gebhart/patrepeval huggingface dataset:
Analysis of TLR4 Polymorphic Variants: New Insights into TLR4/MD-2/CD14 Stoichiometry, Structure, and Signaling (2006)

TLR4 is the signal-transducing receptor for structurally diverse microbial molecules such as bacterial LPS, respiratory syncytial virus fusion (F) protein, and chlamydial heat shock protein 60. Previous studies associated two polymorphic mutations in the extracellular domain of TLR4 (Asp(299)Gly and Thr(399)Ile) with decreased LPS responsiveness. To analyze the molecular basis for diminished responsiveness, site-specific mutations (singly or coexpressed) were introduced into untagged and epitope (Flag)-tagged wild-type (WT) TLR4 expression vectors to permit a direct comparison of WT and mutant signal transduction. Coexpression of WT TLR4, CD14, and MD-2 expression vectors in HEK293T cells was first optimized to achieve optimal LPS-induced NF-kappaB reporter gene expression. Surprisingly, transfection of cells with MD-2 at high input levels often used in the literature suppressed LPS-induced signaling, whereas supraoptimal CD14 levels did not. Under conditions where WT and polymorphic variants were comparably expressed, significant differences in NF-kappaB activation were observed in response to LPS and two structurally unrelated TLR4 agonists, chlamydial heat shock protein 60 and RSV F protein, with the double, cosegregating mutant TLR4 exhibiting the greatest deficiency. Overexpression of Flag-tagged WT and mutant vectors at input levels resulting in agonist-independent signaling led to equivalent NF-kappaB signaling, suggesting that these mutations in TLR4 affect appropriate interaction with agonist or coreceptor. These data provide new insights into the importance of stoichiometry among the components of the TLR4/MD-2/CD14 complex. A structural model that accounts for the diminished responsiveness of mutant TLR4 polymorphisms to structurally unrelated TLR4 agonists is proposed.
Effects of Pulsed Nd:YAG Laser on the Surface of Rabbit Retina (1991)

Six albino rabbits were subjected to pulsed Nd:YAG laser irradiation to the retinal surface to determine whether such treatment would lead to proliferative vitreoretinopathy. Choroidal, retinal, and preretinal hemorrhages, noted at the time of treatment, resolved after 7 to 10 days. Histological examination showed no signs of anterior segment damage or proliferative vitreoretinopathy. These preliminary findings suggest that more extensive experimentation is warranted to determine if pulsed Nd:YAG laser may in fact safely be used to separate vitreoretinal adhesions in the treatment of retinal detachment.
Functional Properties of Human Embryonic Stem Cell–Derived Cardiomyocytes: Intracellular Ca2+ Handling and the Role of Sarcoplasmic Reticulum in the Contraction (2005)

Since cardiac transplantation is limited by the small availability of donor organs, regeneration of the diseased myocardium by cell transplantation is an attractive therapeutic modality. To determine the compatibility of human embryonic stem cell-derived cardiomyocytes (hESC-CMs) (7 to 55 days old) with the myocardium, we investigated their functional properties regarding intracellular Ca2+ handling and the role of the sarcoplasmic reticulum in the contraction. The functional properties of hESC-CMs were investigated by recording simultaneously [Ca2+]i transients and contractions. Additionally, we performed Western blot analysis of the Ca2+-handling proteins SERCA2, calsequestrin, phospholamban, and Na+/Ca2+ exchanger (NCX). Our major findings are, first, that hESC-CMs displayed temporally related [Ca2+]i transients and contractions, negative force-frequency relations, and lack of post-rest potentiation. Second, ryanodine, thapsigargin, and caffeine did not affect the [Ca2+]i transient and contraction, indicating that at this developmental stage, contraction depends on transsarcolemmal Ca2+ influx rather than on sarcoplasmic reticulum Ca2+ release. Third, in agreement with the notion that a voltage-dependent Ca2+ current is present in hESC-CMs and contributes to the mechanical function, verapamil completely blocked contraction. Fourth, whereas hESC-CMs expressed SERCA2 and NCX at levels comparable to those of the adult porcine myocardium, calsequestrin and phospholamban were not expressed. Our study shows for the first time that functional properties related to intracellular Ca2+ handling of hESC-CMs differ markedly from the adult myocardium, probably due to immature sarcoplasmic reticulum capacity.
A low-cost high-performance CMOS timing vernier for ATE (2002)

Current conditions within the test industry impose a difficult combination of design requirements for the next generation of General Purpose Automatic Test Equipment: faster devices require higher tester bandwidth, higher data rates, and higher timing edge accuracy; yet, lower device selling prices and industry economics require lower ATE acquistion and maintenance costs. Emitter Coupled Logic (ECL) based timing systems can achieve high performance, but are expensive and power hungry. The use of CMOS-based ATE has become necessary in order to meet the lower-power and higher integration demands associated with lower cost. However methods of dealing with the high variability of a CMOS process and with the high temperature and voltage dependence of CMOS are required. A new timing vernier combining two different stabilization techniques has been developed using a 0.5 micron process which achieves high performance at low power and low cost.
Use of selective annealing for growing very large grain silicon on insulator films (1982)

The selective annealing technique (laser annealing under a patterned antireflecting coating) has been successfully applied to the growth of very large (20×400 μm) silicon single crystals on SiO2. The grain boundary location is controlled by a conventional lithography step, and the grains obtained have a nearly perfect rectangular shape.
The Programmer as Player: Uncovering Latent Forms of Digital Play Using Structuration and Actor-Network Theory (2014)

Is programming a game considered play? Normally we would say that it is not; play happens when a game is consumed, not when it is produced. But by adopting this perspective we are falling into the trap that popular culture and mass media set when they categorize games as just another entertainment product. What, then, is the true purpose of this division between programming and play? Why do we seem them as different?

In this article, I will explore the early history of computer gaming to show how this dichotomy came about. As it turns out, the computer engineers who worked with the earliest computer systems must shoulder much of the blame. Those programmers who created games such as Spacewar identified themselves as proto-hackers, standing a distance apart from those engaged in more serious computer work. Engineers such as Douglas Engebart, meanwhile, were thinking about the computer as a tool to solve problems, not a platform for artistic endeavour. These two forces enabled outsiders to consider gaming and programming to be wholly separate activities.

For the purposes of this work, both structuration theory and actor-network theory are employed. I found that each methdology offered fresh insights into these issues, which could then be merged to provide a complete picture of this early era in digital computing.
Mechanisms of transthyretin amyloidogenesis. Antigenic mapping of transthyretin purified from plasma and amyloid fibrils and within in situ tissue localizations. (1994)

Transthyretin (TTR) is the major amyloid fibril protein in senile systemic amyloidosis and in several forms of familial amyloidoses. However, the internal organization of the fibrils is virtually unknown. It is not known whether the structure of the TTR molecules is substantially altered within the fibrils. In this study we used various antigenic mapping procedures to determine whether major antigenic sites differ between normal TTR, ATTR (TTR from amyloid fibrils), and in situ amyloid fibrils. Antigenic mapping was achieved using standard immunological procedures (ie, ELISA, Western blot, and immunohistochemistry), synthetic peptides of the TTR molecule, antisera against these synthetic peptides and against normal TTR, ATTR, and alkali-degraded amyloid fibrils. Our results show that the antigenic sites on normal plasma TTR include the AB loop and the CD loop. The amino acid sequences associated with these loops are present on the outside of the TTR molecule. Antiserum against beta-strand H reacted only with TTR in amyloid fibrils and ATTR but not with normal plasma TTR or TTR in the islets of Langerhans. Our results suggest that there is an altered configuration of TTR within amyloid fibrils when compared with plasma TTR.
SEMA4D compromises blood–brain barrier, activates microglia, and inhibits remyelination in neurodegenerative disease (2014)

Multiple sclerosis (MS) is a chronic neuroinflammatory disease characterized by immune cell infiltration of CNS, blood-brain barrier (BBB) breakdown, localized myelin destruction, and progressive neuronal degeneration. There exists a significant need to identify novel therapeutic targets and strategies that effectively and safely disrupt and even reverse disease pathophysiology. Signaling cascades initiated by semaphorin 4D (SEMA4D) induce glial activation, neuronal process collapse, inhibit migration and differentiation of oligodendrocyte precursor cells (OPCs), and disrupt endothelial tight junctions forming the BBB. To target SEMA4D, we generated a monoclonal antibody that recognizes mouse, rat, monkey and human SEMA4D with high affinity and blocks interaction between SEMA4D and its cognate receptors. In vitro, anti-SEMA4D reverses the inhibitory effects of recombinant SEMA4D on OPC survival and differentiation. In vivo, anti-SEMA4D significantly attenuates experimental autoimmune encephalomyelitis in multiple rodent models by preserving BBB integrity and axonal myelination and can be shown to promote migration of OPC to the site of lesions and improve myelin status following chemically-induced demyelination. Our study underscores SEMA4D as a key factor in CNS disease and supports the further development of antibody-based inhibition of SEMA4D as a novel therapeutic strategy for MS and other neurologic diseases with evidence of demyelination and/or compromise to the neurovascular unit.
Mutations in a Specific Human Serum Albumin Thyroxine Binding Site Define the Structural Basis of Familial Dysalbuminemic Hyperthyroxinemia (1996)

The familial dysalbuminemic hyperthyroxinemia (FDH) phenotype results from a natural human serum albumin (HSA) mutant with histidine instead of arginine at amino acid position 218. This mutation results in an enhanced affinity for thyroxine. Site-directed mutagenesis and a yeast protein expression system were used to synthesize wild type HSA and FDH HSA as well as several other HSA mutants. Studies on the binding of thyroxine to these HSA species using equilibrium dialysis and quenching of tryptophan 214 fluorescence suggest that the FDH mutation affects a single thyroxine binding site located in the 2A subdomain of HSA. Site-directed mutagenesis of HSA and thyroxine analogs were used to obtain information about the mechanism of thyroxine binding to both wild type and FDH HSA. These studies suggest that the guanidino group of arginine at amino acid position 218 in wild type HSA is involved in an unfavorable binding interaction with the amino group of thyroxine, whereas histidine at amino acid position 218 in FDH HSA is involved in a favorable binding interaction with thyroxine. Neither arginine at amino acid position 222 nor tryptophan at amino acid position 214 appears to favorably influence the binding of thyroxine to wild type HSA.
Two regions of the adenovirus early region 1A proteins are required for transformation (1988)

Regions of the adenovirus type 5 early region 1A (E1A) proteins that are required for transformation were defined by using a series of deletion mutants. Deletion mutations collectively spanning the entire protein-coding region of E1A were constructed and assayed for their ability to cooperate with an activated ras oncogene to induce transformation in primary baby rat kidney cells. Two regions of E1A (amino acids 1 to 85 and 121 to 127) were found to be essential for transformation. Deletion of all or part of the region from amino acids 121 to 127 resulted in a total loss of transforming ability. An adjacent stretch of amino acids (residues 128 to 139), largely consisting of acidic residues, was found to be dispensable for transformation but appeared to influence the efficiency of transformation. Amino acids 1 to 85 made up a second region of the E1A protein that was essential for transformation. Deletion of all or part of this region resulted in a loss of the transforming activity. Even a mutation resulting in a single amino acid change at position 2 of the polypeptide chain was sufficient to eliminate transformation. Deletion of amino acids 86 to 120 or 128 to 289 did not eliminate transformation, although some mutations in these regions had lowered efficiencies of transformation. Foci induced by transformation-competent mutants could be expanded into cell lines that retained their transformed morphology and constitutively expressed the mutant E1A proteins.
The nucleotide sequence of the gene encoding GCAT from Aeromonas salmonicida ssp. salmonicida (1996)

Abstract The nucleotide sequence of the gene encoding GCAT (glycerophospholipid: cholesterol acetyltransferase) in Aeromonas salmonicida ssp. salmonicida has been determined. The sequence revealed an open reading frame of 1005 bp encoding 335 amino acids, an 18‐amino‐acid signal peptide and a 317‐amino‐acid mature polypeptide with a deduced molecular mass of 35 380 Da and an estimated pI of 6.25. Within the encoding region, the homology with the corresponding gene from Aeromonas hydrophila was 92.9% for the nucleotide sequence and 93.7% for the deduced amino acid sequence.
AP-1 Repressor Protein JDP-2: Inhibition of UV-Mediated Apoptosis through p53 Down-Regulation (2001)

Members of the AP-1 transcription factor family, especially c-Jun and c-Fos, have long been known to mediate critical steps in the cellular response to ultraviolet (UV) irradiation. We sought to examine whether two newly discovered members of the AP-1 family, JDP-1 and JDP-2, also participate in the mammalian UV response. Here we report that JDP-2, but not JDP-1, is transiently induced upon UV challenge and that elevated levels of JDP-2 increase cell survival following UV exposure. This protective function of JDP-2 appears to be mediated through repression of p53 expression at the transcriptional level, via a conserved atypical AP-1 site in the p53 promoter.
PWT-458, a novel pegylated-17-hydroxywortmannin, inhibits phosphatidylinositol 3-kinase signaling and suppresses growth of solid tumors (2005)

Deregulated phosphatidylinositol 3-kinase (PI3K) signaling pathway is widely implicated in tumor growth and resistance to chemotherapy. While a strong rationale exists for pharmacological targeting of PI3K, only a few proof-of-principle in vivo efficacy studies are currently available. PWT-458, pegylated-17-hydroxywortmannin, is a novel and highly potent inhibitor of PI3K in animal models. Upon in vivo cleavage of its poly(ethyleneglycol) (PEG), PWT-458 releases its active moiety 17-hydroxywortmannin (17-HWT), the most potent inhibitor in its class. Here we show that a single intravenous injection of PWT-458 rapidly inhibited PI3K signaling, as measured by a complete loss of AKT (Ser-473) phosphorylation in xenograft tumors grown in nude mice. Following a daily X5 dosing regimen, PWT-458 demonstrated single-agent antitumor activity in nude mouse xenograft models of U87MG glioma, nonsmall cell lung cancer (NSCLC) A549, and renal cell carcinoma (RCC) A498. Efficacious doses ranged from 0.5 mg/kg to 10 mg/kg, achieving a superior therapeutic index over 17-HWT. PWT-458 augmented anticancer efficacy of a suboptimal dose of paclitaxel against A549 and U87MG tumors. Combination treatment of PWT-458 and an mTOR inhibitor, Pegylated-Rapamycin (Peg-Rapa), resulted in an enhanced antitumor efficacy in U87MG. Finally, PWT-458 in combination with interferon-alpha (Intron-A) caused a dramatic regression of RCC A498, which was not achieved by either agent alone. These studies identify PWT-458 as an effective anticancer agent and provide strong proof-of-principle for targeting the PI3K pathway as novel anticancer therapy.
The Book of Ruth, Nahum, Habakkuk, and Zephaniah (1992)

Reviewed Book: Hubbard, Robert L. The Book of Ruth. Grand Rapids: Eerdmans, 1989. New international commentary on the Old Testament. Reviewed Book: Robertson, O Palmer. The Books of Nahum, Habakkuk, and Zephaniah. Grand Rapids: Eerdmans, 1990. New international commentary on the Old Testament.
Abstract 5507: Toll Like Receptor 4 Activation Elicits Pro-atherogenic Gene Activation In Monocytes In Humans (2008)

Introduction: Inflammatory activation of both circulating blood cells as well as vessel wall cells is a hallmark of atherogenesis. Agonists of the Toll-like receptor 4 pathway, present on white blood cells as well as endothelial cells, have been associated with a pro-atherogenic state. Recently, standardized inflammatory challenge models using lipopolysaccharide (LPS) have been suggested to mimick these atherogenic changes. However, similarity between circulating pathways and ’vessel wall’ pathways need further validation. Therefore, we evaluated the effects of in vivo LPS challenge on circulating monocytes in humans. Methods: A bolus of Escherichia coli endotoxin (LPS 1 ng/kg bodyweight) or NaCl was infused intravenously in healthy male volunteers (n=13). Blood was drawn at 0, 1 and 4 hours after the challenge. The monocytes (CD14+ cells) were isolated using positive MACS selection. Subsequently, mRNA sample extraction using RnaseBee was performed. cDNA was prepared, amplified, labeled and then hybridized onto spotted oligonucleotide microarrays before scanning. Data were analyzed using R-project version 2.2.0. Validation Taqman took place. Results: Following LPS challenge, CD14+ count dropped by 48% in the first hour due to margination of monocytes, followed by normalization at 4 hours. Purity of CD14+ fraction approximated 90%. LPS was associated with upregulation of a series of pro-atherogenic genes (BID, DIPA, FRA-1, HSP27, HSP70, ILRN, MIP-1a, MIP1b, S100A9, SLA1, TIMPS, TLR2), immune system related genes (CLP1, DF, CD45-AP, HLA-DPB1, BATF, C3AR1, CD14) as well as a series of unrelated genes. No genes were differentially expressed during saline control experiments. RT-PCR confirmed upregulation of CD14, SLA1, BATF, C3AR1, MIP-B, TLR-2, VCAN and ILRN. Conclusion: TLR4 activation following LPS challenge is associated with potent activation of monocytic pathways involved in chemotaxis and immune activation. These activation patterns bear great resemblance to those reported in atherogenic vessel wall. It is tempting to speculate that circulating cells (’vulnerable blood’) can be used as a surrogate to detect high-risk vessel wall lesions (vulnerable patient).
Recent advances in the pharmacological control of experimental allergic encephalomyelitis (EAE) and the implications for multiple sclerosis treatment (1995)

The autoimmune, cell-mediated condition experimental allergic encephalomyelitis (EAE) is the representative model for the inflammatory central nervous system disease MS. EAE has been extensively employed to determine the efficacy of pharmacological agents that may be of ultimate use in the treatment of MS. A wide variety of drugs has been examined for activity in EAE but, over the last decade, three groups of compounds have emerged with clear and reproducible ability to modify significantly the onset and progression of the disease. The immunosuppressants, the modulators of catecholamine activity and the antineoplastic agents have convincingly altered the course of EAE and, as a consequence, provided understanding of the mechanisms of disease expression and offered further insight into the pathogenesis of MS. The article stresses the usefulness of EAE as a model to identify prospective pharmacological treatments for MS and, in particular, considers those compounds subsequently assessed for their ability to interfere with the progression of the human disease.
Measuring the Forces that Control Protein Interactions (2000)

▪ Abstract Although the force fields and interaction energies that control protein behavior can be inferred indirectly from equilibrium and kinetic measurements, recent developments have made it possible to quantify directly (a) the ranges, magnitudes, and time dependence of the interaction energies and forces between biological materials; (b) the mechanical properties of isolated proteins; and (c) the strength of single receptor-ligand bonds. This review describes recent results obtained by using the atomic force microscope, optical tweezers, the surface force apparatus, and micropipette aspiration to quantify short-range protein-ligand interactions and the long-range, nonspecific forces that together control protein behavior. The examples presented illustrate the power of force measurements to quantify directly the force fields and energies that control protein behavior.
Ligand-assisted Aggregation of Proteins (2005)

A comprehensive series of solution and crystallographic studies reveal how simple, achiral, bivalent ligands of the cyclic pyruvate of glycerol promote face-to-face complex formation of the pentraxin, serum amyloid P component (SAP) into decamers. SAP, a protein of the human innate immune system, is universally present in amyloids, including cerebral amyloid deposits found in the brain of Alzheimer disease patients. Removal of SAP through a specific aggregation mechanism mediated by multivalent ligands appears to provide therapeutic benefit in the progression of this disease. Crystallographic studies reveal that in our novel series of ligands only the methyl and carboxylate moieties of the pyruvate ketal directly interact with the protein, but the geometric constraints imposed by the tether dictate which of two chair conformations are adopted by the pyruvate dioxane ring. Solution studies, as interpreted through a simple thermodynamic model, account for the distribution of pentameric and decameric bound states at different ligand concentrations and indicate that differences in the flexibility of the tether determine the geometry and stability of the specific aggregates formed between SAP and two different bivalent ligands. The factors affecting the design of ligands promoting face-to-face protein dimerization as well as potential biological implications are discussed.