gebhart/patrepeval huggingface dataset:
Biased amino acid distributions in regions of the T cell receptors and MHC molecules potentially involved in their association (1991)

We have analysed, in the context of the available structural information, the frequency of occurrence of different amino acids in functional regions of both the class I MHC antigens and of the TCR alpha and beta chains. We found that in class I MHC molecules, charged residues are found frequently among those which are presumably dedicated to interactions with the TCR, while the aromatic side chain residues are found more in the interior of the groove. In the TCR, the Asn residue appears with high frequency in all the CDR equivalents. The TCR CDR3s of both alpha and beta chains are particularly rich in Gly, whereas the CDR1 and CDR2 loops exhibit strong biases in favour of charged residues. Accordingly, the interactions between the MHC molecule and the peptide antigen appear to be essentially mediated by hydrophobic interactions and hydrogen bonding, while electrostatic interactions between charged residues might be important in the association of TCR and MHC molecules. The observation that each CDR1 and CDR2 is biased towards a particular set of amino acids, taken together with the nature of the protruding residues on the MHC helices, allows us to propose, in the frame of a molecular model of the MHC-TCR complex, several plausible configurations.
[Abnormalities in stomach and duodenal ulcer immunoregulation]. (2005)

The effect of the immunity state on the clinical course of stomach ulcer was studied. The study involved 50 patients (38 men and 12 women being 17-67 years old) with stomach ulcer (n = 14) and duodenal ulcer (n = 36) in the acute condition and 25 healthy blood donors. Twenty-seven patients underwent an immunology study. It was revealed that the evident increase of circulatory lymphocyte apoptosis (> 10), which is associated with the depression of their proliferative activity in vitro culture, is recorded with 40.7% of patients (11/27). It was also revealed that a high level of circulatory lymphocyte apoptosis and apoptosis-associated dysfunctions are found more frequently in people with long-term and complicated clinical course.
An Epidermal Stimulation and Sensing Platform for Sensorimotor Prosthetic Control, Management of Lower Back Exertion, and Electrical Muscle Activation (2015)

The design of an ultrathin, conformal electronic device that integrates electrotactile stimulation with electromyography, temperature, and strain sensing in a single, simple platform is reported. Experiments demonstrate simultaneous use of multiple modes of operation of this type of device in the sensorimotor control of robotic systems, in the monitoring of lower back exertion and in muscle stimulation.
Phase equilibria in iron ternary alloys : a critical assessment of the experimental literature (1988)

Published by The Institute of Materials, London. 39 Fe X-Y systems, originally published by ASM and The Institute of Materials in the International Metals Reviews, now updated and presented in a comprehensive collection.
MALDI-MS redox lipidomics applied to human hair: A first look (2011)

Lipids are an amazingly diverse group of biomolecules with an array of biological functions including protecting and maintaining key properties and structure. Oxidative insult in the form of UV, hydrothermal, or other damage leads to compromised lipid function and can be linked to a wide range of consumer complaints. This proof-of-principle study applied and evaluated redox lipidomic approaches for the characterization and profiling of selected lipids and their oxidation products in human hair. It was observed that cholesterol and cholesterol derivatives regions appeared to be the most susceptible to oxidative damage and this leads to further experiments, including the systematic characterization of oxidative products, and correlation of modifications with damage protocol.
Low Latency ASR for Simultaneous Speech Translation (2020)

User studies have shown that reducing the latency of our simultaneous lecture translation system should be the most important goal. We therefore have worked on several techniques for reducing the latency for both components, the automatic speech recognition and the speech translation module. Since the commonly used commitment latency is not appropriate in our case of continuous stream decoding, we focused on word latency. We used it to analyze the performance of our current system and to identify opportunities for improvements. In order to minimize the latency we combined run-on decoding with a technique for identifying stable partial hypotheses when stream decoding and a protocol for dynamic output update that allows to revise the most recent parts of the transcription. This combination reduces the latency at word level, where the words are final and will never be updated again in the future, from 18.1s to 1.1s without sacrificing performance in terms of word error rate.
Convolutional cost aggregation for robust stereo matching (2017)

Although convolutional neural network (CNN)-based stereo matching methods have become increasingly popular thanks to their robustness, they primarily have been focused on the matching cost computation. By leveraging CNNs, we present a novel method for matching cost aggregation to boost the stereo matching performance. Our insight is to learn the convolution kernel within CNN architecture for cost aggregation in a fully convolutional manner. Tailored to cost aggregation problem, our method differs from handcrafted methods in terms of its convolutional aggregation through optimally learned CNNs. First, the matching cost is aggregated with cost volume unary network, and then optimized with explicit disparity boundary, estimated through disparity boundary pairwise network, within a global energy minimization. Experiments demonstrate that our method outperforms conventional hand-crafted aggregation methods.
An Interaction Instance Oriented Approach for Web Application Integration in Portals (2007)

Currently, the significance of a portal stems not only from being a handy way to access data but also from being the means of facilitating the integration with Web applications. This paper proposes an interaction instance oriented approach for integrating web applications in portals. The key aspect is to enable a user to have the same interaction experiences from a portal that he/she accesses the web application directly. The approach is thus focused on the description of the presentation layer of the interaction instances of a web application and a portlet, which defines an interaction instance as consecutive web pages or fragments. Web application integration is then transformed to the problem that how to translate all web pages of an interaction instance of a Web application to certain view equivalence regions, which form the interaction instance of a portlet. Experiments show that the approach is effective and efficient.
Artificial Neural Networks in the Outcome Prediction of Adjustable Gastric Banding in Obese Women (2010)

ANN models can be successfully applied for prediction of weight loss in obese women treated by LAGB. This approach may constitute a valuable tool for selection of the best candidates for surgery, taking advantage of an integrated multidisciplinary approach.
Genetic engineering of rice capable of synthesizing fructans and enhancing chilling tolerance (2008)

Fructans are water-soluble fructose oligomers and polymers that are based on sucrose, and have been implicated in protecting plants against water stress. Rice (Oryza sativa L.) is highly sensitive to chilling temperatures, and is not able to synthesize fructans. Two wheat fructan-synthesizing enzymes, sucrose:sucrose 1-fructosyltransferase, encoded by wft2, or sucrose:fructan 6-fructosyltransferase, encoded by wft1, were introduced into rice plants, and rice transformants that accumulate fructans were successfully obtained. The mature leaf blades of transgenic rice lines with wft2 or wft1 accumulated 16.2 mg g(-1) FW of oligo- and polysaccharides mainly composed of inulin oligomers of more than DP7, and 3.7 mg g(-1) FW of oligo- and polysaccharides, mainly composed of phlein oligomers of more than DP15, respectively. The transgenic rice seedlings with wft2 accumulated significantly higher concentrations of oligo- and polysaccharides than non-transgenic rice seedlings, and exhibited enhanced chilling tolerance. The oligo- and polysaccharide concentrations of seedlings expressing wft1 were obviously lower than those of lines expressing wft2, and no correlation between oligo- and polysaccharide concentrations and chilling tolerance was detected in wft1-expressing rice lines. The results suggest that transgenic rice lines expressing wheat-derived fructosyltransferase genes accumulated large amounts of fructans in mature leaf blades and exhibited enhanced chilling tolerance at the seedling stage. This is the first report owing that fructan accumulation enhanced tolerance to non-freezing low temperatures.
Commensal microbes drive intestinal inflammation by IL-17–producing CD4 <sup>+</sup> T cells through ICOSL and OX40L costimulation in the absence of B7-1 and B7-2 (2014)

The costimulatory B7-1 (CD80)/B7-2 (CD86) molecules, along with T-cell receptor stimulation, together facilitate T-cell activation. This explains why in vivo B7 costimulation neutralization efficiently silences a variety of human autoimmune disorders. Paradoxically, however, B7 blockade also potently moderates accumulation of immune-suppressive regulatory T cells (Tregs) essential for protection against multiorgan systemic autoimmunity. Here we show that B7 deprivation in mice overrides the necessity for Tregs in averting systemic autoimmunity and inflammation in extraintestinal tissues, whereas peripherally induced Tregs retained in the absence of B7 selectively mitigate intestinal inflammation caused by Th17 effector CD4(+) T cells. The need for additional immune suppression in the intestine reflects commensal microbe-driven T-cell activation through the accessory costimulation molecules ICOSL and OX40L. Eradication of commensal enteric bacteria mitigates intestinal inflammation and IL-17 production triggered by Treg depletion in B7-deficient mice, whereas re-establishing intestinal colonization with Candida albicans primes expansion of Th17 cells with commensal specificity. Thus, neutralizing B7 costimulation uncovers an essential role for Tregs in selectively averting intestinal inflammation by Th17 CD4(+) T cells with commensal microbe specificity.
A Qualitative Study of American Sign Language Interpreting for Deaf Individuals with Disabilities (2020)

There are complexities involved in American Sign Language (ASL) interpreting for the unique population of Deaf individuals with disabilities (DWD), particularly in educational settings, that must be considered. Based on the foundation of existing literature regarding the field of ASL interpreting, educational interpreting, and strategies of working with DWD individuals, the researcher created a theoretical conceptual framework that combined the frameworks of ASL Interpreting and Special Education. The current primary research is aimed at addressing another portion of the gap, that is, research regarding practical experiences in working with this population. This study was conducted through questionnaires sent out through email to ASL interpreters located through snowball sampling. This research seeks to understand the experiences of ASL interpreters who have worked with DWD individuals through participants responses to questions about strategies used, and unique challenges and rewards faced, when working with this population. Responses were dissected through content analysis to uncover trends and themes among the personal experiences of the participants. The researcher uncovered three major themes from these experiences: individualization, flexibility, and collaboration. Much of the data supports the proposed conceptual framework, but more research is needed to corroborate these findings. This research positively impacts the ASL interpreting field by providing insight into an area that currently lacks research and by bringing awareness to the need for more education and training for those who will be working with this exceptional population.
A hierarchical decomposition methodology for single-stage clock circuits (2002)

This paper describes a methodology for designing the interconnect distribution for single-stage clock circuits using a hierarchical decomposition. This new method of splitting the design into global and local distributions improves the optimization efficiency and enhances both wireability and performance. A novel use of the Delaunay triangulation provides a means for efficiently constructing and optimizing the local distribution. The combination of these global and local solutions produces layouts with less wirelength and an average 3/spl times/ performance improvement over flat solutions while keeping the worst case skew below 50 ps. When these designs are wiresized, they achieve a 25% reduction in wire area over their flat circuit counterparts due to the reduction in downstream capacitive wire loading.
Segmentation by nonlinear diffusion. II (2003)

An algorithm that systematically uses nonuniform smoothing to find boundary components in the form of connected, regularized curves is presented. The boundary, represented by a variable continuously defined over the image domain, as well as the smoothing of the image are determined by a nonlinear system of diffusion equations. Nonlinear diffusion is used again to threshold the boundary variable to produce the actual object boundaries. Laplacians of smoothed gradients are the main tool used. Nonuniform smoothing permits the use of multiple smoothings and the use of derivatives of up to order six.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Diagnosis and management of isolated angiitis of the central nervous system (1989)

Isolated angiitis of the central nervous system (IAC) is usually a fatal inflammatory disease with a predilection for small blood vessels. Recurrent cerebral infarction leading to death within a few years is the usual course, but this may be significantly altered by aggressive immunosuppressive therapy with prednisone and cyclophosphamide. Other diseases may, however, present with similar clinical and angiographic features. Because antemortem diagnosis suggests a therapy, establishing the criteria for diagnosis is important. This report describes clinical, angiographic, and biopsy features, and therapy of five successfully treated patients with IAC. The following specific criteria are recommended for establishing an antemortem diagnosis of IAC: (1) clinical pattern of headaches and multifocal neurologic deficits present for at least 6 months, unless the deficits are severe at onset or rapidly progressive; (2) cerebral angiography demonstrating segmental arterial narrowing; (3) exclusion of systemic inflammation or infection; and (4) leptomeningeal/parenchymal biopsy demonstrating vascular inflammation or exclusion of alternate diagnoses. Based upon the successful management of these five previously unreported patients, as well as others in the literature, the following treatment regimens are recommended for the initial 6 weeks of therapy: (1) prednisone 40 to 60 mg/day, and (2) cyclophosphamide 100 mg/day.
MiRonTop: mining microRNAs targets across large scale gene expression studies (2010)

http://www.microarray.fr:8080/miRonTop/index.
Channel estimation technique for OFDM systems spread by chirp sequences (2012)

A frequency domain equalization for multipath fading is widely used for OFDM systems and accurate channel estimation is required. In conventional OFDM systems, pilot symbols are inserted periodically in time and frequency domain by a transmitter for channel estimation. Channel estimation error is quite large, especially in frequency-selective fading channel, because the estimates are interpolated with the restricted pilot subcarriers. The channel estimation error can be decreased by assigning pilot symbols to all subcarriers in specified OFDM blocks. In that case, however, no data symbols can be transmitted in OFDM blocks where pilot symbols are transmitted. In this paper we propose a new channel estimation scheme in which OFDM signal is transmitted after spread by chirp sequences, and channel estimation of all subcarriers is achieved with only one pilot symbol without interpolation. Simulation results show that the MSE performance of channel estimation and the BER performance can be significantly improved by the proposed scheme.
Design Methodologies for 3D Mixed Signal Integrated Circuits (2014)

Three-dimensional (3D) integration technology has been proposed as a promising technology to provide small footprint, reduced wirelength, and the capability of heterogeneous integration. In particular, 3D IC is a good candidate to address the design issues in conventional analog/digital mixed-signal IC designs. In this work, we focus on modeling and analyzing the impacts of through silicon vias (TSVs) on mixed-signal ICs. Based on the analysis, a set of design methodologies for 3D mixed-signal ICs are proposed. The design methodologies are verified with a case study, in which a 12-bit successive approximation register analog-to-digital converter (SAR ADC) is re-designed by partitioning it into three stacked layers for 3D integration. The experimental results show that, compared to the traditional 2D counterpart, our 3D SAR ADC with optimized TSV placement can achieve significant area and power reduction, and performance improvement. Specifically, due to the isolation of substrate noise disturbance in our 3D design, the signal-to-noise-plus-distortion ratio (SNDR) is improved from 68.74 dB to 74.12 dB.
Interface Evaluation for Mobile Robot Teleoperation (2003)

Controlling mobile robots through teleoperation is a challenging task that demands a flexible and efficient user interface. Mobile robots are often equipped with numerous sensors (proximity sensors, system status sensors, positioning and heading devices, multiple cameras, etc.) that provide a high volume of data to the user. Because the amount of data is vastly larger than what can fit on the screen, and because the needed subset of data can change rapidly and unpredictably depending on events in the robot&apos;s environment, modern teleoperation interfaces often display user-selected data with a windowing paradigm that facilitates quick display modification. In this paper, we examine the possibility that too much fine-grained control over window positioning and sizing could hamper user performance by interfering with display modification. To test our hypothesis, three humancomputer interfaces for a mobile robot were designed and then evaluated through performance studies consisting of 12 expert and 24 novice participants. The first two interface designs followed the standard Microsoft Windows graphical user interface design paradigm and provided participants with fine-grained control over the position and sizing of sensor displays. The third interface was designed using principles from cockpit and humanfactors research, and provided participants with limited control over display position and sizing. User performance for each interface was assessed on a display reconfiguration task consisting of adding, removing, positioning, and resizing sensor data windows, a common task in robot navigation and situational assessment. In general, expert participants preferred the interface with limited control over position and sizing, while novice participants preferred the more tradition...
High performance vertical-cavity surface-emitting laser diodes with a Au-plated heat spreading layer (2002)

Etched-pillar vertical-cavity surface-emitting laser diodes exhibit submilliamp threshold currents down to 400 /spl mu/A and high output power levels. A Au-plated heat spreading layer reduces the thermal resistance by a factor of two and increases the maximum output power by approximately 60%. A laser with 660 /spl mu/A threshold current reaches a maximum output power of 3.56 mW. The good heat sinking provides high output power despite relatively large operating voltages over 3 V. Small output power variations over a wide temperature range from 20/spl deg/C to 90/spl deg/C are demonstrated. The best temperature insensitivity of laser output power is achieved in a constant voltage operation mode.
Optimization of the Thermal Dosimetry for Endocavitary HICU Ablation of Sectorial Digestive Tumours (2007)

Effective treatment of malignant tumours demands well controlled energy deposition in the region of interest. Generally, two major steps must be fulfilled: pre‐operative optimal planning of the thermal dosimetry and per‐operative active control of the delivered thermal dose. The first issue is addressed here in the particular case of the ultrasound therapy for endocavitary tumours (oesophagus, colon or rectum) with phased array cylindrical contact applicators. Computation is divided into two main parts: 1. definition of the heating sequence parameters (the total sonication time, the number of independent beams, the orientation and the applied time for every beam), and 2. calculation of the corresponding thermal dose. One slice orthogonal to the symmetry axis of the High Intensity Contact Ultrasound (HICU) device is considered. User defined tumoral geometry is divided into a regular polar grid (5.625 degrees step). The different duration applied for interleaved fast switched beams corresponding to selected orientations is exponentially scaled to the measured depth along each direction. Iterative 2D Fourier transformation of the BHTE equation allows fast calculation of the temperature and thermal dose (computing time accomplished with Matlab language ∼ 3 minutes for a medium size tumour). Border conditions (cooling balloon) are taken into account with a binary mask applied to the simulated temperature at each iteration. The planned thermal dose covered the target region at 300% of lethal threshold with extra margin ranged from 1 to 3 mm. The short computing time allows near real time, in‐situ planning of the dosimetry.
Alzheimer's disease: dysfunction of a signalling pathway mediated by the amyloid precursor protein? (2001)

All individuals with Alzheimer's disease (AD) experience a progressive loss of cognitive function, resulting from a neurodegenerative process characterized by the deposition of beta-amyloid (A beta) in plaques and in the cerebrovasculature, and by the formation of neurofibrillary tangles in neurons. The cause of the neuronal death is unknown but it is thought to be linked in some way to the beta-amyloid precursor protein (APP), which is the source of the A beta that accumulates in the AD brain. There are two pieces of supporting data for this: first, APP is overexpressed in Down's syndrome, which leads to AD-like neuropathology by the age of 40 in virtually all affected individuals; secondly, specific point mutations in APP cause some forms of familial AD. Our laboratory has focused on a specific aspect of APP and its connection with the neuronal destruction seen in AD. We have hypothesized that AD results from a progressive dysfunction of APP. In addition, on the basis of recent data generated by our laboratory and others, we propose that in the normal brain a percentage of APP is present as an integral protein of the plasma membrane that mediates the transduction of extracellular signals into the cell via its A beta-containing C-terminal tail. In AD, accumulation of abnormal levels of the C-terminus in the neuron disturbs this signal-transduction function of APP, causing disorders in the cell-cycle machinery and consequent apoptosis. Here, we discuss the key findings that support this hypothesis, and discuss its therapeutic implications for AD.