gebhart/patrepeval huggingface dataset:
A Novel Method for Improving the Performance of InP/InGaAsP Multiple-Quantum-Well Mach-Zehnder Modulators by Phase Shift Engineering (1996)

Semiconductor external modulators are increasingly employed in high speed and long haul optical fiber communication. A highly desirable feature of an external light modulator is the ability to generate a signal with a negative frequency chirp. Mach-Zehnder (MZ) III-V multiple-quantum-well (MQW) modulators are thus increasingly attractive relative to other modulator designs because of their adjustable frequency chirp, low drive voltage, small size, long term reliability and potential for integration with laser sources[l, 2, 3, 4], Unfortunately, in III-V MQW MZ modulators where the two arms of the interferometer are of equal length and the power splitting ratio 50%, the nonlinear electrooptic effect imparts a small positive chirp under symmetric push-pull operation. While negative chirp can be induced by designing the Y-junction to inject less optical power into the more deeply biased modulator arm and employing a small amount of overdrive, [5] the back-to-back extinction ratio is degraded. In this paper we demonstrate that by increasing the length of one of the modulator arms such that the transmitted optical signal is shifted by π relative to the other arm, an optimal chirp can be obtained while maintaining a high extinction ratio.
Heritable susceptibility to severe Borrelia burgdorferi-induced arthritis is dominant and is associated with persistence of large numbers of spirochetes in tissues (1994)

In human Lyme disease, symptoms with widely varying levels of severity have been observed. A mouse model of Lyme disease has been developed which allows analysis of mice with mild, moderate, and severe pathologies after inoculation with the spirochete Borrelia burgdorferi. To determine whether the differences in symptoms reflect differences in the number of spirochetes persisting in affected tissues, a sensitive PCR technique was developed to detect B. burgdorferi DNA in virtually any tissue of an infected mouse. This analysis, which detects DNA from as few as three spirochetes, revealed the presence of B. burgdorferi DNA in many tissues from severely arthritic C3H/HeJ mice as early as 1 week postinfection. The heart, ear, and ankle were particularly heavily infected, although B. burgdorferi DNA was also detected in spleen, liver, brain, kidney, bladder, uterus, and lymph nodes. In contrast, much lower levels of spirochete DNA were detected in tissues of infected BALB/c mice, which develop less severe arthritis when infected with B. burgdorferi than do C3H/HeJ mice. This difference was evident throughout the 5-week analysis. A competitive PCR method allowed determination of the absolute number of spirochete gene sequences in infected tissues. Ankles and hearts from C3H/HeJ mice were found to harbor 10(7) copies of the B. burgdorferi ospA gene, while these tissues from BALB/c mice contained 5- and 10-fold less B. burgdorferi DNA, respectively. The genetic regulation of severe pathology was analyzed by infecting the offspring of a cross between C3H/HeJ and BALB/c mice. The F1 mice developed severe arthritis and contained high levels of Borrelia DNA in the heart and ankle, similar to the C3H/HeJ parent. These findings indicate that susceptibility to severe arthritis is a dominant trait and suggest that it may correlate with high levels of persisting spirochetes. Models of pathology in Lyme disease should take into consideration the fact that severity of pathology may be directly related to the number of organisms in infected tissues.
Fluidized Bed Sputtering for Particle and Powder Metallization (2013)

Abstract : A system for sputter deposition of thin (10 1000 nm) metal and ceramic coatings onto vibro-fluidized beds of microparticles has been fabricated. Coatings are sputtered onto microparticles of various sizes, shapes, and materials. Experiments show that the coating deposition rate onto particles decreases with decreasing particle size for the case of a fixed total bed mass. Factors affecting particle coating thickness also include sputter power and fluidized bed container size. Coating surface morphology is evaluated using scanning electron microscopy. Lower sputter deposition powers create smoother, less porous coatings. Fluidizing parameters such as driving amplitude and frequency are also shown to affect coating morphology. Barrier coatings on salt microparticles are produced and shown to slow the dissolution of the coated salt particles in water. Dual-layer memetal-ceramicoatings are also demonstrated using the sputter deposition technique. A dual-layer aluminum/tin-oxide coating is produced on glass microspheres, which are then shown to have distinct reflectance characteristics and colors. A model is developed to estimate coating thickness based on size, shape, and number of particles.
Fault localization in ABAP Programs (2011)

In this paper we present an automated technique for localizing faults in data centric programs. Data-centric programs typically interact with databases to get collections of content, process each entry in the collection and output another collection or write entries back to database. Many of the production faults in data centric programs are manifested because of presence of certain data values or data patterns in the database that were not checked for or handled correctly during development of the initial code. Our technique collects the execution trace of the faulty program, uses a novel precise slicing algorithm to break the trace into slices mapping to each entry in the output collection and finally does a semantic difference between the slices corresponding to correct output entries versus incorrect ones to suggest potentially faulty statements. We implemented our approach for ABAP programs. ABAP is the language used to code in SAP systems and interacts heavily with databases. It also contains embedded SQL like commands to work on collections of data. We applied our technique to a suite of 13 ABAP programs with faults from the field and it was able to identify the precise cause in 12 cases.
Comprehensive Analysis and Selection of Anthrax Vaccine Adsorbed Immune Correlates of Protection in Rhesus Macaques (2014)

Humoral and cell-mediated immune correlates of protection (COP) for inhalation anthrax in a rhesus macaque (Macaca mulatta) model were determined. The immunological and survival data were from 114 vaccinated and 23 control animals exposed to Bacillus anthracis spores at 12, 30, or 52 months after the first vaccination. The vaccinated animals received a 3-dose intramuscular priming series (3-i.m.) of anthrax vaccine adsorbed (AVA) (BioThrax) at 0, 1, and 6 months. The immune responses were modulated by administering a range of vaccine dilutions. Together with the vaccine dilution dose and interval between the first vaccination and challenge, each of 80 immune response variables to anthrax toxin protective antigen (PA) at every available study time point was analyzed as a potential COP by logistic regression penalized by least absolute shrinkage and selection operator (LASSO) or elastic net. The anti-PA IgG level at the last available time point before challenge (last) and lymphocyte stimulation index (SI) at months 2 and 6 were identified consistently as a COP. Anti-PA IgG levels and lethal toxin neutralization activity (TNA) at months 6 and 7 (peak) and the frequency of gamma interferon (IFN-γ)-secreting cells at month 6 also had statistically significant positive correlations with survival. The ratio of interleukin 4 (IL-4) mRNA to IFN-γ mRNA at month 6 also had a statistically significant negative correlation with survival. TNA had lower accuracy as a COP than did anti-PA IgG response. Following the 3-i.m. priming with AVA, the anti-PA IgG responses at the time of exposure or at month 7 were practicable and accurate metrics for correlating vaccine-induced immunity with protection against inhalation anthrax.
Interleukin-16 (2000)

Interleukin 16 (IL-16) was initially described in 1982 as the first T cell chemoattractant. Through interaction with CD4, IL-16 has now been characterized as a chemoattractant for a variety of CD4+ immune cells. Recent in vivo studies have more fully characterized IL-16 as an immunomodulatory cytokine that contributes to the regulatory process of CD4+ cell recruitment and activation at sites of inflammation in association with asthma and several autoimmune diseases. Since its cloning in 1994, IL-16 structure and function have been studied extensively. This review addresses the current data regarding IL-16 protein and gene structure; the expanding list of cells capable of generating IL-16; the direct interaction of IL-16 with its receptor, CD4; and the functional bioactivities of IL-16 as they relate to inflammation and HIV-1 infection. In addition, potential therapeutic modalities for IL-16 relating to inflammation and immune reconstitution in HIV-1 infection are also discussed.
Surface‐enhanced Raman scattering for medical diagnostics and biological imaging (2005)

Abstract We present recent development and applications of a surface‐enhanced Raman scattering (SERS) technology for use in medical diagnostics and biological imaging. For medical diagnostics, we use Raman‐active dye‐labeled DNA gene probes and nanostructured metallic substrates as SERS‐active platforms. The surface‐enhanced Raman gene probes can be used to detect DNA biotargets (e.g. gene sequences, bacteria and viral DNA) via hybridization to DNA sequences complementary to these probes. The SERS gene probes eliminate the need for radioactive labels and have great potential to provide both sensitivity, selectivity and label multiplexing for DNA sequencing and clinical assays. We also describe a hyperspectral surface‐enhanced Raman imaging (HSERI) system that combines imaging capabilities with SERS detection to identify cellular components with high spatial and temporal resolution. The HSERI system's application to biological imaging is demonstrated using Raman dye‐labeled silver nanoparticles in cellular systems. Copyright © 2005 John Wiley & Sons, Ltd.
Quantitative assessment of corneal biomechanical properties using optical coherence elastography and a modified Rayleigh Lamb-frequency model (2015)

This study reports the application of a modified Rayleigh-Lamb frequency equation (RLFE) to a noncontact optical coherence elastography (OCE) method for quantitative assessment of the biomechanical properties of a porcine cornea. A focused air-pulse induced an elastic wave in the cornea, which was imaged by a phasestabilized optical coherence tomography (OCT) system. From the displacement data acquired by the OCT system, phase velocities of the mechanical wave were extracted by spectral analysis using a fast Fourier transform. Experiments were conducted on 2% agar phantom samples, and the Young’s moduli were assessed by the Rayleigh-Lamb frequency equation, which was validated using uniaxial mechanical compression testing. The Rayleigh-Lamb frequency equation was then applied to OCE data from a normal porcine cornea, in which the fluid-solid effect was considered. The Young’s modulus of the porcine cornea was measured to be ~60 kPa and the shear viscosity was ~0.33 <i>Pa·s</i>. The combination of OCE and RLFE is a promising noninvasive method for the estimation of the biomechanical properties of the cornea <i>in vivo</i>.
A <i>Vernonia</i> Diacylglycerol Acyltransferase Can Increase Renewable Oil Production (2016)

Increasing the production of plant oils such as soybean oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybean, however, usually results in reduced protein, a second valuable seed component. This study shows that by manipulating a highly active acyl-CoA:diacylglycerol acyltransferase (DGAT) the hydrocarbon flux to oil in oilseeds can be increased without reducing the protein component. Compared to other plant DGATs, a DGAT from Vernonia galamensis (VgDGAT1A) produces much higher oil synthesis and accumulation activity in yeast, insect cells, and soybean. Soybean lines expressing VgDGAT1A show a 4% increase in oil content without reductions in seed protein contents or yield per unit land area. Incorporation of this trait into 50% of soybeans worldwide could result in an increase of 850 million kg oil/year without new land use or inputs and be worth ∼U.S.$1 billion/year at 2012 production and market prices.
The Phenylquinazoline Compound S-4893 is a Non-Competitive Cytokinin Antagonist that Targets Arabidopsis Cytokinin Receptor CRE1 and Promotes Root Growth in Arabidopsis and Rice (2010)

We identified two phenylquinazoline compounds in a large-scale screening for cytokinin antagonists in yeast expressing the Arabidopsis cytokinin receptor cytokinin response 1/histidine kinase 4 (CRE1). After chemical modifications, we obtained compound S-4893, which non-competitively inhibited binding of the natural ligand 2-isopentenyladenine to CRE1. S-4893 antagonized cytokinin-induced activation of the Arabidopsis response regulator 5 promoter in Arabidopsis. Importantly, S-4893 had no detectable intrinsic cytokinin agonist activity in Arabidopsis or in the transformed yeast system. Cytokinin bioassay further demonstrated that S-4893 antagonized cytokinin-induced stimulation of callus formation and inhibition of root elongation. S-4893 also promoted seminal, crown and lateral root growth in rice, suggesting that S-4893 could potentially promote root growth in a variety of agronomically important plants. We believe S-4893 will be a useful tool in functional studies of cytokinin action in a wide range of plants and a lead compound for the development of useful root growth promoters in agriculture.
Improving DBMS Performance through Diverse Redundancy (2006)

Database replication is widely used to improve both fault tolerance and DBMS performance. Non-diverse database replication has a significant limitation - it is effective against crash failures only. Diverse redundancy is an effective mechanism of tolerating a wider range of failures, including many non-crash failures. However it has not been adopted in practice because many see DBMS performance as the main concern. In this paper we show experimental evidence that diverse redundancy (diverse replication) can bring benefits in terms of DBMS performance, too. We report on experimental results with an optimistic architecture built with two diverse DBMSs under a load derived from TPC-C benchmark, which show that a diverse pair performs faster not only than non-diverse pairs but also than the individual copies of the DBMSs used. This result is important because it shows potential for DBMS performance better than anything achievable with the available off-the-shelf servers
Molecular detection and <i>in vivo</i> analysis of the specific T cell response to a protein antigen (1992)

We have analyzed in detail the repertoire of transcripts encoding the V beta chains of the T cell receptor and investigated the T cell response of B10.A mice to pigeon cytochrome c. We were thus able to follow the specific T cell response in vivo after immunization with this protein antigen. The response is first detectable in the draining lymph nodes, then in the spleen and in the blood. It is qualitatively similar in individual animals. It is dominated by a major category of specific T cells harboring a V beta 3-J beta 1.2 rearrangement, and a limited and well-defined set of nucleotide sequences, previously found in several specific T cell hybridomas and clones. This predominance is observed from the onset of the immune response strongly suggesting the notion that there is no variation and, therefore, no maturation of the T cell response in the course of immunization.
Cloned Defective Interfering Influenza Virus Protects Ferrets from Pandemic 2009 Influenza A Virus and Allows Protective Immunity to Be Established (2012)

Influenza A viruses are a major cause of morbidity and mortality in the human population, causing epidemics in the winter, and occasional worldwide pandemics. In addition there are periodic outbreaks in domestic poultry, horses, pigs, dogs, and cats. Infections of domestic birds can be fatal for the birds and their human contacts. Control in man operates through vaccines and antivirals, but both have their limitations. In the search for an alternative treatment we have focussed on defective interfering (DI) influenza A virus. Such a DI virus is superficially indistinguishable from a normal virus but has a large deletion in one of the eight RNAs that make up the viral genome. Antiviral activity resides in the deleted RNA. We have cloned one such highly active DI RNA derived from segment 1 (244 DI virus) and shown earlier that intranasal administration protects mice from lethal disease caused by a number of different influenza A viruses. A more cogent model of human influenza is the ferret. Here we found that intranasal treatment with a single dose of 2 or 0.2 µg 244 RNA delivered as A/PR/8/34 virus particles protected ferrets from disease caused by pandemic virus A/California/04/09 (A/Cal; H1N1). Specifically, 244 DI virus significantly reduced fever, weight loss, respiratory symptoms, and infectious load. 244 DI RNA, the active principle, was amplified in nasal washes following infection with A/Cal, consistent with its amelioration of clinical disease. Animals that were treated with 244 DI RNA cleared infectious and DI viruses without delay. Despite the attenuation of infection and disease by DI virus, ferrets formed high levels of A/Cal-specific serum haemagglutination-inhibiting antibodies and were solidly immune to rechallenge with A/Cal. Together with earlier data from mouse studies, we conclude that 244 DI virus is a highly effective antiviral with activity potentially against all influenza A subtypes.
Ceftibuten: Development of a Commercial Process Based on Cephalosporin C. Part II. Process for the Manufacture of 3-Exomethylene-7(<i>R</i>)-glutaroylaminocepham-4-carboxylic Acid 1(<i>S</i>)-Oxide (2002)

Analysis of several options for the synthesis of Ceftibuten from cephalosporin C-derived starting materials led to the conclusion that the most practical option, leading to the lowest costs, would be realized by trying to resurrect the previously discarded electrochemical reduction process. This contribution describes the preparation of 3-exomethylene-7(R)-glutaroylaminocepham-4-carboxylic acid 1(S)-oxide (10,1(S)-oxide) in almost quantitative yield by the electrochemical reduction of 3-acetoxymethyl-7(R)-glutaroylaminoceph-3-em-4-carboxylic acid 1(S)-oxide (9,1(S)-oxide) using a high-surface area tin mesh cathode. The new product has been shown (see Bernasconi, E.; Lee, J.; Sogli, L.; Walker, D. Org. Process Res. Dev. 2002, 6, 169) to be a superior new intermediate for the preparation of orally active cephalosporins such as Ceftibuten.
Real-time measurement of Brownian relaxation of magnetic nanoparticles by a mixing-frequency method (2011)

A detection scheme for real-time Brownian relaxation of magnetic nanoparticles (MNPs) is demonstrated by a mixing-frequency method in this paper. MNPs are driven into the saturation region by a low frequency sinusoidal magnetic field. A high frequency sinusoidal magnetic field is then applied to generate mixing-frequency signals that are highly specific to the magnetization of MNPs. These highly sensitive mixing-frequency signals from MNPs are picked up by a pair of balanced built-in detection coils. The phase delays of the mixing-frequency signals behind the applied field are derived, and are experimentally verified. Commercial iron oxide MNPs with the core diameter of 35 nm are used for the measurement of Brownian relaxation. The results are fitted well with Debye model. Then a real-time measurement of the binding process between protein G and its antibody is demonstrated using MNPs as labels. This study provides a volume-based magnetic sensing scheme for the detection of binding kinetics and interaction affinities between biomolecules in real time.
The Tufts-MIT Prescription Guide: Assessment of Users to Predict the Suitability of Augmentative Communication Devices (1989)

Under contract to the National Institute of Neurological and Communicative Disorders and Stroke, we developed a system for prescribing augmentative communication devices for motor-impaired, nonvocal people. The system is novel in that it scores devices for their suitability for a client based on assessments that do not involve trial-and-error evaluation of client performance with devices. The “benchmarks” it calculates are designed to be predictive of the overall utility of a device given the client's needs, and of the communication rate the client will achieve with it once it has become completely familiar. The scoring process is performed by a program known as the Tufts-MIT Prescription Guide, which runs on IBM XT-compatible computers. Special-purpose assessment instrumentation has been developed to perform the motor-assessment tasks required by the Guide to estimate expert rate. An exhaustive questionnaire is used to get at the device features and functions that will be useful and preferable to a client. These needs are inferred by the Guide software from answers to questions concerning the client's living circumstances and preferences. Preliminary data show the benchmark scores aligning well with independent measures of expert user satisfaction and communication rate. This article defines the clinical motivation for the work, outlines a general scheme for predictive assessment, presents a brief overview of the Guide, and delineates one aspect of its function in considerable detail as illustration of the general scheme.
Results of a Phase III, Multinational, Double-blind, Placebo-controlled Study in Subjects with Relapsing Forms of Multiple Sclerosis (RMS) to Assess the Efficacy, Safety, and Tolerability of GA Depot, a Long-Acting IM Injection of Glatiramer Acetate, Administered Once Every Four Weeks (P6-3.014) (2023)

To assess efficacy, safety and tolerability of GA Depot, a long-acting IM injection of glatiramer acetate, administered every four weeks, compared to placebo in a phase III randomized double-blind study in subjects with relapsing multiple sclerosis (RMS).
FlexiStickers (2009)

Texturing 3D models using casual images has gained importance in the last decade, with the advent of huge databases of images. We present a novel approach for performing this task, which manages to account for the 3D geometry of the photographed object. Our method overcomes the limitation of both the constrained-parameterization approach, which does not account for the photography effects, and the photogrammetric approach, which cannot handle arbitrary images. The key idea of our algorithm is to formulate the mapping estimation as a Moving-Least-Squares problem for recovering local camera parameters at each vertex. The algorithm is realized in a FlexiStickers application, which enables fast interactive texture mapping using a small number of constraints.
Cloning and Assembly of Complex Libraries of Full-Length HCV cDNA Clones (2003)

Many studies of the molecular biology of hepatitis C virus (HCV) begin by obtaining representative cDNA clones of the viral genome. Most cloning strategies have been devised to deal with the low levels of HCV RNA present in starting material used for RNA isolation and cDNA synthesis. Typical sources include patient sera, liver samples, sera and tissues from infected chimpanzees, or in some cases, viral RNA obtained after replication in cell culture. Thus far, patient samples are the most common source of HCV RNA for cDNA cloning. Titers of HCV RNA in patient sera are low, typically ranging from 10(3) to 10(8) mol/mL. Except for a few instances, where cDNA libraries were obtained directly by isolating RNA from large volumes of high-titer sera (1,2), PCR is used for amplifying HCV cDNA prior to cloning. Since this procedure requires smaller amounts of HCV RNA, it is more generally useful for construction of complex cDNA libraries from a wide variety of HCV-containing samples.