gebhart/patrepeval huggingface dataset:
Five Listeria monocytogenes genes preferentially expressed in infected mammalian cells: plcA, purH, purD, pyrE and an arginine ABC transporter gene, arpJ (1994)

Listeria monocytogenes is a bacterial pathogen that multiplies within the cytosol of eukaryotic cells. To identify Listeria genes with preferentially intracellular expression (pic genes), a library of Tn917-lac insertion mutants was screened for transcriptional fusions to lacZ with higher expression inside a macrophage-like cell line than in a rich broth medium. Five pic genes with up to 100-fold induction inside cells were identified. Three of them (purH, purD and pyrE) were involved in nucleotide biosynthesis. One was part of an operon encoding an ABC (ATP-binding cassette) transporter for arginine. The corresponding mutants were not affected in intracellular growth, cell-to-cell spread or virulence, except for the transporter mutant, whose LD50 after intravenous infection of mice was twofold higher than the wild-type. The fifth gene was plcA, a previously identified virulence gene that encodes a phosphatidylinositol-phospholipase C, and is cotranscribed with prfA, a gene encoding a pleiotropic transcriptional activator of known virulence genes. Although plcA expression is known to depend on PrfA, a prfA promoter-lacZ fusion was highly expressed both inside and outside cells. Furthermore, in the presence of cellobiose, a disaccharide recently shown to repress plcA and hly expression, plcA and hly mRNA levels were dramatically reduced without any decrease in the monocistronic prfA mRNA levels. These results demonstrate that virulence gene activation does not depend only on prfA transcript accumulation.
Strained SOI technology for high-performance, low-power CMOS applications (2003)

Advantages of strained-SOI CMOS and the impact on circuit performance are presented from the viewpoint of ring oscillator speed, floating body effects, threshold voltage control and gate leakage reduction. Circuit performance enhancement of about 1.7 times over conventional SOI CMOS is verified experimentally at 0.95/spl mu/m gate lengths and theoretically expected even at gate lengths of 50nm.
Analysis and design of feedforward power amplifier (2002)

A linear power amplifier is particularly emphasized on the system using a linear modulation scheme, because intermodulation distortion which causes adjacent channel interference and co-channel interference is mostly generated in a nonlinear power amplifier. In this paper, parameters of a linearization loop, such as an amplitude imbalance, a phase imbalance and a delay mismatch, are fully analyzed to get a specific cancellation performance and linearization bandwidth. Experimental results are presented for Korea PCS frequency band. The center frequency of the feedforward amplifier is 1.855 GHz with 30 MHz bandwidth. The cancellation performance of the first linearization loop is more than 40 dB and intermodulation cancellation performance of feedforward amplifier is more than 35 dB.
Distance Measurement Model Based on RSSI in WSN (2010)

The relationship between RSSI (Received Signal Strength Indication) values and distance is the foundation and the key of ranging and positioning technologies in wireless sensor networks. Log-normal shadowing model (LNSM), as a more general signal propagation model, can better describe the relationship between the RSSI value and distance, but the parameter of variance in LNSM is depended on experiences without self-adaptability. In this paper, it is found that the variance of RSSI value changes along with distance regu- larly by analyzing a large number of experimental data. Based on the result of analysis, we proposed the relationship function of the variance of RSSI and distance, and established the log-normal shadowing model with dynamic variance (LNSM-DV). At the same time, the method of least squares(LS) was selected to es- timate the coefficients in that model, thus LNSM-DV might be adjusted dynamically according to the change of environment and be self-adaptable. The experimental results show that LNSM-DV can further reduce er- ror, and have strong self-adaptability to various environments compared with the LNSM.
Contribution of heat shock proteins to cell protection from complement-mediated lysis (2001)

The possible participation of hsc70 and hsp70 in cellular protection from complement damage was studied. Human erythroleukemia K562 cells were pretreated with reagents affecting hsc70 or hsp70, and cell sensitivity to lysis by antibody and human complement was examined. Treatment with deoxyspergualin, an hsc70 inhibitor, sensitized K562 cells to complement lysis, whereas treatment with ethanol, butanol or hemin, inducers of hsc70 synthesis, protected the cells from complement-mediated lysis. Incubation of K562 at either 42 degrees C or with the amino acid analogue L-azetidine-2-carboxylic acid induced synthesis of hsp70, but not of hsc70. The latter treatment also conferred elevated resistance to complement lysis on K562 cells. Pretreatment of K562 cells with sub-lethal doses of complement desensitizes them to lethal complement doses. No effect of sublytic complement on synthesis of hsc70 and hsp70 was found. However, the results demonstrated that complement stress causes translocation of hsc70 from the cytoplasm to the K562 cell surface. Two monoclonal and two polyclonal antibodies identified hsc70 on the surface of intact, viable complement-stressed cells, while antibodies directed to hsp70 did not bind to these cells. Altogether, the results suggest that the heat shock proteins hsc70 and hsp70 play a role in cell defense against complement.
Interleukin‐6 Modulates Plasma Cholesterol and C‐Reactive Protein Concentrations in Nonagenarians (2005)

Objectives: To establish whether the relationship between interleukin‐6 (IL‐6) and plasma lipid and C‐reactive protein (CRP) concentrations is different in Finnish nonagenarians than in middle‐aged subjects with lower inflammatory status. Design: Cross‐sectional. Setting: Observational cohort study concentrating on the oldest old. Participants: Nonagenarians (n=291, mean age±standard deviation 90±1; 68 men, 223 women) who lived in the Tampere municipality in southern Finland and a middle‐aged control population from the same area (n=227, aged 44±8). Measurements: Plasma high sensitive CRP and lipid concentrations were analyzed using an automatic analyzer and IL‐6 levels using enzyme‐linked immunosorbent assay. Results: Plasma concentrations of IL‐6 (4.39±5.25 vs 1.88±1.98 pg/mL) and CRP (3.54±4.98 vs 1.53±1.91 mg/L) were significantly higher in nonagenarians than in middle‐aged subjects ( P&lt; .001). In nonagenarians, plasma CRP levels increased ( P&lt; .001) and plasma total cholesterol ( P= .006), low‐density lipoprotein cholesterol ( P= .02), and high‐density lipoprotein cholesterol ( P= .002) levels decreased according to IL‐6 quartiles. In middle‐aged subjects, similar associations were not found. Conclusion: The relationship between IL‐6 and plasma CRP and cholesterol levels in nonagenarians with enhanced systemic inflammation differs from that of middle‐aged subjects.
Experimental therapy of malignant gliomas using the inhibitor of histone deacetylase MS-275 (2006)

Inhibitors of histone deacetylases are promising compounds for the treatment of cancer but have not been systematically explored in malignant brain tumors. Here, we characterize the benzamide MS-275, a class I histone deacetylase inhibitor, as potent drug for experimental therapy of glioblastomas. Treatment of four glioma cell lines (U87MG, C6, F98, and SMA-560) with MS-275 significantly reduced cell growth in a concentration-dependent manner (IC(90), 3.75 micromol/L). Its antiproliferative effect was corroborated using a bromodeoxyuridine proliferation assay and was mediated by G(0)-G(1) cell cycle arrest (i.e., up-regulation of p21/WAF) and apoptotic cell death. Implantation of enhanced green fluorescent protein-transfected F98 glioma cells into slice cultures of rat brain confirmed the cytostatic effect of MS-275 without neurotoxic damage to the organotypic neuronal environment in a dose escalation up to 20 micromol/L. A single intratumoral injection of MS-275 7 days after orthotopic implantation of glioma cells in syngeneic rats confirmed the chemotherapeutic efficacy of MS-275 in vivo. Furthermore, its propensity to pass the blood-brain barrier and to increase the protein level of acetylated histone H3 in brain tissue identifies MS-275 as a promising candidate drug in the treatment of malignant gliomas.
Small-molecule discovery from DNA-encoded chemical libraries (2011)

Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.
Ta-Doped Li7La3Zr2O12for Water-Stable Lithium Electrode of Lithium-Air Batteries (2014)

Garnet-type high lithium ion conductivity solid electrolytes with nominal compositions of Li7-xLa3Zr2-xTaxO12 (x = 0–0.7) were prepared by using a sol-gel precursor and are proposed as the protective layer for a water-stable lithium electrode for lithium-air rechargeable batteries. The Li6.75La3Zr1.75Ta0.25O12 (LLZ-0.25Ta) composition sintered at 1,180°C for 36 h showed the highest relative density of 96.7% and resistance to water permeation. The LLZ-0.25Ta was stable in contacting with lithium metal and also in a saturated LiOH/10 M LiCl aqueous solution. The total and bulk conductivities of the sintered LLZ-0.25Ta pellet were 5.20 × 10−4 and 6.55 × 10−4 S cm−1 at 25°C, respectively. The Li/LLZ-0.25Ta/Li cell showed a stable cell resistance of 310 Ω cm2 at 25°C for 4 months. However, polarization experiments on the Li/LLZ-0.25Ta/Li cell suggest a lithium dendrite short-circuit after 100 s at 0.5 mA cm−2 and after 2000 s of polarization at 0.1 mA cm−2 at room temperature.
Chimeric Clostridial Cytotoxins: Identification of the N-Terminal Region Involved in Protein Substrate Recognition (1998)

Clostridium sordellii lethal toxin is a member of the family of large clostridial cytotoxins that glucosylate small GTPases. In contrast to Clostridium difficile toxins A and B, which exclusively modify Rho subfamily proteins, C. sordellii lethal toxin also glucosylates Ras subfamily proteins. By deletion analysis and construction of chimeric fusion proteins of C. sordellii lethal toxin and C. difficile toxin B, we localized the enzyme activity of the lethal toxin to the N terminus of the holotoxin and identified the region involved in protein substrate specificity. The toxin fragment of the N-terminal 546 amino acid residues of C. sordellii lethal toxin glucosylated Rho and Ras subfamily proteins, as the holotoxin did. Deletion of a further 30 amino acid residues from the C terminus of this active fragment drastically reduced glucotransferase activity and blocked glucohydrolase activity. Exchange of amino acid residues 364 through 516 of lethal toxin for those in the active toxin B fragment (1 to 546) allowed glucosylation of Ras subfamily proteins. In contrast, the chimera with amino acids 1 to 364 from toxin B, 365 to 468 from lethal toxin, and 469 to 546 from toxin B exhibited markedly reduced modification of Ras subfamily proteins, whereas modification of Rac and Cdc42 was hardly changed. The data indicate that the region of amino acid residues 364 through 516 primarily defines the substrate specificity of C. sordellii lethal toxin.
Low lactate dehydrogenase and high mitochondrial glycerol phosphate dehydrogenase in pancreatic beta-cells. Potential role in nutrient sensing. (1994)

Nutrient metabolism was examined with regard to insulin secretion in purified rat islet beta- and non-beta-cells, beta-cell lines, and hepatocytes. Lactate dehydrogenase (LDH) activity (nanomoles.min-1.mg protein-1) was remarkably low in the glucose-sensitive INS-1 cell line (15.7) and in beta-cells (22.3). Thus, beta-cell LDH was respectively 8-, 122-, 17-, and 136-fold lower than in islet non-beta, liver, HIT-T15, and RINm5F cells. Plasma membrane lactate transport activity was 3-10-fold lower in beta- or INS-1 cells than in the other cell types. Conversely, mitochondrial glycerol phosphate dehydrogenase was strongly expressed only in beta- and INS-1 cells. The significance of these findings to nutrient recognition was explored using INS-1 cells as a model of native beta-cells. Glucose-stimulated lactate output and glucose utilization were, respectively, 12- and 5-fold lower in INS-1 than in RINm5F cells. Each process was entirely blocked by respiratory chain inhibitors in INS-1 cells, whereas glucose utilization was barely affected and lactate output stimulated in RINm5F cells. Glucose oxidation represented 73% of total utilization in INS-1 cells, but only 9% in RINm5F cells. Absolute rates of glucose oxidation, and the extent of mitochondrial NAD(P) reduction, were similar in the two cell types, and glucose stimulated insulin secretion 1.9-fold in INS-1 and 1.4-fold in RINm5F cells. The mitochondrial substrates, monomethyl succinate, pyruvate, and leucine, each triggered secretion in INS-1 cells. The balance of LDH, plasma membrane lactate transport, and mitochondrial glycerol phosphate dehydrogenase activities therefore appear to be important in beta- and INS-1 cell glucose recognition to ensure that mitochondrial oxidation is the principle fate of pyruvate and NADH produced by glycolysis. The resultant close coupling of glycolysis with mitochondrial oxidation explains the absence in beta-cells of Crabtree and Pasteur effects.
Design Languages for Embedded Systems (2003)

Embedded systems are application-specific computers that interact with the physical world. Each has a diverse set of tasks to perform, and although a very flexible language might be able to handle all of them, instead a variety of problem-domain-specific languages have evolved that are easier to write, analyze, and compile. This paper surveys some of the more important languages, introducing their central ideas quickly without going into detail. A small example of each is included.
Magnetic Resonance Imaging of Pulmonary Lesions in Guinea Pigs Infected withMycobacterium tuberculosis (2004)

We utilized magnetic resonance imaging to visualize lesions in the lungs of guinea pigs infected by low-dose aerosol exposure to Mycobacterium tuberculosis. Lesions were prominent in such images, and colorized three-dimensional reconstructions of images revealed a very uniform distribution in the lungs. Lesion numbers after 1 month were approximately similar to the aerosol exposure algorithm, suggesting that each was established by a single bacterium. Numbers of lesions in unprotected and vaccinated animals were similar over the first month but increased thereafter in the control animals, indicating secondary lesion development. Whereas lesion sizes increased progressively in control guinea pigs, lesions remained small in BCG-vaccinated animals. A prominent feature of the disease pathology in unprotected animals was rapid and severe lymphadenopathy of the mediastinal lymph node cluster, which is paradoxical given the strong state of cellular immunity at this time. Further development of this technical approach could be very useful in tracking lesion size, number, and progression in the search for new tuberculosis vaccines.
[Short-term and long-term outcomes of treating bifurcation lesions with two drug eluting stent techniques]. (2006)

Two DES technique for the treatment of bifurcation lesions is safe and effective and short- and long-term outcomes is satisfactory.
The geometry of turbo-decoding dynamics (2000)

The spectacular performance offered by turbo codes sparked intense interest in them. A considerable amount of research has simplified, formalized, and extended the ideas inherent in the original turbo code construction. Nevertheless, the nature of the relatively simple ad hoc turbo-decoding algorithm has remained something of a mystery. We present a geometric interpretation of the turbo-decoding algorithm. The geometric perspective clearly indicates the relationship between turbo-decoding and maximum-likelihood decoding. Analysis of the geometry leads to new results concerning existence of fixed points, conditions for uniqueness, conditions for stability, and proximity to maximum-likelihood decoding.
Characterization of high-affinity receptors for interleukin 5 on interleukin 5-dependent cell lines. (1989)

Interleukin 5 (IL-5) is a glycosylated polypeptide that acts as a key factor for B-cell growth and differentiation. We demonstrated previously that there are two classes (high and low affinity) of IL-5 receptors on murine chronic B-cell leukemic cells (BCL1-B20). Treatment of surface-bound radiolabeled IL-5 with bivalent crosslinkers identified a polypeptide of Mr 92,500. In this study, we analyzed characteristics of high-affinity IL-5 receptors on IL-5-dependent early B-cell lines (T-88 and T88-M), mouse myeloma cells (MOPC-104E), and BCL1-B20 cells. All cell lines had two classes of IL-5 binding sites, but T88-M cells bore the highest number of high-affinity receptors. The number of high-affinity IL-5 receptors on BCL1-B20 cells could be up-regulated 3-fold by lipopolysaccharide and down-regulated by IL-5. Disuccinimidyl tartarate crosslinking of 35S-labeled IL-5 to the receptors on the T88-M and lipopolysaccharide-stimulated BCL1-B20 cells revealed two major 35S-labeled components of Mr 92,500 and Mr 160,000, even when the binding of 35S-labeled IL-5 was carried out under high-affinity conditions (100 pM 35S-labeled IL-5). The Mr 92,500 component, but not the Mr 160,000 component, was detected in the lysates of MOPC-104E and T-88 cells, both of which bore a large number of low-affinity receptors and a limited number of high-affinity receptors. The results suggest that the Mr 92,500 component represents the complex of IL-5 with the low-affinity Mr 46,500 receptor, whereas the high-affinity receptor consists of the Mr 46,500 peptide and an additional peptide.
Hydrophobicity and amphiphilicity in protein structure (1986)

The importance of the hydrophobic interaction in stabilizing native protein structure has long been appreciated. However, more than other component forces, this one has resisted quantitative description. We present two approximate methods of assessing the hydrophobic component to the free energy of protein folding. Both are expressed in terms of what can be called hydrophobic moments of the protein. The first method is intended to yield an approximate value for the hydrophobic energy. This energy is calculated from a set of atomic coordinates in terms of the hydrophobicity (or 0th hydrophobic moment) of each amino acid residue and its accessibility or lack of it to aqueous solvent. The second method considers the first moment of the hydrophobicity of a group of residues, the hydrophobic moment. Segments of secondary structure in folded proteins tend to have hydrophobic moments that oppose each other. For example, alpha-helices on the protein surface tend to have one hydrophobic face and one hydrophilic face, with the hydrophilic face out towards the solvent. This pattern of organization is often apparent from a computer model of the protein that shows the magnitude and direction of the hydrophobic moment of each segment of secondary structure. Examples are given for the incorrectly folded structures of Novotný et al [J Mol Biol 177:787, 1984] and for the correct structures to which they correspond.
Dicer-Dependent Turnover of Intergenic Transcripts from the Human β-Globin Gene Cluster (2005)

The widespread occurrence of intergenic transcription in eukaryotes is increasingly evident. Intergenic transcription in the beta-globin gene cluster has been described in murine and human cells, and models for a role in gene and chromatin activation have been proposed. In this study, we analyze intergenic transcription and the chromatin state throughout the human beta-globin gene cluster and find that the data are not consistent with such activation-linked models. Thus, intergenic transcript levels correlate with neither chromatin activation nor globin gene expression. Instead, we find that intergenic transcripts of the beta-globin gene cluster are specifically upregulated in Dicer-deficient cells. This is accompanied by a shift towards more activated chromatin as indicated by changes in histone tail modifications. Our results strongly implicate RNA interference (RNAi)-related mechanisms in regulating intergenic transcription in the human beta-globin gene cluster and further suggest that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres.
Eccentric contractions induce rapid isometric torque drop in dystrophin‐deficient dogs (2010)

We tested the hypothesis that eccentric contractions (ECCs) rapidly induce greater-than-normal isometric torque drop in dystrophin-deficient golden retriever muscular dystrophy (GRMD) muscles. ECCs were imposed by forcibly stretching activated muscles. The results indicate that isometric torque drop was greater in GRMD versus controls (P < 0.0001). Our findings support the hypothesis that ECCs induce greater-than-normal isometric torque drop in GRMD muscles. The magnitude of ECC-induced isometric torque loss may be an ideal clinical endpoint in the GRMD model.
Effectiveness of recombinant desulphatohirudin in reducing restenosis after balloon angioplasty of atherosclerotic femoral arteries in rabbits. (1991)

Rabbits receiving r-hirudin at the time of experimental balloon angioplasty had significantly less restenosis by angiography and by quantitative histopathology than rabbits receiving heparin.