gebhart/patrepeval huggingface dataset:
Development and Application of a High-Throughput Assay for glmS Riboswitch Activators (2006)

Riboswitches are newly-discovered gene control elements that are promising targets for antibacterial drug development. To facilitate the rapid discovery and development of riboswitch-targeted compounds, modern drug discovery techniques such as structure-based design and high-throughput screening will need to be applied. One promising riboswitch drug target is the glmS riboswitch, which upon binding glucosamine-6-phosphate (GlcN6P) functions as a ribozyme and catalyzes self-cleavage. Herein we report the development of a high-throughput assay for glmS ribozyme cleavage that relies on fluorescence resonance energy transfer (FRET). This assay can be used to screen for compounds that bind to and activate glmS ribozyme cleavage. To validate the screen, we demonstrate that the assay can identify the active compounds from a library of GlcN6P analogs whose affinities for ribozyme were determined by commonly used electrophoretic methods with radiolabeled RNA. Furthermore, the primary screen of a library of 960 compounds previously approved for use in humans identified five active compounds, one of which is a GlcN6P analog known to stimulate ribozyme activity. These results demonstrate that modern high-throughput screening techniques can be applied to the discovery of riboswitch-targeted drug compounds.
Adaptive quantization for low bit rate video coding (2002)

We present a new adaptive quantization scheme in the framework of the visual telephony video coding standards (H.263/H.263+/H.263++). The scheme relies on having multiple sets of uniform quantizers for the lowest quantization levels. The decision about which quantizer to choose is based on the local rate distortion characteristics of the source block being quantized. Two schemes are presented: one which is within the syntax of H.263, and the other which requires a minor change in the syntax of H.263/H.263+. It is shown that up to about 10% savings in bit rates can be achieved by using the second method. With tuned VLC tables, the gains are even higher. Performance is further increased if a second degree of adaptivity is introduced by having multiple sets of VLC tables.
Supporting nested transactional memory in logTM (2006)

Nested transactional memory (TM) facilitates software composition by letting one module invoke another without either knowing whether the other uses transactions. Closed nested transactions extend isolation of an inner transaction until the toplevel transaction commits. Implementations may flatten nested transactions into the top-level one, resulting in a complete abort on conflict, or allow partial abort of inner transactions. Open nested transactions allow a committing inner transaction to immediately release isolation, which increases parallelism and expressiveness at the cost of both software and hardware complexity.This paper extends the recently-proposed flat Log-based Transactional Memory (LogTM) with nested transactions. Flat LogTM saves pre-transaction values in a log, detects conflicts with read (R) and write (W) bits per cache block, and, on abort, invokes a software handler to unroll the log. Nested LogTM supports nesting by segmenting the log into a stack of activation records and modestly replicating R/W bits. To facilitate composition with nontransactional code, such as language runtime and operating system services, we propose escape actions that allow trusted code to run outside the confines of the transactional memory system.
<i>Chlamydia</i> <i>pneumoniae</i> Inhibits Apoptosis in Human Peripheral Blood Mononuclear Cells Through Induction of IL-10 (2000)

Chlamydia pneumoniae is a common cause of pulmonary infection, with serum positivity in at least 50% of the general population. In this study, we report that human PBMCs exposed to C. pneumoniae are resistant to apoptosis induced by the potent photoactivated chemotherapeutic agents 8-methoxypsoralen and hypericin. In contrast, PBMCs treated with a heat-inactivated inoculum exhibit normal susceptibility to apoptosis. We also observed that human PBMCs are responsive to C. pneumoniae infection by secretion of key immune regulatory cytokines, including IL-12 and IL-10. While IL-12 may play an important role in limiting C. pneumoniae proliferation within cells, IL-10 serves an anti-inflammatory function by down-regulating proinflammatory cytokines such as IL-12 and TNF-alpha. Depletion of endogenous IL-10, but not of IL-12, abolished the apoptosis resistance of C. pneumoniae-infected PBMCs. Furthermore, addition of exogenous IL-10, but not IL-12, significantly increased the resistance of control inoculum-treated PBMCs to photoactivated 8-methoxypsoralen- and hypericin-induced apoptosis. Therefore, we conclude that C. pneumoniae possesses an antiapoptotic mechanism. The resistance to apoptosis observed in PBMCs exposed to C. pneumoniae is due, at least partially, to the IL-10 induced during C. pneumoniae infection.
Vascular Endothelial Growth Factor VEGF-like Heparin-Binding Protein from the Venom of <i>Vipera aspis aspis</i> (Aspic Viper) (1999)

The heparin-binding dimeric hypotensive factor (HF) was purified from Vipera aspis aspis (Aspic viper) venom [Komori, Y. and Sugihara, H. (1990) Toxicon 28, 359-369]. In this study, the amino acid sequence, and structure and function of HF, were elucidated. By electrospray ionization mass spectrometry (ESI-MS), the molecular weight of HF was determined to be 25 072.1. The complete amino acid sequence of HF was determined by Edman sequencing of the S-pyridylethylated HF and its peptides derived from enzymatic digestion. The theoretical molecular mass calculated from the primary structure agrees well with the molecular weight determined by ESI-MS. HF consists of two homogeneous monomers bound covalently. The monomer with an N-terminal blocked by pyroglutamic acid contains 110 amino acid residues, including eight cysteine residues, two of which are considered to be involved in intermolecular disulfide bonds. Sequential homology search revealed that the primary structure of HF is similar to that of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) with a sequential homology of 45 and 22%, respectively. When injected intradermally into a rat, an increase in capillary permeability was observed with HF or VEGF. On the other hand, only HF exerted a strong hypotensive effect after intravenous injection of samples into a rat. Purified HF has a mitogenic effect on endothelial cells. Through the use of bovine aortic endothelial cells (BAEC), the half-maximal mitogenic concentration of HF was determined to be 5-5. 5 nM (125-138 ng/mL). Similarly, VEGF had a mitogenic concentration at 0.5-1 nM. When incubated with HF and cycloheximide or HF and heparin, the cell growth was inhibited, suggesting that the mechanism of action of HF is similar to that of VEGF.
A MIM driven Display with Colour Filters on 2″ diagonal Plastic Substrates (1999)

Abstract We report an active‐matrix display with colour filters presumably using plastic substrates for the first time. The fabrication and characterisation of Ta 2 O 5 based and bridge type MIM devices applying an TaAl alloy as new ductile bottom electrode material is described. The realisation of the corresponding low temperature absorptive colour filter, the TN‐cell assembly and TAB bonding techniques on polymer substrates are presented.
Design and characterization of GaN∕InGaN solar cells (2007)

We experimentally demonstrate the III-V nitrides as a high-performance photovoltaic material with open-circuit voltages up to 2.4V and internal quantum efficiencies as high as 60%. GaN and high-band gap InGaN solar cells are designed by modifying PC1D software, grown by standard commercial metal-organic chemical vapor deposition, fabricated into devices of variable sizes and contact configurations, and characterized for material quality and performance. The material is primarily characterized by x-ray diffraction and photoluminescence to understand the implications of crystalline imperfections on photovoltaic performance. Two major challenges facing the III-V nitride photovoltaic technology are phase separation within the material and high-contact resistances.
Application of the Taguchi method on the robust design of molded 225 plastic ball grid array packages (1995)

A three-dimensional nonlinear finite element model of a molded plastic ball grid array (PBGA) has been developed using the ANSYS/sup TM/ finite element simulation code. The model has been used to optimize the package for robust design and to determine design rules to keep package warpage within acceptable limits. An L/sub 18/ Taguchi matrix has been developed to investigate the effect of die attach and mold compound properties along with the substrate, mold compound and die attach thicknesses on the potential defects that would possibly occur during temperature cycling. For package failures, simulations performed represent temperature cycling 165/spl deg/C to -65/spl deg/C. This condition is approximated by cooling the package mounted on a multilayer printed circuit board (PCB) from 165/spl deg/C to -65/spl deg/C. For coplanarity analysis, simulations have been performed without the PCB and the lowest temperature of the cycle is changed to 20/spl deg/C. Predicted results indicate that for an optimum design (low stress in the package and low package warpage) mold compound as well as die attach material should have low Young's modulus and low coefficient of thermal expansion. Furthermore, it is found that the overmold should be kept as thin as possible. In addition to the optimization analysis, plastic strain distribution on each solder ball has been determined to predict the location of the probable first solder ball failure. The results indicate that higher strain levels are obtained in solder balls located one pitch inwards from the edge of the die.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Salivary immunoglobulin G assay to diagnose Helicobacter pylori infection in children (1997)

An in-house enzyme-linked immunosorbent assay (ELISA) for measurement of Helicobacter pylori-specific immunoglobulin G (IgG) and IgA in saliva was evaluated by comparison with histopathologic (Giemsa staining) and biochemical (urease quick test) examination of gastric biopsy specimens obtained from 112 children referred for diagnostic gastroscopy. Serum H. pylori IgG was also measured in a subgroup of 50 children by the same ELISA. Salivary H. pylori IgG levels were significantly higher in H. pylori-positive (n = 57) than in H. pylori-negative (n = 55) children (P < 0.001). The sensitivity and specificity of the salivary IgG test were 93 and 82%, respectively; the positive and negative predictive values were 84 and 92%, respectively; and the accuracy was 87.5%. Salivary H. pylori IgA did not distinguish H. pylori-positive from H. pylori-negative children. The performance of serum H. pylori IgG was slightly (3 to 6%) better than that of salivary H. pylori IgG. The salivary IgG test can be considered a useful tool for the screening of H. pylori infection in children.
Induction of CA125-Specific B and T Cell Responses in Patients Injected with MAb-B43.13—Evidence for Antibody-Mediated Antigen-Processing and Presentation of CA125 in Vivo (2001)

The murine monoclonal anti-CA125 antibody MAb-B43.13 has previously been administered as an immunoscintigraphic agent in order to monitor recurrence of ovarian cancer in patients, and a long-term follow-up demonstrated a survival benefit for these patients. The clinical benefit was initially attributed to the activation of the idiotypic network. The objective of this study was to investigate the role of CA125-MAb-B43.13 immune complex formation on the induction of CA125-specific immune responses. Analysis of patient serum samples from pharmacokinetic studies demonstrated that the antibody forms immune complexes with CA125 in circulation within 30 minutes of injection. Induction of humoral and cellular anti-CA125 responses correlated with the amount of circulating CA125 antigen present at time of antibody injection. Subsequent to the injection of MAb-B43.13, the patients generated anti-CA125 antibodies that were directed against various epitopes on the antigen and were not restricted to the specific epitope recognized by MAb-B43.13. The generation of CA125-specific B and T cell responses after MAb-B43.13 injection correlated with improved survival. The influence of circulating CA125 for the induction of CA125-specific immune responses and the multi-epitopic nature of the human anti-CA125 antibodies suggest that the majority of these antibodies were not induced via the idiotypic network but by the autologous antigen itself. Since antibody and T cell responses to CA125 were not present before injection of MAb-B43.13, it is hypothesized that complex formation of MAb-B43.13 with circulating antigen triggers the induction of CA125-specific immune responses.
Nuclear magnetic resonance spectra of carbanions. Part 10. Dibenzyl-barium, -strontium, and -calcium (1978)

1 H and 13C n.m.r. spectra of three benzyl alkaline earth metal compounds were measured and compared with those of other benzyl compounds. Their aromatic proton resonances are substantially upfield from that of benzene. This higher shielding shift is characteristic of benzyl carbanions. Chemical shift considerations indicate that the carbon–metal bonds of the benzyl carbanions in tetrahydrofuran increase in ionic nature as the counterion varies in the order of magnesium, calcium, strontium, lithium, barium, and potassium.
Genetic determinants of neoplastic transformation by the retroviral oncogene v-erbB. (1988)

The retroviral oncogene v-erbB is a mutant version of the gene (c-erbB or ERBB1) that encodes the cell-surface epidermal growth factor receptor (EGFR). The mutations take three forms: (i) a large deletion that removes the entire ligand-binding domain of EGFR, (ii) smaller deletions that affect the carboxyl-terminal domain of EGFR, and (iii) point mutations that cause conservative substitutions of amino acids. Previous work has shown that, in the absence of the large deletion, ERBB1 cannot transform cells autonomously. Here we report that when the large deletion is present, no other mutation is required for ERBB1 to transform established rodent fibroblasts to a tumorigenic phenotype. In particular, there is no need for deletions affecting the carboxyl terminus of the gene product. It appears, therefore, that removal of the ligand-binding domain from the EGFR suffices to create a transforming protein. Deletions at the carboxyl terminus of the EGFR apparently play only a secondary role in transformation by affecting the host range and perhaps the potency of transformation; and there is as yet no evidence to implicate point mutations in the activation of ERBB1 to an oncogene. Our findings support the view that augmented activity of the EGFR can contribute to tumorigenesis.
A hematopoietic organ-specific 49-kD nuclear antigen: predominance in immature normal and tumor granulocytes and detection in hematopoietic precursor cells (1996)

A 49-kD protein was specifically detected in hematopoietic organs by Western blotting with a novel mouse monoclonal antibody (B92) raised against stromal cells. The protein was found in the immunizing cells using a sensitive method. However, its detection in the bone marrow by the B92 antibody seemed to stem from the abundance of p49 in immature cells of the myeloid lineage. Study of the bone marrow following in vivo irradiation or 5-fluorouracil (5-FU) treatment, in vitro culture with differentiation-inducing factors and long-term culture, and cell sorting all pointed in the same direction: the protein was found in early myeloid cells and in hematopoietic precursor cells. These results were in accordance with the specific presence of p49 in primary radiation-induced myeloid leukemia and its absence in spontaneous B lymphoma. Immunofluorescent staining using B92 antibody detected a nuclear antigen forming a dotted pattern in early myeloid cells and day 12 colony-forming units-spleen (CFU-S). Nuclear localization of p49 was further demonstrated by subcellular fractionation followed by Western blotting. We thus identified a nuclear protein that within the hematopoietic population is detected in hematopoietic precursor cells, predominates in early myeloid cells, and is reduced following differentiation. These properties imply that p49 might be involved in the regulation of hematopoietic cell growth or differentiation.
Tissue Doppler imaging detects early asymptomatic myocardial abnormalities in a dog model of Duchenne?s cardiomyopathy (2004)

These results show that TDI is more sensitive than conventional echocardiography in detecting pre-clinical myocardial abnormalities before occurrence of left ventricular dilation and dysfunction. TDI should be part of the screening techniques for the early diagnosis of cardiomyopathy.
Vertical banded gastroplasty: results in 233 patients. (1986)

The authors describe their experience with vertical banded gastroplasty in 233 patients for whom the follow-up ranged from 12 to 30 months. There were no deaths. Intraoperatively, two gastric perforations and one esophageal perforation occurred; these were closed and drained. A postoperative leak was treated promptly by removal of the collar, drainage and gastrostomy. There were three instances of late obstruction, due in one to mesh adhering to liver and in two to stenoses; gastrogastrostomy was followed by regained weight. Removal of the collar was also associated with failure to lose adequate weight. Rare complications were intraluminal erosion of mesh and staple-line breakdown. The gallbladder was still present in 175 patients; of these, 25 had gallstones and underwent a cholecystectomy at the time of gastroplasty. Of the other 150, symptomatic gallstones subsequently developed in 13. At 12 months after gastroplasty 80% of patients had lost at least 50% of excess weight and at 24 months 83% had lost 50% or more of excess weight (15 patients lost to follow-up). To avoid failures, the collar circumference should not be more than 5.0 cm. A small experience suggests that revision of a failed horizontal gastroplasty to vertical banded gastroplasty is hazardous.
Raloxifene, tamoxifen, nafoxidine, or estrogen effects on reproductive and nonreproductive tissues in ovariectomized rats (1996)

For the first time, four well-characterized compounds from four distinct chemical classes were directly compared for efficacy and potency in hone, uteri, lipids, and adipose tissues in an ovariectomized model with 6 month old rats. Five weeks of oral dosing confirmed that ethynyl estradiol, tamoxifen, and raloxifene are potent inhibitors of the loss in volumetric bone mineral density (BMD, mg/cc) induced by ovariectomy, as measured by computed tomography. In the metaphysis of distal femora from ovariectomized rats, analysis showed a significant 12-20% decrease (P< 0.01) in the BMD. Linear regression analysis was used to calculate half-maximal efficacious doses for ethynyl estradiol ED(50) =0.04mg /kg, which was threefold more potent than tamoxifen, which in turn was threefold more potent than raloxifene, which was more efficacious than nafoxidine. In the uterus, raloxifene had minimal effects on the endometrium and smaller effects on uterine eosinophil peroxidase activity than nafoxidine, tamoxifen, or estrogen, respectively. Estrogen was the most potent in reducing cholesterol levels in ovariectomized rats, whereas tamoxifen and nafoxidine were more effective than raloxifene in blocking gain in body weight. Distinct compounds had advantages in the management of bone, uterine, serum cholesterol, and adipose tissues after ovariectomy. The distinct pattern of pharmacological effects may be best understood in terms of their respective chemical structure, specifically estrogens, benzothiophenes (raloxifene), dihydronapthylenes (nafoxidine), and triphenylethylenes (tamoxifen). These data point to advantages of separate compounds in the management of bone, uterine, serum cholesterol, and adipose tissues after estrogen deficiency, and show that the benzothiophene raloxifene has potentially important advantages over estrogen, tamoxifen, or nafoxidine in the uterus.
Controllable self-organization of colloid microarrays based on finite length effects of electrospun ribbons (2012)

This paper presents a mechanoelectrospinning (MES)-assisted surface-tension driven self-organization to provide a possible route towards inexpensive generation of large-scale ordered microarrays in a controllable manner. To control the self-organization driven by surface tension and Plateau–Rayleigh instability, finite length effects are utilized to manipulate the self-organizing processes and adjust the competition between nucleation and free surface instability. We introduce fine ribbon-lattices to determine the boundary conditions of ribbons to make use of the finite length effects. The ribbon-lattices are electrodeposited precisely by MES, borrowing ideas from the “Chinese kite”, by involving the mechanical drawing force and the electric field force. Then the samples are transferred to a moisture-rich environment in which the ribbons absorb water vapour and become liquid lines. Surface instability emerges and leads the liquid lines to controllable self-organization. We uncover the controllable area to manipulate the self-organization behavior. A uniform or hierarchical microarray with a specific position, gap and droplet-size can be generated in a continuously tunable manner. This bottom-up method provides a digital approach for the fabrication of large-scale ordered microarrays and micropatterns.
Entropy-based anomaly detection for in-vehicle networks (2011)

Due to an increased connectivity and seamless integration of information technology into modern vehicles, a trend of research in the automotive domain is the development of holistic IT security concepts. Within the scope of this development, vehicular attack detection is one concept which gains an increased attention, because of its reactive nature that allows to respond to threats during runtime. In this paper we explore the applicability of entropy-based attack detection for in-vehicle networks. We illustrate the crucial aspects for an adaptation of such an approach to the automotive domain. Moreover, we show first exemplary results by applying the approach to measurements derived from a standard vehicle's CAN-Body network.
Cell Cycle Regulation in Plant Development (2006)

Cell cycle regulation is of pivotal importance for plant growth and development. Although plant cell division shares basic mechanisms with all eukaryotes, plants have evolved novel molecules orchestrating the cell cycle. Some regulatory proteins, such as cyclins and inhibitors of cyclin-dependent kinases, are particularly numerous in plants, possibly reflecting the remarkable ability of plants to modulate their postembryonic development. Many plant cells also can continue DNA replication in the absence of mitosis, a process known as endoreduplication, causing polyploidy. Here, we review the molecular mechanisms that regulate cell division and endoreduplication and we discuss our understanding, albeit very limited, on how the cell cycle is integrated with plant development.
Influence of Co‐Doping on the Sintering Path and on the Optical Properties of a Submicronic Alumina Material (2008)

Sintering in air was performed on pure and CaO/TiO 2 co‐doped slip cast α‐alumina samples. The relative density/grain size relationship, referred to as sintering path, has been obtained for each composition. Fully dense samples were obtained after an additional hot isostatic pressing (HIP) step on the pure and doped materials. After grinding and polishing, the optical properties were measured on flat windows (thickness around 1 mm) in the ultraviolet, visible, close‐infrared, and mid‐infrared ranges. The influence of a tiny residual porosity on the optical properties, impossible to quantify using standard methods, has been investigated.