gebhart/patrepeval huggingface dataset:
Primary and Metastatic Melanoma With NTRK Fusions (2018)

A number of oncogenic driver mutations have been identified in melanocytic nevi and melanoma, but translocations also play a role in tumorigenesis and provide potential therapeutic targets for malignant lesions. Various translocations, such as those involving the anaplastic lymphoma kinase ( ALK ), neurotrophic tropomyosin receptor kinase 1 ( NTRK1 ), and NTRK3 have been reported in spitzoid melanocytic neoplasms leading to kinase-fusion proteins that result in immunohistochemically detectable ALK or NTRK expression. We have previously reported that ALK expression can be found in nonspitzoid primary and metastatic cutaneous melanomas. In this study we report that nonspitzoid metastasizing melanomas of adults may also harbor NTRK fusions and that NTRK expression can be immunohistochemically detected in these tumors. Of 751 melanomas analyzed by next-generation sequencing, 4 metastatic melanomas were identified with NTRK fusions, 3 involving NTRK1 , 1 involving NTRK2 . They occurred in 3 women and 1 man. Two of the corresponding primary tumors were from the trunk, 1 from an extremity and 1 tumor arose in anal skin. One primary tumor displayed features of superficial spreading melanoma and 3 were nodular melanomas. All tumors were cytologically characterized by the presence of large epithelioid melanocytes. All tumors were immunoreactive with anti-Trk antibody. Next-generation sequencing documented that the NTRK1 fusion partners included TRIM63 , DDR2 , and GON4L . One tumor harbored an NTRK2-TRAF2 fusion. Thus, our findings document that NTRK kinase fusions can occur in nonspitzoid metastasizing melanomas of adults. The presence of an NTRK family fusion in these tumors may provide a therapeutic opportunity in a small subset of patients with metastatic melanoma.
An in vivo assay identifies changes in residue accessibility on mechanosensitive channel gating (2004)

MscL is a mechanosensitive channel of large conductance that functions as an "emergency release valve," allowing bacteria to survive acute hypoosmotic stress. Although Escherichia coli MscL is the best-studied mechanosensitive channel, structural rearrangements occurring during gating remain disputed. Introduction of a charged residue into the pore of MscL was shown to result in a reduced-viability phenotype. Here, we probe for residues in the transmembrane domains that are exposed to the aqueous environment in the presence and absence of hypoosmotic shock by reacting a charged sulfhydryl reagent with substituted cysteines. Subsequent analysis of cell viability allows for an assessment of residues exposed in the closed and opening states in vivo. The results suggest that the crystal structure of MscL derived from the Mycobacterium tuberculosis orthologue may reflect a nearly closed rather than fully closed state and support a clockwise rotation of the pore-forming first transmembrane domain on gating.
GABRA1 and STXBP1 : Novel genetic causes of Dravet syndrome (2014)

We show that GABRA1 and STXBP1 make a significant contribution to Dravet syndrome after SCN1A abnormalities have been excluded. Our results have important implications for diagnostic testing, clinical management, and genetic counseling of patients with this devastating disorder and their families.
Lipoprotein fractionation in deuterium oxide gradients: a procedure for evaluation of antioxidant binding and susceptibility to oxidation. (1994)

Oxidative modifications of lipoproteins appear to contribute to their atherogenicity. Very low and low density lipoproteins (VLDL and LDL) are protected against these modifications by antioxidants that can be incorporated in vivo or in vitro into the particles. We describe here ultracentrifugal procedures for isolation of VLDL and LDL that do not require subsequent dialysis or buffer equilibration. Lipoproteins were isolated in buffers with physiological ionic composition prepared in D2O (deuterium oxide). This allowed measurements of the content of antioxidants and of the susceptibility to oxidation of the isolated LDL without further manipulations. Conventional ultracentrifugal methods use high salt concentrations and require additional steps to eliminate them. This introduces uncertainties in the evaluation of antioxidant binding and on measurements of their effect on VLDL and LDL oxidation. With the method described, the composition of the isolated VLDL and LDL was indistinguishable from that of fractions isolated with KBr gradients. Also, the content of alpha-tocopherol was similar. LDL isolated with KBr solutions appeared to bind 20-45% more of the probucol present in serum than LDL isolated in isotonic solutions prepared with D2O. This was the case with probucol incorporated into plasma or serum in vivo or in vitro. Five out of seven LDL isolated with the D2O procedure from different human sera appeared more resistant to Cu(2+)-catalyzed oxidation than those obtained with KBr gradients from the same serum. In addition to the gradient procedure, we also describe a preparative version of the method that can be used with multiple samples.
Assessing the Activity of Cediranib, a VEGFR-2/3 Tyrosine Kinase Inhibitor, against VEGFR-1 and Members of the Structurally Related PDGFR Family (2011)

Cediranib is a potent inhibitor of the VEGF receptor (VEGFR)-2 and VEGFR-3 tyrosine kinases. This study assessed the activity of cediranib against the VEGFR-1 tyrosine kinase and the platelet-derived growth factor receptor (PDGFR)-associated kinases c-Kit, PDGFR-α, and PDGFR-β. Cediranib inhibited VEGF-A-stimulated VEGFR-1 activation in AG1-G1-Flt1 cells (IC(50) = 1.2 nmol/L). VEGF-A induced greatest phosphorylation of VEGFR-1 at tyrosine residues Y1048 and Y1053; this was reversed by cediranib. Potency against VEGFR-1 was comparable with that previously observed versus VEGFR-2 and VEGFR-3. Cediranib also showed significant activity against wild-type c-Kit in cellular phosphorylation assays (IC(50) = 1-3 nmol/L) and in a stem cell factor-induced proliferation assay (IC(50) = 13 nmol/L). Furthermore, phosphorylation of wild-type c-Kit in NCI-H526 tumor xenografts was reduced markedly following oral administration of cediranib (≥1.5 mg/kg/d) to tumor-bearing nude mice. The activity of cediranib against PDGFR-β and PDGFR-α was studied in tumor cell lines, vascular smooth muscle cells (VSMC), and a fibroblast line using PDGF-AA and PDGF-BB ligands. Both receptor phosphorylation (IC(50) = 12-32 nmol/L) and PDGF-BB-stimulated cellular proliferation (IC(50) = 32 nmol/L in human VSMCs; 64 nmol/L in osteosarcoma cells) were inhibited. In vivo, ligand-induced PDGFR-β phosphorylation in murine lung tissue was inhibited by 55% following treatment with cediranib at 6 mg/kg but not at 3 mg/kg or less. In contrast, in C6 rat glial tumor xenografts in mice, ligand-induced phosphorylation of both PDGFR-α and PDGFR-β was reduced by 46% to 61% with 0.75 mg/kg cediranib. Additional selectivity was showed versus Flt-3, CSF-1R, EGFR, FGFR1, and FGFR4. Collectively, these data indicate that cediranib is a potent pan-VEGFR kinase inhibitor with similar activity against c-Kit but is significantly less potent than PDGFR-α and PDGFR-β.
It's a Blog, Blog, Blog World: Users and Uses of Weblogs (2005)

This study surveyed 3,747 Weblog readers online from April 23, 2003, to May 22, 2003, to examine their motives for using Weblogs. Weblog users tend to be young, highly educated men with high incomes. Respondents report moderate to high levels of trust in government, high self-efficacy, and high interest in political and general news. A factor analysis revealed six primary motivations for accessing Weblogs: information seeking and media check, convenience, personal fulfillment, political surveillance, social surveillance, and expression and affiliation. Additionally, hierarchical regression found that political involvement predicted all six Weblog motivations. Further, each of the independent variables predicted at least one of the Weblog motivations.
AKT2, a member of the protein kinase B family, is activated by growth factors, v-Ha-ras, and v-src through phosphatidylinositol 3-kinase in human ovarian epithelial cancer cells. (1998)

Three members have been identified in the protein kinase B (PKB) family, i.e., Akt/PKB alpha, AKT2/PKB beta, and AKT3/PKB gamma. Previous studies have demonstrated that only AKT2 is predominantly involved in human malignancies and has oncogenic activity. However, the mechanism of transforming activity of AKT2 is still not well understood. Here, we demonstrate the activation of AKT2 with several growth factors, including epidermal growth factor, insulin-like growth factor 1, insulin-like growth factor II, basic fibroblast growth factor, platelet-derived growth factor, and insulin, in human ovarian epithelial cancer cells. The kinase activity and the phosphorylation of AKT2 were induced by the growth factors and blocked by the phosphatidylinositol (PI) 3-kinase inhibitor, wortmannin, and dominant-negative Ras (N17Ras). Moreover, the activated Ras and v-Src, two proteins that transduce growth factor-generated signals, also activated AKT2, and this activation was not significantly enhanced by growth factor stimulation but was abrogated by wortmannin. These results indicate that AKT2 is a downstream target of PI 3-kinase and that Ras and Src function upstream of PI 3-kinase and mediate the activation of AKT2 by growth factors. The findings also provide further evidence that AKT2, in cooperation with Ras and Src, is important in the development of some human malignancies.
Transmission of independent signals through a multimode fiber using digital optical phase conjugation (2016)

Multimode fibers are attractive for a variety of applications such as communication engineering and biophotonics. However, a major hurdle for the optical transmission through multimode fibers is the inherent mode mixing. Although an image transmission was successfully accomplished using wavefront shaping, the image information was not transmitted individually for each of the independent pixels. We demonstrate a transmission of independent signals using individually shaped wavefronts employing a single segmented spatial light modulator for optical phase conjugation regarding each light signal. Our findings pave the way towards transferring independent signals through strongly scattering media.
Elevated γ-Aminobutyric Acid, Glutamate, and Vascular Endothelial Growth Factor Levels in the Vitreous of Patients With Proliferative Diabetic Retinopathy (1997)

Levels of glutamate potentially toxic to retinal ganglion cells are found in the vitreous of patients with PDR. Elevated vitreous GABA may reflect amacrine cell dysfunction and underlie electroretinographic oscillatory potential abnormalities seen in diabetic retinopathy. The correlations of glutamate and GABA levels with an elevated VEGF level provide biochemical support for ischemia-induced neovascularization in patients with PDR. These findings present opportunities for novel therapeutic modalities in the treatment of PDR.
(R,S)‐Reticuline 7‐O‐methyltransferase and (R,S)‐norcoclaurine 6‐O‐methyltransferase of Papaver somniferum – cDNA cloning and characterization of methyl transfer enzymes of alkaloid biosynthesis in opium poppy (2003)

S-Adenosyl-L-methionine:(R,S)-reticuline 7-O-methyltransferase converts reticuline to laudanine in tetrahydrobenzylisoquinoline biosynthesis in the opium poppy Papaver somniferum. This enzyme activity has not yet been detected in plants. A proteomic analysis of P. somniferum latex identified a gel spot that contained a protein(s) whose partial amino acid sequences were homologous to those of plant O-methyltransferases. cDNA was amplified from P. somniferum RNA by reverse transcription PCR using primers based on these internal amino acid sequences. Recombinant protein was then expressed in Spodoptera frugiperda Sf9 cells in a baculovirus expression vector. Steady-state kinetic measurements with one heterologously expressed enzyme and mass spectrometric analysis of the enzymatic products suggested that this unusual enzyme is capable of carrying through sequential O-methylations on the isoquinoline and on the benzyl moiety of several substrates. The tetrahydrobenzylisoquinolines (R)-reticuline (4.2 sec(-1) mm(-1)), (S)-reticuline (4.5 sec(-1) mm(-1)), (R)-protosinomenine (1.7 sec(-1) mm(-1)), and (R,S)-isoorientaline (1.4 sec(-1) mm(-1)) as well as guaiacol (5.9 sec(-1) mm(-1)) and isovanillic acid (1.2 sec(-1) mm(-1)) are O-methylated by the enzyme with the ratio kcat/K m shown in parentheses. A P. somniferum cDNA encoding (R,S)-norcoclaurine 6-O-methyltransferase was similarly isolated and characterized. This enzyme was less permissive, methylating only (R,S)-norcoclaurine (7.4 sec(-1) mm(-1)), (R)-norprotosinomenine (4.1 sec(-1) mm(-1)), (S)-norprotosinomenine (4.0 sec(-1) mm(-1)) and (R,S)-isoorientaline (1.0 sec(-1) mm(-1)). A phylogenetic comparison of the amino acid sequences of these O-methyltransferases to those from 28 other plant species suggests that these enzymes group more closely to isoquinoline biosynthetic O-methyltransferases from Coptis japonica than to those from Thalictrum tuberosum that can O-methylate both alkaloid and phenylpropanoid substrates.
Device-to-Device Communications for National Security and Public Safety (2014)

Device-to-device (D2D) communications have been proposed as an underlay to long-term evolution (LTE) networks as a means of harvesting the proximity, reuse, and hop gains. However, D2D communications can also serve as a technology component for providing public protection and disaster relief (PPDR) and national security and public safety (NSPS) services. In the United States, for example, spectrum has been reserved in the 700-MHz band for an LTE-based public safety network. The key requirement for the evolving broadband PPDR and NSPS services capable systems is to provide access to cellular services when the infrastructure is available and to efficiently support local services even if a subset or all of the network nodes become dysfunctional due to public disaster or emergency situations. This paper reviews some of the key requirements, technology challenges, and solution approaches that must be in place in order to enable LTE networks and, in particular, D2D communications, to meet PPDR and NSPS-related requirements. In particular, we propose a clustering-procedure-based approach to the design of a system that integrates cellular and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ad hoc</i> operation modes depending on the availability of infrastructure nodes. System simulations demonstrate the viability of the proposed design. The proposed scheme is currently considered as a technology component of the evolving 5G concept developed by the European 5G research project METIS.
Olefin Metathesis and Beyond (2000)

The advent of well-defined catalysts for olefin metathesis which combine high activity, durability, and excellent tolerance towards polar functional groups has revolutionized the field. The past decade has seen the rapid embrace of these reagents as tools for advanced organic and polymer chemistry and the success of this development is witnessed by a plethora of elegant applications to the synthesis of natural and nonnatural products. This review article provides an overview of these developments and intends to familiarize the reader with some very recent advances which hold the promise to expand the scope of the reaction even further. Moreover, the positive impact of metathesis on the fundamental logic of retrosynthetic planning is demonstrated by means of typical examples. Finally, it will be shown that metathesis is by no means restricted to alkenes as substrates, and some comments on metathesis reactions following unconventional mechanistic pathways will also be presented.
Etanercept improves linear growth and bone mass acquisition in MTX-resistant polyarticular-course juvenile idiopathic arthritis (2010)

Clinical control of disease activity by etanercept in MTX-refractory polyJIA is associated with rapidly instituted catch-up growth and improvement of bone mineralization and body composition. In recently diagnosed polyJIA patients treated with MTX the relation between clinical response and these parameters was less evident. Preliminary data on serum IL-6 and osteoprotegerin levels indicate that the beneficial effects seen with etanercept therapy may be related to its control of systemic IL-6 production and enhancement of osteoblast activity.
A Study on the Failure Definition for the MTBF Evaluation (1988)

MTBF (Mean Time Between Failures) is one of the measures to express the reliability for a repairable system, especially for a military weapon system. But MTBF is meaningless without a clear definition of the system failures. In this paper we discuss two failure definitions, one is defined by US Army Training and Doctrine Command jointly with US Army Materiel Command and the other one is used to M1 Tank.
ELO2 and ELO3, Homologues of theSaccharomyces cerevisiae ELO1 Gene, Function in Fatty Acid Elongation and Are Required for Sphingolipid Formation (1997)

ELO2 and ELO3 were identified from the Saccharomyces cerevisiae genome data base as homologues of ELO1, a gene involved in the elongation of the fatty acid 14:0 to 16:0. Mutations in these genes have previously been shown to produce pleiotropic effects involving a number of membrane functions. The simultaneous disruption of ELO2 and ELO3 has also been shown to produce synthetic lethality, indicating that they have related and/or overlapping functions. Gas chromatography and gas chromatography/mass spectroscopy analyses reveal that null mutations of ELO2 and ELO3 produce defects in the formation of very long chain fatty acids. Analysis of the null mutants indicates that these genes encode components of the membrane-bound fatty acid elongation systems that produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids. Elo2p appears to be involved in the elongation of fatty acids up to 24 carbons. It appears to have the highest affinity for substrates with chain lengths less than 22 carbons. Elo3p apparently has a broader substrate specificity and is essential for the conversion of 24-carbon acids to 26-carbon species. Disruption of either gene reduces cellular sphingolipid levels and results in the accumulation of the long chain base, phytosphingosine. Null mutations in ELO3 result in accumulation of labeled precursors into inositol phosphoceramide, with little labeling in the more complex mannosylated sphingolipids, whereas disruption of ELO2 results in reduced levels of all sphingolipids.
Use of pKa Differences To Enhance the Formation of Base Triplets Involving C−G and G−C Base Pairs (2000)

Two C-nucleosides are employed for the recognition of dC-dG base pairs. Both derivatives are related to dC but lack the O2-carbonyl. The absence of the carbonyl should eliminate any unfavorable steric interactions at this site. One of the derivatives contains a 2-aminopyridine heterocycle (d2APy) while the second contains a 2-aminopyrimidine heterocycle (d2APm). The former with a pK(a) of 6. 8 functions better for the recognition of dG-dC base pairs than it does in the binding to dC-dG base pairs. The d2APm derivative with a pK(a) of 3.3 functions better to form base triplets with dC-dG base pairs than with dG-dC targets. Triplex T(m)'s in both cases are compared with the sequence containing the native dC residue. The dC analogues appear to make two hydrogen bonds to a target dG base residue, one of which requires protonation of the ring nitrogen. Recognition of a target dC residue appears to require the formation of a single hydrogen bond to the C-nucleoside and having that nitrogen largely in the unprotonated state facilitates its formation.
Synaptotagmin Modulation of Fusion Pore Kinetics in Regulated Exocytosis of Dense-Core Vesicles (2001)

In the exocytosis of neurotransmitter, fusion pore opening represents the first instant of fluid contact between the vesicle lumen and extracellular space. The existence of the fusion pore has been established by electrical measurements, but its molecular composition is unknown. The possibility that synaptotagmin regulates fusion pores was investigated with amperometry to monitor exocytosis of single dense-core vesicles. Overexpression of synaptotagmin I prolonged the time from fusion pore opening to dilation, whereas synaptotagmin IV shortened this time. Both synaptotagmin isoforms reduced norepinephrine flux through open fusion pores. Thus, synaptotagmin interacts with fusion pores, possibly by associating with a core complex of membrane proteins and/or lipid.
Focusing processor policies via critical-path prediction (2001)

Although some instructions hurt performance more than others, current processors typically apply scheduling and speculation as if each instruction was equally costly. Instruction cost can be naturally expressed through the critical path: if we could predict it at run-time, egalitarian policies could be replaced with cost-sensitive strategies that will grow increasingly effective as processors become more parallel.This paper introduces a hardware predictor of instruction criticality and uses it to improve performance. The predictor is both effective and simple in its hardware implementation. The effectiveness at improving performance stems from using a dependence-graph model of the microarchitectural critical path that identifies execution bottlenecks by incorporating both data and machine-specific dependences. The simplicity stems from a token-passing algorithm that computes the critical path without actually building the dependence graph.By focusing processor policies on critical instructions, our predictor enables a large class of optimizations. It can (i) give priority to critical instructions for scarce resources (functional units, ports, predictor entries); and (ii) suppress speculation on non-critical instructions, thus reducing “useless” misspeculations. We present two case studies that illustrate the potential of the two types of optimization, we show that (i) critical-path-based dynamic instruction scheduling and steering in a clustered architecture improves performance by as much as 21% (10% on average); and (ii) focusing value prediction only on critical instructions improves performance by as much as 5%, due to removing nearly half of the misspeculations.
Carma1, a CARD‐containing binding partner of Bcl10, induces Bcl10 phosphorylation and NF‐κB activation1 (2001)

Bcl10, a caspase recruitment domain (CARD)-containing protein identified from a breakpoint in mucosa-associated lymphoid tissue (MALT) B lymphomas, is essential for antigen-receptor-mediated nuclear factor kappaB (NF-kappaB) activation in lymphocytes. We have identified a novel CARD-containing protein and interaction partner of Bcl10, named Carma1. Carma1 is predominantly expressed in lymphocytes and represents a new member of the membrane-associated guanylate kinase family. Carma1 binds Bcl10 via its CARD motif and induces translocation of Bcl10 from the cytoplasm into perinuclear structures. Moreover, expression of Carma1 induces phosphorylation of Bcl10 and activation of the transcription factor NF-kappaB. We propose that Carma1 is a crucial component of a novel Bcl10-dependent signaling pathway in T-cells that leads to the activation of NF-kappaB.