gebhart/patrepeval huggingface dataset:
The effect of concanavalin A on the rat electro-olfactogram. Differential inhibition of odorant response (1987)

When the rat olfactory mucosa is treated with concanavalin A, it subsequently shows diminished sensitivity towards 60% of the 112 odorants tested (as judged by the amplitude of the electro-olfactogram response). Odorants containing four to six carbon atoms tend to show the largest (absolute) diminutions, suggesting a receptor for this kind of odorant, although the structural specificity is weak. The receptor seems to be of particular importance in the detection of thiols, carboxylic acids and hydrocarbons of the above size, since these compounds loose the highest proportion of their original signal. The concanavalin A appears to be binding to the glycan of one or more cell-surface proteins. The binding may be at, or close to, at least one odorant receptor.
The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling (2018)

The Ras-extracellular signal-regulated kinase pathway is critical for controlling cell proliferation, and its aberrant activation drives the growth of various cancers. Because many pathogens produce toxins that inhibit Ras activity, efforts to develop effective Ras inhibitors to treat cancer could be informed by studies of Ras inhibition by pathogens. <i>Vibrio vulnificus</i> causes fatal infections in a manner that depends on multifunctional autoprocessing repeats-in-toxin, a toxin that releases bacterial effector domains into host cells. One such domain is the Ras/Rap1-specific endopeptidase (RRSP), which site-specifically cleaves the Switch I domain of the small GTPases Ras and Rap1. We solved the crystal structure of RRSP and found that its backbone shares a structural fold with the EreA/ChaN-like superfamily of enzymes. Unlike other proteases in this family, RRSP is not a metalloprotease. Through nuclear magnetic resonance analysis and nucleotide exchange assays, we determined that the processing of KRAS by RRSP did not release any fragments or cause KRAS to dissociate from its bound nucleotide but instead only locally affected its structure. However, this structural alteration of KRAS was sufficient to disable guanine nucleotide exchange factor-mediated nucleotide exchange and prevent KRAS from binding to RAF. Thus, RRSP is a bacterial effector that represents a previously unrecognized class of protease that disconnects Ras from its signaling network while inducing limited structural disturbance in its target.
SIRT1 Shows No Substrate Specificity in Vitro (2005)

SIR2 is a key regulator of the aging process in many model organisms. The human ortholog SIRT1 plays a pivotal role in the regulation of cellular differentiation, metabolism, cell cycle, and apoptosis. SIRT1 is an NAD(+)-dependent deacetylase, and its enzymatic activity may be regulated by cellular energy. There is a growing number of known SIRT1 substrates that contain epsilon-acetyl lysine but for which no obvious consensus sequence has been defined. In this study, we developed a novel unbiased method to identify deacetylase sequence specificity using oriented peptide libraries containing acetylated lysine. Following incubation with SIRT1, the subset of deacetylated peptides was selectively captured using a photocleavable N-hydroxysuccinimide (NHS)-biotin linker and streptavidin beads and analyzed using mass spectrometry and Edman degradation. These studies revealed that substrate recognition by SIRT1 does not depend on the amino acid sequence proximate to the acetylated lysine. This result brings us one step closer to understanding how SIRT1 and possibly other protein deacetylases chose their substrate.
Aqueous RAFT Polymerization:  Recent Developments in Synthesis of Functional Water-Soluble (Co)polymers with Controlled Structures (2004)

Reversible addition-fragmentation chain transfer (RAFT) polymerization has been the focus of intensive research over the past few years since this methodology allows the synthetic tailoring of macromolecules with complex architectures including block, graft, comb, and star structures with predetermined molecular weight, terminal functionality, and narrow molecular weight distribution. In this paper we recount significant milestones in achieving controlled free radical homopolymerization and block copolymerization of water-soluble and amphiphilic monomers including nonionic, cationic, anionic, and zwitterionic species. It is shown that under aqueous conditions, control of homopolymerization and further blocking to extend the molecular weight or to produce precisely structured block copolymers require not only careful selection of reagents (initiator, chain transfer agent, and monomer) but also regulation or elimination of hydrolysis of the omega-terminal thiocarbonylthio functionality. The technological potential of such systems is illustrated for the stimuli (pH) reversible micellization of amphiphilic block copolymers and for stabilization and stimuli responsive aggregation of gold nanoparticles bearing covalently tethered co(polymers). Given the advantages of RAFT over other controlled free radical techniques for preparation of water-soluble architectures, it may be anticipated that this technology will be at the forefront of nano- and microscale self-assembly in electronics and biotechnology.
Controllable Monodisperse Multiple Emulsions (2007)

A drop within a drop within a drop: A microfluidic technique is used to generate highly controlled multiple emulsions (see picture). The high degree of control and scalability afforded by this method makes it a flexible and promising route for engineering designer emulsions and microcapsules with multiphase structures. Moreover, its generality will enable fabrication of novel materials containing complex internal structures. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701358_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Thematic review series: The Immune System and Atherogenesis. The role of natural antibodies in atherogenesis (2005)

Atherosclerosis is now widely recognized as a chronic inflammatory disease that involves innate and adaptive immune responses. Both cellular and humoral components of the immune system have been implicated in atherogenesis. Natural antibodies can be considered humoral factors of innate immunity, and their functional role in health and disease has been reexamined in recent years. Natural antibodies exhibit a remarkably conserved repertoire that includes a broad specificity for self-antigens. For this reason, they are believed to be a product of natural selection and have been suggested to play an important role in "housekeeping" functions. Recent evidence has revealed that oxidation-specific epitopes are important and maybe immunodominant targets of natural antibodies, suggesting an important function for these antibodies in the host response to consequences of oxidative stress, for example, to the oxidative events that occur when cells undergo apoptosis. This review will focus on these recent findings and discuss the emerging evidence for an important role of natural antibodies in atherogenesis.
Nucleotide Sequence of the Uricase Gene from Bacillus sp. TB-90 (1996)

The nucleotide sequence of the uricase gene from the thermophilic bacterium Bacillus sp. TB-90 was determined. The primary structure of the uricase deduced from the nucleotide sequence comprised 332 amino acids, with a total molecular mass of 37,994 Da. The molecular mass of the subunit of the uricase produced by the transformant of Escherichia coli agreed well with this value. However, the molecular mass of a subunit of the uricase produced by Bacillus sp. TB-90 was found to be 34,000 Da by SDS-PAGE. The difference between these molecular masses was attributed to processing of the C-terminal 13 amino acid residue in Bacillus sp. TB-90. Comparison of the enzymatic properties of both uricases showed that the thermostability of the uricase produced by the transformant was enhanced by about 10 degrees C in comparison to that produced by Bacillus sp. TB-90.
Next-generation sequencing identifies contribution of both class I and II HLA genes on susceptibility of multiple sclerosis in Japanese (2019)

We identified HLA variants associated with the risk of MS and NMOSD. Our study contributes to the understanding of the genetic architecture of MS and NMOSD in the Japanese population.
GMSK Modulation for Digital Mobile Radio Telephony (1981)

This paper is concerned with digital modulation for future mobile radio telephone services. First, the specific requirements on the digital modulation for mobile radio use are described. Then, premodulation Gaussian filtered minimum shift keying (GMSK) with coherent detection is proposed as an effective digital modulation for the present purpose, and its fundamental properties are clarified with the aid of machine computation. The constitution of modulator and demodulator is then discussed from the viewpoints of mobile radio applications. The superiority of this modulation is supported by some experimental test results.
Na+/K+-ATPase regulation in Dahl salt-sensitive and salt-resistant rats. (1988)

Circulating Na+/K+-ATPase inhibitors have been implicated in volume-expanded forms of hypertension. Inhibition of vascular smooth muscle cell Na+/K+-ATPase has been demonstrated to elevate intracellular Ca2+ levels and enhance contractility, thus providing a mechanism of raised peripheral resistance. In cells chronically subjected to Na+/K+-ATPase inhibition, however, new Na+/K+-ATPase molecules are synthesized, which then restore the intracellular milieu to preinsult conditions. Restoral of the preinsult intracellular milieu in vascular smooth muscle cells would then be expected to lead to the reduction of muscle cell contractility and peripheral resistance. Thus circulating Na+/K+-ATPase inhibitors may not be effective in eliciting chronic forms of hypertension unless the target cell "homeostatic response" is impaired. We demonstrate an apparent such impairment in Dahl salt-sensitive rats, a genetic model of salt-sensitive hypertension.
The effect of vagus nerve stimulation upon vulnerability of the canine ventricle: role of sympathetic-parasympathetic interactions. (1975)

The effect of vagus nerve stimulation (VNS) upon ventricular vulnerability was studied in 30 mongrel dogs subjected to varying levels of adrenergic stimulation. Vulnerability was assessed both by determining the minimum current required to produce ventricular fibrillation (VF threshold) and by plotting VF threshold throughout the vulnerable period (VF zone). Chloralose-anesthetized animals were studied by means of sequential pulses applied to the apex of the right ventricular endocardium. Testing was carried out in closed-chest dogs, in open-chest dogs with and without left stellate ganglion stimulation (LSGS), and in open- and closed-chest dogs pretreated with propranolol. In the absence of adrenergic stimulation. VNS was without significant effect on either the VF threshold or the VF zone under closed- or open-chest conditions. During LSGS, however, VNS was associated with a 93 +/- 22% (mean +/- SE) increase in VF threshold (P less than 0.01) and constriction of the VF zone. Vagus nerve stimulation combined with LSGS raised VF threshold to the control value, but not beyond. After beta-adrenergic blockade with propranolol, VNS was without effect on VF threshold in either open- or closed-chest animals. It is concluded that augmented sympathetic tone is a precondition for a VNS-induced elevation in VF threshold. The vagal effect is indirect and is expressed by opposing the effects of heightened adrenergic tone on ventricular vulnerability.
Patterning organic–inorganic thin-film transistors using microcontact printed templates (2001)

We report the simple, low-cost, and parallel fabrication of patterned organic–inorganic thin-film transistors (TFTs) by microcontact printing a molecular template on the substrate surface prior to film deposition. We printed molecules with hydrophobic tail groups on the gate oxide surfaces of TFTs to chemically, differentiate the substrate surface and confine the self-assembly of thin films, deposited from solutions flooded across the entire surface, to the transistor channels. TFTs are fabricated with good device characteristics and no current leakage. This process is more general to the patterning of other solution-deposited thin-film materials.
Visual sensing of continuum robot shape using self-organizing maps (2010)

Shape control of continuum robots requires a means of sensing the the curved shape of the robot. Since continuum robots are deformable, they take on shapes that are general curves in space, which are not fully defined by actuator positions. Vision-based shape-estimation provides a promising avenue for shape-sensing. While this is often facilitated by fiducial markers, sometimes fiducials are not feasible due to either the robot's application or its size. To address this, we present a robust and efficient stereo-vision-based, shape-sensing algorithm for continuum robots that does not rely on fiducials or assume orthogonal camera placement. The algorithm employs self-organizing maps to triangulate three-dimensional backbone curves. Experiments with an object with a known shape demonstrate an average accuracy of 1.53 mm on a 239 mm arc length curve.
A Fast Binary Logarithm Algorithm [DSP Tips & Tricks (2010)

This article presents a computationally fast algorithm for computing logarithms. The algorithm is particularly well suited for implementation using fixed-point processors.
Increased PMN adherence on endothelial cells after hypoxia: involvement of PAF, CD18/CD11b, and ICAM-1 (1993)

Ischemia is a well-known situation occurring in several diseases. There is a large body of evidence for the accumulation of neutrophils in the microvascular injury and the transformation of ischemic tissue into an inflammatory territory. However, the molecular mechanisms underlying this phenomenon are still poorly understood. The effects of hypoxia were investigated on human umbilical vein endothelial cells (HUVEC) in culture, and a very strong activation of these cells was obtained with an induction of the platelet-activating factor (PAF) synthesis which was optimal after 90 min of hypoxia. PAF was chemically identified by gas chromatography-mass spectrometry. Along with incubation under hypoxia, a constant increase in the adherence of unstimulated human polymorphonuclear neutrophils (PMN) to endothelial cells was observed. The role of PAF and of adhesion glycoproteins in this hypoxia-induced neutrophil adherence to HUVEC was then assessed. The adherence was mediated by PAF after 90 min of hypoxia as indicated by the inhibition obtained with PAF receptor antagonists and with PAF synthesis inhibition. When tested on HUVEC incubated for 120 min under hypoxia, PAF antagonists could not inhibit the PMN adherence, whereas inhibition of PAF during hypoxia could block the process, suggesting a role of PAF acting as a second messenger. In addition, the inhibitory effects obtained using monoclonal antibodies indicate that this increased adherence was also mediated by intracellular adhesion molecule 1 on HUVEC and by CD18/CD11b on neutrophils. GMP-140 seems also to be involved after 90 min hypoxia but not after 120 min hypoxia, which correlated well with the presence of PAF.(ABSTRACT TRUNCATED AT 250 WORDS)
INTERFEROME: the database of interferon regulated genes (2008)

INTERFEROME is an open access database of types I, II and III Interferon regulated genes (http://www.interferome.org) collected from analysing expression data sets of cells treated with IFNs. This database of interferon regulated genes integrates information from high-throughput experiments with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information to enable a detailed investigation of the molecular mechanisms underlying IFN biology. INTERFEROME fulfils a need in infection, immunity, development and cancer research by providing computational tools to assist in identifying interferon signatures in gene lists generated by high-throughput expression technologies, and their potential molecular and biological consequences.
Enhancement of radiation response of prostatic carcinoma by taxol: therapeutic potential for late-stage malignancy. (1995)

Radiation therapy for advanced prostate cancer has dose-limiting complications and often results in limited tumor control. A combination of radiation and taxol, a potential radiation sensitizer, may enhance therapeutic efficacy at currently used individual doses. Human prostatic carcinoma lines in vitro, and Dunning rat prostatic adenocarcinoma in vivo, were treated with taxol and radiation individually, and in combination. Cytotoxicity of taxol was comparable between androgen sensitive and insensitive lines, with 50% growth inhibition at 9.6 to 12.7 nM. Combining agents increased cytotoxicity, with a dose modifying ratio of 1.8 at 0.1% survival. Flow cytometry showed an enhancement of radiation toxicity associated with taxol-induced cell cycle phase arrest at G2/M. Injection of taxol (4 mg/kg/day x 5), radiation dose fractionation (1.5 Gy/day x 5) and their combination significantly delayed Dunning tumor growth. Adverse side effects were minimal. The results imply that combination of these agents may have clinical potential in prostate cancer treatment.
Generation of Knockout Rats with X-Linked Severe Combined Immunodeficiency (X-SCID) Using Zinc-Finger Nucleases (2010)

The efficient and rapid generation of gene knockout rats shows that using ZFN technology is a new strategy for creating gene-targeted rat models of human diseases. In addition, the X-SCID rats that were established in this study will be valuable in vivo tools for evaluating drug treatment or gene therapy as well as model systems for examining the treatment of xenotransplanted malignancies.
New amber mutation in a beta-thalassemic gene with nonmeasurable levels of mutant messenger RNA in vivo. (1988)

We have identified a beta-thalassemia gene that carries a novel nonsense mutation in a Chinese patient. This mutation, a G to T substitution at the first position of codon 43, changes the glutamic acid coding triplet (GAG) to a terminator codon (TAG). Based on oligonucleotide hybridization studies of 78 Chinese and Southeast Asian beta-thalassemia chromosomes, we estimate that this mutation accounts for a small minority of the beta-thalassemia mutations in that population. Study of the expression of this cloned gene in a transient expression system demonstrated a 65% decrease in levels of normally spliced mutant beta-globin mRNA. However, the study of reticulocyte RNA isolated from an individual heterozygous for this mutation demonstrated a total absence of this mutant mRNA in vivo. The basis for this big discrepancy between the level of accumulated mRNA in vivo and in vitro is probably the result of differences in the stabilities of the mutant mRNA in erythroid cells.
PREVENTION OF REJECTION OF ALLOGENEIC BONE MARROW TRANSPLANTS BY NK 1.1 ANTISERUM (1983)

We have studied the effect of in vivo administration of NK 1.1 antiserum on two functions of natural killer (NK) cells: (A) in vitro cytotoxicity of B6 mice to T cell lymphoma, YAC-1, and (B) potential of B6 mice to reject allogeneic BALB/c bone marrow transplants. We demonstrated that a single i.v. injection of 0.4 ml of NK 1.1 antiserum significantly reduced in vitro NK cell cytotoxic potential and concomitantly prevented rejection of allogeneic bone marrow transplants. NK 1.1 antiserum was effective in diminishing both of these functions when injected 2, 6, or 24 hr before transplantation and NK cell assay, but it was ineffective when given 48 hr before transplantation or the NK cell test. As a specificity control, we investigated the effect of specific anti-T-cell-directed monoclonal antibodies, Thy 1.2 and Lyt 2.2, in the same systems. Neither of these antibodies exerted any effect on NK cell cytotoxicity to YAC-1 or rejection of allogeneic bone marrow transplants. These studies indicate that NK cells represent one of the major components of the mechanism of bone marrow graft rejection.
Trichome Management to Enhance Camptothecins in Camptotheca Decaisne (2014)

Inducible chemical defenses of plants have received much attention in the last three decades, and these defenses often involve trichomes. It is known that some plant secondary metabolites may accumulate in trichomes which can protect plants from damage by herbivores. However, studies on plant trichomes are largely limited to some major vegetable or cash crops and model species with large glandular trichomes (e.g., Nictotiana and Arabidopsis). In fact, the existing studies on the effect of damage (pruning or defoliation) on trichome density or chemical production in plants are partial and even contradictory. Management strategies to maximize chemical induction in medicinal plants or pharmaceutical crops have not been developed well. Our experiments showed that camptothecins (CPTs) are primarily accumulated in glandular trichomes in Camptotheca. We found that pruning, particularly decapitation pruning (T-pruning) can effectively induce contents and derivatization of CPTs in Camptotheca, and the leveled CPTs caused induced endogenous autotoxicity (abnormal morphogenesis) in the plants. Auxin reduction is a trigging factor for such induced biosynthesis and endogenous autotoxicity. Because trichomes are visible to the naked eye and can be much more easily targeted and measured than CPTs, the term "Trichome Management" is used for strategy development to induce CPTs in Camptotheca.
Effects of long-term PPI treatment on producing bowel symptoms and SIBO (2010)

Prolonged PPI treatment may produce bowel symptoms and SIBO; therefore, the strategy of step-down or on-demand PPI therapy should be encouraged in GERD.
Hepatic molecular effects of rosiglitazone in human non‐alcoholic steatohepatitis suggest long‐term pro‐inflammatory damage (2013)

In NASH patients, hepatic PPAR-γ induction by rosiglitazone was associated with increased hepatic expression of pro-inflammatory genes which may explain the lack of long-term histological benefit shown in human studies with this drug. It is unclear whether these results are a class effect of PPAR-γ agonists or a specific effect of rosiglitazone.
Shielding Strategies for Human Space Exploration (1997)

A group of twenty-nine scientists and engineers convened a 'Workshop on Shielding Strategies for Human Space Exploration' at the Lyndon B. Johnson Space Center in Houston, Texas. The provision of shielding for a Mars mission or a Lunar base from the hazards of space radiations is a critical technology since astronaut radiation safety depends on it and shielding safety factors to control risk uncertainty appear to be great. The purpose of the workshop was to define requirements for the development and evaluation of high performance shield materials and designs and to develop ideas regarding approaches to radiation shielding. The workshop was organized to review the recent experience on shielding strategies gained in studies of the 'Space Exploration Initiative (SEI),' to review the current knowledge base for making shield assessment, to examine a basis for new shielding strategies, and to recommend a strategy for developing the required technologies for a return to the moon or for Mars exploration. The uniqueness of the current workshop arises from the expected long duration of the missions without the protective cover of the geomagnetic field in which the usually small and even neglected effects of the galactic cosmic rays (GCR) can no longer be ignored. It is the peculiarity of these radiations for which the inter-action physics and biological action are yet to be fully understood.