gebhart/patrepeval huggingface dataset:
A single amino-acid substitution in the Ets domain alters core DNA binding specificity of Ets1 to that of the related transcription factors Elf1 and E74 (1993)

Ets proteins form a family of sequence specific DNA binding proteins which bind DNA through a 85 aminoacids conserved domain, the Ets domain, whose sequence is unrelated to any other characterized DNA binding domain. Unlike all other known Ets proteins, which bind specific DNA sequences centered over either GGAA or GGAT core motifs, E74 and Elf1 selectively bind to GGAA corecontaining sites. Elf1 and E74 differ from other Ets proteins in three residues located in an otherwise highly conserved region of the Ets domain, referred to as conserved region III (CRIII). We show that a restricted selectivity for GGAA core-containing sites could be conferred to Ets1 upon changing a single lysine residue within CRIII to the threonine found in Elf1 and E74 at this position. Conversely, the reciprocal mutation in Elf1 confers to this protein the ability to bind to GGAT core containing EBS. This, together with the fact that mutation of two invariant arginine residues in CRIII abolishes DNA binding, indicates that CRIII plays a key role in Ets domain recognition of the GGAA/T core motif and lead us to discuss a model of Ets proteins--core motif interaction.
Withaferin A Strongly Elicits IκB Kinase β Hyperphosphorylation Concomitant with Potent Inhibition of Its Kinase Activity (2006)

The transcription factor NFkappaB plays a critical role in normal and pathophysiological immune responses. Therefore, NFkappaB and the signaling pathways that regulate its activation have become a major focus of drug development programs. Withania somnifera (WS) is a medicinal plant that is widely used in Palestine for the treatment of various inflammatory disorders. In this study we show that the leave extract of WS, as well as its major constituent withaferin A (WA), potently inhibits NFkappaB activation by preventing the tumor necrosis factor-induced activation of IkappaB kinase beta via a thioalkylation-sensitive redox mechanism, whereas other WS-derived steroidal lactones, such as withanolide A and 12-deoxywithastramonolide, are far less effective. To our knowledge, this is the first communication of IkappaB kinase beta inhibition by a plant-derived inhibitor, coinciding with MEK1/ERK-dependent Ser-181 hyperphosphorylation. This prevents IkappaB phosphorylation and degradation, which subsequently blocks NFkappaB translocation, NFkappaB/DNA binding, and gene transcription. Taken together, our results indicate that pure WA or WA-enriched WS extracts can be considered as a novel class of NFkappaB inhibitors, which hold promise as novel anti-inflammatory agents for treatment of various inflammatory disorders and/or cancer.
Preparation and Electrochemical Properties of High-performance LiFePO_4 (2005)

Carbon covered LiFePO4 powders with the microstructure of submicro-particles aggregated 5.01wt% carbon content, and the diameter of aggregated particle of 10μm were synthesized by solid state sintering processing. The capacity and cycle performance were studied at the charge and discharge rate of C/10, C/5, C/2 and 1C. The results show that below the rate of C/2, the voltage platform and capacity is not sensitive to the rate. When the rate is increased to 1C, the capacity is decreased and the voltage platform is increased in charge processing and decreased in discharge processing. Along with the increasing of cycle number, the capacity is increased to its saturate value. After 30 cycles, the capacities are 131.7, 129.1, 123.5 and 114.4 mAh/g, respectively.
Integrated Optimization for Rate Allocation in Reservoir Simulation (2003)

Summary When using a reservoir simulator to predict future field production, one must determine objectives and apply constraints to manage wells and surface facilities. Sequential Quadratic Programming (SQP) methods are used to set well rates in a facility network of a reservoir simulator so that production objectives are maximized (or minimized) subject to constraints on pressures, flow rates, and stream compositions. Actions taken for infeasible conditions are discussed. This method is called Optimized Rate Allocation (ORA). Black-oil and compositional examples are given.
Graphene Nanoplatelet-Polymer Chemiresistive Sensor Arrays for the Detection and Discrimination of Chemical Warfare Agent Simulants (2017)

A cross-reactive array of semiselective chemiresistive sensors made of polymer-graphene nanoplatelet (GNP) composite coated electrodes was examined for detection and discrimination of chemical warfare agents (CWA). The arrays employ a set of chemically diverse polymers to generate a unique response signature for multiple CWA simulants and background interferents. The developed sensors' signal remains consistent after repeated exposures to multiple analytes for up to 5 days with a similar signal magnitude across different replicate sensors with the same polymer-GNP coating. An array of 12 sensors each coated with a different polymer-GNP mixture was exposed 100 times to a cycle of single analyte vapors consisting of 5 chemically similar CWA simulants and 8 common background interferents. The collected data was vector normalized to reduce concentration dependency, z-scored to account for baseline drift and signal-to-noise ratio, and Kalman filtered to reduce noise. The processed data was dimensionally reduced with principal component analysis and analyzed with four different machine learning algorithms to evaluate discrimination capabilities. For 5 similarly structured CWA simulants alone 100% classification accuracy was achieved. For all analytes tested 99% classification accuracy was achieved demonstrating the CWA discrimination capabilities of the developed system. The novel sensor fabrication methods and data processing techniques are attractive for development of sensor platforms for discrimination of CWA and other classes of chemical vapors.
Identifying multiple infection sources in a network (2012)

Estimating which nodes are the infection sources that introduce a virus or rumor into a network, or the locations of pollutant sources, plays a critical role in limiting the potential damage to the network through timely quarantine of the sources. In this paper, we derive estimators for the infection sources and their infection regions based on the infection network geometry. We show that in a geometric tree with at most two sources, our estimator identifies these sources with probability going to one as the number of infected nodes increases. We extend and generalize our methods to general graphs, where the number of infection sources are unknown and there may be multiple sources. Numerical results are presented to verify the performance of our proposed algorithms under different types of graph structures.
Automatic Content Placement in Sports Highlights (2006)

To be viable advertising platforms, methods for in-program content placement in sports video must balance against clutter. We propose viewer relevance (VR) measures of video frames in the temporal and spatial domain. Video sub-segments with low temporal VR are first selected, within which actual content is emplaced on regions with low spatial VR. We compute VR measures using color, motion, texture and domain features, upon which spatio-temporal techniques are used to segment spatial regions for actual content placement. Results from preliminary subjective viewing trials on soccer and tennis video indicate that our approach is promising
BLOOM: BLoom filter based oblivious outsourced matchings (2017)

Both approaches handle practical problem sizes efficiently and are easily parallelized to scale with the elastic resources available in the cloud. The fully homomorphic scheme, FHE-BLOOM, realizes a comprehensive outsourcing to the cloud, while the partially homomorphic scheme, PHE-BLOOM, trades a slight relaxation of security guarantees against performance improvements by at least three orders of magnitude.
<title>Application of backside fiber optic system for in-situ CMP endpoint detection on shallow-trench isolation wafers</title> (1998)

A method of Chemical-Mechanical Planarization (CMP) endpoint detection of shallow trench isolation wafer is discussed in this paper. The detection algorithm was developed based on the interferometric intensity modulation of the light reflected from the wafer being polished. The physical model of the process proved to reliably predict behavior of the reflected signal during successive removal of a silicon oxide film and transition into patterned silicon nitride layer. The model calculates film thickness removed from STI wafers with known layer structure, from the reflected signal recorded during CMP process. The in-situ miniature system incorporating fiber-optic coupled diode laser and InGaAs photodetector was successfully implemented for the purpose of Endpoint Detection. On a patterned wafer the system can control nitride thickness removal with a better than 200 angstrom accuracy. The wireless modular design permits real- time simultaneous multiple points operation in a fully automated mode.
The Role of Stem Cell Factor and Granulocyte-Colony Stimulating Factor in Treatment of Stroke (2013)

Stroke is a serious cerebrovascular disease that causes high mortality and persistent disability in adults worldwide. Stroke is also an enormous public health problem and a heavy public financial burden in the United States. Treatment for stroke is very limited. Thrombolytic therapy by tissue plasminogen activator (tPA) is the only approved treatment for acute stroke, and no effective treatment is available for chronic stroke. Developing new therapeutic strategies, therefore, is a critical need for stroke treatment. This article summarizes the discovery of new routes of treatment for acute and chronic stroke using two hematopoietic growth factors, stem cell factor (SCF) and granulocyte-colony stimulating factor (G-CSF). In a study of acute stroke, SCF and G-CSF alone or in combination displays neuroprotective effects in an animal model of stroke. SCF appears to be the optimal treatment for acute stroke as the functional outcome is superior to G-CSF alone or in combination (SCF+G-CSF); however, SCF+G-CSF does show better functional recovery than G-CSF. In a chronic stroke study, the therapeutic effects of SCF and G-CSF alone or in combination appear differently as compared with their effects on the acute stroke. SCF+G-CSF induces stable and long-lasting functional improvement; SCF alone also improves functional outcome but its effectiveness is less than SCF+G-CSF, whereas G-CSF shows no therapeutic effects. Although the mechanism by which SCF+G-CSF repairs the brain in chronic stroke remains poorly understood, our recent findings suggest that the SCF+G-CSF-induced functional improvement in chronic stroke is associated with a contribution to increasing angiogenesis and neurogenesis through bone marrow-derived cells and the direct effects on stimulating neurons to form new neuronal networks. These findings would assist in developing new treatment for stroke. The article presents some promising patents on role of stem cell factor and granulocyte-colony stimulating factor in treatment of stroke.
FCoE in perspective (2008)

Fibre Channel over Ethernet (FCoE) is a direct mapping of Fibre Channel over lossless Ethernet being defined by the FC-BB-5 working group of the INCITS T11 Technical Committee. This paper presents a summary of the Fibre Channel architecture, elaborates the extensions needed for Ethernet to be lossless, and discusses the architectural models of FCoE, the way in which Fibre Channel frames are mapped into Ethernet frames, the addressing structures used by FCoE, and the control protocol that allows FCoE to be seamlessly integrated in the existing Fibre Channel environments.
Nucleotide sequence of the Escherichia coli recJ chromosomal region and construction of recJ-overexpression plasmids (1991)

The nucleotide sequence of the recJ gene of Escherichia coli K-12 and two upstream coding regions was determined. Three regions were identified within these two upstream genes that exhibited weak to moderate promoter activity in fusions to the galK gene and are candidates for the recJ promoter. recJ appeared to be poorly translated: the recJ nucleotide sequence revealed a suboptimal initiation codon GUG, no discernible ribosome-binding consensus sequence, and relatively nonbiased synonymous codon usage. Comparison of the sequence of this region of the chromosome with DNA data bases identified the gene immediately downstream of recJ as prfB, which encodes translational release factor 2 and has been mapped near recJ at 62 min. No significant homology between recJ and other previously sequenced regions of DNA was detected. However, protein sequence comparisons with a gene upstream of recJ, denoted xprB, revealed significant homology with several site-specific recombination proteins. Its genetic function is presently unknown. Knowledge of the nucleotide sequence of recJ allowed the construction of a plasmid from which overexpression of RecJ protein could be induced. Supporting the notion that translation of recJ is limiting, a strong T7 bacteriophage promoter upstream of recJ did not, by itself, allow high-level expression of RecJ protein. The addition of a ribosome-binding sequence fused to the initiator GTG of recJ in this construction was necessary to promote expression of high levels of RecJ protein.
Responding to Disasters (2009)

Inova Fairfax Hospital for Children, Falls Church, Virginia. Address correspondence to Laura A. Stokowski, RN, MS; [email protected]
Construction and maintaining detailed production plans: Investigations into the development of knowledge-based factory scheduling systems (1986)

To be useful in practice, a factory production schedule must reflect the influence of a large and conflicting set of requirements, objectives and preferences. Human schedulers are typically overburdened by the complexity of this task, and conventional computer-based scheduling systems consider only a small fraction of the relevent knowledge. This article describes research aimed at providing a framework in which all relevant scheduling knowledge can be given consideration during schedule generation and revision. Factory scheduling is cast as a complex constraint-directed activity, driven by a rich symbolic model of the factory environment in which various influencing factors are formalized as constraints. A variety of constraint-directed inference techniques are defined with respect to this model to provide a basis for intelligently compromising among conflicting concerns. Two knowledge-based factory scheduling systems that implement aspects of this approach are described.
“찬란한 폐허”와 이산의 멜랑콜리아: V. S. 나이폴의 『도착의 수수께끼』와 영국성의 공간미학 비판 (2016)

V. S. Naipaul’s autobiographical novel, The Enigma of Arrival, presents a first person narrative of postcolonial migration told by a middle-aged Indian writer who leaves his homeland Trinidad for England at the age of eighteen and later takes up residence in a manorial cottage on the grounds of a Victorian-Edwardian country estate in Wiltshire. Many readers of The Enigma of Arrival have voiced discomfort, locating in the novel Naipaul’s emotional investment in deep old England and his sense of wrongness in postimperial England. The sense of belatedness and wrongness pervasive in the novel, however, does not necessarily mean a politically reactionary position occupied by a conservative essentialist who pines for authentic England and Englishness. This paper aims to acknowledge an idiosyncratic narrative of Naipaul’s postcolonial migration that heavily draws on the localist discourse of Englishness and analyze Naipaul’s landscape aesthetics. Naipaul implicates his novel in the profound sense of melancholia that his narrator experiences in the process of postcolonial dislocation. Melancholia on Naipaul’s part, however, is not a simple retrograde vision of colonial desire but a crucial means of coming to terms with the enigmatic process of departure and arrival that a postcolonial subject experiences. For the melancholia pervasive in The Enigma of Arrival is sparked and shaped by specific cultural concerns and struggles conditioned and framed by postcolonial modernity, thus serving as a paradigm symptomatic of postcolonial modernity that Naipaul’s novel attempts to capture.
Multimode Interference Reflectors: A New Class of Components for Photonic Integrated Circuits (2013)

Multimode interference devices are very versatile components that are often used as components for power splitting or combining in larger circuits. In this paper, we present a new class of multimode interference couplers that are designed to reflect all or part of the light. The components can act as on-chip mirrors with partial out-coupling, or they can act as compact mirrors with full reflection. We present an overview of such devices, the basic theory and practical design guidelines. Their simple layout makes these devices easy to fabricate and tolerant to fabrication errors. We fabricated devices of several types and present the experimental results.
Titanate Nanofibers as Intelligent Absorbents for the Removal of Radioactive Ions from Water (2008)

Layered titanate nanofibers can absorb bivalent ions from waste water via an ion exchange process. The sorption induces a considerable deformation of the layered structure, thus trapping the cations in the fibers permanently. Therefore, the fibers are desirable sorbents for the removal of toxic, radioactive Ra(2+) and Sr(2+) ions from water and subsequent safe disposal thereof.
Effect of Insulin-Like Growth Factor I on Deoxyribonucleic Acid Synthesis and Galactopoiesis in Bovine Undifferentiated and Lactating Mammary Tissue<i>in Vitro</i>* (1988)

We have demonstrated that insulin-like growth factor I (IGF-I), at physiological concentrations, is a potent mitogen of bovine undifferentiated mammary epithelial cells cultured in collagen in serum-free medium. Its activity is independent of insulin, although at pharmacological concentrations insulin may substitute for IGF-I. The maximal [3H]thymidine incorporation stimulated by either IGF-I or insulin was only 25-40% of that in medium supplemented with 10% fetal calf serum (FCS) only. Epidermal growth factor (EGF) exhibited low mitogenic activity which was not synergistic with IGF-I in serum-free medium. IGF-I and EGF had low synergistic activity when added separately to 10% FCS-supplemented medium. Strong synergism (100% or more) was observed, however, when both factors were added simultaneously, indicating that their maximum mitogenic effect is dependent on a simultaneous presence of other factors existing in FCS. The galactopoietic effect of IGF-I was tested in organ culture of bovine lactating mammary gland. Neither fatty acid synthesis nor alpha-lactalbumin secretion was stimulated by IGF-I, even at 2000 ng/ml. These results indicate that, at least in our in vitro system, galactopoiesis is not affected by IGF-I.
The Vitacuff and Intravascular Catheter—Related Infection (1989)

<h3>To the Editor.—</h3> I read with interest the article by Flowers et al<sup>1</sup>inThe Journal. I have several misgivings about the use of the Vitacuff catheter. Guide-wire changes and accepted and effective maintenance technique for central venous catheters and sepsis workups are not possible with the Vitacuff. As a result, the critically ill patient is subjected to repeated "new sticks" and the risks of complications each time a temperature spike occurs. The Vitacuff requires a stab incision for placement. Ten percent of these incisions were not adequate to prevent catheter extrusion in this study. The stab technique is limited to the subclavian approach (stab incisions in the area of the internal jugular or femoral veins are not desirable) and the subclavian approach also carries the highest incidence of pneumothorax. The incidence of candidemia in this study and previous multicenter trials<sup>2</sup>with the Vitacuff is unacceptable. Fifty-three (49%)
Increased Levels of Activated Factor VII and Decreased Plasma Protein S Activity and Circulating Thrombomodulin during Use of Oral Contraceptives (1996)

In the present study the effect of oral contraceptive (OC) treatment on selected factors involved in the activation, i.e. circulating activated factor VII (cFVIIa), and in the inhibition of blood coagulation, i.e. plasma protein S activity and circulating thrombomodulin (cTM), were for the first time measured in OC users in a prospective study. Beside other coagulation variables, these parameters were measured during treatment with three low estrogen formulations containing different gestagen components (norgestimate, gestodene). During OC treatment increases in the activation markers prothrombin fragment F1 + 2 and D-Dimer were found, suggesting an increased activation of blood coagulation and fibrinolysis. Along with elevated plasma levels of FVII antigen, cFVIIa was also found increased in all three treatment groups, while inhibitory components of blood coagulation, plasma protein S activity and cTM, significantly and similarly decreased during treatment in all three treatment groups. We conclude that low dose estrogen pills induce similar changes in the plasma levels of main regulatory components of blood coagulation, despite differences in their gestagen components. Increased levels of activators and decreased activities of inhibitors may contribute to arterial and venous thrombotic complications seen in predisposed OC users.
Chelate-Controlled Synthesis of <i>rac-</i> and <i>meso-</i>Me<sub>2</sub>Si(3-<sup>t</sup>Bu-C<sub>5</sub>H<sub>3</sub>)<sub>2</sub>ZrCl<sub>2</sub> (2003)

The reaction of the chelated bis-amide complex Zr{PhN(CH2)3NPh}Cl2(THF)2 (2) with Li2[Me2Si(3-tBu-C5H3)2] yields meso-Me2Si(3-tBu-C5H3)2Zr{PhN(CH2)3NPh} (meso-3) in >98% yield. In contrast, the reaction of Zr{Me3SiN(CH2)3NSiMe3}Cl2(THF)2 (4) or the related mono-THF adduct Zr{Me3SiN(CH2)3NSiMe3}Cl2(THF) (5) with Li2[Me2Si(3-tBu-C5H3)2] yields rac-Me2Si(3-tBu-C5H3)2Zr{Me3SiN(CH2)3NSiMe3} (rac-6) in quantitative NMR yield and 89% isolated yield. X-ray crystallographic analyses show that the Zr{RN(CH2)3NR} chelate ring in rac-6 has a pronounced twist conformation, while that in meso-3 has a flatter, envelope conformation. It is proposed that the conformations of the Zr{RN(CH2)3NR} chelate rings in the stereodetermining transition states for addition of the second Cp- ring in these reactions are similar to those in the metallocene products and control the diastereoselectivity. meso-3 and rac-6 are converted to meso-Me2Si(3-tBu-C5H3)2ZrCl2 (meso-1) and rac-1, respectively, by reaction with HCl in Et2O.
Antibody responses to an immunodominant nonstructural 1 synthetic peptide in patients with dengue fever and dengue hemorrhagic fever (1999)

Two flaviviruses, dengue (DEN) virus and Japanese encephalitis (JE) virus, are important because of their global distribution and the frequency of epidemics in tropical and subtropical areas. To study the B-cell epitopes of nonstructural 1 (NS1) glycoprotein and anti-NS1 antibody response in DEN infection, a series of 15-mer synthetic peptides from the predicted B-cell linear epitopes of DEN-2 NS1 protein were prepared. Enzyme-linked immunosorbent assay (ELISA) was performed to analyze antibody responses to these peptides from sera of both DEN and JE patients. One peptide derived from DEN-2 NS1, D2 NS1-P1 (amino acids 1-15), was identified as the immunodominant epitope that reacted with sera from dengue fever (DF) patients but not JE patients. The isotype of D2 NS1-P1-specific antibodies was mainly immunoglobulin M (IgM) in all sera that tested positive. A specificity study demonstrated that sera from all four DEN types reacted with D2 NS1-P1. A dynamics study showed that specific antibodies to this peptide could be detected as early as 2 days after the onset of symptoms. We observed significant anti-D2 NS1-P1 antibody responses in 45% of patients with primary and secondary infections with DF or with dengue hemorrhagic fever. This is the first report demonstrating that significant anti-DEN NS1 antibodies can be induced in the sera of patients with primary DEN infection.