gebhart/patrepeval huggingface dataset:
Tyrosine 740 Phosphorylation of Discoidin Domain Receptor 2 by Src Stimulates Intramolecular Autophosphorylation and Shc Signaling Complex Formation (2005)

DDR2 is a receptor tyrosine kinase whose activating ligands are various collagens. DDR2-mediated cellular signaling has been shown to require Src activity. However, the precise mechanism underlying the Src dependence of DDR2 signaling is unknown. Here, using baculoviral co-expression of the DDR2 cytosolic domain and Src, we show that Src targets three tyrosine residues (Tyr-736, Tyr-740, and Tyr-741) in the activation loop of DDR2 for phosphorylation. This phosphorylation by Src stimulates DDR2 cis-autophosphorylation of additional tyrosine residues. In vitro Shc binding assays demonstrate that phosphotyrosines resulting from DDR2 autophosphorylation are involved in Shc binding to the DDR2 cytosolic domain. Mutating tyrosine 740 of DDR2 to phenylalanine stimulates autophosphorylation of DDR2 to an extent similar to that resulting from Src phosphorylation of DDR2. In addition, the DDR2 Y740F mutant protein displays collagen-independent, constitutively activated signaling. These findings suggest that tyrosine 740 inhibits DDR2 autophosphorylation. Collectively, our findings are consistent with the following mechanism for Src-dependent DDR2 activation and signaling: 1) ligand binding promotes phosphorylation of Tyr-740 in the DDR2 activation loop by Src; 2) Tyr-740 phosphorylation stimulates intramolecular autophosphorylation of DDR2; 3) DDR2 autophosphorylation generates cytosolic domain phosphotyrosines that promote the formation of DDR2 cytosolic domain-Shc signaling complexes.
Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria (2011)

The biochemical and structural data presented support that hHOGA utilizes a type I aldolase reaction mechanism, but employs novel residue interactions for substrate binding. A mapping of the PH3 mutations identifies potential rearrangements in either the active site or the tetrameric assembly that would likely cause a loss in activity. Altogether, these data establish a foundation to assess mutant forms of hHOGA and how their activity could be pharmacologically restored.
Pbx Modulation of Hox Homeodomain Amino-Terminal Arms Establishes Different DNA-Binding Specificities across the<i>Hox</i>Locus (1996)

Pbx cofactors are implicated to play important roles in modulating the DNA-binding properties of heterologous homeodomain proteins, including class I Hox proteins. To assess how Pbx proteins influence Hox DNA-binding specificity, we used a binding-site selection approach to determine high-affinity target sites recognized by various Pbx-Hox homeoprotein complexes. Pbx-Hox heterodimers preferred to bind a bipartite sequence 5'-ATGATTNATNN-3' consisting of two adjacent half sites in which the Pbx component of the heterodimer contacted the 5' half (ATGAT) and the Hox component contacted the more variable 3' half (TNATNN). Binding sites matching the consensus were also obtained for Pbx1 complexed with HoxA10, which lacks a hexapeptide but requires a conserved tryptophan-containing motif for cooperativity with Pbx. Interactions with Pbx were found to play an essential role in modulating Hox homeodomain amino-terminal arm contact with DNA in the core of the Hox half site such that heterodimers of different compositions could distinguish single nucleotide alterations in the Hox half site both in vitro and in cellular assays measuring transactivation. When complexed with Pbx, Hox proteins B1 through B9 and A10 showed stepwise differences in their preferences for nucleotides in the Hox half site core (TTAT to TGAT, 5' to 3') that correlated with the locations of their respective genes in the Hox cluster. These observations demonstrate previously undetected DNA-binding specificity for the amino-terminal arm of the Hox homeodomain and suggest that different binding activities of Pbx-Hox complexes are at least part of the position-specific activities of the Hox genes.
Synthesis of complement components (C3, C2, B and C1-inhibitor) and lysozyme by human monocytes and macrophages. (1986)

The synthesis of C3, C2, factor B (B) C1-inhibitor and lysozyme has been studied in monocytes and macrophages isolated from the synovial fluids of patients with rheumatoid arthritis. Concentrations of all 5 proteins in culture supernatants were measured by the sandwich ELISA technique. Kinetic studies showed that only lysozyme and C3 could be detected in monocyte culture supernatants on the first day of culture, whereas C2, B and C1-inhibitor were not present until the third day. In contrast all 5 proteins could be detected in the supernatants of macrophage cultures on day 1. In both monocyte and macrophage cultures synthesis of lysozyme and C1-inhibitor continued throughout the culture period, whereas synthesis of C2, B and C3 appeared to be reduced after the fifth day in culture. Quantitative studies showed that the secretion rates of lysozyme (4,700 X 10(3) molecules/cell/hr) was similar in monocytes and macrophages. Synthesis rates for all 4 complement components in monocyte cultures were less than 0.2% of that for lysozyme. Although the synthetic rates were higher in macrophages, even then they constituted less than 2% of the rate for lysozyme. Synthetic rates for complement components, but not lysozyme, were increased by BSA-anti-BSA antigen-antibody complexes and reduced by serum-treated complexes. Although the functional activity of monocyte B was similar to that for serum, the activity of monocyte C2 was 5 times that of serum C2. As C42 formed with monocyte C2 had a half-life of 13.5 min at 30 degrees C, compared with 4.5 min for the enzyme formed with serum C2, it is probable that monocyte C2 is oxidized by the oxygen products of these cells.
Dipole Modeling of Magnetic Flux Leakage (2009)

In this paper, we present an analytical model to represent the 3-D magnetic flux leakage (MFL) field due to the occurrence of a surface-breaking defect in a ferromagnetic specimen. This situation is frequently encountered in the nondestructive evaluation (NDE) of energy pipelines using the MFL technique. The model is derived from first principles, and utilizes the concept of dipolar magnetic charge induction to yield the 3-D MFL field in terms of surface integrals. The magnetic flux density in the specimen is assumed to be in the saturation region, and the permeability is assumed to be locally constant in the vicinity of the defect. The model uses just two geometric parameters and is capable of reproducing results that have been obtained experimentally in the literature. 3-D MFL field simulations obtained from the model facilitate a better understanding of the effect of a surface-breaking defect on the magnetic field in its vicinity. Furthermore, we simulate and analyze the 3-D MFL field in the 3-D space around the defect. This analysis yields numerous properties regarding the spatial characteristics of the three orthogonal components of the MFL field of the defect.
258. Phthalaldehydes and related compounds. Part II. Synthesis of isogladiolic acid (1953)

J. J. Brown and G. T. Newbold, J. Chem. Soc., 1953, 1285 DOI: 10.1039/JR9530001285
The New OED Project at Waterloo: Old Wine in New Bottles (1988)

The New OED Project at Waterloo: Old Wine in New Bottles
Significant enhancement of the sensing characteristics of In<sub>2</sub>O<sub>3</sub>nanowires by functionalization with Pt nanoparticles (2010)

We report a significant enhancement in the gas sensing properties of In(2)O(3) nanowires by functionalizing their surfaces with Pt nanoparticles. For Pt-functionalization, In(2)O(3)-Pt core-shell nanowires are synthesized by the sputtering deposition of Pt layers on bare In(2)O(3) nanowires. Next, continuous Pt shell layers are transformed into Pt nanoparticles of cubic phase by heat treatment. In an O(2) gas sensing test, the Pt-functionalized In(2)O(3) nanowires reveal exceptionally higher sensitivity and faster response than bare In(2)O(3) nanowires.
Insights into tunnelling rays: outperforming guided rays in fiber-optic sensing device (2009)

We report that, for an evanescent-wave (EW) based fiber-optic sensor, the less skewed tunnelling rays and a small number of very steep guided rays experience total internal reflection (TIR) at one end-face of the air-clad fiber segment. As a result, they demonstrate nine times greater efficiency in collecting EW-power than rays that do not exhibit end-face- TIR. This tunneling ray group originates from a launching ring that is seven times wider than that of end-face-TIR capable guided rays, enabling it to dominate the overall detected EW-power level. Strongly supporting this conclusion is the counter-intuitive experimental observation that the detected power at one end of the fiber abruptly drops 91% when the back reflection at the opposite end is eliminated, while an isotropic light source is placed at the core-cladding interface between these two ends. The mechanism of non-propagating ray excitation accounts for this high efficiency. We also indicate that many highly skewed tunnelling rays are naturally isolated from the external world because, outside the fiber core, they are accessible only via their EW fields even at the fiber end-faces. The findings reported here have significant implications for the design of future high-performance EW-based fiber sensing devices for the analysis of surface-event.
Cc Chemokine Receptor (Ccr)3/Eotaxin Is Followed by Ccr4/Monocyte-Derived Chemokine in Mediating Pulmonary T Helper Lymphocyte Type 2 Recruitment after Serial Antigen Challenge in Vivo (2000)

Isolated peripheral blood CD4 cells from allergic individuals express CC chemokine receptor (CCR)3 and CCR4 after expansion in vitro. In addition, human T helper type 2 (Th2) cells polarized in vitro selectively express CCR3 and CCR4 at certain stages of activation/differentiation and respond preferentially to the ligands eotaxin and monocyte-derived chemokine (MDC). However, controversy arises when the in vivo significance of this distinct expression is discussed. To address the functional role of CCR3/eotaxin and CCR4/MDC during the in vivo recruitment of Th2 cells, we have transferred effector Th cells into naive mice to induce allergic airway disease. Tracking of these cells after repeated antigen challenge has established that both CCR3/eotaxin and CCR4/MDC axes contribute to the recruitment of Th2 cells to the lung, demonstrating the in vivo relevance of the expression of these receptors on Th2 cells. We have shown that involvement of the CCR3/eotaxin pathway is confined to early stages of the response in vivo, whereas repeated antigen stimulation results in the predominant use of the CCR4/MDC pathway. We propose that effector Th2 cells respond to both CCR3/eotaxin and CCR4/MDC pathways initially, but that a progressive increase in CCR4-positive cells results in the predominance of the CCR4/MDC axis in the long-term recruitment of Th2 cells in vivo.
Preparation and Luminescence Properties of SrSi2O2N2:Eu2+ Phosphors for White LEDs (2007)

This work has investigated luminescence properties of SrSi2O2N2: Eu2+ phosphors synthesized by a new method using Sr2SiO4: Eu2+ as a precursor. Compared with a conventional solid-state reaction method, this method provides increased crystallinity and luminescence efficiency. X-ray diffraction analysis has indicated that SrSi2O2N2: Eu2+ formed as an almost single-phase, but chemical analysis has shown that obtained samples have an oxygen/nitrogen atomic ratio deviated from the stoichiometric composition. It can be expected that luminescence efficiency of this phosphor will be higher for the stoichiometric composition than for non-stoichiometric ones. Under 460 nm excitation, this phosphor shows an emission band peaked at 538-564 nm for varied Eu2+ concentration, and shows the maximum at 15 mol% with high integrated photoluminescence intensity, which is about 1.05 times as high as that of the commercial yellow phosphor, (Y,Gd)3Al5O12: Ce3+ (P46-Y3).
A language for document generic layout description and its use for segmentation into regions (2002)

We present a segmentation method guided by a generic layout description expressed in a new language. The proposed language allows to describe a page as superposed layers that may be used to separate the main text body from other components, for example figures. The language's novelty resides in the fact that, instead of describing directly the global topology of generic pages according to their regions, generic separators are described and used as region boundary delimiters. Separators may be declared as white spaces or threads. By doing this, the problem of document segmentation into regions has become a problem of separator determination, solved by analyzing lines and white spaces contained in documents.
Low-power high-accuracy timing systems for efficient duty cycling (2008)

Time keeping and synchronization are important services for networked and embedded systems. High quality timing information allows embedded network nodes to provide accurate time-stamping, fast localization, efficient duty cycling schedules, and other basic but essential functions - all of which are required for low power operation.
Serum immunoglobulin levels in thymus-deficient pituitary dwarf mice. (1970)

Hypopituitary dwarf Snell—Bagg mice have previously been shown to have a reduced capacity to produce antibody to sheep red cells and to reject foreign skin grafts. Their thymuses, spleens and lymph nodes are hypoplastic. However, quantitative estimation of their serum immunoglobulin levels reveals no significant difference from the values seen in normal litter-mates. Immunoelectrophoretic analysis shows no overall differences in immunoglobulin pattern between normal and dwarf mouse serum except a possible alteration in distribution of the IgG subtypes.
An adaptive multiple model approach for fast content-based skin detection in on-line videos (2008)

We propose a straightforward skin detection method for online videos. To overcome varying illumination circumstances and a variety of skin colors, we introduce a multiple model approach which can be carried out independently per model. The color models are initiated by skin detection based on face detection and adapted in real time. Our approach outperforms static approaches both in precision and runtime. If we detect a face in a scene, the number of false positives can be diminished significantly. Evaluation is carried out on publicly available on-line videos showing that adaptive multiple model outperforms static methods in classification precision and suppression of false positives.
Uncertainty-Aware Household Appliance Scheduling Considering Dynamic Electricity Pricing in Smart Home (2013)

High quality demand side management has become indispensable in the smart grid infrastructure for enhanced energy reduction and system control. In this paper, a new demand side management technique, namely, a new energy efficient scheduling algorithm, is proposed to arrange the household appliances for operation such that the monetary expense of a customer is minimized based on the time-varying pricing model. The proposed algorithm takes into account the uncertainties in household appliance operation time and intermittent renewable generation. Moreover, it considers the variable frequency drive and capacity-limited energy storage. Our technique first uses the linear programming to efficiently compute a deterministic scheduling solution without considering uncertainties. To handle the uncertainties in household appliance operation time and energy consumption, a stochastic scheduling technique, which involves an energy consumption adaptation variable , is used to model the stochastic energy consumption patterns for various household appliances. To handle the intermittent behavior of the energy generated from the renewable resources, the offline static operation schedule is adapted to the runtime dynamic scheduling considering variations in renewable energy. The simulation results demonstrate the effectiveness of our approach. Compared to a traditional scheduling scheme which models typical household appliance operations in the traditional home scenario, the proposed deterministic linear programming based scheduling scheme achieves up to 45% monetary expense reduction, and the proposed stochastic design scheme achieves up to 41% monetary expense reduction. Compared to a worst case design where an appliance is assumed to consume the maximum amount of energy, the proposed stochastic design which considers the stochastic energy consumption patterns achieves up to 24% monetary expense reduction without violating the target trip rate of 0.5%. Furthermore, the proposed energy consumption scheduling algorithm can always generate the scheduling solution within 10 seconds, which is fast enough for household appliance applications.
Design and deployment of an integrated data ciphering unit inside a low bit rate voice transcoder for secure voice communications over telephone networks (2003)

It is noted that to provide encryption-based secure communication in telephone networks, one of the basic questions to be faced by telephone companies is where to locate the encryption/decryption devices and also how to interface them with their existing telephone switching and multiplexing equipment so that the cost of providing secure communication service to their customers is affordable. To answer this question, an integrated data ciphering unit (DCU) is presented. In particular, the deployment of a DCU inside low bit rate voice (LBRV) transcoder telephone equipment is discussed. The accuracy of an adaptive differential pulse-code modulation prediction algorithm and the impact of errors due to decoding are analyzed, and a specific scheme for the deployment of the DCU inside an LBRV transcoder is proposed to provide a better level of security for voice communication over telephone networks. Some implementation details and a cost analysis are presented indicating that the percentage incremental cost of providing secure communication service to the customers is quite negligible.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Oxygen Measurements on Acid‐Etched Czochralski‐Grown Silicon Wafers (1992)

Concentrations of oxygen in acid‐etched Czochralski (CZ)‐grown silicon wafers have been determined as precisely as in double‐sided polished wafers, by means of p‐polarized Brewster angle incidence infrared spectroscopy. Furthermore, we have successfully extended this technique to the case where the thickness of an acid‐etched CZ sample wafer or a single‐sided polished one is different from that of reference specimen.
Recent developments and applications of the real-space multigrid method (2008)

The salient features of the real-space multigrid method and its recent applications are described. This method is suitable for very large scale, massively parallel calculations of atomic and electronic structure, as well as quantum molecular dynamics. Its nearly O(N) implementation provides a compact, variationally optimized basis that is also very useful for fully O(N) calculations of quantum transport. Recently, we also developed a hybrid method for simulating biomolecules in solution, in which most of the solvent is inexpensively treated using an approximate density-functional method, while the biomolecule and its first solvation shells are described at the full Kohn–Sham level. Our calculations show excellent parallel efficiency and scaling on massively parallel supercomputers.
Effects of erythropoietin and recombinant cytokines on colony formation and self-renewal by erythroid burst-forming units and granulocyte-macrophage progenitors from mobilized peripheral blood progenitor cells. (2002)

The effects of erythropoietin and recombinant cytokines (G-CSF, SCF, IL-3 and GM-CSF) on colony formation and self-renewal by erythroid burst-forming units (BFU-E) and granulocyte-macrophage progenitors (CFU-GM) from mobilized peripheral blood progenitor cells (PBPCs) of the normal donors and patients were investigated. To better understand how combinations of the cytokines may be appropriate for stem cell manipulation, a model involving replating of individual BFU-E and CFU-GM colonies has been used to study the effects of cytokines on colony formation and self-renewal. Based on granulocyte colony-stimulating factor (G-CSF) and erythropoietin(EPO) alone serve as a baseline with which to compare the effects of the combinations with stem cell factor (SCF), interleukin-3 (IL-3) or granulocyte-macrophage colony-stimulating factor (GM-CSF). The results revealed that: 1. BFU-E derived from PBPCs produced a significantly great numbers of subcolonies in EPO plus IL-3 and EPO+SCF+IL-3, and a difference in EPO+SCF compared with EPO alone. 2. Compared patients to normal donors the self-renewal ability of BFU-E was not influenced after EPO plus SCF or IL-3. 3. There was a significantly increased frequency of CFU-GM in the presence of SCF, IL-3, and GM-CSF used in conjunction with G-CSF. Comparing the frequencies of CFU-GM in patients and donors, patients' PBPCs were more sensitive to G-CSF+SCF and GMix (G-CSF+SCF+IL-3+GM-CSF), especially to G-CSF alone than donors. 4. There was a significant increase in AUC (area under the curve of subcolony distribution) in the presence of G-CSF combined with other cytokines. GMix was identified as the optimal combination of cytokines for both the expansion of CFU-GM as well as the expansion of clonogenic progenitor cells. 5. Donors have a high AUC than patients, especially there was a significant increase AUC in G-CSF alone (P = 0.0067).
Sequence analysis of a mitochondrial DNA fragment isolated from cultured cells of carrot cytoplasmic male-sterile strain. (1991)

2.0 kb Hind III fragment isolated from cytoplasmic male-sterile carrot mitochondria, designated PKT5, was hybridized to ORF13 which is the coding region of a unique polypeptide in maize CMS (Dewey et al., 1986). Sequence analysis indicated that PKT5 is consisted of 3 domains. Domain 1 was identical to the 5'-flanking region of atp6 in maize CMS-TURF2H3 sequence (Dewey et al., 1986). Domain 2 contained a novel ORF encoding 72 amino acids, which was extremely homologous to the amino-terminal 67 amino acids of the unique ORF13 in maize CMS. Domain 3 except an amino acid change (Ile87 = ATT for Asn87 = AAT), was identical to ORF25 polypeptide in maize CMS. Connective sequences of these 3 domains were also highly homologous to the maize CMS-TURF2H3 sequence. Out of 7 recombination points in maize CMS-TURF2H3 sequence, at least 4 points were conserved in PKT5 sequence.
Propagation-mode-controlled fabrication of self-written waveguide in photosensitive polyimide for single-mode operation (2005)

We have developed a new fabrication method of single-mode self-written waveguide by controlling the propagation mode in an optical fiber. This method is very appropriate for repeatable fabrication of the single-mode self-written waveguide. Since a Gaussian-like near-field pattern is required for the fabrication of a tiny and uniform waveguide core, the propagation mode in a conventional optical communication fiber was controlled by coupling with an optical fiber having 3-μm core, which shows a single-mode operation at visible wavelength region. Single-mode propagation at optical communication wavelength was confirmed for the fabricated self-written waveguide. The evaluated core diameter of the self-written waveguide was /spl sim/9.5 μm.