gebhart/patrepeval huggingface dataset:
Lrp, a leucine-responsive protein, regulates branched-chain amino acid transport genes in Escherichia coli (1992)

We investigated the relationship between two regulatory genes, livR and lrp, that map near min 20 on the Escherichia coli chromosome. livR was identified earlier as a regulatory gene affecting high-affinity transport of branched-chain amino acids through the LIV-I and LS transport systems, encoded by the livJ and livKHMGF operons. lrp was characterized more recently as a regulatory gene of a regulon that includes operons involved in isoleucine-valine biosynthesis, oligopeptide transport, and serine and threonine catabolism. The expression of each of these livR- and lrp-regulated operons is altered in cells when leucine is added to their growth medium. The following results demonstrate that livR and lrp are the same gene. The lrp gene from a livR1-containing strain was cloned and shown to contain two single-base-pair substitutions in comparison with the wild-type strain. Mutations in livR affected the regulation of ilvIH, an operon known to be controlled by lrp, and mutations in lrp affected the regulation of the LIV-I and LS transport systems. Lrp from a wild-type strain bound specifically to several sites upstream of the ilvIH operon, whereas binding by Lrp from a livR1-containing strain was barely detectable. In a strain containing a Tn10 insertion in lrp, high-affinity leucine transport occurred at a high, constitutive level, as did expression from the livJ and livK promoters as measured by lacZ reporter gene expression. Taken together, these results suggest that Lrp acts directly or indirectly to repress livJ and livK expression and that leucine is required for this repression. This pattern of regulation is unusual for operons that are controlled by Lrp.
Circulating Myeloperoxidase and Anti-Myeloperoxidase Antibody in Patients with Vasculitis (1999)

To evaluate a role of myeloperoxidase (MPO) and antibody to myeloperoxidase (anti-MPO) in vasculitis, MPO and anti-MPO were determined by enzyme-linked immunosorbent assays in sera from 43 patients with vasculitis, 40 with rheumatoid arthritis, 36 with systemic lupus erythematosus (SLE), 23 with mixed connective tissue disease, 13 with systemic sclerosis, 22 with polymyositis/dermatomyositis, 18 with Sjögren's syndrome, and 30 normal controls. Kidney and lung sections from patients with vasculitis were stained for MPO. Anti-MPO titers were significantly higher (p<0.005) in the patients with vasculitis (mean+/- SD absorbance at 405 nm: 0.53 +/- 0.37) than in any other groups (0.15 +/- 0.04 to approximately 0.21 +/- 0.11). MPO levels in patients with vasculitis were comparable with those in patients with other diseases except SLE. In two patients with vasculitis, anti-MPO decreased sharply with simultaneous increases in MPO 1-2 weeks after they developed pulmonary hemorrhage. Numerous cells positive for MPO infiltrated the Bowman's spaces. These results indicate that MPO may contribute to the pathogenesis of vasculitis and a sudden fall in anti-MPO may predict a poor prognosis in some cases.
A role for endothelin in the maintenance of post‐ischaemic renal failure in the rat. (1991)

1. Endothelin (ET) has been shown to reduce glomerular filtration rate (GFR) and renal blood flow (RBF) and may therefore be a possible mediator of the reduction of GFR and RBF observed in post-ischaemic acute renal failure. 2. We infused a specific ET antibody, i.v., for 1 h before and 1 h after a 60 min period of renal ischemia by clamping the renal artery, and observed the changes in renal function (acute clearance and long-term metabolic cage studies) compared with rats infused with non-immune rabbit serum. 3. In acute and long-term studies, better renal function, as judged by GFR and RBF was observed in rats treated with the ET antibody. Furthermore, ischaemic rats showed higher levels of plasma immunoreactive ET (7.02 +/- 1.17 pg ET (ml plasma)-1; mean +/- S.E.M.) than normal rats where it was undetected. 4. We previously reported that glomeruli and renal platelet-activating factor (PAF) production were increased after renal ischaemia. So, we studied the possible relationship between ET and glomeruli or renal PAF production in post-ischaemic acute renal failure. 5. Glomeruli from ischaemic rats produced greater amounts of PAF than glomeruli from normal or anti-ET antibody-treated ischaemic rats. In addition, total renal PAF production was higher in ischaemic-untreated than in non-ischaemic or anti-ET-treated rats. Glomeruli incubated with 10(-7) M-endothelin produced much more PAF than those incubated in control conditions (138.4 +/- 10.5 vs. 80.2 +/- 9.4 pg PAF (mg protein)-1; means +/- S.E.M.; n = 10). 6. In conclusion, the present study suggests that endothelin plays a role in the persistent renal vasoconstriction that characterizes post-ischaemic acute renal failure. In addition, the observed increase in glomerular PAF production after renal ischaemia may be due to the action of endothelin.
Change in circulating levels of the chemokines macrophage inflammatory proteins 1α and 1β, RANTES, monocyte chemotactic protein-1 and interleukin-16 following treatment of severely immunodeficient HIV-infected individuals with indinavir (1997)

The in vivo demonstration of an association between diminishing plasma HIV-RNA levels and the emergence of a circulating chemokine profile capable of inhibiting HIV replication corroborates recent in vitro observations and provides evidence for the restoration of chemokine capacity by HIV protease inhibitor-based therapy.
Improving the readability of time-frequency and time-scale representations by the reassignment method (1995)

In this paper, the use of the reassignment method, first applied by Kodera, Gendrin, and de Villedary (1976) to the spectrogram, is generalized to any bilinear time-frequency or time-scale distribution. This method creates a modified version of a representation by moving its values away from where they are computed, so as to produce a better localization of the signal components. We first propose a new formulation of this method, followed by a thorough theoretical study of its characteristics. Its practical use for a large variety of known time-frequency and time-scale distributions is then addressed. Finally, some experimental results are reported to demonstrate the performance of this method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
More Recent Progress in the Preparation of Au Nanostructures, Properties, and Applications (2003)

Au nanoparticles exhibit excellent compatibility with biomolecules and some distinct optical properties. Their two popular features, the color change upon aggregation and surface plasmon resonance (SPR) enhancement, have been exploited in analytical chemistry, biosensing platforms, and immunoassays. The preparation of monodispersed Au nanoparticles with improved electronic, optical, and chemical properties is still an on-going and formidable task. This review aims to outline the most significant and recent progress towards the utilization of gold nanoparticles in biosensing.
Vaccines in oncology: background and clinical potential (2001)

Cancer is one of the leading causes of death in Western society. Despite improvements in screening, diagnosis and treatment of cancer, many patients ultimately succumb to their disease. Advances in molecular biology and our increased understanding of how the immune system functions have led to an intense interest in the development of cancer vaccines.
A High Precision Motion Control System With Application to Microscale Robotic Deposition (2006)

Decreasing the minimum feature size of solid free-form (SFF) fabrication techniques requires advancements in both the SFF process and the actuating hardware. Microscale robotic deposition (mu-RD) is an ink-deposition SFF process where recent advances in ink design coupled with a high-precision motion system can lead to the fabrication of parts with microscale-sized features. This paper presents a control algorithm that combines nonlinearity compensation and a learning feedforward approach to achieve high-precision tracking with a standard, off-the-shelf motion system. The off-the-shelf motion system is affected by several nonlinear disturbances that severely inhibit the accuracy of linear models for small motions. Iterative learning control (ILC) is used in an inverse identification procedure to obtain accurate maps of the disturbances. These maps are used in the controller to yield a linear system after nonlinearity cancellation. As a further improvement, ILC is used to increase accuracy in tracking the repetitive portion of specific part trajectories. The combined approach yields extremely low contour tracking errors and is used to fabricate two types of periodic parts demonstrating high aspect ratios and spanning elements. Although high-precision tracking can also be achieved with an expensive, customized system, the off-the-shelf system combined with the control technique presented here provides a more cost-effective solution. The proposed control technique is effective for improving performance of repeatable, but uncertain nonlinear systems
RNA Polymerase I-Driven Minigenome System for Ebola Viruses (2005)

In general, Ebola viruses are well known for their ability to cause severe hemorrhagic fever in both human and nonhuman primates. However, despite substantial sequence homology to other members of the family Filoviridae, Reston ebolavirus displays reduced pathogenicity for nonhuman primates and has never been demonstrated to cause clinical disease in humans, despite its ability to cause infection. In order to develop a tool to explore potential roles for transcription and replication in the reduced pathogenicity of Reston ebolavirus, we developed an RNA polymerase I (Pol I)-driven minigenome system. Here we demonstrate successful Reston ebolavirus minigenome rescue, including encapsidation, transcription, and replication, as well as the packaging of minigenome transcripts into progeny particles. The Pol I-driven Reston ebolavirus minigenome system provides a higher signal intensity with less background (higher signal-to-noise ratio) than a comparable T7-driven Reston ebolavirus minigenome system which was developed simultaneously. Successful Reston ebolavirus minigenome rescue was also achieved by the use of helper plasmids derived from the closely related Zaire ebolavirus or the more distantly related Lake Victoria marburgvirus. The use of heterologous helper plasmids in the Reston ebolavirus minigenome system yielded levels of reporter expression which far exceeded the level produced by the homologous helper plasmids. This comparison between minigenomes and helper plasmids from different filovirus species and genera indicates that inherent differences in the transcription and/or replication capacities of the ribonucleoprotein complexes of pathogenic and apathogenic filoviruses may exist, as these observations were confirmed in a Lake Victoria marburgvirus minigenome system.
New concept for negative-tone electron-beam resist (1996)

Negative tone electron beam resist forms pattern with radical crosslinking brought by electron beam irradiation and succeeding chemical reactions resulting radical species. The important problem of current negative tone resist is insufficient pattern profile because of tailing and scum found after development. We have solved these problems with reducing the unnecessary cross linking by loading particular radical captures in resist. This paper presents the technical result of resolution improvement achieved on the ZEN4000 that consists of p-chloromethylstyrene and p-chlorostyrene negative electron beam resist series.
The retromer component sorting nexin-1 is required for efficient retrograde transport of Shiga toxin from early endosome to the trans Golgi network (2007)

The mammalian retromer complex is a multi-protein complex that regulates retrograde transport of the cation-independent mannose 6-phosphate receptor (CI-MPR) from early endosomes to the trans Golgi network (TGN). It consists of two subcomplexes: a membrane-bound coat comprising sorting nexin-1 (SNX1) and possibly sorting nexin-2 (SNX2), and a cargo-selective subcomplex, composed of VPS26, VPS29 and VPS35. In addition to the retromer, a variety of other protein complexes has been suggested to regulate endosome-to-TGN transport of not only the CI-MPR but a wide range of other cargo proteins. Here, we have examined the role of SNX1 and SNX2 in endosomal sorting of Shiga and cholera toxins, two toxins that undergo endosome-to-TGN transport en route to their cellular targets located within the cytosol. By using small interfering RNA (siRNA)-mediated silencing combined with single-cell fluorescent-toxin-uptake assays and well-established biochemical assays to analyze toxin delivery to the TGN, we have established that suppression of SNX1 leads to a significant reduction in the efficiency of endosome-to-TGN transport of the Shiga toxin B-subunit. Furthermore, we show that for the B subunit of cholera toxin, retrograde endosome-to-TGN transport is less reliant upon SNX1. Overall, our data establish a role for SNX1 in the endosome-to-TGN transport of Shiga toxin and are indicative for a fundamental difference between endosomal sorting of Shiga and cholera toxins into endosome-to-TGN retrograde transport pathways.
Analysis of an in vivo model to study the interaction of host factors with Candida albicans (1981)

Conditions were established under which membrane diffusion chambers surgically implanted into mice could be used to study interactions between host defense factors and Candida albicans within the chambers. Depending on the size of membrane pores, soluble host substances and phagocytic cells entered the chambers during the first 24 h after chamber implantation. By 7 days in vivo, the membranes of chambers appeared impermeable to these host factors. Mouse phagocytic cells were found to be functional within the in vivo chambers whether the cells emigrated to the chambers on their own accord or were placed there before chamber implantation. Opsonic factors such as antibody and complement appeared to be biologically functional within the in vivo chambers. Conditions suitable for harvesting C. albicans from the chambers also were determined.
Metrology of subwavelength photoresist gratings using optical scatterometry (1995)

The widths and overall profiles of dielectric grating lines can be determined by measuring the intensity of diffracted laser light from the sample over a specified range of incident beam angles. This technique, known as 2-Θ scatterometry, is able to accurately and precisely measure photoresist structures in the subhalf micron regime. Moreover, a 2-Θ scatterometer is capable of making measurements in a rapid and nondestructive manner. To test this technique we measured five identically processed wafers with nominal 0.5 μm line/0.5 μm space grating patterns. Each wafer comprised gratings in a Shipley 89131 negative photoresist exposed in a matrix of incremental exposure doses and focus settings. The scatterometry results were consistent with cross-sectional and top-down scanning electron microscopy (SEM) measurements of the same structures. The average deviation of 11 scatterometer linewidth measurements from top-down SEM measurements, over a broad exposure range, is 14.5 nm. In addition, the repeatability (1σ) of the 2-Θ scatterometer is shown to be excellent: 0.5 nm for consecutive measurements and 0.8 nm for day-to-day measurements.
Surfactant protein A and surfactant protein D in health and disease (1998)

Surfactant protein (SP) A and SP-D are collagenous glycoproteins with multiple functions in the lung. Both of these proteins are calcium-dependent lectins and are structurally similar to mannose-binding protein and bovine conglutinin. Both form polyvalent multimeric structures for interactions with pathogens, cells, or other molecules. SP-A is an integral part of the surfactant system, binds phospholipids avidly, and is found in lamellar bodies and tubular myelin. Initially, most research interest focused on its role in surfactant homeostasis. Recently, more attention has been placed on the role of SP-A as a host defense molecule and its interactions with pathogens and phagocytic cells. SP-D is much less involved with the surfactant system. SP-D appears to be primarily a host defense molecule that binds surfactant phospholipids poorly and is not found in lamellar inclusion bodies or tubular myelin. Both SP-A and SP-D bind a wide spectrum of pathogens including viruses, bacteria, fungi, and pneumocystis. In addition, both molecules have been measured in the systemic circulation by immunologic methods and may be useful biomarkers of disease. The current challenges are characterization of the three-dimensional crystal structure of SP-A and SP-D, molecular cloning of their receptors, and determination of their precise physiological functions in vivo.
Synchronizing a database to improve freshness (2000)

In this paper we study how to refresh a local copy of an autonomous data source to maintain the copy up-to-date. As the size of the data grows, it becomes more difficult to maintain the copy \ fresh, “making it crucial to synchronize the copy effectively. We define two freshness metrics, change models of the underlying data, and synchronization policies. We analytically study how effective the various policies are. We also experimentally verify our analysis, based on data collected from 270 web sites for more than 4 months, and we show that our new policy improves the \ freshness” very significantly compared to current policies in use.
Modeling and Control Design of Vsi-Fed Pmsm Drive Systems With Active Load (1998)

A field-oriented control design and detailed analysis of a VSI-fed PMSM drive system with active load is done through simulations of the system model, using modern simulation software packages. A new control method for the speed tracking control based on the estimation of the load torque profile is proposed. A new, multilevel modeling approach for creating simulation models of power electronic circuits is developed for easier analysis and faster simulations. It is based on a modular approach wherein each module can be modeled at any level of complexity, while maintaining full compatibility of the modules. The new approach is applied to modeling of the VSI-fed PMSM drive system. The three-phase VSI-fed PMSM drive system model that is developed and experimentally verified is analyzed in the application of a starter/generator, where the load changes dynamically with motor speed. As a result, a detailed analysis of the field-oriented control design of a two stage cascade digital controller is presented, with an emphasis on the new method for the speed control, large-signal and small-signal analyses of several most popular flux-weakening strategies, and sampling delay effects on the system stability.
Complementation of a human adenovirus early region 4 deletion mutant in 293 cells using adenovirus-polylysine-DNA complexes. (1995)

The E1 deleted adenoviral vectors are efficient at gene transfer to cells in culture or in animals. However, their use is limited because of an immune-mediated loss of transduced cells. This immune response is believed to result from low-level production of viral antigens from these vectors after gene transfer. The early region 4 (E4) of adenovirus produces a number of proteins that play an important role in adenoviral and host gene regulation during infection of mammalian cells. There is interest in developing E4 deficient adenovirus for gene therapy, especially in the context of developing a combined E1/E4 deleted vector. Towards this goal, a method by which to complement and propagate an E4 deficient adenovirus (dl 1014) in the E1 complementing 293 cell line, using a novel and simple rescue technique, has been developed. Purified adenovirus deficient in E4 gene expression (dl 1014) was conjugated to expression plasmids containing the E4-open reading frame 6 gene or complete E4 region to produce adenovirus-polylysine-DNA complexes that were used to transfect 293 cells. The derived virus obtained from this transfection did not replicate on 293 cells but did replicate on W162 cells (E4+) confirming that the virus was indeed deleted for E4. Viral yield was high ranging from 3 x 10(8) to 9 x 10(8) plaque forming units per 10(6) 293 cells. This method has general application to the production of new adenoviral mutants that will be useful for developing second generation adenoviral vectors.
Factors Influencing Parathion Degradation by Recombinant Escherichiacoli with Surface‐Expressed Organophosphorus Hydrolase (1998)

A unique approach for organophosphorus pesticides detoxification was developed previously by anchoring organophosphorus hydrolase (OPH) onto the surface of Escherichia coli with a tightly regulated tac promoter. The resulting recombinant cells degraded parathion very effectively without the diffusional limitation observed in cells expressing OPH intracellularly. However, the precise conditions for surface targeting or pesticide degradation were not fully understood. In this paper, several factors influencing parathion degradation were investigated. Production of active OPH onto the cell surface was highly host-specific; a high rate of parathion degradation was observed from strains JM105 and XL1-Blue, which regulated production of the OPH fusion very tightly. However, in the absence of ampicillin selection, plasmids were only favorably maintained in strain XL1-Blue. OPH activity was highly dependent on growth conditions. Optimal OPH activity was observed when cells were grown in Luria-Bertani (LB)-buffered medium at 37 degrees C. OPH activity was further improved by supplementing the growth medium with cobalt chloride, which favors the formation of the metal active center. The timing of cobalt addition also influenced parathion degradation. Maximum OPH activity was obtained by adding cobalt to induced cultures during the late stationary phase. The resulting cultures grown under the optimized conditions had an eight-fold increase in parathion degradation.
High‐density lipoprotein inhibits mechanical stress‐induced cardiomyocyte autophagy and cardiac hypertrophy through angiotensin II type 1 receptor‐mediated PI3K/Akt pathway (2015)

Mechanical stress triggers cardiac hypertrophy and autophagy through an angiotensin II (Ang II) type 1 (AT1) receptor-dependent mechanism. Low level of high density lipoprotein (HDL) is an independent risk factor for cardiac hypertrophy. This study was designed to evaluate the effect of HDL on mechanical stress-induced cardiac hypertrophy and autophagy. A 48-hr mechanical stretch and a 4-week transverse aortic constriction were employed to induce cardiomyocyte hypertrophy in vitro and in vivo, respectively, prior to the assessment of myocardial autophagy using LC3b-II and beclin-1. Our results indicated that HDL significantly reduced mechanical stretch-induced rise in autophagy as demonstrated by LC3b-II and beclin-1. In addition, mechanical stress up-regulated AT1 receptor expression in both cultured cardiomyocytes and in mouse hearts, whereas HDL significantly suppressed the AT1 receptor. Furthermore, the role of Akt phosphorylation in HDL-mediated action was assessed using MK-2206, a selective inhibitor for Akt phosphorylation. Our data further revealed that MK-2206 mitigated HDL-induced beneficial responses on cardiac remodelling and autophagy. Taken together, our data revealed that HDL inhibited mechanical stress-induced cardiac hypertrophy and autophagy through downregulation of AT1 receptor, and HDL ameliorated cardiac hypertrophy and autophagy via Akt-dependent mechanism.