gebhart/patrepeval huggingface dataset:
Natural Killer Cells Are Essential for the Ability of BRAF Inhibitors to Control BRAFV600E-Mutant Metastatic Melanoma (2014)

BRAF(V600E) is a major oncogenic mutation found in approximately 50% of human melanoma that confers constitutive activation of the MAPK pathway and increased melanoma growth. Inhibition of BRAF(V600E) by oncogene targeting therapy increases overall survival of patients with melanoma, but is unable to produce many durable responses. Adaptive drug resistance remains the main limitation to BRAF(V600E) inhibitor clinical efficacy and immune-based strategies could be useful to overcome disease relapse. Tumor microenvironment greatly differs between visceral metastasis and primary cutaneous melanoma, and the mechanisms involved in the antimetastatic efficacy of BRAF(V600E) inhibitors remain to be determined. To address this question, we developed a metastatic BRAF(V600E)-mutant melanoma cell line and demonstrated that the antimetastatic properties of BRAF inhibitor PLX4720 (a research analogue of vemurafenib) require host natural killer (NK) cells and perforin. Indeed, PLX4720 not only directly limited BRAF(V600E)-induced tumor cell proliferation, but also affected NK cell functions. We showed that PLX4720 increases the phosphorylation of ERK1/2, CD69 expression, and proliferation of mouse NK cells in vitro. NK cell frequencies were significantly enhanced by PLX4720 specifically in the lungs of mice with BRAF(V600E) lung metastases. Furthermore, PLX4720 also increased human NK cell pERK1/2, CD69 expression, and IFNγ release in the context of anti-NKp30 and IL2 stimulation. Overall, this study supports the idea that additional NK cell-based immunotherapy (by checkpoint blockade or agonists or cytokines) may combine well with BRAF(V600E) inhibitor therapy to promote more durable responses in melanoma.
Inductive Representation Learning on Large Graphs (2017)

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.
Stimulation of in vitro human skin collagenase expression by platelet-derived growth factor. (1985)

Platelet-derived growth factor (PDGF) is both chemoattractant and mitogenic for stromal cells. Here, we examined the effects of PDGF on collagenase expression by normal human skin fibroblasts. Culturing cells for 24 hr in the presence of PDGF at 0-180 ng/ml resulted in a dose-dependent, saturable increase in collagenase activity in the culture medium that was paralleled by equal increases in immunoreactive collagenase protein, suggesting enhanced synthesis of a catalytically unaltered enzyme. The specificity of this effect was demonstrated by comparing the collagenase-stimulatory effect with that on total protein synthesis and DNA synthesis. Under in vitro conditions that produced a 2.5-fold increase in collagenase synthesis, there was an approximately equal to 20% increase in total protein synthesis and no change in DNA synthesis. In addition, platelet factor 4, another platelet-derived protein, caused a less than 20% increase in collagenase expression. In time-course studies, stimulation of collagenase synthesis was first observed 8-10 hr after exposure to the growth factor. Conversely, when cells were primed with PDGF for approximately equal to 24 hr and the stimulator was then removed, an increased rate of synthesis was seen for an additional approximately equal to 6 hr, after which the rate reverted to control levels. Since the kinetic data suggested a possible pretranslational effect, fibroblasts cultured with PDGF were used to prepare mRNA. In cell-free translation, total protein synthesis was essentially unaltered; however, the growth factor caused a greater than 2-fold increase in translatable collagenase mRNA. The data suggest that PDGF specifically modulates collagenase synthesis, possibly through a series of events that lead to increased transcription or preferential translation of collagenase mRNA.
Transgenic rabbit producing human growth hormone in milk. (2003)

The gene construct WAP(6xHisThr):hGH containing the entire human growth hormone gene (hGH) under the rat whey acidic protein (WAP) promoter regulating the expression in mammary glands of mammals was prepared. The 5' end of the gene was modified by the addition of a sequence encoding six histidine residues and a sequence recognized by thrombin. The gene construct was introduced by microinjection into the male pronucleus of a fertilized oocyte. The founder male rabbit was obtained with the transgene mapping to chromosome 7. The presence of the growth hormone was confirmed in samples of milk collected during the lactation of F1 generation females. The growth hormone can be easily purified by affinity chromatography and cleavage by thrombin to an active form.
Protein Prosthesis:  1,5-Disubstituted[1,2,3]triazoles as cis-Peptide Bond Surrogates (2007)

[Image: see text] Proline is unique among the natural amino acids in the similar propensity of its peptide bond to be in the cis or trans conformation. This attribute affects many processes, including the rate at which proteins fold, their structures, and their activities. Other aliphatic amino acids can serve as mimics for proline residues with trans peptide bonds. In contrast, chemical synthesis is needed to create surrogates for cis prolyl peptide bonds. Here, 1,5-disubstituted-[1,2,3]-triazoles were assessed as cis-peptide bond surrogates. Huisgen’s 1,3-dipolar cycloaddition reaction of amino alkynes and azido acids and a Ru(II) catalyst were used to synthesize a variety of Xaa–1,5-triazole-Ala modules in moderate-to-high yields. Two of these modules, along with their 1,4-triazole regioisomers, were installed in a turn region of bovine pancreatic ribonuclease by using expressed protein ligation. The resulting semisynthetic enzymes displayed full enzymatic activity, indicating the maintenance of native structure. The 1,5-triazole surrogates instilled conformational stability that was comparable to that of Xaa–cis-Pro segments, whereas the 1,4-triazoles conferred markedly less stability. The stability conferred by both surrogates was independent of the Xaa residue, eliminating an uncertainty in protein design. We conclude that Xaa–1,5-triazole-Ala modules can serve as viable mimics of Xaa–cis-Pro segments. The possibility of synthesizing this surrogate by the ligation of fragments in situ and the emergence of biocompatible catalysts for that process portends its widespread use.
A double-masked comp arison of betaxolol and levobuno lol fo r the treatment of primary open-angle glaucoma. (1990)

SUMMARY This article shows a double masked study between Betaxolol 0.5% drops and Levobunolol 0.5% drops involving 40 glaucomatous patients. 20 randomized patients were given Betaxolol. And other 20 patients were given Levobunolol in a randomized way as well. This work developed over a period of 12 weeks during which time the effects of the above mentioned drugs on the ocular were observed specially over the Intraocular Pressure as well as their possible systemic effects.
Intestinal microflora are necessary for development of spontaneous adenocarcinoma of the large intestine in T-cell receptor beta chain and p53 double-knockout mice. (2001)

This study was conducted to confirm the hypothesis that intestinal microflora are required for the development of adenocarcinoma in the colon of the TCRbeta and p53 double-knockout (TCRbeta-/- p53-/-) mouse. Germ-free TCRbeta-/- p53-/- mice were produced. At 7 weeks of age, the animals were divided into two groups (n = 10/group), and one of these groups was conventionalized. Animals of both groups were subjected to histopathological examination for adenocarcinoma of the colon at 4 months of age. There was no development of adenocarcinoma of the colon among the germ-free mice, whereas in the conventionalized group, adenocarcinomas of the ileocecum and cecum were detected in 70% of animals. These results indicate the usefulness of the TCRbeta-/- p53-/- mouse as a colon cancer animal model that develops spontaneous adenocarcinoma of the colon early in life, and suggest that intestinal microflora play a major role in the development of adenocarcinoma of the colon in this animal model.
Sleepiness, Driving, and Motor Vehicle Crashes (1998)

Increased awareness of the relationship between sleepiness and motor vehicle crashes will promote the health and safety of drivers and highway users. Physicians can contribute by encouraging good sleep habits, recognizing and treating sleep-related problems, and counseling patients about the risks of driving while sleepy. To protect public health and safety, the American Medical Association recommends continued research on devices and technologies to detect the signs of sleepiness and prevent the deterioration of driver alertness and performance. Educational programs about the risks of falling asleep while driving are needed for physicians, the public, and commercial truck drivers.
Combining acoustic echo cancellation and adaptive beamforming for achieving robust speech interface in mobile robot (2008)

This paper proposes a combined scheme in which adaptive beamforming and acoustic echo canceller are integrated in order to achieve a robust full-duplex speech interface between user and mobile robot. In particular, this paper addresses the situation in which an echo signal and the userpsilas voice are propagated from the same direction toward a linear array of microphones. We propose a cascading scheme that uses an acoustic echo canceller followed by an adaptive beamformer. By using the system output to adapt echo canceller, and by controlling the adaptive mode of each adaptive filter in the beamformer and in the echo canceller, we can recover the original speech, which would otherwise have remained contaminated by both noise and echoes. In addition, a double-talk detector is proposed so that effective acoustic echo cancellation may be attained without generating error divergence when the userpsilas voice and the echo are present simultaneously. Representative experimental results with real data demonstrate the validity of the proposed scheme.
Innate immunity to virus infection (2008)

The innate immune system is essential for the initial detection of invading viruses and subsequent activation of adaptive immunity. Three classes of receptors, designated retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), Toll-like receptors (TLRs), and nucleotide oligomerization domain (NOD)-like receptors (NLRs), sense viral components, such as double-stranded RNA (dsRNA), single-stranded RNA, and DNA. RLRs and TLRs play essential roles in the production of type I interferons (IFNs) and proinflammatory cytokines in cell type-specific manners. While the RLRs play essential roles in the recognition of RNA viruses in various cells, plasmacytoid dendritic cells utilize TLRs for detecting virus invasion. NLRs play a role in the production of mature interleukin-1 beta to dsRNA stimulation. Activation of innate immune cells is critical for mounting adaptive immune responses. In this review, we discuss recent advances in our understanding of the mechanisms of viral RNA recognition by these different types of receptors and its relation to acquired immune responses.
Influence of a mixing solvent with tetrahydrofuran and N,N‐dimethylformamide on electrospun poly(vinyl chloride) nonwoven mats (2002)

Abstract We evaluated the effects of the solvent composition with respect to the solution concentration, applied electric field, and tip‐to‐collector distance on the morphology of electrospun poly(vinyl chloride) (PVC) fibers. The solvent volume ratio was strongly correlated with the diameter of the electrospun fibers with respect to the other processing parameters. Electrospun PVC fibers dissolved in tetrahydrofuran (THF) had diameters ranging from 500 nm to 6 μm; those dissolved in N,N ‐dimethylformamide (DMF) had an average diameter of 200 nm. The diameters of the electrospun fibers were obtained from narrow to broad distributions with the solvent composition. Also, the diameters of fibers electrospun from a mixed solvent of THF and DMF were less than 1 μm. The mechanical properties of electrospun PVC nonwoven mats depended on the fiber orientation and linear velocity of the drum surface. With increasing linear velocity of the drum surface, electrospun PVC fibers were arranged toward the machine direction, and the dimensions of the spiral path were shorter. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2259–2268, 2002
Engineered protein scaffolds for molecular recognition (2000)

The use of so-called protein scaffolds has recently attracted considerable attention in biochemistry in the context of generating novel types of ligand receptors for various applications in research and medicine. This development started with the notion that immunoglobulins owe their function to the composition of a conserved framework region and a spatially well-defined antigen-binding site made of peptide segments that are hypervariable both in sequence and in conformation. After the application of antibody engineering methods along with library techniques had resulted in first successes in the selection of functional antibody fragments, several laboratories began to exploit other types of protein architectures for the construction of practically useful binding proteins. Properties like small size of the receptor protein, stability and ease of production were the focus of this work. Hence, among others, single domains of antibodies or of the immunoglobulin superfamily, protease inhibitors, helix-bundle proteins, disulphide-knotted peptides and lipocalins were investigated. Recently, the scaffold concept has even been adopted for the construction of enzymes. However, it appears that not all kinds of polypeptide fold which may appear attractive for the engineering of loop regions at a first glance will indeed permit the construction of independent ligand-binding sites with high affinities and specificities. This review will therefore concentrate on the critical description of the structural properties of experimentally tested protein scaffolds and of the novel functions that have been achieved on their basis, rather than on the methodology of how to best select a particular mutant with a certain activity. An overview will be provided about the current approaches, and some emerging trends will be identified. (c) 2000 John Wiley & Sons, Ltd. Abbreviations used: ABD albumin-binding domain of protein G APPI Alzheimer's amyloid beta-protein precursor inhibitor BBP bilin-binding protein BPTI bovine (or basic) pancreatic trypsin inhibitor BSA bovine serum albumin CBD cellulose-binding domain of cellobiohydrolase I CD circular dichroism Cdk2 human cyclin-dependent kinase 2 CDR complementarity-determining region CTLA-4 human cytotoxic T-lymphocyte associated protein-4 FN3 fibronectin type III domain GSH glutathione GST glutathione S-transferase hIL-6 human interleukin-6 HSA human serum albumin IC(50) half-maximal inhibitory concentration Ig immunoglobulin IMAC immobilized metal affinity chromatography K(D) equilibrium constant of dissociation K(i) equilibrium dissociation constant of enzyme inhibitor LACI-D1 human lipoprotein-associated coagulation inhibitor pIII gene III minor coat protein from filamentous bacteriophage f1 PCR polymerase-chain reaction PDB Protein Data Bank PSTI human pancreatic secretory trypsin inhibitor RBP retinol-binding protein SPR surface plasmon resonance TrxA E. coli thioredoxin
Sensitive Fluorescence Polarization Technique for Rapid Screening of α-Synuclein Oligomerization/Fibrillization Inhibitors (2007)

Parkinson's disease (PD) is characterized by the accumulation of fibrillar alpha-synuclein (alpha-Syn) inclusions known as Lewy bodies (LBs) and Lewy neurites. Mutations in the alpha-Syn gene or extra copies thereof cause familial PD or dementia with LBs (DLB) in rare kindreds, but abnormal accumulations of wildtype alpha-Syn also are implicated in the pathogenesis of sporadic PD, the most common movement disorder. Insights into mechanisms underlying alpha-Syn mediated neurodegeneration link alpha-Syn oligomerization and fibrillization to the onset and progression of PD. Thus, inhibiting alpha-Syn oligomer or fibril formation is a compelling target for discovering disease modifying therapies for PD, DLB, and related synucleinopathies. Although amyloid dyes recognize alpha-Syn fibrils, efficient detection of soluble oligomers remains a challenge. Here, we report a novel fluorescence polarization (FP) technique for examining alpha-Syn assembly by monitoring changes in its relative molecular mass during progression of normal alpha-Syn from highly soluble monomers to higher order multimers and thence insoluble amyloid fibrils. We report that FP is more sensitive than conventional amyloid dye methods for the quantification of mature fibrils, and that FP is capable of detecting oligomeric alpha-Syn, allowing for rapid automated screening of potential inhibitors of alpha-Syn oligomerization and fibrillization. Furthermore, FP can be combined with an amyloid dye in a single assay that simultaneously provides two independent biophysical readouts for monitoring alpha-Syn fibrillization. Thus, this FP method holds potential to accelerate discovery of disease modifying therapies for LB PD, DLB, and related neurodegenerative synucleinopathies.
ChemInform Abstract: Electrostatic Activation of Nucleofuges: Cationic Leaving Groups. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Role of Ca2+-Dependent K+Channels in Cerebral Vasodilatation Induced by Increases in Cyclic GMP and Cyclic AMP in the Rat (1996)

These findings suggest that dilatation of cerebral arterioles by receptor-mediated activation of adenylate cyclase and by direct activation of guanylate cyclase in the rat is mediated in large part by activation of Ca(2+)-dependent K+ channels.
The emergence of nonuniform spatiotemporal fractionation schemes within the standard BED model (2015)

Nonuniform spatiotemporal fractionation schemes represent a novel approach to exploit fractionation effects that deserves further exploration for selected disease sites.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees (1997)

Seq-Gen can be obtained by WWW from http:/(/)evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html++ + or by FTP from ftp:/(/)evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.
Loss of function of the Drosophila zfh-1 gene results in abnormal development of mesodermally derived tissues. (1993)

The Drosophila zfh-1 gene encodes an unusual protein with nine Cys2His2 type zinc-finger motifs and one homeodomain that shows a complex pattern of expression in the embryonic mesoderm and nervous system. To study the function of zfh-1, we generated loss-of-function zfh-1 mutations. Phenotypic analysis of zfh-1 mutant embryos reveals that the gene is not required for the initial segregation of the mesoderm or for the differentiation of mesodermally derived tissues. Rather, loss of zfh-1 function results in various degrees of local errors in cell fate or positioning.
Six1 regulates stem cell repair potential and self-renewal during skeletal muscle regeneration (2012)

Satellite cells (SCs) are stem cells that mediate skeletal muscle growth and regeneration. Here, we observe that adult quiescent SCs and their activated descendants expressed the homeodomain transcription factor Six1. Genetic disruption of Six1 specifically in adult SCs impaired myogenic cell differentiation, impaired myofiber repair during regeneration, and perturbed homeostasis of the stem cell niche, as indicated by an increase in SC self-renewal. Six1 regulated the expression of the myogenic regulatory factors MyoD and Myogenin, but not Myf5, which suggests that Six1 acts on divergent genetic networks in the embryo and in the adult. Moreover, we demonstrate that Six1 regulates the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway during regeneration via direct control of Dusp6 transcription. Muscles lacking Dusp6 were able to regenerate properly but showed a marked increase in SC number after regeneration. We conclude that Six1 homeoproteins act as a rheostat system to ensure proper regeneration of the tissue and replenishment of the stem cell pool during the events that follow skeletal muscle trauma.
Potent Inhibitory Effect of Flavonoids inScutellaria baicalensison Amyloid β Protein-Induced Neurotoxicity (2004)

The free radical scavenging activities of two major flavonoids (baicalein and baicalin) in Scutellaria baicalensis were determined. The antioxidant capacities of baicalein and baicalin were determined by the 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid)(*)(-) scavenging assay and showed about 110 and 70% vitamin C equivalent antioxidant capacity, respectively. Because amyloid beta (Abeta) protein is known to increase free radical production and lipid peroxidation in PC12 nerve cells, leading to apoptosis and cell death, treatment with baicalein and baicalin may result in the prevention of cellular damage by the Abeta-induced reactive oxygen species. We found that baicalein and baicalin resulted in a dose-dependent anti-Abeta toxicity by means of three different assays [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction, lactate dehydrogenase release, and trypan blue exclusion assays]. These results suggest that baicalein as well as baicalin can reduce the cytotoxicity of Abeta protein in PC12 cells, possibly by a reduction of oxidative stress, and these flavonoids may be useful in the chemoprevention of Alzheimer's disease.