gebhart/patrepeval huggingface dataset:
Guillain‐Barré Syndrome and Influenza Virus Infection (2008)

Influenza viruses are infrequent triggering agents of GBS but may play a significant role during major influenza outbreaks. Influenza-related GBS displays specific features and is not associated with antiganglioside antibody response, which suggests the presence of underlying immune mechanisms.
Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering. (1985)

The principal catalytic factor in the activation of tyrosine by the tyrosyl-tRNA synthetase is found to be improved binding of ATP in the transition state. The activation reaction involves the attack of the tyrosyl carboxylate on the alpha-phosphate group of ATP to generate a pentacoordinate transition state. Model building of this complex located a binding site for the gamma-phosphate group of ATP, consisting of hydrogen bonds with the side chains of Thr-40 and His-45. Removal of these groups by protein engineering shows that they contribute no binding energy with unreacted ATP but put all of their binding energy into stabilizing the [tyrosine-ATP] transition state [the mutant tyrosyl-tRNA synthetase (Thr-40----Ala-40; His-45----Gly-45) has the rate of formation of tyrosyl adenylate lowered by 3.2 X 10(5) but KS for ATP is lowered by only a factor of 5]. The side chains of these residues also provide a binding site for pyrophosphate in the reverse reaction. Thus, catalysis is accomplished by stabilization of the transition state by improved binding of a group on the substrate that is distant from the seat of reaction.
A cytoskeleton-related gene, uso1, is required for intracellular protein transport in Saccharomyces cerevisiae. (1991)

The Saccharomyces cerevisiae mutant strains blocked in the protein secretion pathway are not able to induce sexual aggregation. We have utilized the defect of aggregation to concentrate the secretion-deficient cells and identified a new gene which functions in the process of intracellular protein transport. The new mutant, uso1, is temperature sensitive for growth and protein secretion. At the restrictive temperature (37 degrees C), uso1 mutant accumulated the core-glycosylated precursor form of the exported protein invertase in the cells. Ultrastructural study of the mutant fixed by the freeze-substitution method revealed expansion of the nuclear envelope lumen and accumulation of the ER at the restrictive temperature. Abnormally oriented bundles of microtubules were often found in the nucleus. The USO1 gene was cloned by complementation of the uso1 temperature-sensitive growth defect. DNA sequence analysis revealed a hydrophilic protein of 1790 amino acids with a COOH-terminal 1,100-amino acid-long alpha-helical structure characteristic of the coiled-coil rod region of the cytoskeleton-related proteins. These observations suggest that Uso1 protein plays a role as a cytoskeletal component in the protein transport from the ER to the later secretory compartments.
Properties of murine CD8+CD27- T cells (2005)

In humans, loss of CD27 expression is associated with the stable acquisition of effector functions by CD8+ T cells. We found that murine (CD8+)CD27- T cells were confined to the primed CD62L(dull/-)CD44(bright)CCR7- T cell population. (CD8+)CD27- T cells were absent from lymph nodes but could be found in blood, spleen and in non-lymphoid organs such as lung and liver. Late after primary influenza virus infection, low percentages of antigen-specific CD27- cells emerged in the lung and spleen. After recovery from secondary influenza virus infection, high percentages of influenza-specific CD27- T cells were found in the lung and the loss of CD27 on lung CD8+ T cells coincided with high granzyme B expression. After murine cytomegalovirus infection, loss of CD27 expression on virus-specific CD8+ T cell populations was sustained and especially marked in liver and lung. We suggest that in mice, CD27 is lost from CD8+ T cells only after repetitive antigenic stimulation. Moreover, the high expression of both granzyme B and perforin in the CD27- T cells suggests that the lack of CD27 on murine CD8+ T cells can be used to identify memory T cells with expression of cytotoxic effector molecules.
Evidence for Sequential Action of cdc7 and cdk2 Protein Kinases during Initiation of DNA Replication in Xenopus Egg Extracts (2000)

To investigate how the protein kinase cdc7 stimulates DNA replication in metazoans, a soluble cell-free replication system derived from Xenopus eggs was used. DNA was incubated in egg cytosol to form prereplication complexes and then in nucleoplasmic extract to initiate DNA synthesis. We find that cdc7 is greatly enriched in nucleoplasmic extract and that this high concentration is essential for efficient DNA replication, supporting previous models that the nucleus activates replication indirectly by sequestering essential components. cdc7 binds to chromatin at the G(1)/S transition before initiation occurs, and it dissociates from chromatin as S phase progresses. The chromatin association of cdc7 requires chromatin-bound MCM. In turn, cdc7 is required to load the initiation factor cdc45 onto the DNA. Finally, efficient replication is observed when chromatin is exposed first to cdc7 and then to cdk2 but not when it is exposed to cdk2 before cdc7. Therefore, the cdc7- and cdk2-dependent initiation steps can be separated, indicating the existence of a novel, stable initiation intermediate. Moreover, the data suggest that cdk2 can only act after cdc7 has executed its function.
On the Development of a Specialized Flexible Gripper for Garment Handling (2013)

In this paper, we discuss ongoing work on the development of a new griper for garments handling and manipulation tasks. We analyze the specificity of the application determining the requirements for the design and functioning of the grasping system. Textiles do not have a stable shape and cannot be manipulated on the basis of a priori geometric knowledge. Therefore, the grasping task cannot be executed without exploring the material and the environment. This is to be achieved by a vision system, which is part of the robotic work cell, in combination with tactile sensors embedded in the fingertips of the gripper. A possible design for the gripper mechanism is outlined and open research and design problems are identified. 
Return-oriented programming without returns (2010)

We show that on both the x86 and ARM architectures it is possible to mount return-oriented programming attacks without using return instructions. Our attacks instead make use of certain instruction sequences that behave like a return, which occur with sufficient frequency in large libraries on (x86) Linux and (ARM) Android to allow creation of Turing-complete gadget sets.
Interferon is a polypeptide hormone. (1984)

Interferons (IFNs) bind to specific high-affinity receptors on the cell surface. The human IFN-alpha receptor is a highly hydrophobic membrane protein (molecular weight about 100,000). After binding to the receptor, IFN is internalized and degraded by lysosomal proteases. The receptor is also internalized, does not recycle to the cell surface and is gradually inactivated. An unidentified mechanism transduces a signal from the interferon/receptor complex to induce the transcription of specific genes. There are striking similarities between IFN and polypeptide hormones in their interaction with cell surface receptors, internalization of polypeptide/receptor complexes and degradation of the polypeptides in lysosomes.
Steric effects of cis‐trans isomerism on neighboring residues in proline oligopeptides: A 13C‐nmr study of conformational heterogeneity in linear tripeptides (1979)

Abstract A series of proline‐containing linear oligopeptides (4 dipeptides and 15 tripeptides) were synthesized and examined in aqueous and nonaqueous solutions using 13 C‐nmr spectroscopy. Spectra of linear tripeptides showing cis ‐ trans isomerism about the X ‐Pro bond ( X = Pro, Gly, and Ala) also show neighboring effects on the chemical shifts of residues both preceding and following the prolyl moiety. The extent of cis ‐ trans isomerism observed about the X ‐Pro peptide bond correlates not only with the nature of X , but also depends on the size of the residue following proline; the larger substituents favor an increase in cis content about the X ‐Pro bond.
Mainstreaming SOI CMOS technology (1999)

Partially-depleted deep sub-micron CMOS on SOI technology is becoming a mainstream technology. This technology offers 20- 35 percent performance gain over a bulk technology implemented with the same tool set. In this paper, first a review of the SOI technology is given. Next, the partially- depleted SOI device and the reasons why it was chosen over fully depleted SOI device are reviewed. The sources of performance gain on SOI, and SOI-unique circuit issues that a designer must consider and account are discussed next. Finally, a low-power application of SOI is reviewed.
63.2% high efficiency and high linearity two-stage InGaP/GaAs HBT power amplifier for personal digital cellular phone system (2002)

This paper reports on a high efficiency and high linearity two-stage InGaP/GaAs heterojunction bipolar transistor (HBT) power amplifier for the Japanese personal digital cellular phone system (PDC). Our power-stage HBT amplifier exhibited a high power added efficiency (PAE) of 68.8% and an adjacent channel leakage power (ACP) of -48 dBc. The ACP of the two-stage amplifier was improved enough for PDC with keeping a high PAE by combining of a driver-stage and this power-stage amplifiers. Our two-stage HBT power amplifier exhibited the highest PAE of 63.2% ever reported and an ACP at a 50-kHz offset frequency of -52 dBc in 1.5 GHz PDC standard at a Pout of 31 dBm under a supply voltage of 3.5 V.
CD44 promotes progenitor homing into the thymus and T cell maturation (2008)

Regain of immunocompetence after myeloablation and bone marrow cell (BMC) reconstitution essentially depends on T progenitor homing into the thymus and intrathymic T cell maturation. CD44 facilitates progenitor homing and settlement in the bone marrow and is known as a T progenitor marker. In search for improving regain of immunocompetence after BMC reconstitution, we explored whether the CD44 standard (CD44 s) and/or variant isoforms CD44v6 and CD44v7 contribute to thymus repopulation and thymocyte maturation. Antibody-blocking studies and cells/mice with a targeted deletion of CD44v6/7 or CD44v7 revealed that CD44s, but not CD44v6 and CD44v7, has a major impact on progenitor cell homing into the thymus. Instead, CD44v6 strengthens apoptosis resistance and expansion of early thymocytes. CD44v6-induced apoptosis resistance, most strong in double-negative (DN) thymocytes, is accompanied by Akt activation. CD44v6-induced proliferation of DN cells proceeds via activation of the MAPK pathway. At later stages of T cell maturation, CD44 acts as an accessory molecule, initiating and supporting TCR/CD3 complex-mediated signal transduction in double-positive and single-positive thymocytes. Thus, CD44 plays a major role in thymus homing. In addition, CD44v6 is important for survival and expansion of early thymocytes. These findings suggest that strengthening CD44v6 expression on lymphoid progenitors could well contribute to accelerated regain of immunocompetence.
Hepatitis C Virus Targets DC-SIGN and L-SIGN To Escape Lysosomal Degradation (2004)

Hepatitis C virus (HCV) is a major health problem. However, the mechanism of hepatocyte infection is largely unknown. We demonstrate that the dendritic cell (DC)-specific C-type lectin DC-SIGN and its liver-expressed homologue L-SIGN/DC-SIGNR are important receptors for HCV envelope glycoproteins E1 and E2. Mutagenesis analyses demonstrated that both HCV E1 and E2 bind the same binding site on DC-SIGN as the pathogens human immunodeficiency virus type 1 (HIV-1) and mycobacteria, which is distinct from the cellular ligand ICAM-3. HCV virus-like particles are efficiently captured and internalized by DCs through binding of DC-SIGN. Antibodies against DC-SIGN specifically block HCV capture by both immature and mature DCs, demonstrating that DC-SIGN is the major receptor on DCs. Interestingly, internalized HCV virus-like particles were targeted to nonlysosomal compartments within immature DCs, where they are protected from lysosomal degradation in a manner similar to that demonstrated for HIV-1. Lewis X antigen, another ligand of DC-SIGN, was internalized to lysosomes, demonstrating that the internalization pathway of DC-SIGN-captured ligands may depend on the structure of the ligand. Our results suggest that HCV may target DC-SIGN to "hide" within DCs and facilitate viral dissemination. L-SIGN, expressed by THP-1 cells, internalized HCV particles into similar nonlysosomal compartments, suggesting that L-SIGN on liver sinusoidal endothelial cells may capture HCV from blood and transmit it to hepatocytes, the primary target for HCV. We therefore conclude that both DCs and liver sinusoidal endothelial cells may act as reservoirs for HCV and that the C-type lectins DC-SIGN and L-SIGN, as important HCV receptors, may represent a molecular target for clinical intervention in HCV infection.
Micro and macromechanical observation of polycrystalline NiTi using in situ optical microscopy (2003)

An experimental investigation of the micro and macromechanical transformation behavior of binary NiTi was undertaken using in situ optical microscopy. Special attention was paid to macroscopic banding, variant microstructure, effects of cyclic loading, strain rate and temperature effects. The experiments were accomplished with a custom-built loading stage designed to allow simultaneous loading and viewing of transformation behavior on the specimen surface with an optical microscope. The results show clearly that martensitic transformation occurs throughout the material at all strain levels. Macroscopic bands are regions of more intense transformation, but areas outside the bands are not martensite-free. The bands themselves are shown to contain regions (stripes) of higher and lower transformation, especially in the earlier transformation stages. Even at full transformation of the specimen, our results show that a polycrystalline NiTi material is far from being 100 % martensitic. Low level cyclic loading of the NiTi specimens was also pursued which revealed significant microstructural changes in the material after as few as 10 cycles. Furthermore was observed that the variants activated remained the same at the various strain rates tested, however at the highest strain rate possible in our set-up, small redistributions of martensitic plates within grains were seen after loading.
A two photon Microscopy study of raft membranes from rat kidney proximal tubular cells reconstituted into giant unilamellar vesicles (GUVs) (2003)

Melanie A Cheng, Luis A Bagatolli, Hubert K Zajicek, Nabil Halaihel, Moshe Levi, Enrico Gratton, and William W Mantulin. A two photon microscopy study of raft membranes from rat kidney proximal tubular cells reconstituted into Giant Unilamellar Vesicles (GUVs). 47th Annual Meeting of the Biophysical Society, San Antonio, Texas, 2003. Biophys J. 2003; 84(2), 914-Pos/B166. Abstract, Internal PDF Rafts are discrete regions in the plasma membrane that are believed to function as platforms for protein and lipid transport. This research aims to study the structure of rat renal proximal tubular cell membranes using techniques used in characterizing artificial membranes. The study involves the direct visualization of GUVs formed from raft fractions of integral rat kidney brush border membranes obtained through detergent extraction with Triton X-100 at 4C. Imaging of GUVs obtained from detergent resistant membranes (DR) labeled with the fluorescent probe Laurdan using two-photon scanning microscopy resulted in fluorescence intensity images showing an even distribution of Laurdan at physiological temperatures. No domain formation was observed in the DR membranes, whereas membrane domains were clearly present in intact brush border membranes. Membrane fluidity was characterized in terms of Laurdan Generalized Polarization (GP) function and was observed to be in a fairly rigid phase across the temperature range in which the DR GUVs were observed (42°-20°C), which is consistent with the characterization of rafts as regions in the membrane in the liquid ordered phase.
Dynamics of epigenetic regulation at the single-cell level (2016)

Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory.
Patrimonio bibliográfico y documental de la Universidad Complutense de Madrid: Presentación del portal Singularis. Madrid, 18 de enero de 2012 (2012)

El Patrimonio bibliografico y documental de la Universidad Complutense de Madrid es uno de sus valores estrategicos mas relevantes. • Exige el cumplimiento de una responsabilidad social de salvaguarda y difusion que la diferencia del resto de las colecciones.Incluye: manuscritos, incunables, impresos antiguos producidos de forma manual (hasta 1830), grabados, libros de especial reserva del siglo XIX y XX, archivos personales e institucionales y fondos de especial valor. • Se custodia: en la Biblioteca Historica de la Universidad Complutense, y tambien en las bibliotecas de centros y otros depositos que determine la Direccion de la Biblioteca.
Induction of vasculogenesis and hematopoiesis in vitro (1992)

Despite a large number of investigations of embryonic vascular development, in particular in avian embryos, the conditions under which the endothelial and hematopoietic cell lineages emerge remain unknown. As we demonstrate here, both endothelial and hematopoietic cells can be induced by treatment of dissociated quail epiblast with fibroblast growth factors in vitro. These cells aggregate in characteristic blood islands. In long-term culture, the induced endothelial cells gave rise to vascular structures in vitro, i.e. vasculogenesis. No induction was observed in the absence of fibroblast growth factors, and other growth factors like TGF-beta, TGF-alpha and EGF were not capable of inducing blood island formation. Thus, the dissociated quail epiblast provides a remarkably simple test system to investigate cell lineage diversification in higher vertebrates.
Aberration-Free Ultrathin Flat Lenses and Axicons at Telecom Wavelengths Based on Plasmonic Metasurfaces (2012)

The concept of optical phase discontinuities is applied to the design and demonstration of aberration-free planar lenses and axicons, comprising a phased array of ultrathin subwavelength-spaced optical antennas. The lenses and axicons consist of V-shaped nanoantennas that introduce a radial distribution of phase discontinuities, thereby generating respectively spherical wavefronts and nondiffracting Bessel beams at telecom wavelengths. Simulations are also presented to show that our aberration-free designs are applicable to high-numerical aperture lenses such as flat microscope objectives.
Warning, Bias May Occur: A Proposed Approach to Detecting Cognitive Bias in Interactive Visual Analytics (2017)

Visual analytic tools combine the complementary strengths of humans and machines in human-in-the-loop systems. Humans provide invaluable domain expertise and sensemaking capabilities to this discourse with analytic models; however, little consideration has yet been given to the ways inherent human biases might shape the visual analytic process. In this paper, we establish a conceptual framework for considering bias assessment through human-in-the-loop systems and lay the theoretical foundations for bias measurement. We propose six preliminary metrics to systematically detect and quantify bias from user interactions and demonstrate how the metrics might be implemented in an existing visual analytic system, InterAxis. We discuss how our proposed metrics could be used by visual analytic systems to mitigate the negative effects of cognitive biases by making users aware of biased processes throughout their analyses.
<title>Architecture of security management unit for safe hosting of multiple agents</title> (1999)

In such growing areas as remote applications in large public networks, electronic commerce, digital signature, intellectual property and copyright protection, and even operating system extensibility, the hardware security level offered by existing processors is insufficient. They lack protection mechanisms that prevent the user from tampering critical data owned by those applications. Some devices make exception, but have not enough processing power nor enough memory to stand up to such applications (e.g. smart cards). This paper proposes an architecture of secure processor, in which the classical memory management unit is extended into a new security management unit. It allows ciphered code execution and ciphered data processing. An internal permanent memory can store cipher keys and critical data for several client agents simultaneously. The ordinary supervisor privilege scheme is replaced by a privilege inheritance mechanism that is more suited to operating system extensibility. The result is a secure processor that has hardware support for extensible multitask operating systems, and can be used for both general applications and critical applications needing strong protection. The security management unit and the internal permanent memory can be added to an existing CPU core without loss of performance, and do not require it to be modified.
Distinctive expression and functions of the type 4 endothelial differentiation gene-encoded G protein-coupled receptor for lysophosphatidic acid in ovarian cancer. (1999)

Endothelial differentiation gene (edg)-encoded G protein-coupled receptors (Edg Rs)-1, -3, and -5 bind sphingosine 1-phosphate (S1P), and Edg-2 and -4 bind lysophosphatidic acid (LPA). Edg Rs transduce signals from LPA and S1P that stimulate ras- and rho-dependent cellular proliferation, enhance cellular survival, and suppress apoptosis. That high levels of LPA in plasma and ascitic fluid of patients with ovarian cancer correlate with widespread invasion suggested the importance of investigating expression and functions of Edg Rs in ovarian cancer cells (OCCs) as compared with nonmalignant ovarian surface epithelial cells (OSEs). Analyses of Edg Rs by semiquantitative reverse transcription-PCR, a radioactively quantified variant of PCR, and Western blots developed with monoclonal antibodies showed prominent expression of Edg-4 R in primary cultures and established lines of OCCs but none in OSEs. In contrast, levels of Edg-2, -3, and -5 were higher in OSEs than OCCs. LPA stimulated proliferation and signaled a serum response element-luciferase reporter of immediate-early gene activation in OCCs but not OSEs, whereas S1P evoked similar responses in both OSEs and OCCs. Pharmacological inhibitors of Edg R signaling suppressed OCC responses to LPA. A combination of monoclonal anti-Edg-4 R antibody and phorbol myristate acetate, which were inactive separately, evoked proliferative and serum response element-luciferase responses of OCCs but not OSEs. Thus the Edg-4 R may represent a distinctive marker of OCC that transduces growth-promoting signals from the high local concentrations of LPA characteristic of aggressive ovarian cancer.