gebhart/patrepeval huggingface dataset:
Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort (2009)

Our findings suggest that common coding variation in these candidate genes do not make a substantial contribution to breast cancer risk in the general population. Cataloging and testing of coding variants in coactivator and corepressor genes should continue and may serve as a valuable resource for investigations of other hormone-related phenotypes, such as inter-individual response to hormonal therapies used for cancer treatment and prevention.
Chimeric Restriction Enzyme: Gal4 Fusion to <i>Fokl </i>Cleavage Domain (1998)

Gal4, a yeast protein, activates transcription of genes required for metabolism of galactose and melibiose. It binds as a dimer to a consensus palindromic 17-base pair DNA sequence. It is a member of the third family of proteins that contain zinc-mediated peptide loops that interact specifically with nucleic acids. Gal4 has a very distinctive zinc coordination profile and mode of DNA-binding. Here, we report the creation of a novel site-specific endonuclease by linking the N-terminal 147 amino acids of Gal4 to the cleavage domain of FokI endonuclease. The fusion protein is active and under optimal conditions, binds to a 17 bp consensus DNA site and cleaves near this site. As expected, the cleavage occurs on either side of the consensus binding site(s).
Analysis and Design of Weakly Coupled LC Oscillator Arrays Based on Phase-Domain Macromodels (2014)

An array of weakly coupled oscillators can generate multiphase signals, i.e., multiple sinusoidal signals with specific phase separations. Multiphase oscillators are attractive solutions in many electronic applications such as the synchronization of multiple processing units in digital electronics and the frequency synthesis in mixed-signal radio frequency circuits. Due to the complexity of multiphase oscillators and the large number of design parameters, novel simulation techniques are highly desired to efficiently handle such large-scale problems. In this paper, an efficient phase-domain simulation technique is proposed to calculate the phase response of inductance capacitance oscillator array. By some practical examples, it is shown how the proposed method can be exploited to identify the array topologies and parameter settings that guarantee stable phase separations. It is also shown how the proposed technique can be used to evaluate phase-noise performance.
Syntheses and Biological Activities (Topoisomerase Inhibition and Antitumor and Antimicrobial Properties) of Rebeccamycin Analogues Bearing Modified Sugar Moieties and Substituted on the Imide Nitrogen with a Methyl Group (1997)

As a part of studies on structure-activity relationships, several potential topoisomerase I inhibitors were prepared. Different analogues of the antitumor antibiotic rebeccamycin substituted on the imide nitrogen with a methyl group were synthesized. These compounds bore either the sugar residue of rebeccamycin, with or without the chlorine atoms on the indole moieties, or modified sugar residues (galactopyranosyl, glucopyranosyl, or fucopyranosyl) linked to the aglycone via a beta- or alpha-N-glycosidic bond. Their inhibitory properties toward protein kinase C, topoisomerase I, and topoisomerase II were examined, and their DNA-binding properties were investigated. Their in vitro antitumor activities against murine B16 melanoma and P388 leukemia cells were determined. Their antimicrobial activities were tested against Gram-positive bacteria Bacillus cereus and Streptomyces chartreusis, Gram-negative bacterium Escherichia coli, and yeast Candida albicans. These compounds are inactive toward topoisomerase II but inhibit topoisomerase I. A substitution with a methyl group on the imide nitrogen led to a loss of proteine kinase C inhibition in the maleimide indolocarbazole series but did not prevent topoisomerase I inhibition. Compounds possessing a beta-N-glycosidic bond, which fully intercalated into DNA, were more efficient at inhibiting topoisomerase I than their analogues with an alpha-N-glycosidic bond; however, both were equally toxic toward P388 leukemia cells. Dechlorinated rebeccamycin possessing a methyl group on the imide nitrogen was about 10 times more efficient in terms of cytotoxicity and inhibition of topoisomerase I than the natural metabolite.
Development of a Real-Time Hierarchical 3D Path Planning Algorithm for Unmanned Aerial Vehicles (2016)

Unmanned aerial vehicles (UAVs) frequently operate in partially or entirely unknown environments. As the vehicle traverses the environment and detects new obstacles, rapid path replanning is essential to avoid collisions. This thesis presents a new algorithm called Hierarchical D* Lite (HD*), which combines the incremental algorithm D* Lite with a novel hierarchical path planning approach to replan paths sufficiently fast for real-time operation. Unlike current hierarchical planning algorithms, HD* does not require map corrections before planning a new path. Directional cost scale factors, path smoothing, and Catmull-Rom splines are used to ensure the resulting paths are feasible. HD* sacrifices optimality for real-time performance. Its computation time and path quality are dependent on the map size, obstacle density, sensor range, and any restrictions on planning time. For the most complex scenarios tested, HD* found paths within 10% of optimal in under 35 milliseconds.
Ethylene−Norbornene Copolymer Microstructure. Assessment and Advances Based on Assignments of <sup>13</sup>C NMR Spectra (2000)

A best-fitting procedure for the quantitative determination of the molar fractions of the stereosequences that define the microstructure of an ethylene−norbornene (E−N) copolymer from 13C NMR spectra has been set up. The quantitative determination of copolymer microstructure will allow one to clarify the E−N copolymerization mechanism. This method utilizes the observed peak areas of the 13C signals and takes into account the consistency between peak areas and the stoichiometry of the copolymer chain. Thus, a further extension of signal assignments is made possible by guessing assignments of unknown signals and by discarding inconsistent hypotheses. This procedure has been applied to the analysis of the 13C NMR spectra of a large number of E−N copolymers, prepared with catalyst precursors rac-Et(indenyl)2ZrCl2 (1), rac-Me2Si(2-Me-benz[e]indenyl)2ZrCl2 (2), Me2Si(Me4Cp)(NtBu)TiCl2 (3), and Me2C(Flu)(Cp)ZrCl2 (4). An estimate of the molar fractions of the various stereosequences with a standard deviation on the order of 1−2% has been obtained. The comparison between controversial assignments existing in the literature for a number of ethylene signals has confirmed our previous assignments. New signals such as those of the C2/C3 carbons of EENNEE meso sequences (M) and of the external carbons C5 of MM and MR triads in ENNNE sequences have been assigned.
Isolated ε subunit of <i>Bacillus subtilis</i> F<sub>1</sub>‐ATPase binds ATP (2005)

Previously, we demonstrated ATP binding to the isolated epsilon subunit of F1-ATPase from thermophilic Bacillus PS3 [Kato-Yamada Y., Yoshida M. (2003) J. Biol. Chem. 278, 36013]. However, whether it is a general feature of the epsilon subunit from other sources is yet unclear. Here, using a sensitive method to detect weak interactions between fluorescently labeled epsilon subunit and nucleotide, it was shown that the epsilon subunit of F1-ATPase from Bacillus subtilis also bound ATP. The dissociation constant for ATP binding at room temperature was calculated to be 2 mM, which may be suitable for sensing cellular ATP concentration in vivo.
XWRAPComposer: a multi-page data extraction service for bio-computing applications (2005)

This paper presents a service-oriented framework for the development of wrapper code generators, including the methodology of designing an effective wrapper program construction facility and a concrete implementation, called XWRAPComposer. Three unique features distinguish XWRAPComposer from existing wrapper development approaches. First, XWRAPComposer is designed to enable multi-stage and multi-page data extraction. Second, XWRAPComposer is the only wrapper generation system that promotes the distinction of information extraction logic from query-answer control logic, allowing higher level of robustness against changes in the service provider's Web site design or infrastructure. Third, XWRAPComposer provides a user-friendly plug-and-play interface, allowing seamless incorporation of external services and continuous changing service interfaces and data format.
Nonlinear filtering for speaker tracking in noisy and reverberant environments (2002)

This paper addresses the problem of speaker tracking in a noisy and reverberant environment using time delay of arrival (TDOA) measurements at spatially distributed microphone pairs. The tracking problem is posed within a state-space estimation framework, and models are developed for the speaker motion and the likelihood of the speaker location in the light of the TDOA measurements. The resulting state-space model is nonlinear and nonGaussian, and consequently no closed-form solutions exist for the filtering distributions required to perform tracking. Here sequential Monte Carlo (SMC) methods are applied to approximate the true filtering distribution with a set of samples. The resulting tracking algorithm requires no triangulation, is computationally efficient, and can straightforwardly be extended to track multiple speakers.
Virtual array imaging radar azimuth resolution analysis (2009)

this paper, a virtual array technique is proposed for forward-looking imaging, where the virtual aperture is obtained on the multi-input/multi-output (MIMO) theory. The analytical expression of the azimuth resolution of the multi- input/double-output virtual array is derived, which establishes the bridge between the virtual aperture technique and synthetic aperture technique and offers a unified frame to process virtual aperture images and synthetic aperture images. The theoretic analysis on the virtual array imaging radar azimuth resolution has also been validated using real data results. (4 pages)
Calcium phosphate cement delivering zoledronate decreases bone turnover rate and restores bone architecture in ovariectomized rats (2012)

Patients sustaining bony fractures frequently require the application of bone graft substitutes to fill the bone defects. In the meantime, anti-osteoporosis drugs may be added in bone fillers to treat osteoporosis, especially in postmenopausal women and the elderly. The effects of zoledronate-impregnated calcium phosphate cement (ZLN/CPC) on ovariectomized (OVX) rats were evaluated. OVX rats were implanted with ZLN/CPC, containing 0.025 mg ZLN in the greater omentum. Afterward the clinical sign of toxicity was recorded for eight weeks. The rats were sacrificed and blood samples were collected for hematology and serum bone turnover markers analyses. The four limbs of the rats were harvested and micro-computer tomography (micro-CT) scanning and bone ash analyses were performed. No clinical toxicity was observed in the treated rats. Compared to the OVX rats, levels of bone resorption markers (fragments of C-telopeptides of type I collagen) and bone formation markers (alkaline phosphatase and osteocalcin) decreased significantly in the treated rats. Osteopontin, which mediates the anchoring of osteoclasts to the mineral matrix of bones, also decreased significantly. Micro-CT scanning and histologic examinations of the distal femoral metaphyses showed that the cancellous bone architectures were restored, with a concomitant decrease in bone porosity. The bone mineral content in the bone ashes also increased significantly. This study indicates that ZLN-impregnated CPC reduces bone turnover rate and restores bone architecture in OVX rats. CPC may be an appropriate carrier to deliver drugs to treat osteoporosis, and this approach may also reduce rates of post-dosing symptoms for intravenous ZLN delivery.
Two-Parameter Approximations For Multi-Echelon Repairable Inventory Models With Batch Ordering Policy (1987)

Abstract In this paper we present a model for multi-echelon repairable systems with batch ordering policy at the bases. Such an ordering policy is desirable when demand rates and/or the set up cost for ordering are relatively high. Operating characteristics of such a system are analyzed. A two-parameter approximation scheme for the distribution of the number of orders outstanding and consequently backorders is developed, and its performance evaluated. It is found that, under a variety of scenarios including both finite and infinite servers at the repair facility, the approximation scheme is very effective in providing a relatively simple means to determine the stocking levels at both the depot and the bases to minimize the cost of inventory holding and backorders. For the special case when the batch size is one, we confirm the effectiveness of the use of the negative binomial distribution as an approximation for the distribution of orders outstanding, as suggested by recent studies, under a much more general setting.
A two-chip PCM CODEC for per-channel applications (1978)

A two-chip IC PCM CODEC (coder/decoder) using CMOS and bipolar technologies will be discussed. The CODEC includes sample and holds, nonuniform A/D and D/A, precision reference and fast PCM buffers. Performance exceeds CCITT and D3 requirements.
Three-Dimensional Structures of the Free and Antigen-Bound Fab from Monoclonal Antilysozyme Antibody HyHEL-63<sup>,</sup> (2000)

Antigen-antibody complexes provide useful models for studying the structure and energetics of protein-protein interactions. We report the cloning, bacterial expression, and crystallization of the antigen-binding fragment (Fab) of the anti-hen egg white lysozyme (HEL) antibody HyHEL-63 in both free and antigen-bound forms. The three-dimensional structure of Fab HyHEL-63 complexed with HEL was determined to 2.0 A resolution, while the structure of the unbound antibody was determined in two crystal forms, to 1.8 and 2.1 A resolution. In the complex, 19 HyHEL-63 residues from all six complementarity-determining regions (CDRs) of the antibody contact 21 HEL residues from three discontinuous polypeptide segments of the antigen. The interface also includes 11 bound water molecules, 3 of which are completely buried in the complex. Comparison of the structures of free and bound Fab HyHEL-63 reveals that several of the ordered water molecules in the free antibody-combining site are retained and that additional waters are added upon complex formation. The interface waters serve to increase shape and chemical complementarity by filling cavities between the interacting surfaces and by contributing to the hydrogen bonding network linking the antigen and antibody. Complementarity is further enhanced by small (<3 A) movements in the polypeptide backbones of certain antibody CDR loops, by rearrangements of side chains in the interface, and by a slight shift in the relative orientation of the V(L) and V(H) domains. The combining site residues of complexed Fab HyHEL-63 exhibit reduced temperature factors compared with those of the free Fab, suggesting a loss in conformational entropy upon binding. To probe the relative contribution of individual antigen residues to complex stabilization, single alanine substitutions were introduced in the epitope of HEL recognized by HyHEL-63, and their effects on antibody affinity were measured using surface plasmon resonance. In agreement with the crystal structure, HEL residues at the center of the interface that are buried in the complex contribute most to the binding energetics (DeltaG(mutant) - DeltaG(wild type) > 3.0 kcal/mol), whereas the apparent contributions of solvent-accessible residues at the periphery are much less pronounced (<1.5 kcal/mol). In the latter case, the mutations may be partially compensated by local rearrangements in solvent structure that help preserve shape complementarity and the interface hydrogen bonding network.
Development of a Sensitive Peptide-Based Immunoassay:  Application to Detection of the Jun and Fos Oncoproteins (1996)

c-Jun and c-Fos belong to the bZIP class of transcriptional activator proteins, many of which have been implicated in the neoplastic transformation of cells. We are interested in engineering dominant-negative leucine zipper (LZ) peptides as a means of sequestering these proteins in vivo in order to suppress their transcriptional regulatory activity. Toward this end, we have developed a novel immunoassay for measuring the dimerization affinities of dimeric Jun and Fos complexes. This peptide-based ELISA relies on the fact that Jun and Fos preferentially form heterodimers via their leucine zipper domains. Recombinant Jun leucine zipper peptides (either native JunLZ or a V36 --> E point mutant) were labeled with biotin and specifically bound through a leucine zipper interaction to a FosLZ-glutathione S-transferase fusion protein adsorbed onto the wells of an ELISA tray. Jun:Fos complexes were subsequently detected using a recently developed streptavidin-based amplification system known as enzyme complex amplification [Wilson, M. R., & Easterbrook-Smith, S.B. (1993) Anal. Biochem. 209, 183-187]. This ELISA system can detect subnanomolar concentrations of Jun and Fos, thus allowing determination of the dissociation constants for complex formation. The dissociation constant for formation of the native JunLZ:FosLZ heterodimer at 37 degrees C was determined to be 0.99 +/- 0.30 nM, while that for JunLZ(V36E):FosLZ heterodimer was 0.90 +/- 0.13 microM. These results demonstrate that the novel peptide-based ELISA described herein is simple and sensitive and can be used to rapidly screen for potential dominant-negative leucine zipper peptides.
Amidinate Salt of Hexafluoroacetone Hydrate for the Preparation of Fluorinated Compounds by the Release of Trifluoroacetate (2012)

A powerful, new reagent, an amidinate salt of hexafluoroacetone hydrate, is an air-stable salt that can be used for the preparation of fluorinated organic molecules. Nucleophilic trifluoromethylation reactions are demonstrated following the base-promoted release of trifluoroacetate. This reagent is soluble in many polar organic solvents and produces fluoroform, following the release of trifluoroacetate. Reactions with this reagent and common electrophiles provide excellent yields of trifluoromethylated products.
Motion-Driven Electrochromic Reactions for Self-Powered Smart Window System (2015)

The self-powered system is a promising concept for wireless networks due to its independent and sustainable operations without an external power source. To realize this idea, the triboelectric nanogenerator (TENG) was recently invented, which can effectively convert ambient mechanical energy into electricity to power up portable electronics. In this work, a self-powered smart window system was realized through integrating an electrochromic device (ECD) with a transparent TENG driven by blowing wind and raindrops. Driven by the sustainable output of the TENG, the optical properties, especially the transmittance of the ECD, display reversible variations due to electrochemical redox reactions. The maximum transmittance change at 695 nm can be reached up to 32.4%, which is comparable to that operated by a conventional electrochemical potentiostat (32.6%). This research is a substantial advancement toward the practical application of nanogenerators and self-powered systems.
Conformational analysis of hepatitis B surface antigen fusions in an <i>Agrobacterium</i>‐mediated transient expression system (2004)

Vaccine antigens have been successfully produced in transgenic plants for oral immunization. Recently, a fusion strategy has been adopted to produce multicomponent vaccines and to target antigens to mucosal sites for enhanced oral immunogenicity. However, antigen fusions may not be folded correctly due to steric hindrance and may thus lose their potency. Here, we describe an Agrobacterium-mediated transient assay that provides enough antigen-expressing material at 2 days post-transfection to evaluate antigen conformation. Using the hepatitis B surface antigen (HBsAg) as a model antigen and the green fluorescent protein (GFP) as a model fusion partner, we showed that transiently expressed HBsAg and an HBsAg fusion with GFP at the N-terminus (GFP:HBsAg), but not the HBsAg fusion with GFP at the C-terminus (HBsAg:GFP), formed the 'a' determinant and virus-like particles (VLPs), similar to yeast-derived vaccine HBsAg. Thus, it is feasible to modify the HBsAg with an N-terminal fusion of up to 239 amino acids without altering its major antigenic properties. Our results also demonstrate that the Agrobacterium-mediated transient expression system can be used to evaluate the conformation of plant-based vaccines or other pharmaceutical proteins in a high-throughput manner.
Influence of Si doping on characteristics of InGaN/GaN multiple quantum wells (1998)

We have systematically studied the influence of Si doping on the characteristics of InGaN/GaN multiple quantum wells (MQWs) by means of high-resolution x-ray diffraction (HRXRD), photoluminescence (PL), PL excitation (PLE), and time-resolved PL spectroscopy. The twelve- period MQWs were grown by metalorganic chemical vapor deposition. Si doping in the GaN barriers was varied from 1×1017 to 3×1019 cm−3. Information on the structural quality of the MQWs as a function of Si doping was extracted from the linewidth broadening of the higher-order superlattice satellite peaks measured in HRXRD. The HRXRD measurements indicate that increased Si doping results in better interface properties of the MQWs. PL and PLE measurements show a decrease in the Stokes shift with increasing Si doping concentration. The 10 K radiative recombination lifetime was observed to decrease from ∼30 ns (for n&lt;1×1017 cm−3) to ∼4 ns (for n=3×1019 cm−3) with increasing Si doping concentration. The reduced Stokes shift, the decrease in radiative recombination lifetime, and the increase in the interface quality indicate that Si doping results in a decrease in carrier localization at potential fluctuations in the InGaN active layers.
A multilayer control for multirotor UAVs equipped with a servo robot arm (2015)

A multilayer architecture to control multirotor UAVs equipped with a servo robot arm is proposed in this paper. The main purpose is to control the aerial platform taking into account the presence of the moving manipulator. Three layers are considered in this work. First, a novel mechanism is proposed considering a moving battery to counterweight the statics of the robotic arm. Then, in order to overcome the mechanical limitations of the previous layer, the residual of the arm static effects on the UAV is computed and compensated through the given control thrust and torques. Finally, an estimator of external forces and moments acting on the aerial vehicle is considered and the estimations are fed back to the controller to compensate neglected aerodynamic effects and the arm dynamics. The performance of the proposed architecture has been experimentally evaluated.
Short-term intra-individual variability in heidelberg retina tomograph II. (2002)

We determined the short-term intra-individual variability for each parameter of the Heidelberg Retina Tomograph II (HRT II). Therefore we examined prospectively 20 healthy volunteers 3 times within 2 weeks. The variability was expressed as the coefficient of variation for each parameter. The short-term intra-individual variability in normal subjects was < or = 12% in all but 3 parameters. Rim Area was the least variable parameter (2 +/- 1%). Cup Volume had the highest variability (25 +/- 38%).