gebhart/patrepeval huggingface dataset:
The Reciprocal Role of Egr-1 and Sp Family Proteins in Regulation of the PTP1B Promoter in Response to the p210 Bcr-Abl Oncoprotein-tyrosine Kinase (2001)

Protein-tyrosine phosphatase 1B (PTP1B) is an important regulator of protein-tyrosine kinase-dependent signaling pathways. Changes in expression and activity of PTP1B have been associated with various human diseases; however, the mechanisms by which PTP1B expression is regulated have yet to be characterized. Previously, we have shown that the expression of PTP1B is enhanced by p210 Bcr-Abl and that PTP1B is a specific antagonist of transformation induced by this oncoprotein protein-tyrosine kinase. Here we have characterized the PTP1B promoter and demonstrate that a motif with features of a stress-response element acts as a p210 Bcr-Abl-responsive sequence, termed PRS. We have shown that three C(2)H(2) zinc finger proteins, namely Sp1, Sp3, and Egr-1, bind to PRS. Whereas binding of either Sp1 or Sp3 induced promoter function, Egr-1 repressed Sp3-mediated PTP1B promoter activation. The binding of Egr-1 to PRS is suppressed by p210 Bcr-Abl due to the inhibition of Egr-1 expression, resulting in the enhancement of PTP1B promoter activity. Our data indicate that Egr-1 and Sp family proteins play a reciprocal role in the control of expression from the PTP1B promoter.
Adhesion of Streptococcus pneumoniae to human pharyngeal epithelial cells in vitro: differences in adhesive capacity among strains isolated from subjects with otitis media, septicemia, or meningitis or from healthy carriers (1981)

A method was developed to study the adhesion of Streptococcus pneumoniae to human pharyngeal epithelial cells. Epithelial cells from healthy persons, pneumococcal strains from patients with otitis media, meningitis, or septicemia, and pneumococcal cells from the nasopharynx of healthy carriers were used. Adhesion was found to be influenced by changes in the bacterial incubation medium and growth phase, the concentration of bacteria and epithelial cells, the epithelial cell donor, the incubation time and temperature, and the pH and osmolarity of the incubation medium. Pretreatment of bacteria with heat, Formalin, or trypsin decreased adhesion. The highest adhesion was obtained when 10(9) bacteria cultivated for 18 h in streptococcus cultivation broth were added to 10(4) pharyngeal cells and incubated at 37 degrees C for 30 min. S. pneumoniae strains from patients with frequent episodes of otitis media and strains from healthy carriers had the highest adhesion values; septicemia and meningitis strains had the lowest. The capsular polysaccharide type did not determine the adhesive capacity of the strains, but otitis strains belonging to the capsular types often associated with otitis media adhered in high numbers. Adhesion may be important for pneumococci colonizing the nasopharynx or inducing otitis media.
Anthraquinones and Lignans from <i>Cassia occidentalis</i> (2010)

Abstract One new anthraquinone glycoside, 6‐ O ‐( α ‐ L ‐rhamnopyranosyl‐(1→6)‐ β ‐ d‐ glucopyranosyl)emodin ( 1 ), and two new sesquilignans, seslignanoccidentaliols A ( 2 ) and B ( 3 ), were isolated from the whole plant of Cassia occidentalis. The structures of the new compounds were established by means of spectroscopic methods, especially 2D‐NMR data ( 1 H, 1 H‐COSY, HMQC, HMBC, and ROESY), as well as HR‐ESI‐MS analysis. One previously reported sesquilignan, erythro ‐guaiacylglycerol‐ β ‐ O ‐4′‐(5′)‐methoxylariciresinol, was revised to be seslignanoccidentaliol A ( 2 ). The 6‐ O ‐( α ‐ L ‐rhamnopyranosyl‐(1→6)‐ β ‐ d‐ glucopyranosyl)emodin ( 1 ) exhibited moderate anti‐HIV‐1 activity with an EC 50 value of 2.90 μg/ml and a therapeutic‐index ( TI ) value of 260.
Prediction of Churn Behaviour of Bank Customers Using Data Mining Tools (2012)

The customer churn is a common measure of lost customers. By minimizing customer churn, a company can maximize its profits. Companies have recognized that existing customers are the most valuable assets. Customer retention is critical for a good marketing and a customer relationship management strategy. The prevention of customer churn through customer retention is a core issue of Customer Relationship Management (CRM). The paper presents churn prediction based on data mining tools in banking. In this paper, a study on modeling purchasing behavior of bank customers in Indian scenario has been attempted. A detailed scheme is worked out to convert raw customer data into meaningful and useful data that suits modeling buying behavior and in turn, converts this meaningful data into knowledge for which predictive data mining techniques are adopted. In this analysis, the researchers have experimented with 2 classification techniques namely CART, and C 5.0. The prediction success rate of Churn class by CART is quite high but C 5.0 had shown poor results in predicting churn customers. However, the prediction success rate of Active class by C 5.0 is more effective than the other technique. However, for reaping significant benefits, the models have predicted the churn behavior.
Genetics and the logic of evolution (2004)

Preface. Acknowledgments. I. UNDERSTANDING BIOLOGICAL COMPLEXITY: Basic Concepts and Principles. 1. Prospect: The Basic Postulates of Life. 2. Conceptual and Analytic Approaches to Evolution. 3. Evolution By Phenotype: How Change Happens in Life. II. BUILDING BLOCKS OF LIFE: A Genetic Repertoire for Evolving Complexity. 4. The Storage and Flow of Biological Information. 5. Genotypes and Phenotypes. 6. A Cell is Born. 7. A Repertoire of Basic Genetic Mechanisms. III. AN INTERNAL AWARENESS OF SELF: Communication within Organisms. 8. Making More of Life: The Many Aspects of Reproduction. 9. Scaling Up: How Cells Build an Organism. 10. Communicating Between Cells. 11. Detecting and Destroying Internal Invaders. IV. EXTERNAL AWARENESS: Information Transfer between Environment to Organism. 12. Detecting Physical Variability in the Environment. 13. Chemical Signaling and Sensation from the Outside World. 14. Detecting Light. 15. The Development and Structure of Nervous Systems. 16. Perceiving: Integrating Signals from the Environment. V. FINALE: Evolutionary Order and Disorder between Phenotypes and Genotypes. 17. A Great Chain of Beings. References. Index.
On key agreement in wireless sensor networks based on radio transmission properties (2009)

Recently, several research contributions have justified that wireless communication is not only a security burden. Its unpredictable and erratic nature can also be turned against an adversary and used to augment conventional security protocols, especially key agreement. In this paper, we are inspired by promising studies on such key agreement schemes, yet aim for releasing some of their limiting assumptions. We demonstrate the feasibility of our scheme within performance-limited wireless sensor networks. The central idea is to use the reciprocity of the wireless channel response between two transceivers as a correlated random variable. Doing so over several frequencies results in a random vector from which a shared secret is extracted. By employing error correction techniques, we are able to control the trade-off between the amount of secrecy and the robustness of our key agreement protocol. To evaluate its applicability, the protocol is implemented on MicaZ sensor nodes and analyzed in indoor environments. Further, these experiments provide insights into realistic channel behavior, available information entropy, and show a high rate of successful key agreements, up to 95 %.
Strong 8.2 μm infrared intersubband absorption in doped GaAs/AlAs quantum well waveguides (1987)

We have measured the infrared intersubband absorption at 8.2 μm in doped GaAs/AlAs quantum well superlattices. Waveguide geometry experiments demonstrate strong absorption with 95% of the incident infrared energy being absorbed.
Efficient Organic Light‐Emitting Diodes based on Sublimable Charged Iridium Phosphorescent Emitters (2007)

Abstract The synthesis and characterization of two new phosphorescent cationic iridium(III) cyclometalated diimine complexes with formula [Ir( L ) 2 (N‐N)] + (PF 6 – ) ( HL = (9,9‐diethyl‐7‐pyridinylfluoren‐2‐yl)diphenylamine); N‐N = 4,4′‐dimethyl‐2,2′‐bipyridine ( 1 ), 4,7‐dimethyl‐1,10‐phenanthroline ( 2 )) are reported. Both complexes are coordinated by cyclometalated ligands consisting of hole‐transporting diphenylamino (DPA)‐ and fluorene‐based 2‐phenylpyridine moieties. Structural information on these heteroleptic complexes has been obtained by using an X‐ray diffraction study of complex 2 . Complexes 1 and 2 are morphologically and thermally stable ionic solids and are good yellow phosphors at room temperature with relatively short lifetimes in both solution and solid phases. These robust iridium complexes can be thermally vacuum‐sublimed and used as phosphorescent dyes for the fabrication of high‐efficiency organic light‐emitting diodes (OLEDs). These devices doped with 5 wt % 1 can produce efficient electrophosphorescence with a maximum brightness of up to 15 610 cd m –2 and a peak external quantum efficiency of ca. 7 % photons per electron that corresponds to a luminance efficiency of ca. 20 cd A –1 and a power efficiency of ca. 19 lm W –1 . These results show that charged iridium(III) materials are useful alternative electrophosphors for use in evaporated devices in order to realize highly efficient doped OLEDs.
Bacteria Binding by DMBT1/SAG/gp-340 Is Confined to the VEVLXXXXW Motif in Its Scavenger Receptor Cysteine-rich Domains (2004)

The scavenger receptor cysteine-rich (SRCR) proteins form an archaic group of metazoan proteins characterized by the presence of SRCR domains. These proteins are classified in group A and B based on the number of conserved cysteine residues in their SRCR domains, i.e. six for group A and eight for group B. The protein DMBT1 (deleted in malignant brain tumors 1), which is identical to salivary agglutinin and lung gp-340, belongs to the group B SRCR proteins and is considered to be involved in tumor suppression and host defense by pathogen binding. In a previous study we used nonoverlapping synthetic peptides covering the SRCR consensus sequence to identify a 16-amino acid bacteria-binding protein loop (peptide SRCRP2; QGRVEVLYRGSWGTVC) within the SRCR domains. In this study, using overlapping peptides, we pinpointed the minimal bacteria-binding site on SRCRP2, and thus DMBT1, to an 11-amino acid motif (DMBT1 pathogen-binding site 1 or DMBT1pbs1; GRVEVLYRGSW). An alanine substitution scan revealed that VEVL and Trp are critical residues in this motif. Bacteria binding by DMBT1pbs1 was different from the bacteria binding by the macrophage receptor MARCO in which an RXR motif was critical. In addition, the homologous consensus sequences of a number of SRCR proteins were synthesized and tested for bacteria binding. Only consensus sequences of DMBT1 orthologues bound bacteria by this motif.
Mass spectrometry during molecular-beam epitaxy: An alternative to reflection high-energy electron diffraction (1988)

A quadrupole mass spectrometer has been positioned in a commercial molecular-beam epitaxy system so that the desorption of atomic and molecular species, from GaAs substrates, can be monitored at various stages in the growth process. The sharply peaked Ga2O154 thermal desorption spectrum, from the surface oxides, is found to provide a useful temperature calibration, and its width is a measure of the substrate temperature distribution. Gallium desorption from GaAs surfaces, as a function of temperature, can be used to calculate growth rate curves, whereas the desorption flux from GaAlAs surfaces enables the alloy composition to be determined directly. Interfacial transients between layers can be monitored, and results are described which suggest that GaAs/AlAs interfaces are not atomically abrupt. Unlike the reflection high-energy electron diffraction technique, these measurements can all be carried out on rotating, large size, substrates.
Self-Assembled Lipid Superstructures:  Beyond Vesicles and Liposomes (2005)

A unique set of nanoparticle dispersions of self-assembled lipid mesophases with distinctive reversed cubic, hexagonal, and sponge phase structures has been prepared by use of original lipid combinations and a simple, generally applicable and scalable method. All key properties, particle size distributions, shape, phase structure, and stability, are controlled predictably and reproducibly. The results suggest the cross-disciplinary use of nonlamellar particle structures in science and technology as, for instance, biomimetics, in vivo drug delivery vehicles for diagnostic and therapeutic agents, protein crystallization matrices, and soft nanoporous materials.
Experimental proof of current bifurcation and mutual heating in bipolar transistor arrays (2008)

We present experimental proof of the electro-thermal bifurcation and mutual heating in bipolar transistor arrays using photon emission microscopy. With this technique, no electrical probing of each individual transistor in the array is needed but optical measurements allow accurate determination of the electro-thermal effects. For identically processed transistors in an array, we show that current bifurcation and mutual heating can be observed as sequentially optical switching of each transistor. Such optical and electrical switching effect can be explained and described using the individual transistor critical collector current theory after including mutual heating.
Cloning Genes from T-DNA Tagged Mutants (1998)

Insertion mutagenesis has a major advantage over other types of mutagenesis in that it not only causes a disruption of the gene, but the insertion element serves as a vehicle for recovery of the flanking DNA. Two types of insertion mutagens used extensively in plants are T-DN As and transposons. Each of these mutagens has then own advantages and disadvantages. A few of the advantages of T-DNAs are that they are:
Role of antioxidants in generalised anxiety disorder and depression (2012)

The findings suggest that antioxidant supplement therapy as an adjuvant therapy is useful in patients with stress-induced psychiatric disorders and the results have been discussed.
PAR4 antagonists in inflammation (2007)

Slofstra and colleagues employ the Shwartzman model of LPS-induced inflammation in mice to show that inhibition of the thrombin receptor PAR4 reduces neutrophil infiltration into inflamed tissue but does not reduce mortality or prolong survival.

It is a commonly held notion that inflammation-
A forskolin derivative, FSK88, induces apoptosis in human gastric cancer BGC823 cells through caspase activation involving regulation of Bcl-2 family gene expression, dissipation of mitochondrial membrane potential and cytochrome c release (2006)

FSK88, a forskolin derivative, was extracted and purified from cultured tropical plant roots, Coleus forskohlii. Our previous studies have demonstrated that FSK88 can inhibit HL-60 cell proliferation and induce the differentiation of HL-60 cells to monocyte macrophages. In this study, we showed that FSK88 can induce apoptotic death of human gastric cancer BGC823 cells in a dose- and time-dependent manner. Results showed that FSK88-induced apoptosis was accompanied by the mitochondrial release of cytochrome c and activation of caspase-3 in BGC823 cells. Furthermore, treatment with caspase-3 inhibitor (z-DEVD-fmk) was capable of preventing the FSK88-induced caspase-3 activity and apoptosis. FSK88-induced apoptosis in human gastric cancer BGC823 cells was also accompanied by the up-regulation of Bax, Bad and down-regulation of Bcl-2. Theses results clearly demonstrated that the induction of apoptosis by FSK88 involved multiple cellular and molecular pathways and strongly suggest that pro- and anti-apoptotic Bcl-2 family genes, mitochondrial membrane potential (Deltapsi(m)), cytochrome c, and caspase-3, participate in the FSK88-induced apoptotic process in human gastric cancer BGC823 cells.
Metronidazole for bacterial vaginosis. A comparison of vaginal gel vs. oral therapy. (2000)

The efficacy of 0.75% metronidazole vaginal gel twice daily for five days in treating BV was similar to that of standard oral metronidazole treatment and was associated with fewer gastrointestinal complaints.
Peptomer Aluminum Oxide Nanoparticle Conjugates as Systemic and Mucosal Vaccine Candidates:  Synthesis and Characterization of a Conjugate Derived from the C4 Domain of HIV-1<sub>MN</sub>Gp120 (1997)

Peptomers are polymers composed of peptides that are specifically cross-linked in a head-to-tail fashion. Recently, a peptomer composed of an amphipathic peptide from the C4 domain of HIV-1MN gp120 was shown to display a prominent alpha-helical conformation that, as an immunogen, elicited rabbit antibodies recognizing native and recombinant gp120 [Robey et al. (1995) J. Biol. Chem. 270, 23918-23921]. For the present study, we synthesized a conjugate composed of the C4 peptomer covalently linked to calcinated aluminum oxide nanoparticles. The nanoparticles were first reacted with (3-aminopropy])-triethoxysilane to provide an amine load of 15.9 mmol of R-NH2/g of solid. The amine-modified aluminum oxide nanoparticles then were reacted with N-acetylhomocysteine thiolactone at pH 10 to place a reactive thiol on the nanoparticles. A bromoacetylated C4 peptomer, modified at the epsilon-amines of lysine residues, then was reacted with the thiolated nanoparticles to give the peptomer covalently linked to aluminum oxide via a thioether bond. The peptomer load was determined to be 16 mg of peptomer/g of particles, a 55% theoretical yield. Particle shape and size of the peptomer-conjugated alumina were analyzed by electron microscopy and displayed a mean maximum diameter of 355 nm and a mean minimum diameter of 113 nm, well within the desired size range of 300 nm believed to be optimal for mucosal immunization purposes. Experimentally determined values of mean particle diameters, specific surface area, and specific peptomer load provided the information necessary to calculate the mean antigen load, which was determined to be 53000 +/- 42000 peptomer epitopes per particle. Peptomer-alumina conjugates, such as that described here, could form the basis of a new class of biomaterial that combines a chemically defined organic immunogen with a nontoxic chemically defined inorganic adjuvant.
On the Design of a Compact Neural Network-Based DOA Estimation System (2009)

A system to measure the direction of arrival (DOA) of a signal within a 45-degree conical sector is demonstrated. The system is compact and uses only four circularly polarized patch elements. A printed beamforming network is used to create a set of partially overlapping beams allowing DOA estimation without ambiguity. Neural networks are used to first classify the antenna signals and then estimate the DOA. The proposed system was validated experimentally in C band and, in spite of the highly disturbed beams caused by the finite size of the antenna platform, it was shown that DOA estimation errors in the order of one degree were achievable under signal-to-noise ratios of 10 dB.
Detection of a Point Mutation Associated with High-Level Isoniazid Resistance in <i>Mycobacterium tuberculosis</i> by Using Real-Time PCR Technology with 3′-Minor Groove Binder-DNA Probes (2003)

Tuberculosis remains one of the leading infectious causes of death worldwide. The emergence of drug-resistant strains of Mycobacterium tuberculosis is a serious public health threat. Resistance to isoniazid (INH) is the most prevalent form of resistance in M. tuberculosis and is mainly caused by mutations in the catalase peroxidase gene (katG). Among high-level INH-resistant isolates (MIC > or = 2), 89% are associated with a mutation at codon 315 of katG. There is a need to develop rapid diagnostic tests to permit appropriate antibiotic treatment and to improve clinical management. Therefore, a single-tube real-time PCR, using a novel kind of probe (3'-minor groove binder-DNA probe), was developed to detect either the wild-type or the mutant codon directly in Ziehl-Neelsen-positive sputum samples. The detection limit of the assay for purified DNA was 5 fg per well (one mycobacterial genome), and with spiked sputum samples, it was 20 copies per well, corresponding to 10(3) mycobacteria per ml of sputum. Sputum samples from 20 patients living in Kazakhstan or Moldova and infected with monodrug- or multidrug-resistant M. tuberculosis and 20 sputum samples from patients infected with INH-susceptible M. tuberculosis were tested. The sensitivities and specificities of the probes were 70 and 94% for the wild-type probe and 82 and 100% for the mutant probe. Binding to either probe was nonambiguous. This real-time PCR allows the rapid identification of a mutant katG allele and can easily be implemented in a clinical microbiology laboratory.
Optimizing Jan Jannink's Implementation of B <sup>+</sup> -tree deletion (1995)

In this note we propose optimization strategies for the B + -tree deletion algorithm. The optimizations are focused on even order B + -trees and on the reduction of the number of block accesses.
Eyedraw (2003)

This paper describes the design and development of EyeDraw, a software program that will enable children with severe mobility impairments to use an eye tracker to draw pictures with their eyes so that they can have the same creative developmental experiences as nondisabled children. EyeDraw incorporates computer-control and software application advances that address the special needs of people with motor impairments, with emphasis on the needs of children. The contributions of the project include (a) a new technique for using the eyes to control the computer when accomplishing a spatial task, (b) the crafting of task-relevant functionality to support this new technique in its application to drawing pictures, and (c) a user-tested implementation of the idea within a working computer program. User testing with nondisabled users suggests that we have designed and built an eye-cursor and eye drawing control system that can be used by almost anyone with normal control of their eyes. The core technique will be generally useful for a range of computer control tasks such as selecting a group of icons on the desktop by drawing a box around them.
Network radar (2004)

Knowledge of link specific traffic characteristics is important in the operation and design of wide area networks. Network tomography is a powerful method for measuring characteristics such as delay and loss on network-internal links using end--to--end active probes. Prior work has established the basic mechanisms for the use of tomographic inference techniques in the networking context. However, the measurement methods described in prior network tomography studies require cooperation between sending and receiving end-hosts, which limits the scope of the paths over which the measurements can be made. In this paper, we describe a new network tomographic technique based on round trip time (RTT) measurements which eliminates the need for special-purpose cooperation from receivers. Our technique uses RTT measurements from TCP SYN and SYN-ACK segments to estimate the delay variance of the shared network segment in the standard one sender - two receivers configuration. We call this approach Network Radar since it is analogous to standard radar. We present an analytic evaluation of Network Radar that specifies the variance bounds within which the technique is effective. We also evaluate Network Radar in a series of tests conducted in a controlled laboratory environment using live end hosts and IP routers. These tests demonstrate the boundaries of effectiveness of the RTT-based approach.