gebhart/patrepeval huggingface dataset:
The Mechanism of Mineralization and the Role of Alkaline Phosphatase in Health and Disease (2010)

Biomineralization is the process by which hydroxyapatite is deposited in the extracellular matrix. Physiological mineralization occurs in hard tissues, whereas pathological calcification occurs in soft tissues. The first step of mineralization is the formation of hydroxyapatite crystals within matrix vesicles that bud from the surface membrane of hypertrophic chondrocytes, osteoblasts, and odontoblasts. This is followed by propagation of hydroxyapatite into the extracellular matrix and its deposition between collagen fibrils. Extracellular inorganic pyrophosphate, provided by NPP1 and ANKH, inhibits hydroxyapatite formation. Tissue-nonspecific alkaline phosphatase (TNAP) hydrolyzes pyrophosphate and provides inorganic phosphate to promote mineralization. Inorganic pyrophosphate, pyridoxal phosphate, and phosphoethanolamine are thought to be the physiologic substrates of TNAP. These accumulate in the event of TNAP deficiency, e.g., in cases of hypophosphatasia. The gene encoding TNAP is mapped to chromosome 1, consists of 12 exons, and possesses regulatory motifs in the 5'-untranslated region. Inhibition of TNAP enzymatic activity suppresses TNAP mRNA expression and mineralization in vitro. Hypophosphatasia is an inherited systemic bone disease characterized by hypomineralization of hard tissues. The phenotype of hypophosphatasia is varied. To date, more than 200 mutations in the TNAP gene have been reported. Knockout mice mimic the phenotypes of severe hypophosphatasia. Among the mutations in the TNAP gene, c.1559delT is frequent in the Japanese population. This frameshift mutation results in the expression of an abnormally long protein that is degraded in cells. DNA-based prenatal diagnosis using chorionic villus sampling has been developed, but requires thorough genetic counseling. Although hypophosphatasia is untreatable at present, the recent success of enzyme replacement therapy offers promise. The problems presented by impaired mineralization in age-related chronic diseases, such as pathologic calcification and decreasing physiological mineralization are growing in importance. Strategies for preventing pathologic calcification using TNAP and NPP1 are in development. A nutrigenomic approach, based on the relationship between TNAP gene polymorphism and bone mineral density, is also discussed.
Response-Specific and Ligand Dose-Dependent Modulation of Estrogen Receptor (ER) α Activity by ERβ in the Uterus (2003)

Estrogen is of great importance in the regulation of uterine function. The aim of this study was to examine the individual physiological roles of each of the two receptors for estradiol, estrogen receptor (ER) alpha and ERbeta, and their potential comodulatory effects on gene expression and uterine growth using recently developed ER subtype-selective agonist ligands. The use of ER subtype-selective ligands provides an alternative, complementary approach to the use of receptor knockout mice. Administration of the ERalpha-selective ligand propyl pyrazole triol (PPT) to immature mice resulted in a significant increase in uterine weight, as well as bromodeoxyuridine incorporation and proliferating cell nuclear antigen expression in luminal epithelial cells. PPT also increased complement component 3, lactoferrin, and glucose-6-phosphate dehydrogenase (G6PDH), and decreased androgen receptor (AR) and progesterone receptor (PR) mRNA levels in uterine tissue, as did estradiol (E(2)). However, when compared with E(2), PPT was less effective in stimulating uterine weight, complement component 3, and G6PDH expression but was as effective as E(2) in regulating lactoferrin, AR, and PR expression. In contrast to the action of the ERalpha agonist PPT, the ERbeta agonist diarylpropionitrile (DPN) did not increase uterine weight or luminal epithelial cell proliferation at a dose that reduced G6PDH and elicited a decrease in PR and AR mRNA and protein expression. Interestingly, DPN reduced the uterine weight stimulation by PPT, and enhanced the effect of PPT in decreasing uterine PR and AR mRNA. These findings with ER subtype-selective ligands indicate that ERalpha is the major regulator of estrogen function in the uterus, but that ERbeta does exert effects on some uterine markers of estrogen action. In addition, ERbeta can modulate ERalpha activity in a response-specific and dose-dependent manner.
Reversible Burn Injury (1992)

Treatment of the patient with burns has advanced dramatically during the last several decades. Patients with burns that cover a greater percentage of the body surface area are now surviving. Cardiac, pulmonary, and vascular insults are better understood and more adequately treated. Nutritional requirements of the patient with burns can be fulfilled, and physical therapy is providing improved quality of life. In spite of these advances, care of burned tissue has progressed only moderately. The introduction of silver nitrate and other topical antibiotics and early excision significantly improved burn care. Other advances are not in widespread use in spite of research data that detail beneficial alternatives or additions to current therapies. Specifically, reversal of burn injury is possible. The research in this field had progressed considerably to the present. Reversal of dermal vascular occlusion in burned tissue seems to preserve that tissue.
Reduced amino acid content in transgenic potato tubers due to antisense inhibition of the leaf H+/amino acid symporter StAAP1 (2003)

Transport processes across the plasma membrane of leaf vascular tissue are essential for transport and distribution of assimilates. In potato, leaves are the predominant sites for nitrate reduction and amino acid biosynthesis. From there, assimilated amino acids are exported through the phloem to supply tubers with organic nitrogen. To study the role of amino acid transporters in long-distance transport and allocation of organic nitrogen in potato plants, a gene encoding a functional, leaf-expressed amino acid permease StAAP1 was isolated. Similar to the sucrose transporter SUT1, StAAP1 expression was induced during the sink-to-source transition, indicating a role in phloem loading. To test the role of StAAP1, expression was inhibited by an antisense approach. Transgenic plants with reduced StAAP1 expression were phenotypically indistinguishable from wild type, as were photosynthetic capacity and tuber yield. However, tubers from antisense StAAP1 plants showed up to 50% reduction in free amino acid contents. In comparison, starch content was not affected or tended to increase relative to wild type. The reduction in all amino acids except aspartate in the antisense plants is consistent with the properties of amino acid permeases (AAPs) found in heterologous systems. The results demonstrate an important role for StAAP1 in long-distance transport of amino acids and highlight the importance of plasma membrane transport for nutrient distribution in plants.
Dynamic Compartmentalization of Base Excision Repair Proteins in Response to Nuclear and Mitochondrial Oxidative Stress (2008)

DNAs harbored in both nuclei and mitochondria of eukaryotic cells are subject to continuous oxidative damage resulting from normal metabolic activities or environmental insults. Oxidative DNA damage is primarily reversed by the base excision repair (BER) pathway, initiated by N-glycosylase apurinic/apyrimidinic (AP) lyase proteins. To execute an appropriate repair response, BER components must be distributed to accommodate levels of genotoxic stress that may vary considerably between nuclei and mitochondria, depending on the growth state and stress environment of the cell. Numerous examples exist where cells respond to signals, resulting in relocalization of proteins involved in key biological transactions. To address whether such dynamic localization contributes to efficient organelle-specific DNA repair, we determined the intracellular localization of the Saccharomyces cerevisiae N-glycosylase/AP lyases, Ntg1 and Ntg2, in response to nuclear and mitochondrial oxidative stress. Fluorescence microscopy revealed that Ntg1 is differentially localized to nuclei and mitochondria, likely in response to the oxidative DNA damage status of the organelle. Sumoylation is associated with targeting of Ntg1 to nuclei containing oxidative DNA damage. These studies demonstrate that trafficking of DNA repair proteins to organelles containing high levels of oxidative DNA damage may be a central point for regulating BER in response to oxidative stress.
Structure of Tobacco Mosaic Virus at 3.6 Å Resolution: Implications for Assembly (1986)

X-ray fiber diffraction analysis of tobacco mosaic virus (TMV) has led to the building of a molecular model of the intact virus, based on a map at 3.6 A resolution derived from five separated Bessel orders. This has been made possible by advances in the solution of the fiber diffraction phase problem. It is now possible to understand much of the chemical basis of TMV assembly, particularly in terms of intersubunit electrostatic interactions and RNA binding. Consideration of the molecular structure in conjunction with physical chemical studies by several groups of investigators suggests that the nucleating aggregate for initiation of TMV assembly is a short (about two turns) helix of protein subunits, probably inhibited from further polymerization in the absence of RNA by the disordering of peptide loop near the inner surface of the virus.
Gene Fusions of Signal Sequences with a Modified β-Glucuronidase Gene Results in Retention of the β-Glucuronidase Protein in the Secretory Pathway/Plasma Membrane (1997)

Signal sequences and endoplasmic reticulum (ER) retention signals are known to play central roles in targeting and translocation in the secretory pathway, but molecular aspects about their involvement are poorly understood. We tested the effectiveness of deduced signal sequences from various genes (hydroxyproline-rich glycoprotein [HRGP] from Phaseolus vulgaris; Serpin from Manduca sexta) to direct a modified beta-glucuronidase (GUS) protein into the secretory pathway in transgenic tobacco (Nicotiana tabacum L.). The reporter protein was not secreted to the cell wall/extracellular space as monitored using extracellular fluid analysis (low- or high-ionic-strength conditions) but occurred in membranes with a density of 1.16 to 1.20 g/mL. Membrane-bound GUS equilibrated with the plasma membrane (PM) and the ER on linear sucrose gradients with or without ethylenediaminetetraacetic acid, suggesting that GUS associates with the ER and the PM. Confocal microscopy of fixed cultured cells prepared from GUS control and HRGP signal peptide (SP)-GUS-expressing plants suggested only cytosolic localization in GUS-expressing plants but substantial peripheral localization in HRGP SP-GUS plants, which is consistent with GUS being associated with the PM. Aqueous two-phase partitioning of microsomal membranes from HRGP SP-GUS and Serpin SP-GUS transgenic leaves also indicated that GUS activity was enriched in the ER and the PM. These observations, together with hydrophobic moment plot analysis, suggest that properties of the SP-GUS protein result in its retention in the secretory pathway and PM.
Palladium-Catalyzed Cleavage Reaction of Carbon−Carbon Triple Bond with Molecular Oxygen Promoted by Lewis Acid (2008)

A new Lewis acid promoted and palladium-catalyzed cleavage reaction of carbon-carbon triple bond with molecular oxygen was reported, in which alkyne or 1.3-diynes is split into carboxylic ester in various alcohols.
Fidaxomicin versus Vancomycin for Clostridium difficile Infection (2011)

The rates of clinical cure after treatment with fidaxomicin were noninferior to those after treatment with vancomycin. Fidaxomicin was associated with a significantly lower rate of recurrence of C. difficile infection associated with non–North American Pulsed Field type 1 strains. (Funded by Optimer Pharmaceuticals; ClinicalTrials.gov number, NCT00314951.)
Phosphorylated Proteins as Physiological Effectors (1978)

A variety of neurotransmitters, hormones, and other regulatory agents affect the phosphorylation of specific proteins in their target tissues. The types of stimuli that share this common effect on protein phosphorylation include numerous substances that do not act through cyclic AMP. These and other observations suggest that many different classes of regulatory substances achieve certain of their biological effects by altering the phosphorylation of specific proteins.
Prevention and Treatment of Experimental Autoimmune Encephalomyelitis by Soluble CD83 (2004)

CD83 is up-regulated on the surface of dendritic cells (DCs) during maturation and has been widely used as a marker for mature DCs. Recently, we reported the recombinant expression of the extracellular immunoglobulin domain of human CD83 (hCD83ext). Using this soluble form of CD83, allogeneic as well as specific cytotoxic T lymphocyte proliferation could be blocked in vitro. Here we report the functional analysis of soluble CD83 in vivo, using murine experimental autoimmune encephalomyelitis (EAE) as a model. Strikingly, only three injections of soluble CD83 prevented the paralysis associated with EAE almost completely. In addition, even when the EAE was induced a second time, CD83-treated mice were protected, indicating a long-lasting suppressive effect. Furthermore, soluble CD83 strongly reduced the paralysis in different therapeutic settings. Most important, even when the treatment was delayed until the disease symptoms were fully established, soluble CD83 clearly reduced the paralyses. In addition, also when EAE was induced a second time, soluble CD83-treated animals showed reduced disease symptoms. Finally, hCD83ext treatment almost completely reduced leukocyte infiltration in the brain and in the spinal cord. In summary, this work strongly supports an immunosuppressive role of soluble CD83, thereby indicating its therapeutic potential in the regulation of immune disorders in vivo.
Pharmacokinetics of progesterone after its administration to ovariectomized rhesus monkeys by injection, infusion, or nasal spraying. (1982)

The pharmacokinetics of progesterone (dose: 10 microgram per animal) were studied in blood and cerebrospinal fluid of adult ovariectomized rhesus monkeys after the administration of the steroid as an intravenous injection, intravenous infusion (duration of infusion: 10 min), or nasal spray. The bioavailability of progesterone, in terms of area under the time--concentration curve and the maximal concentration in the two body fluids, was significantly higher when the steroid was infused or sprayed intranasally than when it was injected intravenously. The clearance of the steroid from the serum, as estimated by its elimination rate constant, elimination half-life, and total body clearance, did not differ for the three methods of administration. These findings suggest that the bioavailability of progesterone is enhanced by extending the duration over which the steroid is delivered into the hemic circulation.
Serogroup W-135 Meningococcal Disease during the Hajj, 2000 (2003)

An outbreak of serogroup W-135 meningococcal disease occurred during the 2000 Hajj in Saudi Arabia. Disease was reported worldwide in Hajj pilgrims and their close contacts; however, most cases were identified in Saudi Arabia. Trends in Saudi meningococcal disease were evaluated and the epidemiology of Saudi cases from this outbreak described. Saudi national meningococcal disease incidence data for 1990 to 2000 were reviewed; cases from January 24 to June 5, 2000, were retrospectively reviewed. The 2000 Hajj outbreak consisted of distinct serogroup A and serogroup W-135 outbreaks. Of 253 identified cases in Saudi Arabia, 161 (64%) had serogroup identification; serogroups W-135 and A caused 93 (37%) and 60 (24%) cases with attack rates of 9 and 6 cases per 100,000 population, respectively. The 2000 Hajj outbreak was the first large serogroup W-135 meningococcal disease outbreak identified worldwide. Enhanced surveillance for serogroup W-135, especially in Africa, is essential to control this emerging epidemic disease.
Simple and Table Feline: Fast Elliptical Lines for Anisotropic Texture Mapping (1999)

Research group. Our focus is research on information technology that is relevant to the technical strategy of the Corporation and has the potential to open new business opportunities. Research at WRL ranges from Web search engines to tools to optimize binary codes, from hardware and software mechanisms to support scalable shared memory paradigms to graphics VLSI ICs. As part of WRL tradition, we test our ideas by extensive software or hardware prototyping. We publish the results of our work in a variety of journals, conferences, research reports and technical notes. This document is a research report. Research reports are normally accounts of completed research and may include material from earlier technical notes, conference papers, or magazine articles. We use technical notes for rapid distribution of technical material; usually this represents research in progress. You can retrieve research reports and technical notes via the World Wide Web at:
Procedural Modeling Using Autoencoder Networks (2015)

Procedural modeling systems allow users to create high quality content through parametric, conditional or stochastic rule sets. While such approaches create an abstraction layer by freeing the user from direct geometry editing, the nonlinear nature and the high number of parameters associated with such design spaces result in arduous modeling experiences for non-expert users. We propose a method to enable intuitive exploration of such high dimensional procedural modeling spaces within a lower dimensional space learned through autoencoder network training. Our method automatically generates a representative training dataset from the procedural modeling rule set based on shape similarity features. We then leverage the samples in this dataset to train an autoencoder neural network, while also structuring the learned lower dimensional space for continuous exploration with respect to shape features. We demonstrate the efficacy our method with user studies where designers create content with more than 10-fold faster speeds using our system compared to the classic procedural modeling interface.
A Single Domain in Human DNA Polymerase ι Mediates Interaction with PCNA: Implications for Translesion DNA Synthesis (2005)

DNA polymerases (Pols) of the Y family rescue stalled replication forks by promoting replication through DNA lesions. Humans have four Y family Pols, eta, iota, kappa, and Rev1, of which Pols eta, iota, and kappa have been shown to physically interact with proliferating cell nuclear antigen (PCNA) and be functionally stimulated by it. However, in sharp contrast to the large increase in processivity that PCNA binding imparts to the replicative Pol, Poldelta, the processivity of Y family Pols is not enhanced upon PCNA binding. Instead, PCNA binding improves the efficiency of nucleotide incorporation via a reduction in the apparent K(m) for the nucleotide. Here we show that Poliota interacts with PCNA via only one of its conserved PCNA binding motifs, regardless of whether PCNA is bound to DNA or not. The mode of PCNA binding by Poliota is quite unlike that in Poldelta, where multisite interactions with PCNA provide for a very tight binding of the replicating Pol with PCNA. We discuss the implications of these observations for the accuracy of DNA synthesis during translesion synthesis and for the process of Pol exchange at the lesion site.
Functionalized Graphene Sheet Colloids for Enhanced Fuel/Propellant Combustion (2009)

We have compared the combustion of the monopropellant nitromethane with that of nitromethane containing colloidal particles of functionalized graphene sheets or metal hydroxides. The linear steady-state burning rates of the monopropellant and colloidal suspensions were determined at room temperature, under a range of pressures (3.35-14.4 MPa) using argon as a pressurizing fluid. The ignition temperatures were lowered and burning rates increased for the colloidal suspensions compared to those of the liquid monopropellant alone, with the graphene sheet suspension having significantly greater burning rates (i.e., greater than 175%). The relative change in burning rate from neat nitromethane increased with increasing concentrations of fuel additives and decreased with increasing pressure until at high pressures no enhancement was found.
Redox-Dependent Regulation of the Conformation and Function of Human Heat Shock Factor 1 (2002)

We present here evidence that redox-dependent thiol-disulfide exchange can provide a mechanism regulating the conformation and activity of the human heat shock transcription factor 1 (HSF1). Diamide and dithiothreitol were reagents used respectively to promote and reverse disulfide cross-link, and the resolution and detection of redox conformers of HSF1 were done according to recently published methods [Manalo, D. J., and Liu, A. Y.-C. (2001) J. Biol. Chem. 276, 23554-23561]. We showed that preincubation of the latent HSF1 monomer with diamide inhibited the in vitro heat-induced activation and trimerization of HSF1 and caused the formation of ox-hHSF1, a compact, disulfide cross-linked HSF1 conformer detectable in immuno-Western blot assay. These effects of diamide were dose-dependent and were rapidly and quantitatively reversed by dithiothreitol. Cysteine site-specific mutants of HSF1 were constructed and used to determine which of the five cysteine residues may be engaged in disulfide cross-link. Analysis of the in vitro transcribed and translated HSF1 proteins showed that while mutation of C1 (amino acid 36) and C2 (amino acid 103) had no effect on the redox sensitivity of HSF1, the mutation of C3 (amino acid 153) or double mutation of C4 and C5 (amino acids 373 and 378, respectively) to serine rendered HSF1 insensitive to diamide and prevented its conversion to ox-HSF1. HSF1 with a single cysteine to serine mutation at either the C4 or C5 position gave different ox-HSF1 conformers in the presence of diamide, suggesting that C3 could be disulfide cross-linked to either C4 or C5. The possibility that HSF1 may have integrated redox chemistry of cysteine sulfhydryl into its functional response in higher mammalian cells is discussed.
Implantable Neural Signal Amplifier for Epileptic Seizure Prediction (2012)

Abstract This paper deals with the design of low power low noise Neural signal amplifier for Epileptic Seizure Prediction. The advent of Micro-electro Arrays has driven the need for implantable electronic circuitry to detect those Extracellular neural signals(ENG). We proposed a preamplifier of fully differential LNA with gm boosting in order to enhance the gain as well as reduce the power consumption. Low frequency high pass function has been realized with anti-parallel Diode connected PMOS. Simulation results shows that the input referred noise is 1.24uVrms from 100Hz to 5KHz, mid-band voltage gain of 44.6dB and the power consumption is 18.24uw. The results are validated using Cadence spectre simulator with 180nm technology. Inductive coupled rail-to-rail power supply circuits are discussed with a rectifier circuits. Simulation results shows that this implantable amplifier is suitable for Epileptic seizure prediction.