gebhart/patrepeval huggingface dataset:
Approximation and Compression With Sparse Orthonormal Transforms (2015)

We propose a new transform design method that targets the generation of compression-optimized transforms for next-generation multimedia applications. The fundamental idea behind transform compression is to exploit regularity within signals such that redundancy is minimized subject to a fidelity cost. Multimedia signals, in particular images and video, are well known to contain a diverse set of localized structures, leading to many different types of regularity and to nonstationary signal statistics. The proposed method designs sparse orthonormal transforms (SOTs) that automatically exploit regularity over different signal structures and provides an adaptation method that determines the best representation over localized regions. Unlike earlier work that is motivated by linear approximation constructs and model-based designs that are limited to specific types of signal regularity, our work uses general nonlinear approximation ideas and a data-driven setup to significantly broaden its reach. We show that our SOT designs provide a safe and principled extension of the Karhunen-Loeve transform (KLT) by reducing to the KLT on Gaussian processes and by automatically exploiting non-Gaussian statistics to significantly improve over the KLT on more general processes. We provide an algebraic optimization framework that generates optimized designs for any desired transform structure (multiresolution, block, lapped, and so on) with significantly better n -term approximation performance. For each structure, we propose a new prototype codec and test over a database of images. Simulation results show consistent increase in compression and approximation performance compared with conventional methods.
Biological Evidence that Scrapie Agent Has an Independent Genome (1987)

There are many distinct strains of scrapie agent, identified by their relative incubation periods and quantitative and qualitative neuropathological properties in inbred mice of particular genotypes. When serially passaged under specified conditions of mouse strain, route of infection and dose of infectivity these properties are stable. However, they may change in a predictable manner if the passage strategy is altered. The scrapie strain 87A shows what has previously been defined as Class III stability; it is stable when passaged at low dose in C57BL mice, but often suddenly changes its properties in the course of a single passage if high doses are used, always resulting in the same new strain. The latter, designated 7D, has shorter incubation periods and more extensive pathology than 87A, properties which are subsequently stable on serial passage even at high dose. This phenomenon has been seen repeatedly using scrapie isolates from six different natural cases in five different breeds of sheep. These isolates are closely similar in all their properties, showing them to be independent isolations of the 87A strain; there have been no isolations of 87A in which the phenomenon did not occur. On the other hand, none of the many other scrapie strains used in the same laboratory have shown this change. 87A brain samples consistently behave as if they contain 87A together with a smaller amount of 7D. This is so even after 87A has previously been passaged at high dilution, well beyond the limiting dilution for 7D, a procedure which would eliminate any minor agent strain originally present in the isolate. Therefore it is highly likely that the 7D in tissues of mice infected with 87A is generated de novo at each passage by mutational change from 87A during the incubation period. The established fact that many different strains exist and the considerable evidence that mutation can occur lead to the conclusion that scrapie agent has its own independently replicating genome.
Remarkable Influence of Silver Islands on the Enhancement of Fluorescence from Eu3+ Ion-Doped Silica Gels (1999)

A simple methodology has been developed to enable a greater enhancement of fluorescence from europium (Eu3+)-doped silica gels containing adsorbed silver (Ag) islands. The procedure involves the preparation of Eu3+-doped silica gels by a sol−gel method and then immersion in a Ag sol for ca. 48 h to allow the adsorption of Ag islands on the pore surfaces of silica gels. UV−vis spectra show the characteristic surface plasmon resonance of the Ag at around 390 nm, and transmission electron microscopy (TEM) presents Ag islandlike particles on the surface of silica gels. The photoluminescence studies reveal the fact that the enhanced fluorescence originates from the local field enhancement around Eu3+ ions, caused by the electronic plasmon resonance of the Ag islands.
Abstract 2420: Modified vaccinia Ankara (MVA) expressing survivin combined with gemcitabine generates specific antitumor effects in a murine pancreatic carcinoma model (2010)

Abstract Survivin is overexpressed by 70-80% of pancreatic cancers, and is associated with resistance to chemotherapy and a poor prognosis. Gemcitabine has been a standard treatment for patients with advanced pancreatic cancer for a decade. Recent reports have demonstrated that gemcitabine treatment attenuates the tumor-suppressive environment by eliminating CD11b+/Gr-1+ myeloid derived suppressor cells (MDSCs). It may also enhance the effect of cancer vaccines. The highly attenuated strain of vaccinia, modified vaccinia Ankara (MVA) has been employed as a vaccine vector to deliver a tumor associated antigen, and MVA vaccines have demonstrated safety, immunogenicity, and evidence of clinical benefit in patients with cancer. We hypothesize that a cancer vaccine targeting survivin can achieve enhanced efficacy when use in combination with gemcitabine. In this study, we tested this hypothesis using an MVA expressing full-length murine survivin. The poorly immunogenic mouse pancreas adenocarcinoma cell line, Pan02, which express murine survivin and syngeneic to C57BL/6, was used for this study. To develop an established tumor model, mice were challenged with 2.5 × 105 Pan02 cells by subcutaneous injection. When the tumors were palpable and reached 4 to 5 mm in diameter, mice were immunized twice at a 1-week interval with 5 × 107 pfu of MVA-survivin or control MVA. Immunization with MVA-survivin resulted in a modest therapeutic antitumor effect on established Pan02 tumors. Gemcitabine (60mg/kg) was administrated 48 hours before first immunization. Mice treated with a control MVA or PBS with gemcitabine all died of progressive tumor by day 35. When administered with gemcitabine, MVA-survivin immunization resulted in significant tumor regression and prolonged survival. The enhanced vaccine efficacy is in part due to decreased CD11b+/Gr-1+ MDSCs. To analyze the survivin specific immune response to MVA-survivin immunization, we utilized a peptide library of 15mers with 11 residues overlapping from full-length murine survivin. Splencytes from mice immunized with MVA-survivin produced intracellular γ-interferon in response to in vitro stimulation with the overlapping peptide library. These data suggest that vaccination with MVA-survivin in combination with gemcitabine represents an attractive strategy to overcome tumor-induced peripheral immune tolerance, and this effect may be associated with a clinical benefit in pancreatic cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2420.
Human apolipoprotein A-I gene expression increases high density lipoprotein and suppresses atherosclerosis in the apolipoprotein E-deficient mouse. (1994)

Atherosclerosis is a complex disease with both genetic and environmental determinants. Apolipoprotein (Apo) E-deficient mice have been created that are highly susceptible to atherosclerosis. In order to assess the role of human apolipoprotein (hApo) A-I and high density lipoprotein (HDL) in atherosclerosis susceptibility, transgenic mice overexpressing the hApo A-I gene were crossed with Apo E-deficient mice. Apo E-/-, hApo A-I mice with two-fold elevation in HDL cholesterol have markedly diminished atherosclerosis with less fibroproliferative lesions by 8 months of age. A strong reciprocal relationship between HDL cholesterol levels and atherosclerosis was found with HDL levels accounting for 78% of the observed variance in mean lesion area. The effect of HDL on atherosclerosis resistance was independent of non-HDL cholesterol.
A Blood-Based Test for Epidermal Growth Factor Receptor Mutations in Lung Cancer (2006)

In this issue of Clinical Cancer Research , Kimura et al. ([1][1]) report on a blood-based assay to detect epidermal growth factor receptor (EGFR) mutations in patients with advanced non–small cell lung cancer (NSCLC).

The development of effective molecular therapeutic targeting strategies in
Active endoscope with SMA (Shape Memory Alloy) coil springs (2002)

This paper describes the development of an active endoscope which allows a large bending angle for practical application and has a simple structure for miniaturization. An active endoscope (image fiber with 4200 pixels and light guide fiber) 2 mm in outer diameter with a shape memory alloy (SMA) actuator was designed and fabricated. The practical specifications of the SMA coil spring were determined based on a design chart and equation. The active endoscope consists of a bending part, the SMA actuator, and an endoscope. The mechanical properties of the bending part were investigated. The shear modulus of the SMA at room temperature and in the parent phase were determined in designing the actuators.
Diversity ofATM gene mutations detected in patients with ataxia-telangiectasia (1997)

The ataxia-telangiectasia mutated (ATM) gene, which is mutated in the autosomal recessive disorder ataxia-telangiectasia (AT), was isolated in 1995 by positional cloning. Although in vitro cell fusion studies had suggested that AT was genetically heterogeneous, all AT patients studied to date have been found to harbor mutations in the ATM gene. More that 100 ATM mutations occurring in AT patients have been documented. The mutations are broadly distributed throughout the ATM gene. Except for patients from families with known consanguinity, most AT patients are compound heterozygotes. The majority (> 70%) of mutations are predicted to lead to protein truncation. A significant number of the reported mutations affect mRNA splicing with at least half of the coding exons (32/62) having been observed to undergo exon skipping. The large size of the ATM gene, 66 exons spanning approximately 150 kb of genomic DNA, together with the diversity and broad distribution of mutations in AT patients greatly limits the utility of direct mutation screening as a diagnostic tool, or method of carrier identification, except where founder effect mutations are involved.
Optimization of Antibacterial Cyclic Decapeptides (2004)

A previously developed method for cyclic peptide synthesis was demonstrated to be able to provide convenient access to large combinatorial libraries of analogues, and this methodology was applied to the optimization of natural product cyclic decapeptides. Using this method, a 192-member library was designed and successfully constructed on the basis of the natural products tyrocidines, streptocidins, and loloatins to increase the therapeutic indices of these antibiotics. Library screening identified nine analogues whose therapeutic indices were increased by up to 90-fold in comparison to the natural products. Three of these analogues showed significant increase in antibacterial potency and concurrent drastic decrease in hemolytic activity. Since the natural products target the bacterial cell wall, the newly discovered analogues are promising leads for drug development against drug-resistant bacteria.
Electrophore Mass Tag Dideoxy DNA Sequencing (1997)

Toward a goal of dideoxy sequencing DNA utilizing electrophore labels, we prepared four electrophore-labeled DNA oligonucleotide primers. Each primer has a different electrophore and DNA sequence but a common glycol keto (alpha,beta-dihydroxyketo) release group. Cleavage of this latter group by either periodate oxidation or a thermal retroaldol reaction releases the electrophores for detection by mass spectrometry. Successful sequencing data with these primers was obtained by capillary electrophoresis on an ABI Model 310 after fluorescence dideoxy terminator cycle sequencing reactions were conducted. In a separate experiment, it was demonstrated that a cocktail of the four electrophore DNA primers could be detected as a dried sample spot by CO2 laser desorption/capillary collection/gas chromatography electron capture mass spectrometry. These results establish some feasibility for our long-term goal of high-speed multiplex electrophore mass tag dideoxy DNA sequencing. Ultimately we plan to use a higher number of electrophore mass tags and to rely on direct detection of the desorbed electrophores by electron capture time-of-flight mass spectrometry.
Hormone Replacement Therapy and the Risk for First Hip Fracture (1990)

Treatment with potent estrogens, both alone and possibly when combined with progestogens, reduces the risk for both cervical and trochanteric hip fractures within the first decade after menopause.
Design Considerations for Silica-Particle-Doped Nitric-Oxide-Releasing Polyurethane Glucose Biosensor Membranes (2016)

Nitric oxide (NO)-releasing polymers have proven useful for improving the biocompatibility of in vivo glucose biosensors. Unfortunately, leaching of the NO donor from the polymer matrix remains a critical design flaw of NO-releasing membranes. Herein, a toolbox of NO-releasing silica nanoparticles (SNPs) was utilized to systematically evaluate SNP leaching from a diverse selection of biomedical-grade polyurethane sensor membranes. Glucose sensor analytical performance and NO-release kinetics from the sensor membranes were also evaluated as a function of particle and polyurethane (PU) chemistries. Particles modified with N-diazeniumdiolate NO donors were prone to leaching from PU membranes due to the zwitterionic nature of the NO donor modification. Leaching was minimized (<5% of the entrapped silica over 1 month) in low water uptake PUs. However, SNP modification with neutral S-nitrosothiol (RSNO) NO donors lead to biphasic leaching behavior. Particles with low alkanethiol content (<3.0 wt % sulfur) leached excessively from a hydrogel PU formulation (HP-93A-100 PU), while particles with greater degrees of thiol modification did not leach from any of the PUs tested. A functional glucose sensor was developed using an optimized HP-93A-100 PU membrane doped with RSNO-modified SNPs as the outer, glucose diffusion-limiting layer. The realized sensor design responded linearly to physiological concentrations of glucose (minimum 1-21 mM) over 2 weeks incubation in PBS and released NO at >0.8 pmol cm<sup>-2</sup> s<sup>-1</sup> for up to 6 days with no detectable (<0.6%) particle leaching.
Siglec-H is an IPC-specific receptor that modulates type I IFN secretion through DAP12 (2005)

Natural interferon (IFN)-producing cells are the primary cell type responsible for production of type I IFN in response to viruses. Herein we report the identification of the first molecular marker of mouse natural interferon-producing cells (IPCs), a novel member of the sialic acid-binding immunoglobulin (Ig)-like lectin (Siglec) family termed Siglec-H. Siglec-H is expressed exclusively on IPCs and is unique among Siglec proteins in that it associates with the adaptor protein DAP12. Moreover, we show that DAP12 modulates the type I IFN response of IPCs to a Toll-like receptor 9 (TLR9) agonist. This observation explains our previous finding that stimulation of IPCs with 440c, a Siglec-H-specific antibody, reduces IPC secretion of type I IFN. Moreover, it supports a model in which engagement of DNAX-activation protein 12 (DAP12)-associated receptors with antibodies or low avidity endogenous ligands interferes with TLR-mediated cellular activation.
Strength Measurement of Optical Fibers by Bending (1986)

A bending technique for the strength measurement of glass fibers is described and an analysis is presented which determines the effective tested length as a function of the statistical parameters which describe the fracture properties of the fiber. The analysis is used to compare strength data determined in both tension and bending for various representative fibers. It is found that the tensile strength cannot be predicted from the strength in bending and vice versa because the tested lengths differ by at least 3 orders of magnitude. Thus, while bending does not replace tension as a measurement technique, it does provide additional valuable information about the flaw size distribution.
Multiple Structural Coloring of Silk‐Fibroin Photonic Crystals and Humidity‐Responsive Color Sensing (2013)

Abstract In the biological world, numerous creatures such as butterflies, insects, and birds have exploited photonic structures to produce bicolor reflections with important biofunctions in addition to unique brilliant structural coloration. Although the mimicking of bistructural color reflection is possible, the fabrication involves a process of combined layer deposition techniques, which is complicated and less flexible. Here, a bistructural color mimicking, based on silk fibroin, is reported using a simple and inexpensive self‐assembly method. Silk‐fibroin inverse opals with different spectral positions of bistructural color reflection (i.e., ultraviolet and visible peaks, ultraviolet and near infrared peaks, and visible and near infrared peaks) are obtained by simply controlling their lattice constants. Furthermore, the inline and continuous tuning of the peak positions of bistructural color reflection can be achieved by the humidity‐induced cyclic contraction of silk fibroin. The potential applications of silk‐fibroin photonic structures in eco‐dying and multifunctional silk fabrics are also demonstrated.
Effect of Lesions of the Ventrolateral Preoptic Nucleus on NREM and REM Sleep (2000)

Neurons in the ventrolateral preoptic nucleus (VLPO) in rats show c-fos activation after sleep and provide GABAergic innervation of the major monoamine arousal systems, suggesting that they may be a necessary part of the brain circuitry that produces sleep. We examined the effects on sleep behavior in rats of cell-specific damage to the VLPO by microinjection of ibotenic acid. Severe lesions of the central cell cluster of the VLPO ( approximately 80-90% cell loss bilaterally) caused a 60-70% decrease in delta power and a 50-60% decrease in nonrapid-eye-movement (NREM) sleep time (p < 0.001). The number of remaining Fos-immunoreactive neurons in the VLPO cell cluster was linearly related to NREM sleep time (r = 0.77; p < 0.001) and total electroencephalogram delta power (r = 0. 79; p < 0.001) but not to rapid-eye-movement (REM) sleep (r = 0.35; p > 0.10). Lesions in the region containing scattered VLPO neurons medial or dorsal to the cell cluster caused smaller changes in NREM sleep time (24.5 or 15%, respectively) but were more closely associated with loss of REM sleep (r = 0.74; p < 0.01). The insomnia caused by bilateral VLPO lesions persisted for at least 3 weeks. Lesions of the VLPO caused no change in mean body temperature or its circadian variation; after small lesions of the ventromedial preoptic nucleus, body temperature showed normal circadian variation but a wider temperature range, and sleep behavior was not affected. These experiments delineate distinct preoptic sites with primary effects on the regulation of NREM sleep, REM sleep, and body temperature.
Complete Genome Sequence ofTreponema pallidum, the Syphilis Spirochete (1998)

The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.
Hierarchical Generative Modeling for Controllable Speech Synthesis (2018)

This paper proposes a neural sequence-to-sequence text-to-speech (TTS) model which can control latent attributes in the generated speech that are rarely annotated in the training data, such as speaking style, accent, background noise, and recording conditions. The model is formulated as a conditional generative model based on the variational autoencoder (VAE) framework, with two levels of hierarchical latent variables. The first level is a categorical variable, which represents attribute groups (e.g. clean/noisy) and provides interpretability. The second level, conditioned on the first, is a multivariate Gaussian variable, which characterizes specific attribute configurations (e.g. noise level, speaking rate) and enables disentangled fine-grained control over these attributes. This amounts to using a Gaussian mixture model (GMM) for the latent distribution. Extensive evaluation demonstrates its ability to control the aforementioned attributes. In particular, we train a high-quality controllable TTS model on real found data, which is capable of inferring speaker and style attributes from a noisy utterance and use it to synthesize clean speech with controllable speaking style.
Antipeptide antibodies that recognize a lymphocyte substance P receptor. (1989)

In an effort to investigate the presence of substance P (SP) receptors on lymphocytes, polyclonal antibodies against SP receptors were developed. The immunogen used to generate these antibodies was a peptide encoded by an RNA complementary to the mRNA for SP. The rationale for using this SP complementary peptide (termed SP CP) as an immunogen resulted from the observation that 3H-SP bound to microtiter wells coated with SP CP in a dose dependent and saturable fashion. Furthermore, binding was blocked with excess unlabeled SP or SP antagonist, D-Pro2-D-Phe7-D-Trp9-SP. Inasmuch as the peptide, SP CP, specifically bound 3H-SP, we hypothesized that antibodies against this peptide might recognize a SP receptor binding site. Using the SP receptor positive lymphoblast cell line, IM-9, affinity-purified antibodies against SP CP but not antibodies against keyhole limpet hemocyanin recognized a molecule on the surface of IM-9 cells. Anti-SP CP binding to IM-9 cells was blocked with excess SP antagonist, suggesting that the antibody and the SP antagonist were competing for the same binding site. In support of this possibility, anti-SP CP antibodies blocked 3H-SP binding to IM-9 cells. An immunoaffinity column coupled with antibodies against SP CP bound protein from solubilized IM-9 cells. This isolated protein bound 125I-Tyr8-SP and binding was specifically blocked with SP as well as by SP antagonist, neurokinin A, and eledoisin. Passthrough material did not bind SP suggesting that a SP receptor had been purified. Western blot analysis of solubilized IM-9 cell proteins using anti-SP CP antibodies but not preimmune IgG recognized a single protein of 58,000 D. Taken together, these results demonstrate that antibodies against SP CP recognize a SP receptor present on the lymphocyte cell line, IM-9.