gebhart/patrepeval huggingface dataset:
Synthesis of Some 2-Aryl-1,2,4-triazolo[1,5-c][1,3]benzoxazin-5-ones as Tools To Define the Essential Pharmacophoric Descriptors of a Benzodiazepine Receptor Ligand (1995)

The synthesis and benzodiazepine receptor (BZR) affinity of some 1,2,4-triazolo[1,5-c][1,3]benzoxazin-5-ones, 2-22, are reported. Compounds 2-22 are devoid of the proton donor group, which according to a BZR schematic model was one of the pharmacophoric descriptors for receptor-ligand interaction. The binding data show that 2-(2-fluorophenyl)-9-chloro-1,2,4-triazolo[1,5-c][1,3]benzoxazin-5 -one (12) and some other compounds display nanomolar BZR affinity, indicating that the hydrogen donor group is not essential for the anchoring of 6,6,5-tricyclic systems to the BZR but only affects the potency of a ligand.
Predictive Model for Wall-Bounded Turbulent Flow (2010)

The behavior of turbulent fluid motion, particularly in the thin chaotic fluid layers immediately adjacent to solid boundaries, can be difficult to understand or predict. These layers account for up to 50% of the aerodynamic drag on modern airliners and occupy the first 100 meters or so of the atmosphere, thus governing wider meteorological phenomena. The physics of these layers is such that the most important processes occur very close to the solid boundary--the region where accurate measurements and simulations are most challenging. We propose a mathematical model to predict the near-wall turbulence given only large-scale information from the outer boundary layer region. This predictive capability may enable new strategies for the control of turbulence and may provide a basis for improved engineering and weather prediction simulations.
Influence of viscosity on the diffraction of sound by a periodic array of screens (2005)

The paper contains an analysis of the transmission of a pressure wave through a periodic grating including the influence of the air viscosity. The system of equations in this case consists of the compressible Navier-Stokes equations associated with no-slip boundary conditions on solid surfaces. The problem is reduced to two hypersingular integral equations for determining the velocity components along the slits. These equations are solved by using Galerkin's method with some special trial functions. The results can be applied in designing protective screens for miniature microphones realized in the technology of micro-electro-mechanical systems (MEMS). In this case, the physical dimensions of the device are on the order of the viscous boundary layer so that the viscosity cannot be neglected. The microfluidic model of the screen consists of a periodic array of slits in a substrate. The analysis indicates that the openings in the screen should be on the order of 10 microm in order to avoid excessive attenuation of the signal.
Blocking effects of polyunsaturated fatty acids on Na+ channels of neonatal rat ventricular myocytes. (1995)

Recent evidence indicates that polyunsaturated long-chain fatty acids (PUFAs) prevent lethal ischemia-induced cardiac arrhythmias in animals and probably in humans. To increase understanding of the mechanism(s) of this phenomenon, the effects of PUFAs on Na+ currents were assessed by the whole-cell patch-clamp technique in cultured neonatal rat ventricular myocytes. Extracellular application of the free 5,8,11,14,17-eicosapentaenoic acid (EPA) produced a concentration-dependent suppression of ventricular, voltage-activated Na+ currents (INa). After cardiac myocytes were treated with 5 or 10 microM EPA, the peak INa (elicited by a single-step voltage change with pulses from -80 to -30 mV) was decreased by 51% +/- 8% (P < 0.01; n = 10) and 64% +/- 5% (P < 0.001; n = 21), respectively, within 2 min. Likewise, the same concentrations of 4,7,10,16,19-docosahexaenoic acid produced the same inhibition of INa. By contrast, 5 and 10 microM arachidonic acid (AA) caused less inhibition of INa, but both n - 6 and n - 3 PUFAs inhibited INa significantly. A monounsaturated fatty acid and a saturated fatty acid did not. After washing out EPA, INa returned to the control level. Raising the concentration of EPA to 40 microM completely blocked INa. The IC50 of EPA was 4.8 microM. The inhibition of this Na+ channel was found to be dose and time, but not use dependent. Also, the EPA-induced inhibition of INa was voltage dependent, since 10 microM EPA produced 83% +/- 7% and 29% +/- 5% inhibition of INa elicited by pulses from -80 to -30 mV and from -150 to -30 mV, respectively, in single-step voltage changes. A concentration of 10 microM EPA shifted the steady-state inactivation curve of INa by -19 +/- 3 mV (n = 7; P < 0.01). These effects of PUFAs on INa may be important for their antiarrhythmic effect in vivo.
DALDA analogues containing alpha-hydroxymethylamino acids. (2001)

To evaluate the role of aromatic amino-acids residues, four analogues of the mu-selective opioid peptide agonist DALDA (H-Tyr-D-Arg-Phe-Lys-NH2) containing the amphiphilic, a,a-disubstituted amino acid (R)- or (S)-alpha-hydroxymethyltyrosine (HmTyr) in position 1 and (R)- or (S)-alpha-hydroxymethylphenylalanine (HmPhe) in position 3 of the peptide sequence were synthesized. Only the [(R)-HmPhe3)]DALDA analogue displayed full agonistic activity in both the guinea pig ileum and the mouse vas deferens assays and turned out to be a delta receptor-selective opioid agonist.
Chronic vagus nerve stimulation induces neuronal plasticity in the rat hippocampus (2009)

Vagus nerve stimulation (VNS) is used to treat pharmacotherapy-resistant epilepsy and depression. However, the mechanisms underlying the therapeutic efficacy of VNS remain unclear. We examined the effects of VNS on hippocampal neuronal plasticity and behaviour in rats. Cell proliferation in the hippocampus of rats subjected to acute (3 h) or chronic (1 month) VNS was examined by injection of bromodeoxyuridine (BrdU) and immunohistochemistry. Expression of doublecortin (DCX) and brain-derived neurotrophic factor (BDNF) was evaluated by immunofluorescence staining. The dendritic morphology of DCX+ neurons was measured by Sholl analysis. Our results show that acute VNS induced an increase in the number of BrdU+ cells in the dentate gyrus that was apparent 24 h and 3 wk after treatment. It also induced long-lasting increases in the amount of DCX immunoreactivity and in the number of DCX+ neurons. Neither the number of BrdU+ cells nor the amount of DCX immunoreactivity was increased 3 wk after the cessation of chronic VNS. Chronic VNS induced long-lasting increases in the amount of BDNF immunoreactivity and the number of BDNF+ cells as well as in the dendritic complexity of DCX+ neurons in the hippocampus. In contrast to chronic imipramine treatment, chronic VNS had no effect on the behaviour of rats in the forced swim or elevated plus-maze tests. Both chronic and acute VNS induced persistent changes in hippocampal neurons that may play a key role in the therapeutic efficacy of VNS. However, these changes were not associated with evident behavioural alterations characteristic of an antidepressant or anxiolytic action.
The effect of chelating agents on iron mobilization in Chang cell cultures (1976)

The investigation of chelating agents with potential therapeutic value in patients with transfusional iron overload has been facilitated by the use of Chang cell cultures. These cells have been incubated with [59Fe]transferrin for 22 hr, following which most of the intracellular radioiron is found in the cytosol, distributed between a ferritin and a nonferritin form. Iron release from the cells depends on transferrin saturation in the medium, but when transferrin is 100% saturated, which normally does not allow iron release, desferrioxamine, 2,3- dihydroxybenzoic acid, rhodotorulic acid, cholythydroxamic acid, and tropolone all promote the mobilization of ferritin iron and its release from cells. They are effective to an approximately equal degree. The incubation of [59Fe]transferrin with tropolone in vitro at a molar ratio of 1:500 results in the transfer of most of the labeled iron to the chelator, reflecting the exceptionally high binding constant of this compound. How far these phenomena relate to therapeutic potentially remains to be seen.
The PeptideAtlas project (2005)

The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.
An inverse relation between blood pressure and birth weight among 5 year old children from Soweto, South Africa (1999)

These data from a disadvantaged urbanised community in Southern Africa extend the reported observations of an inverse relation between birth weight and systolic blood pressure. The study adds to the evidence that influences in fetal life and early childhood influence systolic blood pressure. Further research is required to assess whether efforts to reduce the incidence of low birthweight babies will attenuate the prevalence of hypertension in future generations.
Management of reactive arthritis (2004)

Reactive arthritis (ReA) is an aseptic form of articular inflammation induced by infections mainly localised in the gastrointestinal (enteroarthritis) or urogenital (uroarthritis) tracts. The bacteria principally involved as causative agents are Chlamydia, Salmonella, Shigella, Campylobacter and Yersinia. The clinical picture is usually characterised by a mono-oligoarthritis of the lower limbs. Axial involvement is possible and extra-articular manifestations such as enthesitis, tenosynovitis, bursitis and dactylitis are frequent. NSAIDs and sulfasalazine are still the drugs most commonly used in the treatment of ReA. Steroids are administered when inflammatory symptoms are resistant to NSAIDs. Experiences with other DMARDs (disease modifying antirheumatic drugs) such as azathioprine, methotrexate and cyclosporin, have been sporadically reported and they can be employed in patients that are unresponsive to the more usual medicaments. The intake of antibacterials (tetracyclines) may be useful in uroarthritis but have not been so successful in enteroarthrits. In more aggressive cases, or when ReA evolves towards ankylosing spondylitis, TNF-α blockers could represent an effective choice.
Disruption of mesoderm and axis formation in fish by ectopic expression of activin variants: the role of maternal activin. (1994)

Formation of mesoderm in Xenopus embryos is the result of an induction event in which peptides such as FGF or activins have been implicated. It was recently demonstrated, by the ectopic expression of a truncated activin receptor, that activin receptor signaling pathways are involved in the processes of mesoderm and axis formation in vivo. However, this approach does not directly address the role of activin itself nor the involvement of activins in the formation of mesoderm in embryos from other vertebrates. In addition, activins are expressed maternally as a protein component of the egg as well as transcribed zygotically, and it is not clear which of the two forms is involved in mesoderm formation. To address those three issues, we analyzed the role of activins in the development of fish embryos by generating two activin dominant-negative variants. One of the variants behaves as an inhibitor of activin protein. The second variant was found to deplete the activin pool when cotranslated with wild-type activin. Injection of RNA encoding these variants into the two-cell embryo of the small teleost fish Oryzias latipes (Japanese medaka) demonstrates that only the maternally provided activin protein is required for mesoderm and axis formation in fish in vivo.
OpenFlow (2008)

This whitepaper proposes OpenFlow: a way for researchers to run experimental protocols in the networks they use every day. OpenFlow is based on an Ethernet switch, with an internal flow-table, and a standardized interface to add and remove flow entries. Our goal is to encourage networking vendors to add OpenFlow to their switch products for deployment in college campus backbones and wiring closets. We believe that OpenFlow is a pragmatic compromise: on one hand, it allows researchers to run experiments on heterogeneous switches in a uniform way at line-rate and with high port-density; while on the other hand, vendors do not need to expose the internal workings of their switches. In addition to allowing researchers to evaluate their ideas in real-world traffic settings, OpenFlow could serve as a useful campus component in proposed large-scale testbeds like GENI. Two buildings at Stanford University will soon run OpenFlow networks, using commercial Ethernet switches and routers. We will work to encourage deployment at other schools; and We encourage you to consider deploying OpenFlow in your university network too
Acid-induced folding of proteins. (1990)

The addition of HCl, at low ionic strength, to the native state of apomyoglobin, beta-lactamase, and cytochrome c caused these proteins to adopt an essentially fully unfolded conformation in the vicinity of pH 2. However, contrary to expectation, the addition of further acid resulted in refolding to a compact conformation with the properties of a molten globule. The major factor responsible for the refolding is believed to be the binding of the anion, which minimizes the intramolecular charge repulsion that initially brought about the unfolding.
Lifileucel, a Tumor-Infiltrating Lymphocyte Therapy, in Metastatic Melanoma (2021)

Lifileucel demonstrated durable responses and addresses a major unmet need in patients with metastatic melanoma with limited treatment options after approved therapy, including the primary refractory to anti-PD-1 or PD-L1 therapy subset.
Recombinant Human mRNA Cap Methyltransferase Binds Capping Enzyme/RNA Polymerase IIo Complexes (1998)

Guanine N-7 methylation is an essential step in the formation of the m7GpppN cap structure that is characteristic of eukaryotic mRNA 5' ends. The terminal 7-methylguanosine is recognized by cap-binding proteins that facilitate key events in gene expression including mRNA processing, transport, and translation. Here we describe the cloning, primary structure, and properties of human RNA (guanine-7-)methyltransferase. Sequence alignment of the 476-amino acid human protein with the corresponding yeast ABD1 enzyme demonstrated the presence of several conserved motifs known to be required for methyltransferase activity. We also identified a Drosophila open reading frame that encodes a putative RNA (guanine-7-)methyltransferase and contains these motifs. Recombinant human methyltransferase transferred a methyl group from S-adenosylmethionine to GpppG 5'ends, which are formed on RNA polymerase II transcripts by the sequential action of RNA 5'-triphosphatase and guanylyltransferase activities in the bifunctional mammalian capping enzyme. Binding studies demonstrated that the human cap methyltransferase associated with recombinant capping enzyme. Consistent with selective capping of RNA polymerase II transcripts, methyltransferase also formed ternary complexes with capping enzyme and the elongating form of RNA polymerase II.
A Combined Macro and Microvascular Model for Whole Limb Heat Transfer (1988)

A new prototype model for whole limb heat transfer is proposed wherein the countercurrent heat exchange from the large central arteries and veins in the core of the limb is coupled to microvascular models for the surrounding muscle and the cutaneous tissue layers. The local microvascular temperature field in the muscle tissue is described by the bioheat equation of Weinbaum and Jiji. The new model allows for an arbitrary axial variation of cross-sectional area and blood distribution between the muscle and cutaneous tissue, accounts for the blood flow to and heat loss from the hand and treats the venous return temperature and surface temperature distribution as unknowns that are determined as part of the solution to the overall boundary value problem. Representative solutions are presented for a wide range of environmental conditions for a limb in both the resting state and during exercise.
Collagen Crosslinks in Human Lumbar Intervertebral Disc Aging (1998)

Alterations in concentrations of pyridinoline and pentosidine collagen crosslinks occur with intervertebral disc aging and degeneration. These changes may contribute to the loss of disc integrity and play a role in the pathogenesis of the degenerative process.
Vascular endothelial growth factor-trap decreases tumor burden, inhibits ascites, and causes dramatic vascular remodeling in an ovarian cancer model. (2003)

Ovarian cancer is the most lethal gynecological malignancy and the fifth most common cause of cancer in women. It is characterized by diffuse peritoneal carcinomatosis and often by large volumes of i.p. ascites. Because vascular endothelial growth factor (VEGF), also known as vascular permeability factor, increases vascular permeability and stimulates endothelial cell growth, its role in ovarian cancer has been evaluated in a number of studies. However, questions remain regarding the ability of VEGF alone to cause ascites formation and the ability of VEGF blockade to inhibit the growth of disseminated cancer. We have used retroviral technology to create cell populations that overproduce VEGF and report that enforced expression of VEGF by ovarian carcinoma cells dramatically reduces the time to onset of ascites formation. In fact, even tumor-free peritoneal overexpression of VEGF, created by using adenoviral vectors, is sufficient to cause ascites to accumulate. We have found that systemic administration of the VEGF-Trap, a recently described high-affinity soluble decoy receptor for VEGF, prevents ascites accumulation and also inhibits the growth of disseminated cancer. Remarkably, much as is observed in s.c. tumor models, VEGF blockade results in dramatic remodeling of the blood vessels in disseminated ovarian carcinoma. The potent effects of the VEGF-Trap in reducing both ascites and tumor burden suggest that it will be of value in a regimen for treatment of women with ovarian cancer and ascites.
Spectral Norm Regularization for Improving the Generalizability of Deep Learning (2017)

We investigate the generalizability of deep learning based on the sensitivity to input perturbation. We hypothesize that the high sensitivity to the perturbation of data degrades the performance on it. To reduce the sensitivity to perturbation, we propose a simple and effective regularization method, referred to as spectral norm regularization, which penalizes the high spectral norm of weight matrices in neural networks. We provide supportive evidence for the abovementioned hypothesis by experimentally confirming that the models trained using spectral norm regularization exhibit better generalizability than other baseline methods.
Modeling hepatitis C virus infection using human induced pluripotent stem cells (2012)

Human pathogens impact patient health through a complex interplay with the host, but models to study the role of host genetics in this process are limited. Human induced pluripotent stem cells (iPSCs) offer the ability to produce host-specific differentiated cells and thus have the potential to transform the study of infectious disease; however, no iPSC models of infectious disease have been described. Here we report that hepatocyte-like cells derived from iPSCs support the entire life cycle of hepatitis C virus, including inflammatory responses to infection, enabling studies of how host genetics impact viral pathogenesis.
Two-stage physical synthesis for FPGAs (2006)

This paper presents an overview of an industrial physical synthesis CAD flow for FPGAs. The flow provides a performance speedup of 10%-15% for most circuits, and a significant number of circuits show a speedup of 20%-180%. We describe the algorithms used to achieve this result including: incremental retiming, BDD-based resynthesis, local rewiring, and logic replication. The effectiveness of these operations depends on the ability to accurately determine which portions of logic are timing critical at a stage of the CAD flow where there is still freedom to perform logic restructuring. We show how this problem can be effectively solved by inserting prediction and restructuring operations at multiple points of the FPGA CAD flow.
von Willebrand factor mediates platelet adhesion to virally infected endothelial cells. (1993)

von Willebrand factor is an adhesive glycoprotein critical to normal hemostasis. It is stored in the Weibel-Palade body of endothelial cells and upon release may mediate platelet adhesion. Herpesvirus-infected endothelium is known to be prothrombotic and to support enhanced platelet adherence. We previously identified P-selectin as a monocyte receptor that is translocated from the Weibel-Palade body to the endothelial cell surface in response to the local generation of thrombin on herpesvirus infected cells. In this study, we show that viral injury to vascular endothelial cells induces secretion of von Willebrand factor which mediates enhanced platelet adhesion to these cells.
Identification of novel hrp ‐regulated genes through functional genomic analysis of the Pseudomonas syringae pv. tomato DC3000 genome (2002)

Pseudomonas syringae pv. tomato (Pst) strain DC3000 infects the model plants Arabidopsis thaliana and tomato, causing disease symptoms characterized by necrotic lesions surrounded by chlorosis. One mechanism used by Pst DC3000 to infect host plants is the type III protein secretion system, which is thought to deliver multiple effector proteins to the plant cell. The exact number of type III effectors in Pst DC3000 or any other plant pathogenic bacterium is not known. All known type III effector genes of P. syringae are regulated by HrpS, an NtrC family protein, and the HrpL alternative sigma factor, which presumably binds to a conserved cis element (called the "hrp box") in the promoters of type III secretion-associated genes. In this study, we designed a search motif based on the promoter sequences conserved in 12 published hrp operons and putative effector genes in Pst DC3000. Seventy-three predicted genes were retrieved from the January 2001 release of the Pst DC3000 genome sequence, which had 95% genome coverage. The expression of the 73 genes was analysed by microarray and Northern blotting, revealing 24 genes/operons (including eight novel genes), the expression of which was consistently higher in hrp-inducing minimal medium than in nutrient-rich Luria-Bertani broth. Expression of all eight genes was dependent on the hrpS gene. Most were also dependent on the hrpL gene, but at least one was dependent on the hrpS gene, but not on the hrpL gene. An AvrRpt2-based type III translocation assay provides evidence that some of the hrpS-regulated novel genes encode putative effector proteins.