gebhart/patrepeval huggingface dataset:
Feedback Inhibition of G Protein-coupled Receptor Kinase 2 (GRK2) Activity by Extracellular Signal-regulated Kinases (1999)

G protein-coupled receptor kinase (GRK)-mediated receptor phosphorylation and beta-arrestin binding uncouple G protein-coupled receptors (GPCRs) from their respective G proteins and initiates the process of receptor internalization. In the case of the beta(2)-adrenergic receptor and lysophosphatidic acid receptor, these processes can lead to ERK activation. Here we identify a novel mechanism whereby the activity of GRK2 is regulated by feedback inhibition. GRK2 is demonstrated to be a phosphoprotein in cells. Mass spectrometry and mutational analysis localize the site of phosphorylation on GRK2 to a carboxyl-terminal serine residue (Ser(670)). Phosphorylation at Ser(670) impairs the ability of GRK2 to phosphorylate both soluble and membrane-incorporated receptor substrates and dramatically attenuates Gbetagamma-mediated activation of this enzyme. Ser(670) is located in a peptide sequence that conforms to an ERK consensus phosphorylation sequence, and in vitro, in the presence of heparin, ERK1 phosphorylates GRK2. Inhibition of ERK activity in HEK293 cells potentiates GRK2 activity, whereas, conversely, ERK activation inhibits GRK2 activity. The discovery that ERK phosphorylates and inactivates GRK2 suggests that ERK participates in a feedback regulatory loop. By negatively regulating GRK-mediated receptor phosphorylation, beta-arrestin-mediated processes such as Src recruitment and clathrin-mediated internalization, which are required for GPCR-mediated ERK activation, are inhibited, thus dampening further ERK activation.
DNA sequencing of the gene encoding a bacterial superantigen, <i>Yersinia pseudotuberculosis</i>-derived mitogen (YPM), and characterization of the gene product, cloned YPM. (1995)

Previously, we found a novel bacterial superantigen from Yersinia pseudotuberculosis, designated Y. pseudotuberculosis-derived mitogen (YPM). In the present study, we analyzed the DNA sequence of the gene encoding YPM. The YPM gene was cloned into a plasmid vector pMW119 and expressed in Escherichia coli DH10B. Like the native YPM, the cloned YPM required the expression of MHC class II molecules on accessory cells in the induction of IL-2 production by human T cells. TCR-V beta repertoire of human T cells reactive with the cloned YPM was V beta 3, V beta 9, V beta 13.1, and V beta 13.2. This repertoire is the same as that of T cells reactive with the native YPM. These results indicate that the cloned YPM expressed in E. coli is identical to the native YPM. Sequencing of the YPM gene revealed that the gene contained an open reading frame of 456 base pairs encoding a precursor form of 151 amino acid residues with m.w. 16,679 that is processed into a mature form of 131 amino acid residues with m.w. 14,529. Homology analysis revealed that the homology of amino acid sequence is quite low among YPM and other well known bacterial superantigens. We designated the gene encoding YPM as ypm.
Nonvolatile delay flip-flop using spin-transistor architecture with spin transfer torque MTJs for power-gating systems (2011)

The power-gating (PG) ability of the authors' previously proposed nonvolatile delay flip-flop (NV-DFF) using pseudo-spin-transistors with spin transfer torque magnetic tunnel junctions (STT-MTJs) is computationally analysed. Break-even time (BET) for nonvolatile logic circuits, which is an important index of energy performance for PG systems, is also formulated for the first time. The BET of the proposed NV-DFF can be effectively reduced by the design of the pseudo-spin-transistor parts of the cell. The NV-DFF is applicable to coarse- and fine-grained PG architectures owing to its potential BET of sub-microseconds in practical CMOS logic applications.
Design of Noncovalent Inhibitors of Human Cathepsin L. From the 96-Residue Proregion to Optimized Tripeptides (2002)

A novel series of noncovalent inhibitors of cathepsin L have been designed to mimic the mode of autoinhibition of procathepsin L. Just like the propeptide, these peptide-based inhibitors have a reverse-binding mode relative to a substrate and span both the S' and S subsites of the enzyme active site. In contrast to previous studies in which even moderate truncation of the full-length propeptide led to rapid reduction in potency, these blocked tripeptide-sized inhibitors maintain nanomolar potency. Moreover, these short peptides show higher selectivity (up to 310-fold) for inhibiting cathepsin L over K versus only 2-fold selectivity of the 96-residue propeptide of cathepsin L. A 1.9 A X-ray crystallographic structure of the complex of cathepsin L with one of the inhibitors confirms the designed reverse-binding mode of the inhibitor as well as its noncovalent nature. Enzymatic analysis also shows the inhibitors to be resistant to hydrolysis at elevated concentrations of the enzyme. The mode of inhibition of these molecules provides a general strategy for inhibiting other cathepsins as well as other proteases.
A Bayesian Framework for Simultaneous Matting and 3D Reconstruction (2007)

Conventional approaches to 3D scene reconstruction often treat matting and reconstruction as two separate problems, with matting a prerequisite to reconstruction. The problem with such an approach is that it requires taking irreversible decisions at the first stage, which may translate into reconstruction errors at the second stage. In this paper, we propose an approach which attempts to solve both problems jointly, thereby avoiding this limitation. A general Bayesian formulation for estimating opacity and depth with respect to a reference camera is developed. In addition, it is demonstrated that in the special case of binary opacity values (background/foreground) and discrete depth values, a global solution can be obtained via a single graph-cut computation. We demonstrate the application of the method to novel view synthesis in the case of a large-scale outdoor scene. An experimental comparison with a two-stage approach based on chroma-keying and shape-from-silhouette illustrates the advantages of the new method.
Real-Time Travel Time Estimates Using Media Access Control Address Matching (2008)

Although travel time is a widely-used highway performance measure, it can be difficult to estimate. Since consumer electronics such as cell phones, MP3 players and global positioning system devices with Wi-Fi or Bluetooth capability already contain unique digital fingerprints called media access control (MAC) addresses, they offer promise as a way to collect link travel times. This paper reports on the use of a prototype system to log and time-stamp wireless MAC addresses at selected sample locations. If these unique MAC addresses are simultaneously logged at multiple locations, the unique MAC addresses can be matched using traditional matching algorithms, and the difference in time stamps can be used to estimate travel time. A field study was conducted at arterial and freeway corridor locations in Indianapolis to evaluate the use of time-stamped MAC addresses acquired from Bluetooth devices to estimate freeway and arterial travel times. Findings indicate that travel time trends were easy to discern by visual inspection and demonstrate the feasibility of using MAC address matching for travel time estimation. Data from arterial highways showed a significantly larger variance compared to data from the freeways due to the impacts of traffic signals and the noise that is introduced when motorists divert from the network. Potential future applications of this technology are described.
Inhibition of MAO and COMT by Hypericum Extracts and Hypericin (1994)

The influence of hypericin, hypericum total extract, and hypericum fractions on the activity of MAO and COMT, prepared in vitro from pork liver, were investigated in several concentration steps. An inhibition of MAO could be shown in the following concentrations (extract correlated to a mean molecular value of 500): hypericin to 10 -3 mol/ L, hypericum total extract to 10 -4 mol/L, one extract fraction up to 10 -5 . A COMT inhibition could not be shown for hypericin, with hypericum extract to 10 -4 mol/L and with two extract fractions also up to 10 -4 mol/L. The MAO inhibiting fraction contained hypericins as well as flavonols, the COMT-inhibition fraction being mainly flavonols and xanthones. The concentrations of inhibition shown might not be sufficient to explain the clinically proven antidepressive effect of hypericum particularly with regard to the inhibition of MAO activity.
Atomic layer deposition of zinc oxide: Understanding the reactions of ozone with diethylzinc (2013)

To understand the reactions involved in the atomic layer deposition (ALD) of zinc oxide films using ozone as the oxygen source, two model systems were examined at the M06-L and M06 levels of density functional theory. The first model involved a two-coordinate zinc complex, HO-Zn-Et, and the second, [(HO)7Zn4(Et)], a cluster having a cubane-like geometry in which each of the zinc ions is four-coordinate. In both cases, the ozone reaction requires two distinct steps to generate a new hydroxyl ligand, which is required for the second phase of the ALD process (reaction with Et2Zn). In step 1, an exothermic insertion of O3 into the Zn-C bond produces an ethyltrioxide (EtOOO–) ligand as an intermediate. Subsequently, a mildly exothermic elimination of singlet oxygen produces an ethoxide complex. In step 2, a second equivalent of ozone abstracts a methylene hydrogen from the ethoxide ligand, resulting in the elimination of acetaldehyde and the formation of a hydrotrioxide (HOOO−) ligand that ultimately eliminates O2 and leaves a hydroxide group bound to the zinc. To simulate one complete ALD cycle, Et2Zn was subsequently reacted with the hydroxyl terminated products from step 1, i.e., Zn(OH)2 or Zn4(OH)8. In the cubane-like model, the geometric availability of additional OH groups opens a 1,4 ethane elimination pathway with an activation energy 7.1 kcal/mol lower than that for 1,2-elimination. A series of experimental ZnO depositions using Et2Zn and O3 were run in a reactor that was modified to allow collection of condensable organic products of the reaction. Acetaldehyde was detected, and quantitative nuclear magnetic resonance established a linear correlation between the amount of acetaldehyde and the number of ALD cycles, consistent with the mechanism inferred on the basis of the computational models.
Solid-state electrochemical nanoimprinting of copper (2007)

For the first time, the authors report highly selective dry etching of copper with a resolution of 80nm using solid-state electrochemical nanoimprint technology. By exploiting the high mobility of copper ions in solid electrolytes such as copper sulfide, they are able to obtain etching rates up to 5Å∕s without the use of contaminating liquids and excessive mechanical forces. Given the dearth of dry etch processes for metals in general and the fact that nanopatterning of metals is typically achieved indirectly using multistep processes, such a direct patterning technique offers potential application in a number of process steps in metallic interconnects and other nanoscale device fabrication.
Detection of Differences in the Nucleotide and Amino Acid Sequences of Diphtheria Toxin from<i>Corynebacterium diphtheriae</i>and<i>Corynebacterium ulcerans</i>Causing Extrapharyngeal Infections (2003)

While Corynebacterium ulcerans can mimic classical diphtheria, extrapharyngeal infections are extremely rare. Sequencing of the diphtheria toxin (DT)-encoding tox gene of two C. ulcerans isolates from extrapharyngeal infections revealed differences from C. diphtheriae DT sequences, mainly in the translocation and receptor-binding domains. C. ulcerans supernatants were much less potent than supernatant from C. diphtheriae. A C. ulcerans DT-specific PCR is described below.
Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii (2015)

Inflammatory bowel diseases (IBD) are characterized by low proportions of F. prausnitzii in the gut microbiome. This commensal bacterium exhibits anti-inflammatory effects through still unknown mechanisms. Stable monoassociated rodents are actually not a reproducible model to decipher F. prausnitzii protective effects. We propose a new gnotobiotic rodent model providing mechanistic clues. In this model, F. prausnitzii exhibits protective effects against an acute colitis and a protective metabolic profile is linked to its presence along the digestive tract. We identified a molecule, salicylic acid, directly involved in the protective effect of F. prausnitzii. Targeting its metabolic pathways could be an attractive therapeutic strategy in IBD.
Multivalent Antigens for Promoting B and T Cell Activation (2015)

Efficacious vaccines require antigens that elicit productive immune system activation. Antigens that afford robust antibody production activate both B and T cells. Elucidating the antigen properties that enhance B-T cell communication is difficult with traditional antigens. We therefore used ring-opening metathesis polymerization to access chemically defined, multivalent antigens containing both B and T cell epitopes to explore how antigen structure impacts B cell and T cell activation and communication. The bifunctional antigens were designed so that the backbone substitution level of each antigenic epitope could be quantified using (19)F NMR. The T cell peptide epitope was appended so that it could be liberated in B cells via the action of the endosomal protease cathepsin D, and this design feature was critical for T cell activation. Antigens with high BCR epitope valency induce greater BCR-mediated internalization and T cell activation than did low valency antigens, and these high-valency polymeric antigens were superior to protein antigens. We anticipate that these findings can guide the design of more effective vaccines.
MIGRAINE: DIAGNOSIS AND MANAGEMENT (2002)

One in 10 people have migraine. The patient’s history is the essential diagnostic tool. Treatment options include acute rescue, lifestyle strategies, alternative remedies, and prophylactic drugs. Most patients are managed in primary care; many never consult a doctor. The triptans have improved acute treatment, and renewed scientific interest in migraine. Overuse of acute rescue medication can lead to chronic daily headache.

Spontaneous overactivity and abnormal amplification in pain and other, predominantly sensory, pathways in the brainstem, leads to migraine. Current opinion favours a primarily neural cause, involving feedback loops through innervation of cranial arteries in the trigeminovascular system.1 A relative deficiency of 5-hydroxytriptamine (5-HT) may be near the root cause, and is linked to the action of most drug treatments. Ongoing research is studying the relevance of calcium channel abnormalities, and peptides such as calcitonin gene related peptide, which may be closer than 5-HT to the underlying cause, offering hope for improved treatment in the future. Migraine is usually polygenic. Uncommon migraine variants, such as familial hemiplegic migraine and CADASIL, are single gene disorders. These are neurodegenerative, not primarily headache conditions.

Migraine is typically manifest by episodic disabling headache, though it is more than just head pain. Differential diagnosis is from tension type headache (TTH), with which migraine is co-morbid (this differential is also discussed from the other perspective elsewhere in this supplement). Migraine lasts hours or days, and is absent more often than it is present; the average attack frequency is once a month. TTH is often chronic and it is present more often than it is absent. Migraine should be distinguished from cluster headache, which is relatively rare and causes recurrent unilateral headache with autonomic dysfunction. The third, common though often challenging differential diagnosis is medication overuse headache (MOH). This typically complicates migraine which is then transformed …
A proposal for error-tolerating codes (2002)

An extended concept of error-tolerating codes is presented and some examples of error-tolerating codes are introduced. An erroneous codeword of the proposed error-tolerating code may occur in the codespace; however, in this case, the erroneous codeword is required to be in a defined neighborhood of the original codeword. When no error is detected in a word, the word may differ from the original codeword, but it is trustworthy and can be used in a system without any error-correction or error-recovery procedures. An error-tolerating code is presented as an example. This code can be used for to implement analog-to-digital converting devices which are useful for dependable high-speed real-time control systems.
A new information theoretic clustering algorithm using k-nn (2013)

We develop a new non-parametric hierarchical information theoretic clustering algorithm based on implicit estimation of cluster densities using k-nearest neighbors (k-nn). Compared to a kernel-based procedure, our k-nn approach is very robust with respect to the parameter choices, with a key ability to detect clusters of vastly different scales. Of particular importance is the use of two different values of k, depending on the evaluation of within-cluster entropy or a cross-cluster cross-entropy in order to obtain the final clustering. We conduct clustering experiments, and report promising results, focusing in particular on the proposed algorithm's robustness to scale.
Is DNA ploidy an independent prognostic indicator in infiltrative node-negative breast adenocarcinoma? (1990)

To evaluate DNA content as an independent, long-term prognostic indicator in infiltrative, node-negative adenocarcinoma of the breast, flow cytometric DNA analyses were performed retrospectively in 165 patients. The exclusive use of paraffin-embedded tissue permitted the study of patients for whom 3 to 15 years' follow-up was available. Other investigators have shown a relationship between DNA nuclear content and well-known prognostic indicators of breast carcinoma, such as estrogen receptors, age, menopausal status, and stage of tumor. However, very few of these studies were based on patients with long-term clinical follow-up and investigated the independent prognostic value of DNA nuclear content. The frequency of aneuploidy in the patients in this study was 57%, with DNA indices ranging from 0.73 to 2.59. Survival in patients with localized breast carcinoma with DNA aneuploid tumors was 84.1% at 5 years and 75.5% at 10 years. Those with diploid tumors showed survival of 87.8% at 5 years and 73.4% at 10 years. These data show no independent prognostic value for DNA nuclear content. The relationship between DNA content, tumor histologic type, and age was also investigated. High-grade tumors were more often aneuploid. There was no association between DNA content and age. Of 165 patients, information regarding estrogen receptor status was available in only 77; 45% of those with aneuploid tumors and 35% with diploid tumors were estrogen receptor-negative. This difference was not significant. The authors conclude that simple determination of DNA ploidy fails to indicate prognosis for infiltrative, node-negative breast carcinoma.
Nutrition power not an alternative. (1996)

Some nutritional therapy is considered alternative or experimental, but basic good nutrition is essential to effectively combat HIV. The gastrointestinal tract is susceptible to a variety of opportunistic infections. Common medical problems of the gastrointestinal system are listed, and patients are advised to choose foods that give them adequate nutrients and calories to maintain their body mass.
Faster-Than-Nyquist Precoded CAP Modulation Visible Light Communication System Based on Nonlinear Weighted Look-Up Table Predistortion (2018)

In this paper, we have experimentally demonstrated faster-than-Nyquist carrierless amplitude and phase modulation quadrature phase-shift keying visible light communication system over 1.5-m free space transmission. Weighted look-up table is used to mitigate nonlinear impairment caused by amplifiers and electro-optical components. At the receiver side, recursive least square is employed to improve the decision precision. By combining these techniques, a data rate of 1.01 Gb/s is experimentally achieved with a bit error rate less than 7% forward error correction limit of 3.8 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . To the best of our knowledge, this is the first time that weighted look-up table is proposed and used in visible light communication system.
Epinephrine Induces von Willebrand Factor Release from Cultured Endothelial Cells: Involvement of Cyclic AMP-dependent Signalling in Exocytosis (1997)

von Willebrand factor (vWf) is released from endothelial cell storage granules after stimulation with thrombin, histamine and several other agents that induce an increase in cytosolic free calcium ([Ca2+]i). In vivo, epinephrine and the vasopressin analog DDAVP increase vWf plasma levels, although they are thought not to induce vWf release from endothelial cells in vitro. Since these agents act via a cAMP-dependent pathway in responsive cells, we examined the role of cAMP in vWf secretion from cultured human umbilical vein endothelial cells. vWf release increased by 50% in response to forskolin, which activates adenylate cyclase. The response to forskolin was much stronger when cAMP degradation was blocked with IBMX, an inhibitor of phosphodiesterases (+200%), whereas IBMX alone had no effect. vWf release could also be induced by the cAMP analogs dibutyryl-cAMP (+40%) and 8-bromo-cAMP (+25%); although their effect was weak, they clearly potentiated the response to thrombin. Epinephrine (together with IBMX) caused a small, dose-dependent increase in vWf release, maximal at 10(-6) M (+50%), and also potentiated the response to thrombin. This effect is mediated by adenylate cyclase-coupled beta-adrenergic receptors, since it is inhibited by propranolol and mimicked by isoproterenol. In contrast to thrombin, neither forskolin nor epinephrine caused an increase in [Ca2+]i as measured by fura-2 fluorescence. In addition, the effects of forskolin and thrombin were additive, suggesting that they act through distinct signaling pathways. We found a close correlation between cellular cAMP content and vWf release after stimulation with epinephrine and forskolin. These results demonstrate that cAMP-dependent signaling events are involved in the control of exocytosis from endothelial cells (an effect not mediated by an increase in [Ca2+]i) and provide an explanation for epinephrine-induced vWf release.
Metamaterial-Inspired Efficient Electrically Small Antennas (2008)

Planar two-dimensional (2D) and volumetric three-dimensional (3D) metamaterial-inspired efficient electrically-small antennas that are easy to design; are easy and inexpensive to build; and are easy to test; are reported, i.e., the EZ antenna systems. The proposed 2D and 3D electrical- and magnetic-based EZ antennas are shown to be naturally matched to a 50 source, i.e., without the introduction of a matching network. It is demonstrated numerically that these EZ antennas have high radiation efficiencies with very good impedance matching between the source and the antenna and, hence, that they have high overall efficiencies. The reported 2D and 3D EZ antenna designs are linearly scalable to a wide range of frequencies and yet maintain their easy-to-build characteristics. Several versions of the 2D EZ antennas were fabricated and tested. The measurement results confirm the performance predictions. The EZ antennas systems may provide attractive alternatives to existing electrically-small antennas.