gebhart/patrepeval huggingface dataset:
Locally Applied Leptin Induces Regional Aortic Wall Degeneration Preceding Aneurysm Formation in Apolipoprotein E–Deficient Mice (2012)

Leptin is locally synthesized in human AAA wall. Paravisceral aortic leptin in ApoE(-/-) mice induces local medial degeneration and augments angiotensin II-induced AAA, thus suggesting novel mechanistic links between leptin and AAA formation.
Pain relief by somatostatin in attacks of cluster headache (1984)

The pain relieving effect of somatostatin treatment during 72 attacks of cluster headache in 8 male patients was compared to treatment with ergotamine or placebo in a double-blind study. Infusion of somatostatin (25 micrograms/min for 20 min i.v.) reduced the maximal pain intensity and the duration of pain significantly compared to placebo treatment, and to a degree comparable to ergotamine tartrate treatment (250 micrograms i.m.). The results obtained provide new information concerning the possible mechanism of cluster headache attacks and suggest a new therapeutic approach.
Biosynthesis of Polyhydroxyalkanoate (PHA) Copolymer from Fructose Using Wild‐Type and Laboratory‐Evolved PHA Synthases (2005)

Eleven laboratory-evolved polyhydroxyalkanoate (PHA) synthases which originated from Pseudomonas sp. 61-3 enzyme (PhaC1(Ps)), together with the wild-type enzyme, were applied for PHA synthesis from fructose using Ralstonia eutropha PHB(-)4 as a host strain. The evolved PhaC1(Ps) mutants had amino acid substitution(s) at position 325 and/or position 481. In these mutants, serine-325 (S325) was replaced by cysteine (C) or threonine (T), while glutamine-481 (Q481) was replaced by lysine (K), methionine (M) or arginine (R). All recombinant strains harboring the genes of the evolved PhaC1(Ps) mutants produced a significantly increased amount of PHA (55-68 wt.-%) compared with the one harboring the wild-type gene (49 wt.-%). Particularly, those evolved PhaC1(Ps) mutants having multiple amino acid substitutions showed higher activities for PHA synthesis. Characterization of the PHA by NMR spectroscopy revealed that they were copolymers consisting of (R)-3-hydroxybutyrate (98-99 mol-%) and medium-chain-length comonomers (1-2 mol-%). This study also confirmed that amino acid substitution at position 481 in PhaC1(Ps) led to an increasing molecular weight of PHA. The number-average molecular weight (Mn) of PHA (Mn = 240,000) synthesized by the evolved PhaC1(Ps) (Q481K) mutant was 4.6-fold greater than that (Mn = 52,000) synthesized by the wild-type enzyme.
Cancerous Immunoglobulins in Cancer Immunology (2014)

The expression of immunoglobulins by cancer cells have been known for two decades. However, the mechanisms of action behind these Cancerous Immunoglobulins (cIgG) are not well understood and may be different from immunoglobulins secreted by normal B lymphocytes. Therefore, the structural and functional roles of cIgG have been actively investigated to resolve this mystery. A monoclonal antibody, RP215, was generated in 1987 and was shown to react with a carbohydrate-associated epitope localized mainly on the heavy chains of cIgG but not on normal immunoglobulins. The knowledge of cIgG has been greatly advanced by using RP215 as a unique probe. Not only was RP215 shown to act as an anti-cIgG to induce apoptosis of cultured cancer cells in vitro/in vivo, it was also shown to elicit Complement-Dependent Cytotoxicity (CDC) reactions to trigger lysis of cancer cells. It has now been established that besides serving to preserve growth/proliferation of cancer cells by capturing growth factors from the human serum, cIgG may also interact with certain human serum proteins which may be harmful to cancer cells. Thus, the hypothesis of dual functional roles of cIgG can be adequately explained in cancer immunology. Furthermore, RP215 may also be used to target cancer cells with surface bound cIgG for development of antibody-based anti-cancer drugs, provided that bioequivalent humanized RP215 is available for preclinical and clinical studies of immunotherapy.
Generation of high-performance protocol-aware analyzers with applications in intrusion detection systems (2010)

Traditional Intrusion Detection and Prevention (IDP) systems scan packets quickly by applying simple byte-wise pattern signatures to network flows. Such a protocol-agnostic approach can be compromised with polymorphic attacks: slight modifications of exploits that bypass pattern signatures but still reach corresponding vulnerabilities. To protect against these attacks, a solution is to provision the IDP system with protocol awareness, at the risk of degrading performance. To balance vulnerability coverage against network performance, we introduce a hardware-aware, compiler-based platform that leverages hardware engines to accelerate the core functions of protocol parsing and protocol-aware signature evaluation.
Regulation of human embryonic stem cell differentiation by BMP-2 and its antagonist noggin (2004)

Human embryonic stem cells differentiate spontaneously in vitro into a range of cell types, and they frequently give rise to cells with the properties of extra-embryonic endoderm. We show here that endogenous signaling by bone morphogenetic protein-2 controls the differentiation of embryonic stem cells into this lineage. Treatment of embryonic stem cell cultures with the bone morphogenetic protein antagonist noggin blocks this form of differentiation and induces the appearance of a novel cell type that can give rise to neural precursors. These findings indicate that bone morphogenetic protein-2 controls a key early commitment step in human embryonic stem cell differentiation, and show that the conservation of developmental mechanisms at the cellular level can be exploited in this system--in this case, to provide a facile route for the generation of neural precursors from pluripotent cells.
Copolymerization of Ethylene with 1-Hexene Using Sterically Hindered Tris(pyrazolyl)borate Titanium (IV) Compounds (2001)

The copolymerization of ethylene/1-hexene was studied using {TpMs}TiCl3 (1) (TpMs = hydridotris(3-mesitylpyrazol-1-yl) and {TpMs*}TiCl3 (2) (TpMs* = hydridobis(3-mesitylpyrazol-1-yl)(5-mesitylpyrazol-1-yl)) com- pounds in the presence of methylaluminoxane at 65°C. For both catalysts it was observed that the productivities decreased with increasing the 1-hexene concentration in the milieu exhibiting a negative comonomer effect. The highest productivities and 1-hexene incorporations were achieved in the case of {TpMs*}TiCl3 catalyst system. The resulting copolymers were not soluble in TCB even at 165°C. 1-hexene incorporations were very low: ca. 1.2 and 3.3 mol-%, respectively for (1) and (2). The r1 and r2 parameters for both (1) and (2)/MAO catalyst systems clearly indicated a strong tendency of these catalytic precursors to preferentially promote ethylene homopolymerization. According to X-ray photoelectron spectroscopy, from the analysis of the Ti2p3/2 peak, TpMs* catalyst seems to present a stronger cationic character after MAO treatment, which can explain in part its higher catalyst activity.
Critical Contributions of Amino-terminal Extracellular Domains in Agonist Binding and Activation of Secretin and Vasoactive Intestinal Polypeptide Receptors. STUDIES OF CHIMERIC RECEPTORS (1995)

Secretin and vasoactive intestinal polypeptide (VIP) receptors are closely related G protein-coupled receptors in a recently described family possessing a large amino-terminal ectodomain. We postulated that this domain might be critical for agonist recognition and therefore constructed a series of six chimeric receptors, exchanging the amino terminus, the first extracellular loop, or both in secretin and VIP receptors. Constructs were expressed in COS cells and characterized by cAMP generation and binding of both secretin and VIP radio-ligands. Wild type receptors demonstrated high affinity binding of respective ligands (IC50 values (in nM): at the secretin receptor: 2.2 for secretin, > 1000 for VIP; at the VIP receptor: 2.2 for VIP, > 1000 for secretin) and appropriately sensitive and selective biological responses (EC50 values (in nM): at the secretin receptor: 1.5 for secretin, 127 for VIP; at the VIP receptor: 1.0 for VIP, 273 for secretin). Replacement of the secretin receptor amino terminus with that of the VIP receptor resulted in biological responsiveness typical of the VIP receptor (EC50 = 120 nM for secretin, 1.7 nM for VIP). The converse was not true, with this domain of the secretin receptor not able to provide the same response when incorporated into the VIP receptor (EC50 = 50 nM for VIP, 30 nM for secretin). The addition of both the first loop and the amino terminus of the secretin receptor was effective in yielding a secretin receptor-like response (EC50 = 2.0 nM for secretin, 47 nM for VIP). All chimeric constructs expressing selectivity for secretin-stimulated activity bound this hormone with high affinity (IC50 = 0.2-2.2 nM); however, there was divergence between VIP binding and biological activity. Thus, the amino terminus of secretin and VIP receptors plays a key role in agonist recognition and responsiveness, with the first loop playing a critical complementary role for the secretin receptor.
ICE-LAP3, a Novel Mammalian Homologue of the Caenorhabditis elegans Cell Death Protein Ced-3 Is Activated during Fas- and Tumor Necrosis Factor-induced Apoptosis (1996)

Members of the ICE/ced-3 gene family have been implicated as components of the cell death pathway. Based on similarities with the structural prototype interleukin-1 beta-converting enzyme (ICE), family members are synthesized as proenzymes that are proteolytically processed to form active heterodimeric enzymes. In this report, we describe a novel member of this growing gene family, ICE-LAP3, which is closely related to the death effector Yama/CPP32/Apopain. Pro-ICE-LAP3 is a 35-kDa protein localized to the cytoplasm and expressed in a variety of tissues and cell lines. Overexpression of a truncated version of ICE-LAP3 (missing the pro-domain) induces apoptosis in MCF7 breast carcinoma cells. Importantly, upon receipt of a death stimulus, endogenous ICE-LAP3 is processed to its subunit forms, suggesting a physiological role in cell death. This is the first report to demonstrate processing of a native ICE/ced-3 family member during execution of the death program and the first description of the subcellular localization of an ICE/ced-3 family member.
Experimental Road Test of a Noncontacting Method of Measuring I-C Engine Torque Nonuniformity (1985)

&lt;div class="htmlview paragraph"&gt;This paper presents the experimental results of measurement of the nonuniformity in diesel engine torque. Measurements were made for an engine driving a water brake dynamometer as well as for a diesel engine (with a manual transmission) in an actual vehicle on roads of varying surface quality. These nonuniformity measurements are a measure of engine performance and have potential application in electronic engine control, maintenance/diagnostic functions and can serve as an indicator of incipient failure of the engine or of certain components.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The instrumentation includes a noncontacting (magnetic field system) sensor which can be mounted on the engine with minimal modification. The computation of the nonuniformity index can be implemented with an 8-bit or 1-6-bit microcomputer&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper presents the theory of the method, explains the necessary instrumentation, and gives results of the experimental study.&lt;/div&gt;
Carbon Nanotube Sponges (2009)

Carbon nanotube sponges are synthesized by chemical vapor deposition, in which nanotubes are self-assembled into a three-dimensionally interconnected framework. The sponges are very light, highly porous, hydrophobic in pristine form, and can be elastically and reversibly deformed into any shape. The sponges can float on water surfaces and absorb large-area spreading oil films (see images), suggesting promising environmental applications. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Magnetic Stimulation Of Finite Neuronal Structures (2005)

In this paper we present an analysis of magnetic stimulation of finite length neuronal structures using computer simulations. Models of finite neuronal structures in the presence of extrinsically applied electric fields indicate that excitation can be characterized by two driving functions: field gradient driving functions and boundary field driving functions. It is found that boundary field driving functions play an important role in governing excitation by magnetic stimulation.
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes (2015)

Recent studies indicate that DNA methylation can be used to identify transcriptional enhancers, but no systematic approach has been developed for genome-wide identification and analysis of enhancers based on DNA methylation. We describe ELMER (Enhancer Linking by Methylation/Expression Relationships), an R-based tool that uses DNA methylation to identify enhancers and correlates enhancer state with expression of nearby genes to identify transcriptional targets. Transcription factor motif analysis of enhancers is coupled with expression analysis of transcription factors to infer upstream regulators. Using ELMER, we investigated more than 2,000 tumor samples from The Cancer Genome Atlas. We identified networks regulated by known cancer drivers such as GATA3 and FOXA1 (breast cancer), SOX17 and FOXA2 (endometrial cancer), and NFE2L2, SOX2, and TP63 (squamous cell lung cancer). We also identified novel networks with prognostic associations, including RUNX1 in kidney cancer. We propose ELMER as a powerful new paradigm for understanding the cis-regulatory interface between cancer-associated transcription factors and their functional target genes.
Influence of nutrient media on the chemical composition of the exopolysaccharide from mucoid and non-mucoid Pseudomonas aeruginosa (1992)

Two mucoid Pseudomonas aeruginosa strains and their non-mucoid revertants isolated from two different clinical origins (cystic fibrosis and bronchiectasis) were grown in various chemically defined media. The extracted exopolysaccharide was characterized by gas-liquid chromatography and 1H-NMR spectroscopy. The exopolysaccharide was always heterogeneous, with an alginate fraction and a neutral fraction essentially composed of glucose, galactose, rhamnose and hexosamines. The alginate composition (mannuronate/guluronate ratio and O-acetylation degree) changed according to the carbon source in nutrient media and whether the strains tested were responding differently to these environmental stimuli. In all cases, the best carbon source for the alginate production was glycerol: the two cystic fibrosis strains produced a predominantly O-acetylated alginate whereas only the mucoid bronchiectasis strain produced a polymannuronate exopolysaccharide
3D Holographic Imaging and Trapping for Non-Invasive Cell Identification and Tracking (2010)

Real-time high-throughput identification, screening, characterization, and processing of biological specimen is of great interest to a host of areas spanning from cell biology and medicine to security and defense. Much like human biometrics, microorganisms exhibit natural signatures that can be used for identification. In this paper, we first overview two optical techniques, namely digital holographic microscopy and holographic optical tweezers which can non-invasively image, manipulate, and identify microorganisms in three dimensions. The two methods bear similarities in their optics and implementation. Thus, we have proposed a new approach to identification of micro/nano organisms and cells by combining the two methods of digital holographic microscopy and holographic optical tweezers which can be integrated into a single compact hardware. The proposed system can simultaneously sense, control, identify, and track cells and microorganisms in three dimensions. New possibilities that arise from the proposed method are discussed.
Macrophage activation by culture in an anoxic environment (1995)

The extracellular amino acid composition of experimental wounds in rats during peak macrophage infiltration bears the imprint of the elevated arginase activity present in wound fluid: L-arginine is found in this space in concentrations markedly lower, and L-ornithine in concentrations markedly higher, than those that are detectable in plasma. No evidence, in the form of L-citrulline or NO2- accumulation, can be found at this time for nitric oxide synthase (NOS) activity. Wound-derived macrophages, however, metabolize L-arginine through both arginase and NOS in culture. Given the requirements of NOS for O2 and the reduced O2 tension in wounds, experiments were performed to determine the role of O2 availability on the metabolism of L-arginine by wound-derived macrophages. Results demonstrated that, beyond inhibiting NOS, culture of wound-derived macrophages in an anoxic environment provided an activation signal, markedly increasing total L-arginine metabolism, arginase activity, NOS protein content, and the release of TNF-alpha and IL-6. Neither resident nor Corynebacterium parvum-elicited peritoneal macrophages responded to anoxic culture with increases in L-arginine utilization, arginase activity or, in the case of resident macrophages, in NOS protein content. The enhanced TNF-alpha and IL-6 release induced by anoxia in wound-derived macrophages was also found in resident peritoneal macrophages. Anoxia appears to act, then, as an inducer of activation-associated traits in macrophages obtained from different sites.
Inhibition of UV light- and Fenton Reaction-induced oxidative DNA damage by the soybcan isoflavone genistein (1996)

We have investigated the effect of the soybean isoflavone genistein on 8-hydroxy-2'-deoxyguanosine (8-OHdG) formation in calf thymus DNA exposed to either UV irradiation or the Fenton reaction system. Under the conditions used we observed that UV light and the Fenton reaction significantly increase 8-OHdG formation in DNA. Co-incubation with genistein inhibits the formation of 8-OHdG induced by either UV light irradiation or the Fenton reaction in a dose-dependent manner. The quenching effect of genistein on 8-OHdG formation induced by UV light is much more potent than that by the Fenton reaction, suggesting that the mechanisms of 8-OHdG formation may differ between the two systems. We further compared the antioxidant activities and quenching effect on 8-OHdG formation of genistein with biochanin A. Genistein potently scavenges both hydrogen peroxide in the medium and superoxide anion generated by xanthine/xanthine oxidase, whereas biochanin A has either a weak or no scavenging effect on these reactive oxygen species. However, both genistein and biochanin A display a similar quenching effect on UV light-induced 8-OHdG formation. These results suggest that the quenching effect of genistein and biochanin A on UV light-induced 8-OHdG formation is different from their ability to scavenge hydrogen peroxide and superoxide anion. The potent inhibition of UV light-induced oxidative DNA damage by genistein suggests its potential anticarcinogenic role in photocarcinogenesis.
Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody (2015)

The MERS-CoV is an emerging virus, which already infected more than 1,300 humans with high (∼36%) mortality. Here, we show that m336, an exceptionally potent human anti-MERS-CoV antibody, is almost germline with only one somatic mutation in the heavy chain. The structure of Fab m336 in complex with the MERS-CoV receptor-binding domain reveals that its IGHV1-69-derived heavy chain provides more than 85% binding surface and that its epitope almost completely overlaps with the receptor-binding site. Analysis of antibodies from 69 healthy humans suggests an important role of the V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of binding at such low levels of somatic hypermutation. Our results also have important implications for development of vaccine immunogens based on the newly identified m336 epitope as well as for elucidation of mechanisms of neutralization by m336-like antibodies and their elicitation in vivo.
Determination of Mixed Venous CO2 Tensions by Rebreathing (1956)

A rapid infrared CO2 analyzer has been used to evaluate a bag rebreathing method for the determination of mixed venous CO2 tension. Using small bag volumes and an initial bag CO2 tension averaging 11 mm Hg above effective alveolar tension, a plateau of CO2 concentration was obtained during normal spontaneous breathing in 18 seconds or less in 16 out of 18 trials during cardiac catheterization. The plateau so obtained was compared with the CO2 tension of a mixed venous sample drawn approximately 1 minute before the rebreathing procedure. The mean difference between the two was +0.1 mm Hg with a standard deviation of 3.1 mm Hg. This accuracy is not sufficient for the determination of cardiac output. Recirculation of blood within the rebreathing period did not introduce apparent errors. The mixed venous CO2 tension by the rebreathing method was determined with greater accuracy than was the effective alveolar CO2 tension from the peak end-tidal CO2 tensions. Abnormalities of distribution of the blood and gas in the lung interfered less with the determination of mixed venous tension by this method than with the determination of alveolar CO2 tension. Thus it is possible to utilize the mixed venous CO2 tension as obtained from rebreathing plateaus to evaluate the ventilatory status of subjects with moderate abnormalities of distribution of gas and blood in the lungs. Submitted on November 14, 1955