gebhart/patrepeval huggingface dataset:
Eukaryotic regulatory elements lurking in plasmid DNA: the activator protein-1 site in pUC. (1994)

Imagine that a Cartesian demon is trying to fool molecular biologists who study gene regulation. He inserts a potent regulatory site into their standard plasmids, a site that can confer transcription regulation via a wide variety of agents on a linked core promoter. These agents include growth factors, neurotransmitters, oxidative stress, UV irradiation, cytokines, phorbol esters, cyclic nucleotides, and steroid/thyroid hormones. Then the demon watches as innocent investigators insert their favorite promoter fragment into the booby-trapped plasmids, transfect the construct into mammalian cells, and analyze gene regulation. Confusion ensues. Parts of this tale are real. Plasmids of the pUC series contain a binding site for activator protein-l (AP-1). a potent and widespread transcription factor that is composed of the Jun and Fos proteins and whose activity is subject to many avenues of regulation (1, 2). The “demon” site, located at basepair 37 in the standard sequence (3) is only a few hundred basepairs from the multiple cloning site where promoter sequences are typically inserted for study. The plasmid AP-1 site, TGACACA, was first suspected on the basis of sequence (Ref. 2, p. 1200) and by its seeming ability to confer responsiveness to UV irradiation (Ref. 4, p. 5175). Its biological activity has now been studied and independently confirmed. The site confers activation by phorbol esters and by transfected Jun on promoters inserted into the multiple cloning site. Jun activation is potentiated by unliganded thyroid hormone receptor and liganded estrogen receptor, but is repressed by thyroid hormone (1) (our unpublished findings). Repression by thyroid hormone is unique to the plasmid site and not conferred by a consensus AP-1 site (TGACTCA). Thus, whereas the demon site can be expected to confer the full range of AP-1 effects, in-
Design and Implementation of A Focused Crawler—TargetCrawler (2014)

Adopting focused crawler to search web sites is the trend of next generation search engines. Design and implementation of a focused crawler -TargetCrawler is introduced in detail, including its overall architecture, main modules, working processes and two key algorithms, duplicate removing algorithm based on the Bloom filter and ranking algorithm based on priority which are designed to ensure accuracy and efficiency of web search. Experimental results show the effectiveness of the scheme.
Computational Power And Accuracy Trade-Offs In Optical Numerical Processors (1986)

The comparison between the capabilities of optical versus electronic signal processors is usually the first issue that is addressed when one considers using optics in a particular signal processing application. In general, it is necessary that optics offers a clear advantage over electronics in order to be able to justify opting for an optical approach. The comparison between optics and electronics is based on a number of related criteria whose relative importance depends on the application. These include processing power (e.g. the number of elementary operations performed per unit time), algorithmic flexibility, accuracy, power consumption, weight, cost. The primary advantage of analog optical systems is the extremely high processing power that can be achieved (in excessof 104 analog multiplication per second is possible with acoustooptic technology) with relatively small power and size requirements. The major disadvantages of conventional analog optical processors are lack of algorithmic flexibility (limited to linear transformations) and low accuracy. These two limitations along with immature device technologies have restricted the utilization of optical signal processors to only a small number of areas, such as synthetic aperture radar and acoustooptic spectrum analyzers. Thus there is strong motivation to find ways to improve the accuracy and extend the range of signal processing operations that can be optically performed in order to extend the applicability of optical techniques. In this paper we examine the method of digital multiplication by analog convolution (DMAC) [l] [4] which has received attention in recent years as a technique for building accurate optical processors. We will show that DMAC is fundamentally limited because it can provide accuracy only at the expense of using post-detection electronics that are more sophisticated than the electonics required to build the entire system electronically in the first place.
Gaussian random fields in spherical coordinates (1991)

The problem of constructing realizations of a random density field in the neighborhood of a peak of specified over-density simplifies dramatically when formulated in spherical coordinates. The problem can now be solved exactly rather than iteratively, and it is practicable to specify also the shape of the peak. The present formalism both facilitates the setting up of initial conditions for numerical simulations of galaxy- and cluster-formation, and analytic investigations of the statistical properties of fields around peaks.
Non-negative matrix factorization for highly noise-robust ASR: To enhance or to recognize? (2012)

This paper proposes a multi-stream speech recognition system that combines information from three complementary analysis methods in order to improve automatic speech recognition in highly noisy and reverberant environments, as featured in the 2011 PASCAL CHiME Challenge. We integrate word predictions by a bidirectional Long Short-Term Memory recurrent neural network and non-negative sparse classification (NSC) into a multi-stream Hidden Markov Model using convolutive non-negative matrix factorization (NMF) for speech enhancement. Our results suggest that NMF-based enhancement and NSC are complementary despite their overlap in methodology, reaching up to 91.9% average keyword accuracy on the Challenge test set at signal-to-noise ratios from -6 to 9 dB-the best result reported so far on these data.
Biosensor Applications to Antitachycardia Devices (1991)

Current arrhythmia detection algorithms are unable to adequately distinguish stable from unstable tachycardias; therefore application of a biosensor to antitachycardia devices has been proposed to improve their performance. Right heart pressures and impedance have been investigated for incorporation into these systems. Integration of other parameters (oxygen saturation, preejection period, pH, cardiac output, flow, and temperature) into these devices might also prove useful. The status of these biosensor arrhythmia detection algorithms and their application to antitachycardia devices are described below.
New multilevel DCT, feature vectors, and universal blind steganalysis (2005)

Universal blind steganalysis can detect hidden messages without using prior information about the steganographic system. Recently, Farid developed a wavelet coefficient, higher-order statistics based, universal blind steganalysis method. This approach is a global method which demonstrated a high-quality in performance standards. Fridrich and Goljan also presented a DCT based local targeted steganalysis method to break the F5 algorithm. However, both Farid’s and Fridrich and Goljan’s methods have some limitations. This paper presents a local universal steganalysis technique combining the advantages of both methods. The basic components of the presented method are: novel DCT multilevel decomposition with wavelet structure; a new set of feature vectors; and a modified kernel function in the Kernel Fisher Discriminant. Experimental results show the presented method offers better performance than commonly used schemes. Inherently, the presented method has the ability to localize the hidden information, it can capture stego information in small blocks, and it is functional using only a small training set.
Energy storage optimization strategies for smart grids (2013)

The efficient management of the supply and demand in electricity networks is becoming a pivotal issue with important fallbacks both in the technological and financial domains. An interesting topic in this domain is the use of large batteries at the end users premises to reduce the average cost of energy supply, by storing energy when its cost is low and releasing it when the cost is high. In this paper, we wish to gain insights on the impact of some system model parameters, such as battery capacity, charge/discharge rate, power request process, and cost functions, on the cost saving that can be achieved by some selected energy storage algorithms. The study shows that the battery capacity has a direct and rather linear impact on cost reduction, while the effect of charge/discharge rates is less straightforward to predict. Furthermore, we show that, with piecewise, convex and non-decreasing cost functions, the optimal energy storage strategy has a threshold structure, where the number of thresholds depend on the shape of the cost function and the constraints of the battery.
Hydrophobic interaction in Candida albicans and Candida tropicalis adherence to various denture base resin materials (1985)

The effects of hydrophobicities of substrate surfaces on microbial adherence were examined by using Candida albicans and Candida tropicalis and 21 denture base resin materials. With increasing surface free energy of resin plates, increasing adherence of C. albicans and decreasing adherence of C. tropicalis were observed. The surface free energy of C. albicans is higher than that of all resin material surfaces, and C. tropicalis has surface free energy lower than that of all materials used. In calculation of the changes of free energy accompanying the adherence, the higher adherence tendency was accompanied by a lower value for the free energy change in both species. From a different standpoint, the closer the surface free energy of the substrate surface and the microorganism, the higher was the probability of adherence.
A novel broadside coupler model for MMIC impedance transformer design (2011)

Broadside coupled impedance transformers offer the potential for significantly improving the loss and bandwidth of matching networks for high power, broadband power amplifiers. There are currently no adequate scalable models available for prototyping designs. This work presents a novel method for developing an accurate, scalable, process specific, broadside coupler model which can be used to design impedance transformers. The empirical broadside coupler model presented in this work is used to construct an example impedance transformer and is compared to electromagnetic simulation and measured data.
Decreased Secretion of ApoB Follows Inhibition of ApoB−MTP Binding by a Novel Antagonist (2000)

Apolipoprotein B (apoB) and microsomal triglyceride transfer protein (MTP) are essential for the efficient assembly of triglyceride-rich lipoproteins. Evidence has been presented for physical interactions between these proteins. To study the importance of apoB-MTP binding in apoB secretion, we have identified a compound, AGI-S17, that inhibited (60-70% at 40 microM) the binding of various apoB peptides to MTP but not to an anti-apoB monoclonal antibody, 1D1, whose epitope overlaps with an MTP binding site in apoB. AGI-S17 had no significant effect on the lipid transfer activity of the purified MTP. In contrast, another antagonist, BMS-200150, did not affect apoB-MTP binding but inhibited MTP's lipid transfer activity. The differential effects of these inhibitors suggest two functionally independent, apoB binding and lipid transfer, domains in MTP. AGI-S17 was then used to study its effect on the lipid transfer and apoB binding activities of MTP in HepG2 cells. AGI-S17 had no effect on cellular lipid transfer activities, but it inhibited coimmunoprecipitation of apoB with MTP. These studies indicate that AGI-S17 inhibits apoB-MTP binding but has no effect on MTP's lipid transfer activity. Experiments were then performed to study the effect of inhibition of apoB-MTP binding on apoB secretion in HepG2 cells. AGI-S17 (40 microM) did not affect cell protein levels but decreased the total mass of apoB secreted by 70-85%. Similarly, AGI-S17 inhibited the secretion of nascent apoB by 60-80%, but did not affect albumin secretion. These studies indicate that AGI-S17 decreases apoB secretion most likely by inhibiting apoB-MTP interactions. Thus, the binding of MTP to apoB may be important for the assembly and secretion of apoB-containing lipoproteins and can be a potential target for the development of lipid-lowering drugs. It is proposed that the apoB binding may represent MTP's chaperone activity that assists in the transfer from the membrane to the lumen of the endoplasmic reticulum and in the net lipidation of nascent apoB, and may be essential for lipoprotein assembly and secretion.
Calculation of the magnetic gradient tensor from total field gradient measurements and its application to geophysical interpretation (1988)

Abstract The very low inherent noise levels of superconducting quantum interference device (SQUID) sensors have led to proposals for the use of airborne SQUID magnetic gradiometers as geophysical interpretation tools. The quantity measured by such systems will be the gradient tensor, the spatial rate of change of the vector components of the magnetic field. By contrast, existing airborne gradiometers measure the spatial rate of change of the magnitude of the total field.This work describes a technique whereby the gradient tensor can be calculated from measurements of either the vertical or horizontal total field gradients throughout a plane. The signal-to-noise ratio of the calculated tensor components is essentially the signal-to-noise ratio of the original total field gradient measurements. The resulting tensor components may be upward or downward continued with standard techniques.Two advantages of using the tensor gradients instead of the total field gradients have been determined. Because the tensor components are not a function of the direction of the Earth's field, contour plots do not suffer the skewing problems that total field or vertical gradient plots do. Thus, tensor gradient contour plots may be easier to interpret or may enhance the information obtained from total field or vertical gradient maps. In addition, the dipole-tracking algorithm developed by Wynn et al. (1975) has been shown to be quite successful in determining the depth and horizontal location of block-shaped bodies. The error in depth estimation is a strong inverse function of the ratio of the closest point of approach to largest dimension of the body. However, if the smallest separation is more than twice the largest dimension of the body, errors in depth estimation are less than 10 percent. Because the tensor components are calculated on a horizontal plane, they can be upward continued to meet this condition.
Characterization of an endolysin, LysBPS13, from a Bacillus cereus bacteriophage (2012)

Use of bacteriophages as biocontrol agents is a promising tool for controlling pathogenic bacteria including antibiotic-resistant bacteria. Not only bacteriophages but also endolysins, the peptidoglycan hydrolyzing enzymes encoded by bacteriophages, have high potential for applications as biocontrol agents against food-borne pathogens. In this study, a putative endolysin gene was identified in the genome of the bacteriophage BPS13, which infects Bacillus cereus. In silico analysis of this endolysin, designated LysBPS13, showed that it consists of an N-terminal catalytic domain (PGRP domain) and a C-terminal cell wall binding domain (SH3_5 domain). Further characterization of the purified LysBPS13 revealed that this endolysin is an N-acetylmuramyl-l-alanine amidase, the activity of which was not influenced by addition of EDTA. In addition, LysBPS13 demonstrated remarkable thermostability in the presence of glycerol, and it retained its lytic activity even after incubation at 100 °C for 30 min. Taken together, these results indicate that LysBPS13 can be considered a favorable candidate for a new antimicrobial agent to control B. cereus.
Evolution in the Palladium‐Catalyzed Cross‐Coupling of sp‐ and sp<sup>2</sup>‐Hybridized Carbon Atoms (2003)

Palladium-catalyzed bond-formation between alkynes and aryl halides and triflates is as fascinating today as it was nearly 30 years ago when such reactions were introduced by Sonogashira (see scheme; OTf=CF3SO3). More facile procedures, new acetylide coupling partners, and more efficient catalysts and ligand systems all combine to expand the limits of this versatile reaction.
Myopathy in critically ill patients (1999)

Myopathic changes are surprisingly frequent in critically ill patients. The clinical importance of this finding is still unknown, but it is likely that weakness caused by myopathy prolongs ICU stay and rehabilitation. Because corticosteroids and muscle relaxants appear to trigger some types of ICU myopathy, they should be avoided or administered at the lowest doses possible. Sepsis, denervation, and muscle membrane inexcitability may be additional factors. Studies addressing the pathophysiology of myopathy in critically ill patients are urgently needed.
Simultaneous Tailoring of Surface Topography and Chemical Structure for Controlled Wettability (2004)

Wettability was controlled in a rational manner by individually and simultaneously manipulating surface topography and surface chemical structure. The first stage of this research involved the adsorption of charged submicrometer polystyrene latex particles to oppositely charged poly(ethylene terephthalate) (PET) film samples to form surfaces with different topographies/roughness; adsorption time, solution pH, solution ionic strength, latex particle size, and substrate charge density are external variables that were controlled. The introduction of discrete functional groups to smooth and rough surfaces through organic transformations was carried out in the second stage. Amine groups (-NH(2)) and alcohol groups (-OH) were introduced onto smooth PET surfaces by amidation with poly(allylamine) and adsorption with poly(vinyl alcohol) (PVOH), respectively. On latex particle adsorbed surfaces, a thin layer of gold was evaporated first to prevent particle redistribution before chemical transformation. Reactions with functionalized thiols and adsorption with PVOH on patterned gold surfaces successfully enhanced surface hydrophobicity and hydrophilicity. Particle size and biomodal particle size distribution affect both hydrophobicity and hydrophilicity. A very hydrophobic surface exhibiting water contact angles of 150 degrees /126 degrees (theta(A)/theta(R)) prepared by adsorption of 1-octadecanethiol and a hydrophilic surface with water contact angles of 18 degrees /8 degrees (theta(A)/theta(R)) prepared by adsorption of PVOH were prepared on gold-coated surfaces containing both 0.35 and 0.1 microm latex particles. The combination of surface topography and surface-chemical functionality permits wettability control over a wide range.
IPv6 over Network based Mobile IPv4 (2007)

There is a growing demand for routable IP addresses to support large
wireless user base today. Wireless operators are looking for ways to
leverage the IPv6 address space to meet the ever increasing number of
wireless data users. The operators who have network-based IPv4
mobility solutions can leverage the same scheme to provide mobility
access service with larger address pool using IPv6 addressing. The
proposed approach solves both, by allowing provision of the network-
based mobility service, and the IPv6 address acquisition for the MNs.
The mobility contolling function may be located either at the
dedicated Access Node (achieving a virtual link-layer to the HA) or at
the first hop Access Router.
Ultra-Deep Pyrosequencing Detects Conserved Genomic Sites and Quantifies Linkage of Drug-Resistant Amino Acid Changes in the Hepatitis B Virus Genome (2012)

UDPS methodology enabled quantification of HBV quasispecies variants, even those harboring complex combinations of amino acid changes. The high percentage of potentially defective genomes, especially in the surface region, suggests effective trans-complementation of these variants.
Voiding disorders and unstable bladder in children. (1993)

A total of 42 neurologically normal children with different voiding problems have been studied urodynamically during the last 4 years. Seventeen patients had unstable bladder, with significantly decreased capacity. The degree of volume decrease depended on the severity of instability and on the type of micturition problems. Eight patients had trabeculation of the bladder wall and 2 had wide bladder neck. Six children had vesicoureteral reflux in 8 ureters. Eleven patients were treated with Ditropan. Four children had repeated cystomanometry after treatment. They had stable bladder and its capacity has increased.
Designing a Packed Dividing Wall Column for an Aromatics Processing Plant (2011)

This paper introduces a comprehensive design method assembled using facilities of a commercial software package that complemented by Excel programs, which contain own column dimensioning and well established cost estimation procedures, enables proper assessment of the industrial viability of a dividing wall column (DWC) equipped with corrugated sheet structured packings. The heart of the performance simulation tool is a detailed four-column model that in conjunction with a simple, theoretically founded short-cut method providing reliable initial values for liquid and vapor splits and a simple but effective objective function for design optimality indication allows determination of the adequate stage and reflux requirement of a DWC. The proposed dimensioning method enables a close approach in accuracy to that required at the stage of conceptual design for purposes of making a bid by an equipment manufacturer. Compared to a two-columns-in-series configuration, as employed in an aromatics processing complex within a refinery, a DWC equipped with state-of-the-art structured packing and auxiliary internals requires approximately 43% less energy to deliver three fractions at required product specifications. This, accompanied by savings of nearly 51% based on total annualized costs, indicates that implementing a DWC could lead to a significant increase in profitability of aromatics processing plants.
The invisible fray: a critical analysis of the use of reflectometry for fray location (2006)

Significant international research and development efforts have been devoted to methods and equipment for locating wiring faults, particularly those on aging aircraft. Several reflectometry methods that send high frequency signals down the line and analyze the returned reflections have risen to the forefront of these technologies. While these methods are proving to be accurate for location of "hard" faults (open and short circuits), the location of "soft" faults such as frays and chafes remains elusive. This paper analyzes the impedance of several types of soft faults and their resultant reflectometry returns, which are shown to be smaller than returns from other sources of physical and electrical noise in the system. Through numerical simulations verified by measurement, it is shown that soft faults are virtually impossible to locate using today's reflectometry methods including time domain reflectometry, frequency domain reflectometry, and spread spectrum time domain reflectometry. The methods used in this analysis can be extended to other types of reflectometry as they emerge.