gebhart/patrepeval huggingface dataset:
A Unified Mechanism of Tyrosine Kinase Regulation by the Gatekeeper Residue. (2007)

Abstract Protein kinase inhibitors achieve binding specificity through contact with a hydrophobic pocket within the ATP-binding cleft. Access to the pocket is dictated by an amino acid residue dubbed the “gatekeeper”, which is threonine in many kinases. Drug resistance is often due to substitution of the gatekeeper threonine with a bulkier amino acid residue that sterically hinders the binding of some drugs. Here we show that substituting a bulky hydrophobic residue in place of threonine in the native cellular forms of c-ABL, c-SRC, PDGFRA, PDGFRB, and EGFR activates kinase activity and promotes malignant transformation of BaF3 cells. Structural modelling and crystallographic analysis reveal that a network of hydrophobic interactions characteristic of the active kinase conformation is stabilized by the gatekeeper substitution. In the inactive kinase conformation, this hydrophobic interactions are dismantled. A small molecule inhibitor that maximizes complementarity with the dismantled spine (Compound #14) inhibits the gatekeeper mutation of BCR/ABL (T315I). These results demonstrate that mutation of the gatekeeper threonine is a common mechanism of activation for tyrosine kinases, and provide structural insights to guide the development of novel inhibitors.
Freeze-out radii extracted from three-pion cumulants in pp, p–Pb and Pb–Pb collisions at the LHC (2014)

come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destine au dpt et la diffusion de documents scientifiques de niveau recherche, publis ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.
Microencapsulation using an oil-in-water-in-air ‘dry water emulsion’ (2011)

We describe the first example of a tri-phasic oil-in-water-in-air 'dry water emulsion'. The method combines highly stable oil-in-water emulsions prepared using branched copolymer surfactants, with aqueous droplet encapsulation using 'dry water' technology.
Polarization‐Selective Patterning in an Anisotropic Smectic B Film (2016)

The versatility of optical lithography can be expanded by using the polarization state of light as an additional parameter next to the intensity of light. This result is confirmed by exposing a highly polarization-selective photoreactive material with polarization holography which results in the formation of defined grating structures.
Measuring Copolymer Formation from End-Functionalized Chains at a PS/PMMA Interface Using FRES and SEC (2000)

Two experimental techniques, forward recoil spectrometry (FRES) and size exclusion chromatography with fluorescence detection (SEC/fluorescence), have been used to monitor independently the extent of reaction between model end-functional polymers at a PS/PMMA interface. Bilayer samples comprising a polystyrene layer containing ca. 8.4 wt % of amino-terminal deuterated polystyrene (dPS-NH2, M = 22 000 g/mol) on an anhydride-terminal fluorescent poly(methyl methacrylate) (*PMMA-anh, M = 31 200 g/mol) layer were annealed at 174 °C for various periods. An interfacial excess observed in the FRES concentration profiles of the dPS-NH2 in the PS layer was used to determine an interfacial coverage of diblock copolymer and a conversion of dPS-NH2 to diblock copolymer. Similarly, the conversion of the fluorescent *PMMA-anh to diblock copolymer was measured using SEC coupled with a fluorescence detector. Both techniques indicate similar reaction kinetics: the formation of copolymer in the interfacial region continued over several hours and approached a steady-state value after 24 h. Interfacial coverages determined from both methods typically agreed to within 15−20%. This validation of the fluorescence approach is important for further investigation of polymer−polymer reaction kinetics and interfacial segregation during in situ reactive polymer compatibilization.
Biotin-Bearing pH-Sensitive Liposomes: High-Affinity Binding to Avidin Layer (1989)

A procedure is described for the preparation of biotin-bearing pH-sensitive liposomes. Liposomes were composed of phosphatidylethanolamine/oleic acid/ cholesterol/biotinaminocaproyl phosphatidylethanolamine (molar ratio 7:3:3:0.1) and contained the fluorescent dye calcein in self-quenched concentrations. these liposomes rapidly destabilized in weakly acidic media (pH 5.7). Liposomes were also readily agglutinated by acetylated avidin. Addition of biotin blocked the agglutination process. Binding of liposomes to a plastic surface coated with acetylated avidin was studied. the high-affinity binding with an apparent KD value up to 10−11 M liposomes was demonstrated by Scatchard analysis of the binding curves. A method of efficiently coating polyvinyl chloride microELisA plates with acylated avidin is also described.
The Vitamin B12-Binding Proteins of Some Amphibians (1971)

Three immunologically distinct unsaturated (without vitamin) vitamin B12-binding proteins have been demonstrated in humans. Intrinsic factor, the best known, has a molecular weight of 55,000 and promotes the uptake of vitamin B12 by the intestinal epithelium (1, 2). Transcobalamin II, a liver-synthesized serum B12 binder with a molecular weight of 35,000, is apparently responsible for the uptake of the vitamin by the tissues (1, 2). A third binder, R binder or transcobalamin I, has a molecular weight of 110,000 and is found in serum, saliva, gastric juice, and a variety of other body fluids (1, 2). The function of this binder is not known. It has been shown recently that chickens have a single unsaturated serum B12 binder with a molecular weight of 113,000 and an immunologically similar proventriculus B12 binder with a molecular weight of 96,000 (3). These binders superficially resemble the human R binders. They are approximately the same size as the human R binder, and in both cases immunologically similar forms occur in both the serum and gastric juice. However, antibody against the chicken binder does not react with human R binder (3). The present study demonstrates the presence of unsaturated B12 binders in amphibians. These resemble neither the human binders nor the chicken binders. Materials and Methods. Levels of unsaturated vitamin B12 (B12) binders were measured using zirconyl phosphate gel (Z-gel), a highly negatively charged gel that binds proteins below their isoelectric point (4, 5). B12-57Co was purchased from Philips-Duphar, Holland, and was diluted with unlabeled B12 to give solutions containing either 100 ng/ml (1000 counts/ng) or 10 ng/ml (10,000 counts/ng). B12-60Co was used as purchased (1 μCi/1.484 μg or 0.652 μCi/μg; E. R. Squibb and Sons, New York).
Supplementary Table S2 from A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non–Small Cell Lung Cancer and Serum DNA (2023)

&lt;p&gt;Supplementary Table S2.Thirty genes for further analyses selected from LUAD TCGA dataset.&lt;/p&gt;
Lawful-Intercept Support for SP Wi-Fi Deployments (2013)

Lawful Intercept stands for legally authorized capture & delivery of
subscriber communications data by a communications provider to a law
enforcement agency.This document describes Generic Lawful Intercept
Architecture Models & implementation considerations for Service
Provider Wi-Fi deployments.
Finding probably best system configurations quickly (2006)

Computer systems often have many possible configurations, and designing a high performance system often requires selecting the best configuration. Unfortunately, the performance of complex systems can often be estimated only via simulations, or with measurements of real systems. Since longer simulation times are required to estimate the performance more accurately, it is often computationally intractable to estimate the performance of all configurations accurately via simulations. (Measurements of real systems can take even longer.)
Concept of Analog-to-Information (2016)

In this chapter the concept of analog-to-information (A-to-I) is introduced. The name A-to-I comes from the Analog-to-Information Receiver Development concept presented in a Defense Advanced Research Projects Agency (DARPA) program. The goal of A-to-I is to use a low sampling frequency to cover a wide input frequency band beyond the Nyquist sampling rate allowed [2-5]. In this chapter we present the analysis results of one of the A-to-I technology development concepts by Northrop Grumman. We would like to acknowledge its contribution and the support of the Air Force Research Laboratory (AFRL).
Impact of RTOS parameters on end-to-end timing performance (2008)

For accurate end-to-end (e2e) analysis of a real-time embedded system (RTES), we need a method to precisely reflect the effects of the underlying real-time operating system (RTOS). In timing analysis, RTOS can be viewed as a matrix of parameters that could affect the timing of the RTES. In this paper, we consider various RTOS parameters that may affect the temporal behavior of the RTES, and propose RTOS modeling as a viable approach to account for the impact of RTOS on e2e timing.
Unmeasurable C-reactive Protein as a Clue in Diagnosis of Severe Hematology Pathologies in Children in Primary Settings (2023)

Abstract Fever is among the most common symptoms which lead parents and their children to the pediatrician. The most common cause of fever in children is acute infection (bacterial or viral). However, sometimes fever can be the manifestation of much more serious diseases. C-reactive protein is a marker widely used in clinical pediatric practice which helps to decide if any antibiotic treatment is needed or not. The authors present 3 case reports of children with fever from the pediatric emergency department, when the result unmeasurable capillary C-reactive protein was one of the clues in the diagnosis of severe hematology pathologies.
Toll-Like Receptor 3 Agonist Protection against ExperimentalFrancisella tularensisRespiratory Tract Infection (2010)

We investigated whether Toll-like receptor 3 (TLR3) stimulation would protect the host from inhaled Francisella tularensis. TLR3 is expressed by respiratory epithelial cells and macrophages and can be activated by a synthetic double-stranded RNA ligand called polyinosine-polycytosine [poly(I:C)]. Thus, we evaluated poly(I:C) as a novel treatment against inhaled F. tularensis. In vivo, BALB/c mice intranasally (i.n.) treated with poly(I:C) (100 microg/mouse) 1 h before or after Schu 4 or LVS (100 CFU) i.n. challenge showed that poly(I:C) treatment significantly reduced bacterial load in the lungs (P < 0.05). Bronchoalveolar lavage from poly(I:C)-treated mice alone or combined with F. tularensis infection significantly increased cytokine secretion and enhanced neutrophil influx to lung tissues. Poly(I:C) responses were transient but significantly prolonged the survival of treated mice after i.n. F. tularensis challenge relative to mock treated animals. This prolonged survival providing a longer window for initiation of levofloxacin (LEVO) treatment (40 mg/kg). Animals treated with poly(I:C), challenged with F. tularensis, and then treated with LEVO 5 days later had 100% survival relative to 0% survival in animals receiving LEVO alone. Mechanistically, poly(I:C) given to human monocyte-derived macrophages before or after Schu 4 or LVS challenge (multiplicity of infection, 20:1) had significantly reduced intracellular bacterial replication (P < 0.05). These data suggest that poly(I:C) may represent a potential therapeutic agent against inhaled F. tularensis that prolongs survival and the opportunity to initiate standard antibiotic therapy (i.e., LEVO).
III-V Semiconductor Photonic Crystals (2000)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. Noda, "III-V Semiconductor Photonic Crystals," in Integrated Photonics Research, T. Li, ed., Vol. 45 of OSA Trends in Optics and Photonics (Optica Publishing Group, 2000), paper IFA4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Multiple Sample Data Spectroscopic Clustering of Large Datasets Using Nyström Extension (2012)

In this article, we focus on computational aspects of spectral clustering algorithms that have recently shown promising results in machine learning, statistics, and computer vision. These algorithms cluster observations (of size n) into groups by investigating eigenvectors of an affinity matrix or its Laplacian matrix, both of which are size n × n. However, when the sample size is large, the computation involved in the matrix eigen-decomposition is expensive or even infeasible. To overcome the computation hurdle, subsampling techniques, such as the Nyström extension, have been used to approximate eigenvectors of large matrices. We study statistical properties of this approximation and their influence on the accuracy of various spectral clustering algorithms. We show that the perturbation of the spectrum due to subsampling could lead to a large discrepancy among clustering results. In order to provide accurate and stable results for large datasets, we propose a method to combine multiple subsamples using data spectroscopic clustering and the Nyström extension. In addition, we propose a sparse approximation of the eigenvectors to further speed up computation. Simulation and experiments on real datasets show that our approaches work quickly and provide reasonable results that are more stable across samples than the single sample approach. This article has supplementary material online.
Stimulation of Growth Hormone Release and Synthesis by Estrogens in Rat Anterior Pituitary Cells in Culture (1986)

We have investigated the potential effect of estrogens in the control of GH secretion in rat anterior pituitary cells in primary culture. We have found that a 72-h preincubation with 17 beta-estradiol (E2) caused an approximately 2- to 3-fold stimulation of basal and GH-releasing factor (GRF)-induced GH release as well as cellular GH content at EC50 values of 44, 35, and 15 pM, respectively. Estrone and estriol also increased GH release at respective EC50 values of 100 and 250 pM. The stimulatory effects of these steroids on GH release and cellular GH content were competitively blocked by simultaneous incubation with the antiestrogen LY156758. In contrast to thyroid and glucocorticoid hormones, a 72-h pretreatment with E2 failed to potentiate GRF-induced cAMP accumulation or enhance the sensitivity of the GH response to GRF. However, E2 increased the stimulatory effect of submaximal concentrations of dexamethasone on spontaneous and GRF-induced GH release as well as on total GH, but did not further increase the effect of maximal dexamethasone concentrations. As determined by a 60-min pulse labeling with [35S]methionine performed after a 72-h preincubation with E2, GH and PRL synthesis were increased by about 50% above control values (P less than 0.005). The present data clearly indicate for the first time that E2, at physiological concentrations, exerts a stimulatory effect on spontaneous and GRF-induced GH release as well as on cellular GH content, probably resulting, at least in part, from stimulation of GH synthesis.
On the Rate-Distortion Performance of Compressed Sensing (2007)

Encouraging recent results in compressed sensing or compressive sampling suggest that a set of inner products with random measurement vectors forms a good representation of a source vector that is known to be sparse in some fixed basis. With quantization of these inner products, the encoding can be considered universal for sparse signals with known sparsity level. We analyze the operational rate-distortion performance of such source coding both with genie-aided knowledge of the sparsity pattern and maximum likelihood estimation of the sparsity pattern. We show that random measurements induce an additive logarithmic rate penalty, i.e., at high rates the performance with rate R + O(log R) and random measurements is equal to the performance with rate R and deterministic measurements matched to the source.
A unified theory of bone healing and nonunion (2016)

This article presents a unified clinical theory that links established facts about the physiology of bone and homeostasis, with those involved in the healing of fractures and the development of nonunion. The key to this theory is the concept that the tissue that forms in and around a fracture should be considered a specific functional entity. This 'bone-healing unit' produces a physiological response to its biological and mechanical environment, which leads to the normal healing of bone. This tissue responds to mechanical forces and functions according to Wolff's law, Perren's strain theory and Frost's concept of the "mechanostat". In response to the local mechanical environment, the bone-healing unit normally changes with time, producing different tissues that can tolerate various levels of strain. The normal result is the formation of bone that bridges the fracture - healing by callus. Nonunion occurs when the bone-healing unit fails either due to mechanical or biological problems or a combination of both. In clinical practice, the majority of nonunions are due to mechanical problems with instability, resulting in too much strain at the fracture site. In most nonunions, there is an intact bone-healing unit. We suggest that this maintains its biological potential to heal, but fails to function due to the mechanical conditions. The theory predicts the healing pattern of multifragmentary fractures and the observed morphological characteristics of different nonunions. It suggests that the majority of nonunions will heal if the correct mechanical environment is produced by surgery, without the need for biological adjuncts such as autologous bone graft. Cite this article: Bone Joint J 2016;98-B:884-91.
The macrophage in the persistence and pathogenesis of HIV infection (1989)

Gendelrnan, Howard E.; Orenstein, Jan M.; Baca, Lisa M.; Weiser, Barbara; Burger, Harold; Kalter, D. Chester; Meltzer, Monte S.
A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes (2022)

Globally, autosomal recessive IFNAR1 deficiency is a rare inborn error of immunity underlying susceptibility to live attenuated vaccine and wild-type viruses. We report seven children from five unrelated kindreds of western Polynesian ancestry who suffered from severe viral diseases. All the patients are homozygous for the same nonsense IFNAR1 variant (p.Glu386*). This allele encodes a truncated protein that is absent from the cell surface and is loss-of-function. The fibroblasts of the patients do not respond to type I IFNs (IFN-α2, IFN-ω, or IFN-β). Remarkably, this IFNAR1 variant has a minor allele frequency >1% in Samoa and is also observed in the Cook, Society, Marquesas, and Austral islands, as well as Fiji, whereas it is extremely rare or absent in the other populations tested, including those of the Pacific region. Inherited IFNAR1 deficiency should be considered in individuals of Polynesian ancestry with severe viral illnesses.
Finding good linear approximations of block ciphers and its >>> application to cryptanalysis of reduced round DES (2009)

International audience
Synthesis of Isoindigo-Based Oligothiophenes for Molecular Bulk Heterojunction Solar Cells (2010)

Isoindigo, as a new electron acceptor unit for organic electronic materials, was integrated into two low-energy gap oligothiophenes. Optical and electrochemical studies of the newly synthesized oligomers demonstrate broad absorption through the visible spectrum, along with appropriate energy levels, as desired for light harvesting donors for organic solar cells when blended with [6,6]-phenyl-C(61)-butyric acid methyl ester (PC(60)BM). Molecular heterojunction solar cells were fabricated using these oligomers and exhibit a power conversion efficiency up to 1.76% with a V(oc) of 0.74 V, I(sc) of 6.3 mA/cm(2) and fill factor of 0.38.
Ultrahigh-stability photonic sampling streams from an actively-modelocked semiconductor diode ring laser (2001)

Summary form only given. Future analog-to-digital conversion needs have inspired recent focus on hybrid optoelectronic systems. The use of short optical pulses for sampling temporal signals promises more accuracy than high-speed electronic comparators. Additional requirements for achieving high precision in high-speed sampling streams are ultralow amplitude and phase noise. Semiconductor optical amplifiers (SOAs) have exhibited proficiency in each of these areas. We report the experimental achievement of optical sampling streams capable of resolving 8.6 bits at a 10 GHz repetition rate. Such accuracy results from ultrashort pulsewidths (1.2 ps), ultralow amplitude noise (0.12% RMS), and ultralow residual jitter (43 fs RMS). A phaselocked-loop (PLL) tested at 2 GHz has further reduced jitter by 91% (from 88 fs to 8 fs).
High Performance Flat Plate Solar Thermal Collector Evaluation (2016)

This report was prepared for the General Services Administration by the National Renewable Energy Laboratory. The Honeycomb Solar Thermal Collector (HSTC) is a flat plate solar thermal collector that shows promising high efficiencies over a wide range of climate zones. The technical objectives of this study are to: 1) verify collector performance, 2) compare that performance to other market-available collectors, 3) verify overheat protection, and 4) analyze the economic performance of the HSTC both at the demonstration sites and across a matrix of climate zones and utility markets.
Ultralow Calcium Requirements of Fungi Facilitate Use of Calcium Regulating Agents to Suppress Host Calcium-Dependent Defenses, Synergizing Infection by a Mycoherbicide (2002)

Infection by many fungi activates a variety of calcium dependent defenses in the hosts, slowing or suppressing the attacker and limiting the efficacy of mycoherbicides. The calcium requirement for fungal growth is so low that it could only be implied based on fungi containing calcium-dependent signaling enzymes. Analytical grade media contain <2 microM calcium, and the addition of specific chelators does not affect fungal growth. Hydrophobic derivatives of the calcium-specific chelator BAPTA designed to traverse plant cuticles were synthesized in order to chelate calcium internally during fungal attack. Some chelators as well as calcium precipitating oxalate and channel blocker verapamil were applied with a weakly mycoherbicidal Colletotrichum coccodes to cotyledons of compatible Abutilon threophrasti. They suppressed calcium dependent callose biosynthesis in the weed and increased virulence but may have affected other calcium-dependent processes that facilitate virulence. The low calcium requirement of fungi, and their high affinity for calcium, allows the application of calcium-regulating agents as synergists for mycoherbicides where the weed uses calcium-dependent defenses.
Amplification method for crosstalk reduction in multi‐core fibre amplifier (2013)

Proposed is a multi‐core fibre amplification method that can reduce crosstalk, in which the optical amplified signals in two adjacent cores propagate in opposite directions. By employing the proposed method, confirmed is a crosstalk improvement of more than 4 dB using the outer six cores of a seven‐core erbium‐doped fibre.