gebhart/patrepeval huggingface dataset:
Probing the Escherichia coli glnALG upstream activation mechanism in vivo. (1988)

In vivo "footprints" of the glnA regulatory region under activating conditions demonstrate that the three most upstream activator sequences bind the protein NRI in the cell. Together, protections at these sites span six of seven consecutive major grooves and lie on the same helix face. E sigma 54 protects two major grooves of DNA approximately 60 base pairs downstream at the glnAp2 promoter and primarily on the opposite helix face. Experiments using potassium permanganate to probe open complex formation in vivo demonstrate that NRI is absolutely required for E sigma 54 to open the promoter DNA. Together, the dimethyl sulfate and permanganate studies verify [Reitzer, L. J., Bueno, R., Cheng, W. D., Abrams, S. A., Rothstein, D. M., Hunt, T. P., Tyler, B. & Magasanik, B. (1987) J. Bacteriol. 169, 4279-4284] that E sigma 54 occupies the glnAp2 promoter in a closed complex in vivo even in the presence of excess nitrogen and the absence of NRI. Furthermore, the slow step in transcriptional activation is shown to be an NRI-dependent conformational change in the downstream promoter DNA, which results in DNA melting. These observations place interesting restrictions on models describing the mechanism by which NRI activates transcription from glnAp2 at a distance.
Engineering Mathematics, 3rd edn (2002)

Engineering Mathematics is a comprehensive textbook for technological and vocational mathematics courses, and is also well designed for self-study objectives. John Bird's approach, based on numerous worked examples and problems, is intended for students of a wide range of abilities and interests. The emphasis is on problem-solving skills, keeping the theory to a minimum, for a thoroughly practical introduction to core mathematics needed for engineering studies and practice. The third edition has been reorganized to present a more logical introduction of the topics, including recent course specifications in the latest National and Vocational Certificate of Education syllabuses.
1-Methylcyclopropene Interactions with Diphenylamine on Diphenylamine Degradation, α-Farnesene and Conjugated Trienol Concentrations, and Polyphenol Oxidase and Peroxidase Activities in Apple Fruit (2005)

1-Methylcyclopropene (1-MCP) is a new technology that is applied commercially to inhibit ethylene action in apple fruit, but its interactions with existing technologies such as diphenylamine (DPA) for control of superficial scald development in fruit during and after storage is unknown. To investigate possible interactions between 1-MCP and DPA, Delicious apples were untreated or treated with 2 g L(-1) DPA, and then with or without 1 microL L(-1) 1-MCP. Ethylene production and respiration rates of fruit were measured immediately following treatment, and fruit was stored at 0.5 degrees C for 12 weeks. Internal ethylene concentrations (IEC), alpha-farnesene and conjugated trienol (CTol) concentrations, activities of peroxidase and polyphenol oxidase (PPO), and DPA levels in the skin of the fruit were measured at intervals during storage. 1-MCP reduced the rate of DPA loss from peel tissue so that by 12 weeks of storage concentrations of the chemical were 25% higher than in untreated fruit. 1-MCP, with and without DPA, markedly inhibited ethylene production and respiration rates, maintained low IEC and alpha-farnesene and CTol concentrations, while DPA had little effect on these factors except inhibition of CTol accumulation. Treatment effects on peroxidase and PPO activities were inconsistent.
Calculations of ion chamber displacement effect corrections for medium-energy X-ray dosimetry (1995)

This paper investigates the displacement effect corrections for ionization chambers calibrated in air in terms of air kerma and used at a depth in a phantom irradiated by medium-energy x-rat beams for tube potentials between 100 kV and 300 kV. The EGS4 (electron gamma shower version 4) Monte Carlo code system has been used to simulate the coupled transport of photons and electrons. The chamber displacement correction factor, pdis, has been calculated both using a simple photon attenuation and scattering method and by direct Monte Carlo calculation of the ration of the water kerma at a depth in a phantom to the water kerma in a low-density (the same density as that of air) water cavity with its centre placed at the same depth in the phantom irradiated by medium-energy x-ray beams. Good agreement has been achieved between the pdis factors obtained using the simple method and those obtained by the direct Monte Carlo simulation. In contrast to the values recommended by the IAEA code of practice, which exceed unity by up to 10%, our pdis values for a stemless NE2571 chamber vary between 0.994 and 1.001 for the same energy range and for a stemless NE2561 chamber between 0.974 and 0.993. The beam quality correction factor and stem correction factor have been investigated in separate works. The ratios of the overall correction factors calculated in this work for an NE2571 chamber to that for an NE2561 chamber are consistent with the recent experimental results.
Multi-Level Mediator-Based Technique for Classes Hot Swapping in Java Applications (2006)

It is software system nature to be updated over time; the usual way of updating software is to shut down the system and install the new version, then restart it. This poses problems for applications that have limited down-time. In this paper, we present an approach for building dynamic Java application where its classes can be updated while the program is running. Our approach is based on the features supported by Java language such as dynamic linking, class loader, and Java reflection
Holographic Memories (1975)

Recent work in holographic memories is reviewed. Erasable, digital holographic stores have major remaining problem areas of increasing the memory capacity and developing a good storage material. The modular memory concept and the superposition of holograms in a thick storage media are two approaches to increasing the capacity of a holographic store. There have been several very interesting read-only holographic memories developed for specialized systems applications. The properties of these specialized holographic stores are compared with some bit-oriented optical memories as well as more standard technologies such as semiconductor storage and magnetic disk storage. The advantages and dis-advantages of holographic storage are reviewed. The associa-tive property of holograms should make this form of storage very useful for parallel search type memories and also create the potential for parallel data processing in applications of the future.
Multiple Crack Growth in a Functionally Graded Material under Thermal Shock (2000)

This paper examines the problem of thermal cracking under a transient temperature field in a ceramic/metal functionally graded plate. When the functionally graded plate is cooled from high temperature, it could be observed that curved or stright multiple cracks occur on the ceramic surface. In addition, those multiple cracks influence each other and form complex arrays. To investigate mutual effect among multiple cracks, crack paths are simulated in a mode I and II state using finite element method. Transient thermal stress field and crack growth are treated as a linear quasi-static thermoelastic problem for a plane strain state.
Structural Studies of the Monolayers and Bilayers Formed by a Novel Cholesterol-Phospholipid Chimera (2011)

Langmuir isotherm, neutron reflectivity, and small angle neutron scattering studies have been conducted to characterize the monolayers and vesicular bilayers formed by a novel chimeric phospholipid, ChemPPC, that incorporates a cholesteryl moeity and a C-16 aliphatic chain, each covalently linked via a glycerol backbone to phosphatidylcholine. The structures of the ChemPPC monolayers and bilayers are compared against those formed from pure dipalmitoylphoshatidylcholine (DPPC) and those formed from a 60:40 mol % mixture of DPPC and cholesterol. In accord with previous findings showing that very similar macroscopic properties were exhibited by ChemPPC and 60:40 mol % DPPC/cholesterol vesicles, it is found here that the chimeric lipid and lipid/sterol mixture have very similar monolayer structures (each having a monolayer thickness of ∼26 Å), and they also form vesicles with similar lamellar structure, each having a bilayer thickness of ∼50 Å and exhibiting a repeat spacing of ∼65 Å. The interfacial area of ChemPPC, however, is around 10 Å(2) greater than that of the combined DPPC/cholesterol unit in the mixed lipid monolayer (viz., 57 ± 1 vs 46 ± 1 Å(2), at 35 mN·m(-1)), and this difference in area is attributed to the succinyl linkage which joins the ChemPPC steroid and glyceryl moieties. The larger area of the ChemPPC is reflected in a slightly thicker monolayer solvent distribution width (9.5 vs 9 Å for the DPPC/cholesterol system) and by a marginal increase in the level of lipid headgroup hydration (16 vs 13 H(2)O per lipid, at 35 mN·m(-1)).
On-line submicron profile measurements from safe distances with conoscopic holography: feasibility and potential problems (2008)

On-line noncontact surface inspection with high precision is still an open problem. Usual methods are, in general, not applicable in hostile environments or not adequate for on-line measurement, as they are either slow in nature or need to work from very short, unsafe distances, providing small depths of field and apertures. The ongoing work toward the development of a noncontact optical profile measuring sensor that could be used for submicron measurements in on-line applications is presented here. Our approach is based on conoscopic holography and triangulation, and uses a very simple method for removing speckle noise, which is key for obtaining high precisions from safe distances (several centimeters).
A Wearable SSVEP-Based BCI System for Quadcopter Control Using Head-Mounted Device (2018)

Restoring the interaction between disabled people and the 3-D physical world via a brain-computer interface (BCI) is an exciting topic. To this end, we designed a wearable BCI system based on the steady-state visual evoked potential (SSVEP), which enables 3-D navigation of quadcopter flight with immersive first-person visual feedback using a head-mounted device. In addition, to alleviate the user’s operational burden, this paper provides asynchronous switch control for the users. The transitional state due to head movement in an asynchronous BCI was isolated online and translated into hover to eliminate its influence. The experimental results in the physical environment showed that the subjects could accomplish the 3-D flight tasks accurately and smoothly using our system. In particular, in this paper, we proposed an information transfer rate metric that is suitable for the asynchronous task. We demonstrated the feasibility of using the head-mounted device and a proper control strategy to facilitate the portability and practicability of the SSVEP-based BCI system for its navigation utility.
ChemInform Abstract: Dynamic Resolution of α‐Substituted Carboxylic Acids and Esters (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The statistical mechanics of polymerized material (1967)

It is argued that a solid consisting of fully entangled long chain molecules will show elastic properties similar to those of cross linked, i.e. vulcanized material, provided that elastic moduli are studied in periods short compared with creep times. An appropriate formula for the free energy is deduced, and calculated for a model in which each chain is confined to an environment formed by the others. Under deformation this environment changes and the elastic energy can be deduced. If 1, 2, 3 are the principal strains, that part of the free energy due to the polymer entanglements is shown to be ΔF = - BκT(12 + 22 + 32)L(σl/m)1/2 for small strains, where B is a numerical constant, L is the total length of polymer present, σ the density of polymer, and l, m the effective length and mass of one of the submolecules from which the polymer is made. An expression is also given for the case of a strain of arbitrary size.
THE RELATION OF INSTRUMENTAL and SYMBOLIC ATTRIBUTES TO A COMPANY'S ATTRACTIVENESS AS AN EMPLOYER (2003)

This study adds a new marketing‐based angle to the study of the attractiveness of organizations in the early stages of the recruitment process. Drawing on the instrumental‐symbolic framework from the marketing literature, we expected that the meanings (in terms of inferred traits) that prospective applicants associate with employing organizations would play an important role in applicants' attractiveness to these organizations. Two groups of prospective applicants (275 final‐year students and 124 bank employees) were drawn from the applicant population targeted by the bank industry. These applicants were asked to rate a randomly assigned bank in terms of job/organizational factors and to ascribe traits to this bank. In both samples, trait inferences about organizations accounted for incremental variance over job and organizational attributes in predicting an organization's perceived attractiveness as an employer. Moreover, it was easier to differentiate among organizations on the basis of trait inferences versus traditional job and organizational attributes. Practical implications for image audit and image management are discussed.
Automated Construction of Macromodels from Frequency Data for Simulation of Distributed Interconnect Networks (2004)

As the complexity of interconnects and packages increases and the rise and fall time of the signal decreases, the electromagnetic effects of distributed passive devices are becoming an important factor in determining the performance of gigahertz systems. The electromagnetic behavior extracted using an electromagnetic simulation or from measurements is available as frequency dependent data. This information can be represented as a black box called a macromodel, which captures the behavior of the passive structure at the input/output ports. In this dissertation, the macromodels have been categorized as scalable, passive and broadband macromodels. The scalable macromodels for building design libraries of passive devices have been constructed using multidimensional rational functions, orthogonal polynomials and selective sampling. The passive macromodels for time-domain simulation have been constructed using filter theory and multiport passivity formulae. The broadband macromodels for high-speed simulation have been constructed using band division, selector, subband reordering, subband dilation and pole replacement. An automated construction method has been developed. The construction time of the multiport macromodel has been reduced. A method for reducing the order of the macromodel has been developed. The efficiency of the methods was demonstrated through embedded passive devices, known transfer functions and distributed interconnect networks.
Evaluation of markers of beige adipocytes in white adipose tissue of the mouse (2016)

While most putative beige markers are clearly expressed in beige adipocytes in vitro, in vivo the small dynamic range of most of these markers, the strength of the beigeing stimulus, and the age of the mice may limit their utility, although this limitation may be overcome by specifically evaluating these markers in the adipocyte fraction. Thermoregulatory markers like UCP1, CIDEA, or Cox8b represent the best options to evaluate the beigeing of white adipose tissue in vivo.
String matching with multicore CPUs: Performing better with the Aho-Corasick algorithm (2013)

Multiple string matching is known as locating all the occurrences of a given number of patterns in an arbitrary string. It is used in bio-computing applications where the algorithms are commonly used for retrieval of information such as sequence analysis and gene/protein identification. Extremely large amount of data in the form of strings has to be processed in such bio-computing applications. Therefore, improving the performance of multiple string matching algorithms is always desirable. Multicore architectures are capable of providing better performance by parallelizing the multiple string matching algorithms. The Aho-Corasick algorithm is the one that is commonly used in exact multiple string matching algorithms. The focus of this paper is the acceleration of Aho-Corasick algorithm through a multicore CPU based software implementation. Through our implementation and evaluation of results, we prove that our method performs better compared to the state of the art.
Conduction in non-crystalline systems (1971)

Abstract A summary is given of mechanisms which may be responsible for non-ohmic conduction due to strong fields in thin films of non-crystalline semi-conductors. This is used for a discussion of the mechanism of threshold switching in thin films of chalcogenide semicondutors. The predictions of the thermal mechanism are outlined, as is also the author's earlier electronic (double injection) model for the on-state. It is suggested that both a thermal on-state and an electronic on-state are possible, and that both have been observed. The on-state in the switches described by Ovshinsky (1968) we believe to be electronic; the thermal model makes predictions quite different from those observed, particularly with respect to the transition to a memory state. On the other hand the process leading up to switching into an electronic state normally involves heating and perhaps a thermal instability; and as a consequence the dependence on temperature and film thickness of the voltages leading to electronic and thermal breakdown can in many cases be similar.
[Perinatal corticosteroid therapy: modalities, efficacy, consequences]. (2001)

During perinatal period, corticosteroid treatment has two major indications: first antenatally to improve fetal maturity and then to treat postnatal bronchopulmonary dysplasia. Antenatal corticosteroid treatment is widely proved to be efficient in reducing hyaline membrane disease and perinatal mortality incidence. Moreover, it has positive effects on intraventricular hemorrhage incidence, on hemodynamic failure, on persistent patent ductus arteriosus and on necrotizing enterocolitis. Side-effects are few and mild considering expected benefits and they usually occurs after multiple courses. Contra-indications are rare. Bronchopulmonary dysplasia comes with early, important and prolonged inflammatory processes. Corticotherapy allows decreasing significantly length of mechanical ventilation and oxygenotherapy among ventilated premature infants diagnosed with bronchopulmonary dysplasia. In the meantime, acute side-effects are frequent and benefits on mortality rate and long term outcome are not obvious. Main concern remains on possible long-term deleterious consequences on growth, lung and central nervous system development. In this field, clinical data are still insufficient as animal experimentation data promote caution and search for a minimal efficient therapeutic pathway.
Fusion of multispectral and panchromatic images by local mean and variance matching filtering techniques (1998)

peer reviewed
Building 3D subsurface models conforming to seismic structural and stratigraphic features (2017)

Subsurface modeling from seismic and borehole data is important for reservoir prediction, geophysical exploration, and production. A reasonable model should honor borehole rock properties and conform to seismic structural and stratigraphic features. Such a subsurface model can be difficult to build in cases complicated by faults and unconformities. Automatic and semiautomatic methods have been proposed to build subsurface models from seismic and borehole data; however, seismic structural and stratigraphic features and borehole measurements are not fully used in most methods. I have developed a workflow to fully use seismic and borehole data to build subsurface models that honor borehole measurements and conform to seismic horizons, faults, unconformities, and stratigraphic features such as channels. In this workflow, I first automatically remove the faulting and folding in seismic and borehole data and map them into an unfaulted and flattened space, in which seismic reflectors and borehole measurements corresponding to the same geologic layers are horizontally aligned. I then build a subsurface model in this unfaulted and flattened space by computing a sequence of 2D horizontal interpolations of borehole data. Each horizontal interpolation is guided by the stratigraphic features apparent in the corresponding horizontal seismic slice, so that the interpolant conforms to the seismic stratigraphic features. I finally map the interpolated model back into the input space and obtain a subsurface model that honors the seismic and borehole data. I demonstrate the proposed workflow using synthetic and real examples complicated by faults and unconformities.
Computing the merger of black-hole binaries: The IBBH problem (1998)

Gravitational radiation arising from the inspiral and merger of binary black holes (BBH's) is a promising candidate for detection by kilometer-scale interferometric gravitational wave observatories. This Rapid Communication discusses a serious obstacle to searches for such radiation and to the interpretation of any observed waves: the inability of current computational techniques to evolve a BBH through its last \ensuremath{\sim}10 orbits of inspiral (\ensuremath{\sim}100 radians of gravitational-wave phase). A new set of numerical-relativity techniques is proposed for solving this ``intermediate binary black hole'' (IBBH) problem: (i) numerical evolutions performed in coordinates co-rotating with the BBH, in which the metric coefficients evolve on the long timescale of inspiral, and (ii) techniques for mathematically freezing out gravitational degrees of freedom that are not excited by the waves.
Randomized, double-blind phase II study of anti-endotoxin antibody (E5) as adjuvant therapy in humans with serious gram-negative infections. (1991)

Xomen-E5 (E5) is a murine monoclonal IgM antibody (MAb) that binds to the lipid A epitope of endotoxin. The MAb was developed by immunization against the J5 mutant of Escherichia coli. Prior studies in humans have shown safety and T1/2 of 18.4 hours. In this double blind study patients suspected to have life threatening gram-negative infections were randomized to receive 2 doses, 24 hours apart, of placebo (P), 2.5 mg/kg E5, or 7.5 mg/kg E5. Overall 23 patients had a documented serious gram-negative infection and received at least one dose of study drug. Mortality 3 days after last infusion was 2 of 9 for P, 0 of 9 for 2.5 mg/kg, and 0 of 5 for 7.5 mg/kg. By 21 days after therapy one E5 treated patient had died. Wheezes occurred in one E5 treated patient. Eight of 15 E5 patients treated had IgG anti-murine antibodies by 3 weeks after therapy. These data suggest the need to pursue studies designed to verify that E5 reduced mortality and morbidity in seriously ill patients with gram-negative infections.
Characterization of the major antigens of<i>Haemophilus equigenitalis</i>(contagious equine metritis organism) (1982)

Immunoelectrophoresis of ultrasonically disrupted Haemophilus equigenitalis (contagious equine metritis organism) cells against rabbit and equine antisera disclosed at least 11 precipitating antigens. Two of these, a polysaccharide and a lipopolysaccharide-protein complex, were of high molecular weight and located on the cell surface. The remaining antigens were intracellular and were small- to medium-sized proteins. The surface antigens were the most significant in relation to the serological response in infected horses. They also reacted with sera from apparently healthy cattle, but the reason for this was not determined. No serological cross-reaction between H. equigenitalis and species of Achromobacter and Moraxella was detected.