmaceuticals because of potential immunogenicity concerns. A major effort has been invested in humanizing plant glycosylation, and several groups have been able to reduce or eliminate immunogenic glycans while introducing mammalian-specific glycans. Finally, biosafety issues and public perception are essential for the acceptance of plants as bioreactors for the production of proteins. Over recent years, it has become clear that food and feed plants carry an inherent risk of contaminating our food supply, and thus much effort has focused on the use of non-food plants. Presently, Nicotiana benthamiana has emerged as the preferred host for transient expression, while tobacco is most frequently used for chloroplast transformation. In this review, we focus on the main issues hindering the economical production of recombinant proteins in plants, describing the current efforts for addressing these limitations, and we include an extensive list of recent patents generated with the intention of solving these limitations.
The ContikiMAC Radio Duty Cycling Protocol (2011)

Low-power wireless devices must keep their radio transceivers off as much as possible to reach a low power consumption, but must wake up often enough to be able to receive communication from their neighbors. This report describes the ContikiMAC radio duty cycling mechanism, the default radio duty cycling mechanism in Contiki 2.5, which uses a power efficient wake-up mechanism with a set of timing constraints to allow device to keep their transceivers off. With ContikiMAC, nodes can participate in network communication yet keep their radios turned off for roughly 99 % of the time. This report describes the ContikiMAC mechanism, measures the energy consumption of individual ContikiMAC operations, and evaluates the efficiency of the fast sleep and phase-lock optimizations. 1
Object detection and tracking for a vision guided automated suspended cell injection process (2010)

Object detection and tracking under the microscopic field of view is an important part in a vision based automated cell injection system. This paper introduces a novel method for recognizing and tracking the cell, the holding pipette and the injection pipette in an Intracytoplasmic Sperm Injection (ICSI) process. The algorithm for identification firstly automatically segmented the microscopic image by Otsu's method, and then calculated the roundness and elongation features of every separated region after removing tiny blobs by judging their areas. The holding pipette was identified by a modified template matching technique, which used the contour information of the object instead of the whole body, resulting in a shorter processing time. The objects were tracked by applying identification method to every frame of the video, with a movement estimation constraint of the holding pipette when performing the matching. Experiment was carried out and the performance of the proposed method was evaluated.