gebhart/patrepeval huggingface dataset:
The PI3K/Akt Pathway: Recent Progress in the Development of ATP-Competitive and Allosteric Akt Kinase Inhibitors (2008)

This article describes recent advances in the development and biological evaluation of allosteric and ATP-competitive small molecule inhibitors for the serine/threonine kinase Akt (protein kinase B, PKB). Unregulated activation of the PI3K/Akt/PTEN pathway is a prominent feature of many human cancers and Akt is over-expressed or activated in all major cancers making Akt an exciting new target for cancer therapy. The development of Akt inhibitors has been complicated and hampered by the presence of three Akt isozymes, (Akt1, Akt2 and Akt3) which differ in function and tissue distribution, as well as a lack of Akt specific inhibitors. In the past 18 months, a large number of reports have appeared describing the discovery and development of allosteric Akt kinase inhibitors and classical ATP-competitive Akt kinase inhibitors. This review will discuss the PI3K/Akt/PTEN pathway, allosteric and ATP-competitive Akt kinase inhibitors, their biological evaluation and progress towards target validation.
<title>Video coding using the MPEG-2 compression standard</title> (1993)

The second phase of the Moving Picture Experts Group (MPEG-2) is ongoing and so far has resulted in completion of algorithmic tools for video coding with this standard. This standard is generic in nature and is organized around the concept of profiles and levels to address a wide range of applications and bit-rates. It not only supports coding of interlaced and progressive format video as a single layer, but also supports scalable video coding. The MPEG-2 standard, like the MPEG-1 standard, specifies a syntax for the bitstream and the semantics of the decoding process; encoders can be designed for best tradeoff of performance versus complexity, based on the application. We describe the various tools available in the MPEG-2 standard and discuss the potential of each tool for improving coding performance or enabling new applications.
A fast and efficient fuzzy color transfer method (2005)

Each image has its own color content that greatly influences the perception of human observer. Being able to transfer the color content of an image into another image, while preserving other features, (like texture), opens a new horizon in human-perception-based image processing. In this paper, after a brief review on the few efficient works performed in the field, a novel fuzzy principle component analysis (PCA) based color transfer method is proposed. The proposed method accomplishes the transformation based on a set of corresponding user-selected regions in images along with a blending ratio parameter set by the user. Results show more robustness and higher speed when comparing our proposed method with other available approaches.
High-sensitivity-coherent optical frequency-domain reflectometry for characterization of fiber-optic network components (1995)

The authors have performed high-sensitivity-coherent optical frequency-domain reflectometry (OFDR) measurements of pig-tailed optical devices with centimeter resolution. The oscillations of the Rayleigh backscattering level produced by coherent fading noise was eliminated, strongly improving the capability of OFDR measurements of low level reflections and losses. Sensitivities down to -105 dB were achieved with minute measurement times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficient exact set-similarity joins (2006)

Given two input collections of sets, a set-similarity join (SSJoin) identifies all pairs of sets, one from each collection, that have high similarity. Recent work has identified SSJoin as a useful primitive operator in data cleaning. In this paper, we propose new algorithms for SSJoin. Our algorithms have two important features: They are exact, i.e., they always produce the correct answer, and they carry precise performance guarantees. We believe our algorithms are the first to have both features; previous algorithms with performance guarantees are only probabilistically approximate. We demonstrate the effectiveness of our algorithms using a thorough experimental evaluation over real-life and synthetic data sets.
Specific interaction of the new fluorescent dye 10‐N‐nonyl acridine orange with inner mitochondrial membrane (1990)

The fluorescent dye 10-N-nonyl acridine orange (NAO), known as specifically associated with mitochondria, has been reported to have a cytotoxic effect when high doses were applied to cells. Presently, the biochemical basis of its toxicity was investigated on isolated rat liver mitochondria. At low concentrations, NAO strongly inhibited state 3 respiration and ATP synthesis. At high concentrations, electron transport, ATP hydrolysis, Pi-transport and adenine nucleotide activities were also decreased. All these inhibitions can be explained by probe-cardiolipin interactions which could induce the collapse of energy conversion and/or the modification of membrane fluidity.
(R)- and (S)-enantiomers of 11-hydroxy- and 10,11-dihydroxy-N-allylnoraporphine: synthesis and affinity for dopamine receptors in rat brain tissue (1991)

The R-(-)- and S-(+)-enantiomers of 11-hydroxy-N-allyl (4), and 10,11-dihydroxy-N-allyl (3) congeners of 11-hydroxy-N-n-propylnorapomorphine (11-OH-NPa, 2) or N-n-propylnorapomorphine (NPA, 1) were synthesized. Binding affinity of these compounds at dopamine (DA) receptor sites was evaluated with a membrane preparation of corpus striatum from rat brain. The R/S enantiomeric receptor affinity ratio was enhanced by allylic substitution of 3 and 4 and their R isomers had high DA receptor affinity similar to that of the N-n-propyl congeners. These N-allylnoraporphines are proposed as useful precursors to the preparation of their tritiated N-n-propyl enantiomers.
Dynamics of the optical damage of output mirrors of ridge semiconductor lasers based on strained quantum-well heterostructures (1998)

An investigation of the dynamics of catastrophic optical damage of a laser diode facet showed that the characteristic energy-evolution time of optical damage was 40–80 ns under pulsed operating conditions. When the pulse duration was less than this characteristic time, the damage was governed by the critical energy of a pulse. An estimate of the thickness of an overheated region gave less than 0.6 μm.
Protected interactive 3D graphics via remote rendering (2004)

Valuable 3D graphical models, such as high-resolution digital scans of cultural heritage objects, may require protection to prevent piracy or misuse, while still allowing for interactive display and manipulation by a widespread audience. We have investigated techniques for protecting 3D graphics content, and we have developed a remote rendering system suitable for sharing archives of 3D models while protecting the 3D geometry from unauthorized extraction. The system consists of a 3D viewer client that includes low-resolution versions of the 3D models, and a rendering server that renders and returns images of high-resolution models according to client requests. The server implements a number of defenses to guard against 3D reconstruction attacks, such as monitoring and limiting request streams, and slightly perturbing and distorting the rendered images. We consider several possible types of reconstruction attacks on such a rendering server, and we examine how these attacks can be defended against without excessively compromising the interactive experience for non-malicious users.
Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont (2005)

Germ-free mice were maintained on polysaccharide-rich or simple-sugar diets and colonized for 10 days with an organism also found in human guts, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling of bacteria and mass spectrometry of cecal glycans. We found that these bacteria assembled on food particles and mucus, selectively induced outer-membrane polysaccharide-binding proteins and glycoside hydrolases, prioritized the consumption of liberated hexose sugars, and revealed a capacity to turn to host mucus glycans when polysaccharides were absent from the diet. This flexible foraging behavior should contribute to ecosystem stability and functional diversity.
A biological function for glucagon-like peptide-2 (1998)

Journal Article A biological function for glucagon-like peptide-2 Get access M A Hussain M A Hussain Laboratory of Molecular Endocrinology, Massachusetts General Hospital, Harvard Medical School, Wellman 320, 50 Blossom Street, Boston, Massachusetts 02114, USA Search for other works by this author on: Oxford Academic Google Scholar European Journal of Endocrinology, Volume 139, Issue 3, Sep 1998, Pages 265–267, https://doi.org/10.1530/eje.0.1390265 Published: 01 September 1998
Quinoxalinediones: Potent Competitive Non-NMDA Glutamate Receptor Antagonists (1988)

The N-methyl-D-aspartate (NMDA)-subtype of glutamate receptors has been well described as a result of the early appearance of NMDA antagonists, but no potent antagonist for the "non-NMDA" glutamate receptors has been available. Quinoxalinediones have now been found to be potent and competitive antagonists at non-NMDA glutamate receptors. These compounds will be useful in the determination of the structure-activity relations of quisqualate and kainate receptors and the role of such receptors in synaptic transmission in the mammalian brain.
Satellite Communications Change Drilling Operations and Procedures (1986)

ABSTRACT This paper describes the Critical Drilling Facility (CDF) communications system design. Different field configurations for active and semi-active operations on the north slope of Alaska, in the Anschutz Ranch of Wyoming, and on semi-submersible drilling rigs in the Bering Sea will be discussed. Historically, oil drilling has operated without any significant communications between the personnel at the rig and the experts and supervisors in regional headquarters. This is still standard practice in the drilling industry today. A drilling system based upon complete communications and team-work has been developed. It exploits the technologies of digital satellite communications, digital video bandwidth compression, drilling data sensor and computer systems, and real-time data transmission. Full-motion video of rig operations and personnel, facsimile, voice, forms entry and access, and drilling data transmissions are available. Also, real-time cementing and well-test data are available at CDF central for resident expert analysis. The CDF not only supports real-time drilling decisions, but provides reproducible technology transfer for drilling future wells in the same field. Although the CDF was originally designed and implemented for drilling, it has become so successful that exploration geologists and managers are finding themselves right-there at the rig without leaving headquarters.
Identification of a new 130 bp cis-acting element in the TsVP1 promoter involved in the salt stress response from Thellungiella halophila (2010)

The TsVP1 promoter had strong activity in almost all tissues except the seeds. In addition, its activity was induced by salt stress in leaves and roots, especially in root tips. A 130 bp region (-667 to -538) was identified as the key region for responding to salt stress.
Isolation of the porcine heparin tetrasaccharides with glucuronate 2-O-sulfate. (1995)

Eleven tetrasaccharides were isolated from the repeating disaccharide region of porcine intestinal heparin after strong digestion with Flavobacterium heparinase. Their structures were determined by composition analysis, enzymatic analysis, and 1H NMR spectroscopy. Nine of them have the common tetrasaccharide backbone, delta HexA alpha 1-4GlcN alpha 1-4IdoA alpha 1-4GlcN, where delta HexA and IdoA represent 4,5-unsaturated hexuronic acid and L-iduronic acid, respectively, and their structural variations are based upon the positions of sulfate groups. The nine compounds include one hexasulfated, three pentasulfated and five tetrasulfated compounds, and four of them have not been isolated previously as discrete structures. The other two of the 11 tetrasaccharides have the following hitherto unreported structures with novel glucuronate 2-O-sulfate at the internal position: delta HexA(2-sulfate) alpha 1- 4GlcN(N,6-disulfate) alpha 1-4GlcA(2-sulfate) beta 1-4GlcN(N-sulfate) and delta HexA(2-sulfate) alpha 1-4GlcN(N,6-disulfate) alpha 1-4GlcA(2-sulfate) beta 1-4GlcN(N,6-disulfate). Thus, 2-O-sulfated glucuronate in the highly sulfated tetrasaccharide structures typical of heparin has been demonstrated. The former and the latter tetrasaccharides account for 0.31 and 0.32% (w/w) of the starting heparin, respectively. Their yield, however, is an underestimation, since these tetrasaccharide structures in longer sequences will be degraded by heparinase. Although the latter tetrasaccharide described above was unexpectedly cleaved by heparinase into two disaccharide units, the former was not degraded by the enzyme most likely due to the lack of the 6-O-sulfate group on the GlcN residue at the reducing terminus. The results indicate its capability of catalyzing both anti and syn elimination, a property shared by heparitinases I and II and chondroitinase ABC. Both tetrasaccharides were degraded into disaccharides by heparitinase II. Therefore, it is necessary to reevaluate the disaccharide composition of heparin/heparan sulfate or oligosaccharide structures, which were previously determined after heparinase or heparitinase II digestion. It is no longer possible to conclude that the 2-O-sulfated unsaturated uronic acid residues obtained from heparin/heparan sulfate by lyase digestions are always derived from iduronate 2-O-sulfate residues in the original polymer. It is quite possible that the novel glucuronate 2-O-sulfate structure in the highly sulfated region of heparin is involved in some of the biological activities of heparin.
Interstitial murine cytomegalovirus pneumonia after irradiation: characterization of cells that limit viral replication during established infection of the lungs (1985)

Interstitial pneumonia associated with viral replication in lung tissue was observed after cytomegalovirus infection of total-body gamma-irradiated mice, whereas in noncompromised hosts the lungs were not affected and virus multiplication was restricted to the salivary glands. The radiation damage could either predispose normally nonpermissive cell types for productive infection or abrogate an immune control of the tissue manifestation of infection by elimination of lymphocytes. Adoptive transfer of lymphoid cells into irradiated, infected recipients supported the second alternative. Even when infection was established in the lungs, as manifested by the presence of infected lung tissue cells in the alveolar septa, an antiviral effect could be assigned to the Lyt-2+, L3T4- subset of T lymphocytes specifically sensitized in the immunocompetent donor. These cells did not require in vitro propagation to perform effector cell functions in vivo and were operative under physiological conditions in comparatively low numbers. Hence, there is reason to assume that T lymphocytes are responsible for the tissue distribution of cytomegalovirus replication during infection.
Efficacy of interleukin-13 receptor–targeted liposomal doxorubicin in the intracranial brain tumor model (2009)

Human glioblastoma tumors selectively express receptors for interleukin 13 (IL-13). In a previous study, we showed that liposomes, when conjugated with IL-13, will deliver chemotherapeutics to a subcutaneous glioma tumor model in mice much more effectively than conventional unconjugated liposomes. Based on this observation, we developed an intracranial brain tumor model in nude mice using human U87 glioma cells. Mice receiving weekly i.p. injections of 15 mg/kg of doxorubicin encapsulated in IL-13-conjugated liposomes had a 5-fold reduction in the intracranial tumor volume over 6 weeks and four of seven animals survived >200 days after tumor implantation. In contrast, the animals receiving unconjugated liposomes with the same doxorubicin concentration did not survive beyond 35 days and there was no evidence of tumor size reduction. The presence of liposomes with doxorubicin in the tumor was shown by taking advantage of the selective expression of IL-13 receptors on the tumor cells and the endogenous fluorescence of doxorubicin. There was no increase in the indices of toxicity in animals receiving the doxorubicin-containing liposomes. Finally, a model of the blood-brain barrier was used to show that the nanovesicles do not harm the endothelial cells yet maintain their toxicity to astrocytoma cells. This approach is necessary to show the efficacy of this targeting platform for tumors in which the blood-brain barrier is not compromised and as a potential use of the nanovesicle system as a surveillance mechanism to prevent recurrence. These data show that IL-13 targeted nanovesicles are a viable option for the treatment of brain tumors.
Multispectral and hyperspectral image analysis with convex cones (1999)

A new approach to multispectral and hyperspectral image analysis is presented. This method, called convex cone analysis (CCA), is based on the bet that some physical quantities such as radiance are nonnegative. The vectors formed by discrete radiance spectra are linear combinations of nonnegative components, and they lie inside a nonnegative, convex region. The object of CCA is to find the boundary points of this region, which can be used as endmember spectra for unmixing or as target vectors for classification. To implement this concept, the authors find the eigenvectors of the sample spectral correlation matrix of the image. Given the number of endmembers or classes, they select as many eigenvectors corresponding to the largest eigenvalues. These eigenvectors are used as a basis to form linear combinations that have only nonnegative elements, and thus they lie inside a convex cone. The vertices of the convex cone will be those points whose spectral vector contains as many zero elements as the number of eigenvectors minus one. Accordingly, a mixed pixel can be decomposed by identifying the vertices that were used to form its spectrum. An algorithm for finding the convex cone boundaries is presented, and applications to unsupervised unmixing and classification are demonstrated with simulated data as well as experimental data from the hyperspectral digital imagery collection experiment (HYDICE).
Improvement in a quantitative measure of bradykinesia after microelectrode recording in patients with Parkinson's disease during deep brain stimulation surgery (2006)

It is widely accepted that patients with Parkinson's disease experience immediate but temporary improvement in motor signs after surgical implantation of subthalamic nucleus (STN) deep brain stimulating electrodes before the electrodes are activated, although this has never been formally studied. Based on anecdotal observations that limb mobility improved just after microelectrode recording (MER) during deep brain stimulation (DBS) procedures, we designed a prospective study to measure upper extremity bradykinesia using a quantitative measure of angular velocity. Measurements were made pre- and post-MER and during intraoperative DBS. Analysis of 98 STN DBS procedures performed on 61 patients showed that MER did not create adverse clinical symptoms despite concerns that MER increases morbidity. Quantitative upper extremity bradykinesia improved after MER alone, and further improvement was seen during intraoperative DBS. Electrophysiological data from each case were then compared to the improvement in bradykinesia post-MER alone and a significant correlation was found between the improvement in arm bradykinesia, the number of passes through the STN with somatosensory driving, and also with the number of arm cells with somatosensory driving in the STN, but not with total number of passes, total number of passes through the STN, or total number of cells with somatosensory driving in the STN. This study demonstrates that there is a significant improvement in upper extremity bradykinesia just after MER, before inserting or activating the DBS electrode in patients with Parkinson's disease who undergo STN DBS.
Wise teachers train better DNN acoustic models (2016)

Automatic speech recognition is becoming more ubiquitous as recognition performance improves, capable devices increase in number, and areas of new application open up. Neural network acoustic models that can utilize speaker-adaptive features, have deep and wide layers, or more computationally expensive architectures, for example, often obtain best recognition accuracy but may not be suitable for the given budget of computational and storage resources or latency required by the deployed system. We explore a straightforward training approach which takes advantage of highly accurate but expensive-to-evaluate neural network acoustic models by using their outputs to relabel training examples for easier-to-deploy models. Experiments on a large vocabulary continuous speech recognition task offer relative reductions in word error rate of up to 16.7 % over training with the hard aligned labels by effectively making use of large amounts of additional untranscribed data. Somewhat remarkably, the approach works well even when only two output classes are present. Experiments on a voice activity detection task give relative reductions in equal error rate of up to 11.5 % when using a convolutional neural network to relabel training examples for a feedforward neural network. An investigation into the hidden layer weight matrices finds that soft target-trained networks tend to produce weight matrices having fuller rank and slower decay in singular values than their hard target-trained counterparts, suggesting that more of the network’s capacity is utilized for learning additional information giving better accuracy.
Functional Heterogeneity of Memory CD4 T Cell Responses in Different Conditions of Antigen Exposure and Persistence (2005)

Memory CD4 T cell responses are functionally and phenotypically heterogeneous. In the present study, memory CD4 T cell responses were analyzed in different models of Ag-specific immune responses differing on Ag exposure and/or persistence. Ag-specific CD4 T cell responses for tetanus toxoid, HSV, EBV, CMV, and HIV-1 were compared. Three distinct patterns of T cell response were observed. A dominant single IL-2 CD4 T cell response was associated with the model in which the Ag can be cleared. Polyfunctional (single IL-2 plus IL-2/IFN-gamma plus single IFN-gamma) CD4 T cell responses were associated with Ag persistence and low Ag levels. A dominant single IFN-gamma CD4 T cell response was associated with the model of Ag persistence and high Ag levels. The results obtained supported the hypothesis that the different patterns observed were substantially influenced by different conditions of Ag exposure and persistence.
Cortical Lesions and Atrophy Associated With Cognitive Impairment in Relapsing-Remitting Multiple Sclerosis (2009)

The burden of CLs and tissue loss are among the major structural changes associated with cognitive impairment in relapsing-remitting MS.