gebhart/patrepeval huggingface dataset:
Application Of Neural Networks To Adaptive Control (2005)

Neural network-based control architectures have been developed that can autonomously learn to perform kinematic and dynamic control of unknown systems and/or adapt to systems that change over time. Kinematic control of non-linear, time varying systems is demonstrated. The controller can control continuous-valued system variables to arbitrary accuracy using a small number of neurons. It learns to control the system more accurately than an analytically calculated control function. It is fault tolerant in the presence of a large number (e.g. 30%) of component failures. The architecture has been used to learn to control a simulated robot arm of initially unknown characteristics. Dynamic feed forward control of a second order system is also demonstrated. The simulations run in near real time, and custom VLSI hardware is under development.
Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer? (2011)

Mutations in the adenomatous polyposis coli (APC) tumor suppressor gene strongly predispose to development of gastro-intestinal tumors. Central to the tumorigenic events in APC mutant cells is the uncontrolled stabilization and transcriptional activation of the protein β-catenin. Many questions remain as to how APC controls β-catenin degradation. Remarkably, the large C-terminal region of APC, which spans over 2000 amino acids and includes critical regions in downregulating β-catenin, is predicted to be natively unfolded. Here we discuss how this uncommonly large disordered region may help to coordinate the multiple cellular functions of APC. Recently, a significant number of germline and somatic missense mutations in the central region of APC were linked to tumorigenesis in the colon as well as extra-intestinal tissues. We classify and localize all currently known missense mutations in the APC structure. The molecular basis by which these mutations interfere with the function of APC remains unresolved. We propose several mechanisms by which cancer-related missense mutations in the large disordered domain of APC may interfere with tumor suppressor activity. Insight in the underlying molecular events will be invaluable in the development of novel strategies to counter dysregulated Wnt signaling by APC mutations in cancer.
Heightened efficacy of nitric oxide-based therapies in type II diabetes mellitus and metabolic syndrome (2008)

Type II diabetes mellitus (DM) and metabolic syndrome are associated with accelerated restenosis following vascular interventions due to neointimal hyperplasia. The efficacy of nitric oxide (NO)-based therapies is unknown in these environments. Therefore, the aim of this study is to examine the efficacy of NO in preventing neointimal hyperplasia in animal models of type II DM and metabolic syndrome and examine possible mechanisms for differences in outcomes. Aortic vascular smooth muscle cells (VSMC) were harvested from rodent models of type II DM (Zucker diabetic fatty), metabolic syndrome (obese Zucker), and their genetic control (lean Zucker). Interestingly, NO inhibited proliferation and induced G0/G1 cell cycle arrest to the greatest extent in VSMC from rodent models of metabolic syndrome and type II DM compared with controls. This heightened efficacy was associated with increased expression of cyclin-dependent kinase inhibitor p21, but not p27. Using the rat carotid artery injury model to assess the efficacy of NO in vivo, we found that the NO donor PROLI/NO inhibited neointimal hyperplasia to the greatest extent in type II DM rodents, followed by metabolic syndrome, then controls. Increased neointimal hyperplasia correlated with increased reactive oxygen species (ROS) production, as demonstrated by dihydroethidium staining, and NO inhibited this increase most in metabolic syndrome and DM. In conclusion, NO was surprisingly a more effective inhibitor of neointimal hyperplasia following arterial injury in type II DM and metabolic syndrome vs. control. This heightened efficacy may be secondary to greater inhibition of VSMC proliferation through cell cycle arrest and regulation of ROS expression, in addition to other possible unidentified mechanisms that deserve further exploration.
Purification and Characterization of Mouse Hematopoietic Stem Cells (1988)

Mouse bone marrow hematopoietic stem cells were isolated with the use of a variety of phenotypic markers. These cells can proliferate and differentiate with approximately unit efficiency into myelomonocytic cells, B cells, or T cells. Thirty of these cells are sufficient to save 50 percent of lethally irradiated mice, and to reconstitute all blood cell types in the survivors.
(1S,2R/1R,2S)-cis-Cyclopentyl PNAs (cpPNAs) as Constrained PNA Analogues:  Synthesis and Evaluation of aeg-cpPNA Chimera and Stereopreferences in Hybridization with DNA/RNA (2004)

Conformationally constrained chiral PNA analogues were designed on the basis of stereospecific imposition of a 1,2-cis-cyclopentyl moiety on an aminoethyl segment of aegPNA. It is known that the cyclopentane ring is a relatively flexible system in which the characteristic puckering dictates the pseudoaxial/pseudoequatorial dispositions of substituents. Hence, favorable torsional adjustments are possible to attain the necessary hybridization-competent conformations when the moiety is imposed on the conventional PNA backbone. The synthesis of the enantiomerically pure 1,2-cis-cyclopentyl PNA monomers (10a and 10b) was achieved by stereoselective enzymatic hydrolysis of a key intermediate ester 2. The chiral (1S,2R/1R,2S)-aminocyclopentylglycyl thymine monomers were incorporated into PNA oligomers at defined positions and through the entire sequence. Hybridization studies with complementary DNA and RNA sequences using UV-Tm measurements indicate that aeg-cpPNA chimera form thermally more stable complexes than aegPNA with stereochemistry-dependent selective binding of cDNA/RNA. Differential gel shift retardation was observed on hybridization of aeg-cpPNAs with complementary DNA.
Trusted Display on Untrusted Commodity Platforms (2015)

A trusted display service assures the confidentiality and authenticity of content output by a security-sensitive application and thus prevents a compromised commodity operating system or application from surreptitiously reading or modifying the displayed output. Past approaches have failed to provide trusted display on commodity platforms that use modern graphics processing units (GPUs). For example, full GPU virtualization encourages the sharing of GPU address space with multiple virtual machines {\em without} providing adequate hardware protection mechanisms; e.g., address-space separation and instruction execution control. This paper proposes a new trusted display service that has a minimal trusted code base and maintains full compatibility with commodity computing platforms. The service relies on a GPU separation kernel that (1) defines different types of GPU objects, (2) mediates access to security-sensitive objects, and (3) emulates object whenever required by commodity-platform compatibility. The separation kernel employs a new address-space separation mechanism that avoids the challenging problem of GPU instruction verification without adequate hardware support. The implementation of the trusted-display service has a code base that is two orders of magnitude smaller than other similar services, such as those based on full GPU virtualization. Performance measurements show that the trusted-display overhead added over and above that of the underlying trusted system is fairly modest.
Small pixel development for novel CMOS image sensors (2008)

Modern trends in camera module design for both mobile and DSC applications are driving the race to shrink pixel and increase pixel array size. At the same time higher demands on the quality of color images - DSC-like quality for mobile applications - require maintaining a large pixel capacity, quantum efficiency (QE), and sensitivity to preserve color image quality. This becomes extremely difficult as the size of the pixel shrinks. This paper discusses the Common Element Pixel Architecture (CEPA) for image sensors with small pixels as well as new pixel designs and process changes, that have enabled a new generation of image sensors with high performance 2.2-&mu;m, 1.75-&mu;m, and smaller pixels. Advanced algorithms of capturing the image help to overcome the challenges associated with the limited pixel capacity of small pixels. The paper considers an HDR mode of operation for the small pixel and its effect on the image quality. Achieving good color crosstalk performances is one of the big challenges in CMOS Image Sensors with small pixels. The paper presents results of an experimental study of crosstalk for different pixel sizes, analyzes the effect of crosstalk on the quality of color image and signal-to-noise ratio after color processing, and discusses ways of cross talk reduction for small pixels.
A Mutational Analysis of the Binding of Staphylococcal Enterotoxins B and C3 to the T Cell Receptor β Chain and Major Histocompatibility Complex Class II (1998)

The three-dimensional structure of the complex between a T cell receptor (TCR) beta chain (mouse Vbeta8.2Jbeta2.1Cbeta1) and the superantigen (SAG) staphylococcal enterotoxin C3 (SEC3) has been recently determined to 3.5 resolution. To evaluate the actual contribution of individual SAG residues to stabilizing the beta-SEC3 complex, as well as to investigate the relationship between the affinity of SAGs for TCR and MHC and their ability to activate T cells, we measured the binding of a set of SEC3 and staphylococcal enterotoxin B (SEB) mutants to soluble recombinant TCR beta chain and to the human MHC class II molecule HLA-DR1. Affinities were determined by sedimentation equilibrium and/or surface plasmon detection, while mitogenic potency was assessed using T cells from rearrangement-deficient TCR transgenic mice. We show that there is a clear and simple relationship between the affinity of SAGs for the TCR and their biological activity: the tighter the binding of a particular mutant of SEC3 or SEB to the TCR beta chain, the greater its ability to stimulate T cells. We also find that there is an interplay between TCR-SAG and SAG-MHC interactions in determining mitogenic potency, such that a small increase in the affinity of a SAG for MHC can overcome a large decrease in the SAG's affinity for the TCR. Finally, we observe that those SEC3 residues that make the greatest energetic contribution to stabilizing the beta-SEC3 complex ("hot spot" residues) are strictly conserved among enterotoxins reactive with mouse Vbeta8.2, thereby providing a basis for understanding why SAGs having other residues at these positions show different Vbeta-binding specificities.
N- and O-glycosylation muteins of recombinant human erythropoietin secreted from BHK-21 cells (1995)

Single-site glycomuteins of recombinant human erythropoietin (rhuEpo) were constructed and transiently and stably expressed in BHK-21 cells. The transient expression levels varied among muteins, being highest for mutein rhuEpoGln24 followed by wild-type rhuEpo (rhuEpowt). All other glycomuteins, including rhuEpoGln38, rhuEpoGln83, rhuEpoThr126, and rhuEpoGly126, were secreted at lower levels than rhuEpowt. Muteins expressed in stable cell lines showed similar differences in expression levels. Also each mutein could be affinity-purified from culture supernatants, and was biologically active in vivo. Based on secretion rates from BHK-21 cells, the most potent erythropoietin was rhuEpoGln24. This mutein is also considered to have biologic activities that are superior to rhuEpowt.
Anti-idiotypic antibodies induce neutralizing antibodies to rabies virus glycoprotein (1983)

Rabbit anti-idiotypic antibodies (alpha Id Ab) were prepared against five murine monoclonal antibodies (mAb) specific for the rabies virus glycoprotein. Four of the mAb were directed against three known, type-specific, neutralizing sites on the glycoprotein, and the other mAb was directed against a topographically uncharacterized, nonneutralizing epitope. An absence of significant cross-reactivity among the alpha Id Ab for heterologous mAb suggested that the alpha Id Ab were highly specific for unique variable region determinants. The binding of three of the five alpha Id Ab to their homologous mAb could be inhibited by rabies virus-soluble glycoprotein, suggesting that the alpha Id Ab possessed subpopulations similar or adjacent to the antigen-binding site of the mAb. Two of the five alpha Id Ab injected into mice elicited a specific virus-neutralizing antibody response. Mechanisms to account for the induction of the virus-neutralizing antibody by alpha Id Ab are discussed.
Anti‐La Monoclonal Antibodies Recognizing Epitopes Within the RNA‐Binding Domain of the La Protein Show Differential Capacities to Immunoprecipitate RNA‐Associated La Protein (1995)

The La (SS-B) autoimmune antigen is an RNA-binding protein that is present in both the nucleus and cytoplasm of eukaryotic cells, where it is found associated with RNA polymerase III transcripts. We have investigated the capacity of anti-La monoclonal antibodies SW1, SW3, and SW5 to immunoprecipitate human La ribonucleoprotein particles. Distinct differences were observed for SW3 in comparison with SW1 and SW5. While SW1 and SW5 precipitated ribonucleoproteins containing pre-tRNA, pre-5S rRNA, hY RNAs, pre-U6 snRNA or the viral EBER1 and VA RNAs, SW3 precipitated only ribonucleoproteins containing VA RNAs or (the precursor of) 7-2 RNA. Mapping of the epitopes recognized by SW1, SW3, and SW5 revealed that all three monoclonal antibodies recognize an epitope within the domain of the protein formed by the ribonucleoprotein motif. Cross-competition studies suggested that the epitope recognized by SW1 and SW5 are identical but distinct from the epitope recognized by SW3. Further analyses of the recognition of La from other species by these monoclonal antibodies revealed that they all reacted with bovine La and were not reactive with La from rodents and Xenopus laevis. Replacement of a single amino acid in the human protein by its murine counterpart abolished recognition by SW1 and SW5, but had no effect on recognition by SW3. Taken together, our results indicate that SW1 and SW5 recognize the same epitope and that SW3 recognizes a distinct epitope, both of which are located in the RNA-binding domain of La, and that the accessibility of these epitopes is differentially influenced by the association of La with various RNA polymerase III transcripts.
Replication and pathogenicity of human immunodeficiency virus type 1 accessory gene mutants in SCID-hu mice (1996)

The functional roles of the human immunodeficiency virus type 1 (HIV-1) accessory genes (nef, vpr, vpu, and vif) are as yet unclear. Using the SCID-hu model system, we have examined the infectivity, replicative capacity, and pathogenicity of strains of the molecular clone HIV-1NL4-3 that contain deletion mutations in these individual accessory genes. We determined that deletion of these genes had differential effects on both infectivity and pathogenicity. Deletion of vpr had little or no effect on viral infectivity, replication, and pathogenicity; however, deletion of vpu or vif had a significant effect on infectivity and moderate effects on pathogenicity. nef-minus strains were the most attenuated in this system, demonstrating significantly lower levels of infectivity and pathogenicity. However, deletion of these individual genes attenuated but did not abrogate the pathogenic properties of HIV-1. Mutant viruses still retained the ability to induce thymocyte depletion to various degrees if implants were infected with higher doses of virus or observed for longer periods of time. The relative contributions of these genes to in vivo pathogenic potential should be taken into consideration when one is contemplating a live attenuated vaccine for HIV-1.
Systematic Low Temperature Silicon Bonding using Pressure and Temperature (1998)

We have developed a systematic three-step process to low temperature direct bond silicon and/or SiO 2 surfaces. The process activates the surface with ammonia, argon and oxygen plasma. While these activation processes allow a very strong low temperature bond to be created, they require techniques distinctly different from those found in previous work for reproducible results. The plasma processes do not result in a bond that propagates as a wave resulting from a point source initiation. A substantial pressure is required to initiate the bond. We have found that a three-step process using pressure and temperature results in very strong, reproducible bonds.
Treatment of Focal Cerebral Ischemia With Synthetic Oligopeptide Corresponding to Lectin Domain of Selectin (1996)

Our data demonstrate that administration of a synthetic oligopeptide corresponding to the lectin domain of selectin decreases the size of ischemic injury after transient, but not after permanent, focal cerebral ischemia as evaluated at 24 hours after onset of ischemia. These effects were associated with an improved CBF at the dorsolateral cerebral cortex after partial reperfusion.
Electromechanical interactions in a carbon nanotube based thin film field emitting diode (2007)

Carbon nanotubes (CNTs) have emerged as promising candidates for biomedical x-ray devices and other applications of field emission. CNTs grown/deposited in a thin film are used as cathodes for field emission. In spite of the good performance of such cathodes, the procedure to estimate the device current is not straightforward and the required insight towards design optimization is not well developed. In this paper, we report an analysis aided by a computational model and experiments by which the process of evolution and self-assembly (reorientation) of CNTs is characterized and the device current is estimated. The modeling approach involves two steps: (i) a phenomenological description of the degradation and fragmentation of CNTs and (ii) a mechanics based modeling of electromechanical interaction among CNTs during field emission. A computational scheme is developed by which the states of CNTs are updated in a time incremental manner. Finally, the device current is obtained by using the Fowler-Nordheim equation for field emission and by integrating the current density over computational cells. A detailed analysis of the results reveals the deflected shapes of the CNTs in an ensemble and the extent to which the initial state of geometry and orientation angles affect the device current. Experimental results confirm these effects.
<title>Absolute measurement using field-shifted moiré</title> (1992)

Phase shifted moire interferometry is one of the most effective tools for obtaining a full-field depth map. The major draw back of the technique is the two pi ambiguity which limits the measurement depth range to one fringe or requires the counting of fringes across the image. In either case, only a relative measurement is obtained, no information is available about the absolute distance to the camera. By moving the moire projection system (field shifting) the period of the moire pattern is changed allowing extraction of absolute depth information. We have built an instrument, employing field shifted moire to produce a full field depth map with 12 bits of depth resolution. The performance and applications of this instrument are discussed.
Sensorless Sliding-Mode MTPA Control of an IPM Synchronous Motor Drive Using a Sliding-Mode Observer and HF Signal Injection (2009)

This paper proposes a nonlinear sliding-mode speed-control scheme for interior permanent-magnet synchronous motor (IPMSM) drives incorporating the maximum-torque-per-ampere trajectory. The drive uses an adaptive sliding-mode observer (SMO) for rotor-speed estimation. The global asymptotic stabilities of both the controller and observer are guaranteed by Lyapunov stability analysis. The very low speed and standstill performance of the drive is further enhanced by combining high-frequency signal injection with the SMO. Hence, the sensorless drive is capable of exhibiting high dynamic and steady-state performances over a wide speed range. Experimental results confirm the effectiveness of the proposed method.
Human liver protein map: A reference database established by microsequencing and gel comparison (1992)

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.
TOC1: Characterization of a Selective Oligomeric Tau Antibody (2013)

The work presented herein addresses a specific portion of the tau pathology, pre-fibrillar oligomers, now thought to be important pathological components in Alzheimer's disease and other neurodegenerative tauopathies. In previous work, we generated an antibody against purified recombinant cross-linked tau dimers, called Tau Oligomeric Complex 1 (TOC1). TOC1 recognizes tau oligomers and its immunoreactivity is elevated in Alzheimer's disease brains. In this report, we expand upon the previous study to show that TOC1 selectively labels tau oligomers over monomers or polymers, and that TOC1 is also reactive in other neurodegenerative tauopathies. Using a series of deletion mutants spanning the tau molecule, we further demonstrate that TOC1 has one continuous epitope located within amino acids 209-224, in the so-called proline rich region. Together with the previous study, our data indicates that TOC1 is a conformation-dependent antibody whose epitope is revealed upon dimerization and oligomerization, but concealed again as polymers form. This characterization of the TOC1 antibody further supports its potential as a powerful biochemical tool that can be used to better investigate the involvement of tau in neurodegenerative diseases.
The 1.51-Å structure of the poxvirus L1 protein, a target of potent neutralizing antibodies (2005)

Although eradicated from nature more than two decades ago, the threat of smallpox has reemerged because of concerns over its use as a biological weapon. We present the structure of the poxvirus L1 protein, a molecule that is conserved throughout the poxvirus family and is nearly identical in vaccinia virus and in variola virus, which causes smallpox. L1 is a myristoylated envelope protein that is a potent target for neutralizing antibodies and an important component of current experimental vaccines. The L1 structure reveals a hydrophobic cavity located adjacent to its N terminus. The cavity would be capable of shielding the myristate moiety, which is essential for virion assembly. The structure of L1 is a step in the elucidation of molecular mechanisms common to all poxviruses that may stimulate the design of safer vaccines and new antipoxvirus drugs.
Maternal hypertension and associated pregnancy complications among african-american and other women in the United States (1996)

The excess incidence of maternal hypertension, particularly chronic hypertension, may contribute to adverse maternal and fetal pregnancy outcomes and the disparity in outcomes observed between African-American and other women in the U.S. These findings provide a specific focus for further clinical outcomes research and assessment of prenatal management in African-American women.