gebhart/patrepeval huggingface dataset:
Biochemical characterization of three stimulatory GTP-binding proteins. The large and small forms of Gs and the olfactory-specific G-protein, Golf. (1990)

The biochemical properties of three stimulatory guanine nucleotide-binding protein (G-protein) alpha subunits, the large and small forms of Gs, Gs-l (52 kDa) and Gs-s (45 kDa), and the olfactory specific G-protein, Golf, have been compared. Complementary DNAs (cDNAs) encoding each alpha subunit were independently expressed in a mammalian cell line deficient in endogenous stimulatory G-proteins (S49 cyc-kin-). Gs-l and Gs-s respond similarly to activation by the beta-adrenergic agonist isoproterenol (EC50 = 80 and 60 nM, respectively) and the receptor-independent G-protein activators guanosine 5-O-3-(thio)triphosphate) (GTP gamma S) and AlF-4. The ability of Golf to interact with the beta-adrenergic receptor was also examined. Surprisingly, Golf interacts with beta-adrenergic receptors and is activated by isoproterenol (EC50 = 120 nM). All three G-proteins respond similarly to treatment with different alpha, beta, and gamma thiophosphoryl analogs of GTP. Specifically, (R)-GTP alpha S and GTP gamma S activate each G-protein, whereas (S)-GTP alpha S and (R)- or (S)-GTP beta S are inactive. In addition, similar to Gs alpha, Golf alpha is covalently modified and constitutively activated by cholera toxin. These studies demonstrate that all three stimulatory G-proteins are functionally and structurally similar, however, subtle differences between Golf and the two forms of Gs appear to modulate their interactions with receptors.
A simple, efficient method to create a cDNA library. (1992)

The simplified "All In One Tube" protocol for constructing a cDNA library combines the advantages of the "Classic method" and the Okayama-Berg method while overcoming some of their drawbacks. In this method, adding adapters, linkers or enzyme digestion steps are no longer necessary after cDNA synthesis, thus making it quicker and especially useful when dealing with small samples of mRNA.
Improvement of bonding strength between Au/Ti and SiO2 films by Si layer insertion (1999)

In the fabrication of broad band optical waveguide modulators, a certain technology must be used to prepare 15–20-μm-thick Au electrodes on the SiO2 surface covering the waveguides. A thin transition metal film is commonly inserted between the Au and SiO2 to improve adhesive strength. The transition metal film used in this study is Ti. Here, the SiO2 surface is precoated with Si prior to the Ti film formation, demonstrating a significant improvement in adhesive strength. The Si layer works as a barrier against oxidation of the Ti film due to the SiO2, leading to a homogenous film growth of metallic Ti.
Modeling the Relationship between User Comments and Edits in Document Revision (2019)

Xuchao Zhang, Dheeraj Rajagopal, Michael Gamon, Sujay Kumar Jauhar, ChangTien Lu. Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). 2019.
Digital antenna architectures using commercial off-the-shelf hardware (2004)

The use of the AD8346 and AD8347 modulator and demodulator chips as phase shifters and variable attenuators has been demonstrated. Insertion loss and phase were measured over the entire operating band of the AD8346 modulator board. Although the insertion loss was high over most of the band, it was within the manufacturer's specifications. In practice, some type of equalizing amplifier would most likely have to be used. A prototype transmit array was built, and phase scanning was verified by pattern measurements. The pattern simulations using measured modulator data showed unacceptable beam squint with frequency due to the lack of true time delay. Therefore, it appears that the AD8346EVAL modulator can only be used over a portion of the specified band. That is, the tunable bandwidth may be from 0.8 to 2.5 GHz, but the instantaneous bandwidth will be significantly less. This observation agrees with the manufacture's 60 MHz modulation bandwidth specification for the devices. Some digital time delay compensation may be possible in the receiver signal processing.
Characteristic Bleaching Profiles of Cyanine Dyes Depending on Active Oxygen Species in the Controlled Fenton Reaction. (1993)

The bleaching of cyanine-type pentamethine trinuclear dyes by active oxygen species (AOS), superoxide and hydroxyl radical, were studied under the xanthine-xanthine oxidase system and the Fenton reaction, respectively. The gradual bleaching of dyes occurred as the result of superoxide produced in the xanthine-xanthine oxidase system. However, the bleaching of cyanine dyes by Fenton reagent varied depending on the reaction conditions. If a normal Fenton reaction of Fe(II) and hydrogen peroxide (H2O2) took place, a hydroxyl radical was generated instantly. A Fenton reaction with an excess of [H2O2] over [Fe(II)] resulted in a gradual bleaching of the dye initiated by the hydroxyl radical, Fe(III) and H2O2. In this reaction, cyanine dyes with shorter side chains were bleached faster than those with longer ones. We controlled the Fenton reaction condition (Fe(II) or Fe(IIO)/H2O2 at pH 3.5 in the dark) to generate a specific AOS such as a hydroxyl radical (.OH) or superoxide (.O2-). Studies using xanthine-xanthine oxidase (pH 7.8), the Fe(II)-dipyridyl complex and various scavengers such as superoxide dismutase (SOD) and hyaluronic acid, revealed that .O2- was the primary radical responsible for this controlled Fenton reaction. This finding shows that this controlled Fenton reaction would be an effective AOS generation method, and that cyanine dyes may be hopeful probes for the detection of AOS.
Acyl Azolium Fluorides for Room Temperature Nucleophilic Aromatic Fluorination of Chloro- and Nitroarenes (2015)

The reaction of acid fluorides with N-heterocyclic carbenes (NHCs) produces anhydrous acyl azolium fluorides. With appropriate selection of acid fluoride and NHC, these salts can be used for the room temperature SNAr fluorination of a variety of aryl chlorides and nitroarenes.
Anodic oxidation of substituted adamantanes (1977)

Photoelectron spectra and voltammetric data are reported for a series of 1-alkyladamantanes. Anodic oxidation of the scries in either trifluoroacetic acid or acetonitrile gives charge-delocalised cation radicals. Whereas adamantane, 1-ethyladamantane. and 1-isopropyladamantane gave products by proton loss from the cation radical, other more highly substituted derivatives, e.g. 1-t-butyladamantane. give products preferentially by fragmentation of a carbon–carbon bond. Competition between deprotonation and fragmentation is controlled by the stability of the leaving carbocation; only if a tertiary group leaves is fragmentation dominant.
Regulation of T cell activation and tolerance by PDL2 (2006)

T cell activation and tolerance are regulated by costimulatory molecules. Although PD-1 serves as a crucial negative regulator of T cells, the function of its ligands, PDL1 and PDL2, is still controversial. In this study, we created a PDL2-deficient mouse to characterize its function in T cell activation and tolerance. Antigen-presenting cells from PDL2-/- mice were found to be more potent in activation of T cells in vitro over the wild-type controls, which depended on PD-1. Upon immunization with chicken ovalbumin, PDL2-/- mice exhibited increased activation of CD4(+) and CD8(+) T cells in vivo when compared with WT animals. In addition, T cell tolerance to an oral antigen was abrogated by the lack of PDL2. Our results thus demonstrate that PDL2 negatively regulates T cells in immune responses and plays an essential role in immune tolerance.
Therapeutic inhibition of the miR-34 family attenuates pathological cardiac remodeling and improves heart function (2012)

MicroRNAs are dysregulated in a setting of heart disease and have emerged as promising therapeutic targets. MicroRNA-34 family members (miR-34a, -34b, and -34c) are up-regulated in the heart in response to stress. In this study, we assessed whether inhibition of the miR-34 family using an s.c.-delivered seed-targeting 8-mer locked nucleic acid (LNA)-modified antimiR (LNA-antimiR-34) can provide therapeutic benefit in mice with preexisting pathological cardiac remodeling and dysfunction due to myocardial infarction (MI) or pressure overload via transverse aortic constriction (TAC). An additional cohort of mice subjected to MI was given LNA-antimiR-34a (15-mer) to inhibit miR-34a alone as a comparison for LNA-antimiR-34. LNA-antimiR-34 (8-mer) efficiently silenced all three miR-34 family members in both cardiac stress models and attenuated cardiac remodeling and atrial enlargement. In contrast, inhibition of miR-34a alone with LNA-antimiR-34a (15-mer) provided no benefit in the MI model. In mice subjected to pressure overload, LNA-antimiR-34 improved systolic function and attenuated lung congestion, associated with reduced cardiac fibrosis, increased angiogenesis, increased Akt activity, decreased atrial natriuretic peptide gene expression, and maintenance of sarcoplasmic reticulum Ca(2+) ATPase gene expression. Improved outcome in LNA-antimiR-34-treated MI and TAC mice was accompanied by up-regulation of several direct miR-34 targets, including vascular endothelial growth factors, vinculin, protein O-fucosyltranferase 1, Notch1, and semaphorin 4B. Our results provide evidence that silencing of the entire miR-34 family can protect the heart against pathological cardiac remodeling and improve function. Furthermore, these data underscore the utility of seed-targeting 8-mer LNA-antimiRs in the development of new therapeutic approaches for pharmacologic inhibition of disease-implicated miRNA seed families.
Urinary Proteomics in Diabetes and CKD (2008)

Urinary biomarkers for diabetes, diabetic nephropathy, and nondiabetic proteinuric renal diseases were sought. For 305 individuals, biomarkers were defined and validated in blinded data sets using high-resolution capillary electrophoresis coupled with electrospray-ionization mass spectrometry. A panel of 40 biomarkers distinguished patients with diabetes from healthy individuals with 89% sensitivity and 91% specificity. Among patients with diabetes, 102 urinary biomarkers differed significantly between patients with normoalbuminuria and nephropathy, and a model that included 65 of these correctly identified diabetic nephropathy with 97% sensitivity and specificity. Furthermore, this panel of biomarkers identified patients who had microalbuminuria and diabetes and progressed toward overt diabetic nephropathy over 3 yr. Differentiation between diabetic nephropathy and other chronic renal diseases reached 81% sensitivity and 91% specificity. Many of the biomarkers were fragments of collagen type I, and quantities were reduced in patients with diabetes or diabetic nephropathy. In conclusion, this study shows that analysis of the urinary proteome may allow early detection of diabetic nephropathy and may provide prognostic information.
Vaccinia recombinant virus expressing the rabies virus glycoprotein: safety and efficacy trials in Canadian wildlife. (1990)

Twenty-six meadow voles (Microtus pennsylvanicus), ten woodchucks (Marmota monax), thirteen grey squirrels (Sciurus carolinensis), thirteen ring-billed gulls (Larus delawarensis), six red-tailed hawks (Buteo jamaicensis) and eight great horned owls (Bubo virginianus) received vaccinia virus recombinant expressing the rabies virus glycoprotein (V-RG) by direct instillation into the oral cavity. Each of ten coyotes (Canis latrans) received the virus in two vaccine-laden baits. Several voles and most of the gulls died from diseases unrelated to vaccination during the observation period, but all other animals remained healthy and survived. These deaths from causes other than vaccination and the absence of any lesions suggestive of vaccinia infection indicate that it is unlikely that any animal suffered or died as a result of V-RG administration. In addition several animals showed an unexpected high level of rabies neutralizing antibodies.
A New PERKspective on Neurodegeneration (2013)

Targeting stress-induced kinases that regulate protein synthesis may be a new therapeutic strategy for treating neurodegenerative diseases.
A Real-Time Obstacle Detection and Reactive Path Planning System for Autonomous Small-Scale Helicopters (2007)

This paper presents the design of a comprehensive Multi-layer Architecture for Trajectory Replanning and Intelligent eXecution (MATRIX) system and its evaluation through high-delity simulations of the R-50 helicopter in the Real-time Interactive Prototype Technology Integration/Development Environment (RIPTIDE). The main feature of the MATRIX system is that it assures effective real-time obstacle detection & avoidance in a cluttered environment. Specically , this paper discusses the (i) Design of the MATRIX System; (ii) Design, implementation & testing of individual modules; (iii) Integration & implementation under RIPTIDE; and (iv) Study of the features and limitations of the proposed architecture and algorithms. The MATRIX system consists of several subsystems including: Path Planner based on Rapidly-exploring Random Trees (RRT), shortest path algorithm for pruning of redundant waypoints, a safety corridor for preventing collisions with obstacles, 4D trajectory generator, nonlinear adaptive outer-loop controller, representation of obstacles using Quadtrees, and obstacle detection using a scanning laser and Interacting Multiple Model Kalman Filters (IMM-KF). These subsystems were developed and integrated within RIPTIDE, and extensive testing was carried out using R-50 helicopter dynamics. It was found that the MATRIX system rapidly generates new paths and trajectories to avoid unknown obstacles, is highly robust, and achieves excellent overall performance.
Cyclic Stretch and Hypertension Induce Retinal Expression of Vascular Endothelial Growth Factor and Vascular Endothelial Growth Factor Receptor—2 (2001)

Systemic hypertension exacerbates diabetic retinopathy and other coexisting ocular disorders through mechanisms that remain largely unknown. Increased vascular permeability and intraocular neovascularization characterize these conditions and are complications primarily mediated by vascular endothelial growth factor (VEGF). Because systemic hypertension increases vascular stretch, we evaluated the expression of VEGF, VEGF-R2 (kinase insert domain-containing receptor [KDR]), and VEGF-R1 (fms-like tyrosine kinase [Flt]) in bovine retinal endothelial cells (BRECs) undergoing clinically relevant cyclic stretch and in spontaneously hypertensive rat (SHR) retina. A single exposure to 20% symmetric static stretch increased KDR mRNA expression 3.9 +/- 1.1-fold after 3 h (P = 0.002), with a gradual return to baseline within 9 h. In contrast, BRECs exposed to cardiac-profile cyclic stretch at 60 cpm continuously accumulated KDR mRNA in a transcriptionally mediated, time-dependent and stretch-magnitude-dependent manner. Exposure to 9% cyclic stretch increased KDR mRNA expression 8.7 +/- 2.9-fold (P = 0.011) after 9 h and KDR protein concentration 1.8 +/- 0.3-fold (P = 0.005) after 12 h. Stretched-induced VEGF responses were similar. Scatchard binding analysis demonstrated a 180 +/- 40% (P = 0.032) increase in high-affinity VEGF receptor number with no change in affinity. Cyclic stretch increased basal thymidine uptake 60 +/- 10% (P < 0.001) and VEGF-stimulated thymidine uptake by 2.6 +/- 0.2-fold (P = 0.005). VEGF-NAb reduced cyclic stretch-induced thymidine uptake by 65%. Stretched-induced KDR expression was not inhibited by AT1 receptor blockade using candesartan. Hypertension increased retinal KDR expression 67 +/- 42% (P < 0.05) in SHR rats compared with normotensive WKY control animals. When hypertension was reduced using captopril or candesartan, retinal KDR expression returned to baseline levels. VEGF reacted similarly, but Flt expression did not change. These data suggest a novel molecular mechanism that would account for the exacerbation of diabetic retinopathy by concomitant hypertension, and may partially explain the principal clinical manifestations of hypertensive retinopathy itself. Furthermore, these data imply that anti-VEGF therapies may prove therapeutically effective for hypertensive retinopathy and/or ameliorating the deleterious effects of coexistent hypertension on VEGF-associated disorders such as diabetic retinopathy.
Role of Endogenous Angiotensin II on Glutamatergic Actions in the Rostral Ventrolateral Medulla in Goldblatt Hypertensive Rats (2003)

In this study, we investigated the cardiovascular responses mediated by rostral ventrolateral medulla neurons (RVLM) in the Goldblatt hypertension model (2K-1C) treated or not treated with captopril. The actions of glutamate into the RVLM were tested, injecting glutamate (0.1 mol/L, 100 nL) and its antagonist kynurenic acid (0.02 mol/L, 100 nL). Glycine (0.5 mol/L, 100 nL) was also microinjected. Experiments were performed in male Wistar rats (weight, 250 to 300 g); 5 groups were studied: (1) 2K-1C nontreated (H, n=6); (2) 2K-1C treated with captopril, 10 mg/kg per day (Ht10, n=10); (3) 2K-1C treated with captopril, 50 mg/kg per day (Ht50, n=7); (4) control normotensive rats (N, n=7); and (5) normotensive rats treated with captopril, 50 mg/kg per day (Nt50, n=8). All experiments in 2K-1C were performed 6 weeks after renal surgery; captopril treatment lasted for the last 2 weeks. In urethane-anesthetized rats (1.2 g/kg IV), bilateral microinjection of glycine into the RVLM caused a depressor response; there was no difference between groups in relation to the change of variation (N: 54+/-2; H: 46+/-12; Ht10: 50+/-3, and Ht50: 42+/-7 mm Hg). Only in the H group, kynurenic acid microinjection into the RVLM caused a depressor response (H: 158+/-8 to 132+/-8 mm Hg). Glutamate response was larger in hypertensive than in normotensive rats (N: 38+/-2.6 and H: 55+/-6); no difference was observed between hypertensive groups. The data suggest that glutamate acts tonically to drive the RVLM in 2K-1C rats, and this action is modulated by endogenous angiotensin II. The increase in the glutamate actions within the RVLM may contribute to the pathogenesis of renovascular hypertension.
Increasing the Throughput Capacity of Mesh Networks by Cross-layer Routing (2005)

International audience
C5A Protects Macaques from Vaginal Simian-Human Immunodeficiency Virus Challenge (2015)

A safe and effective vaginal microbicide could decrease human immunodeficiency virus (HIV) transmission in women. Here, we evaluated the safety and microbicidal efficacy of a short amphipathic peptide, C5A, in a rhesus macaque model. We found that a vaginal application of C5A protects 89% of the macaques from a simian-human immunodeficiency virus (SHIV-162P3) challenge. We observed no signs of lesions or inflammation in animals vaginally treated with repeated C5A applications. With its noncellular cytotoxic activity and rare mechanism of action, C5A represents an attractive microbicidal candidate.
Tridentate SCS Palladium(II) Complexes:  New, Highly Stable, Recyclable Catalysts for the Heck Reaction (1999)

A new pincer-type SCS ligand containing Pd(II) is a simple, robust catalyst for Heck chemistry using a variety of alkene acceptors and aryl iodides. It is less active with aryl bromides. While certain palladium(II) species insert slowly into the aryl C−H bond of an unsubstituted version of this ligand, the introduction of activating groups into the 5 position of the aromatic ring readily allows quantitative metal insertion. These ligands were synthesized and attached to soluble polymers by simple modification of inexpensive starting materials. For example, both 5-oxy and 5-amido SCS ligands were successfully appended to 5000 Mn poly(ethylene glycol) via ether or amide linkages, respectively. Both the 5-oxo and 5-amido complexes are active as Heck catalysts in DMF solution in air. The PEG-bound 5-amido-SCS−Pd complex was recycled via solvent precipitation three times with no observed catalyst deactivation. While the 5-amido-SCS−Pd complexes are very robust, their 5-oxo counterparts decompose slowly under certain conditions. These SCS catalysts are analogous to PCP-type catalysts previously reported in the literature but avoid the requirement of an air-sensitive phosphine synthesis.
A Modern Approach to Searching the World Wide Web: Ranking Pages by Inference over Content. (2001)

The Hypertext-based Webs such as Intranets contain a vast amount of information pertaining to an enormous number of subjects. It is, however, an organically grown and thus essentially structureless environment that is in a constant state of flux. Therefore, finding useful information pertaining to a particular topic is oftentimes a difficult task. Search engines were designed with the intent of easing the burden on the individuals perusing the Web for specific topics. Traditionally, Web search engines have used straightforward--and relatively nave--approaches towards indexing and ranking pages pertaining to a particular subject. As our understanding of hyperlinked environments has improved, algorithmic tools have been developed that more effectively distill the plethora of information that exists within this environment. We will briefly discuss the history of the World Wide Web, the approaches employed by &quot;traditional &quot; search engines, and how alternative techniques can improve upon older approaches. We find that new techniques build upon, rather than replace, previous approaches, and that the problem of searching the Web is one that evolves as our understanding of the Web&apos;s structure improves. 1
Refractoriness to Antivascular Endothelial Growth Factor Treatment: Role of Myeloid Cells (2008)

CD11b+Gr1+ cells, which include neutrophils, macrophages, and myeloid-derived suppressor cells, have been shown to contribute to tumor angiogenesis. Recently, we found that accumulation of CD11b+Gr1+ in tumors renders them refractory to angiogenic blockade by vascular endothelial growth factor (VEGF) antibodies. This effect was traced to a pathway of CD11b+Gr1+-mediated angiogenesis that is, at least in part, driven by the secreted protein Bv8, which is up-regulated by the important myeloid growth factor granulocyte colony-stimulating factor (G-CSF). Thus, G-CSF may promote tumor angiogenesis through a Bv8-dependent pathway that bypasses VEGF and renders tumors refractory to anti-VEGF therapy.
A Conserved, Lipid‐Mediated Sorting Mechanism of Yeast Ist2 and Mammalian STIM Proteins to the Peripheral ER (2009)

Sorting of yeast Ist2 to the plasma membrane (PM) or the cortical endoplasmic reticulum (ER) requires a cortical sorting signal (CSS(Ist2)) that interacts with lipids including phosphatidylinositol-4,5-bisphosphate (PI(4,5)P(2)) at the PM. Here, we show that the expression of Ist2 in mammalian cells resulted in a peripheral patch-like localization without any detection of Ist2 at the cell surface. Attached to C-termini of mammalian integral membrane proteins, the CSS(Ist2) targeted these proteins to PM-associated domains of the ER and abolished trafficking via the classical secretory pathway. The interaction of integral membrane proteins with PI(4,5)P(2) at the PM created ER-PM contacts. This process is similar to the regulated coupling of ER domains to the PM via stromal interaction molecule (STIM) proteins during store-operated Ca(2+) entry (SOCE). The CSS(Ist2) and the C-terminus of the ER-located Ca(2+) sensor STIM2 were sufficient to bind PI(4,5)P(2) and PI(3,4,5)P(3) at the PM, showing that an evolutionarily conserved mechanism is involved in the sorting of integral membrane proteins to PM-associated domains of the ER. Yeast Ist2 and STIM2 share a common basic and amphipathic signal at their extreme C-termini. STIM1 showed binding preference for liposomes containing PI(4,5)P(2), suggesting a specific contribution of lipids to the recruitment of ER domains to the PM during SOCE.