gebhart/patrepeval huggingface dataset:
Hapten–protein binding: from theory to practical application in the in vitro prediction of skin sensitization (2005)

In view of the forthcoming European Union ban on in vivo testing of cosmetic and toiletry ingredients, following the publication of the 7th amendment to the Cosmetics Directive, the search for practical, alternative, non-animal approaches is gathering pace. For the end-point of skin sensitization, the ultimate goal, i.e. the development and validation of alternative in vitro/in silico assays by 2013, may be achieved through a better understanding of the skin sensitization process on the cellular and molecular levels. One of the key molecular events in skin sensitization is protein haptenation, i.e. the chemical modification of self-skin protein(s) thus forming macromolecular immunogens. This concept is widely accepted and in theory can be used to explain the sensitizing capacity of many known skin sensitizers. Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. In this review, we consider some of the theoretical aspects of protein haptenation, how mechanisms of protein haptenation can be investigated experimentally and how we can use such knowledge in the development of novel, alternative approaches for predicting skin sensitization potential in the future.
Histone deacetylase inhibitors modulate renal disease in the MRL-lpr/lpr mouse (2003)

Studies in human systemic lupus erythematosus (SLE) suggest a possible role for histone deacetylases (HDACs) in skewed gene expression and disease pathogenesis. We used the MRL-lpr/lpr murine model of lupus to demonstrate that HDACs play a key role in the heightened levels of both Th1 and Th2 cytokine expression that contribute to disease. The availability of specific HDAC inhibitors (HDIs) such as trichostatin A (TSA) and suberonylanilide hydroxamic acid (SAHA) permits the study of the role of HDACs in gene regulation. Our results indicate that HDIs downregulate IL-12, IFN-gamma, IL-6, and IL-10 mRNA and protein levels in MRL-lpr/lpr splenocytes. This effect on gene transcription is associated with an increased accumulation of acetylated histones H3 and H4 in total cellular chromatin. To elucidate the in vivo effects of TSA on lupuslike disease, we treated MRL-lpr/lpr mice with TSA (0.5 mg/kg/d) for 5 weeks. Compared with vehicle-treated control mice, TSA-treated mice exhibited a significant reduction in proteinuria, glomerulonephritis, and spleen weight. Taken together, these findings suggest that increased expression of HDACs leading to an altered state of histone acetylation may be of pathologic significance in MRL-lpr/lpr mice. In addition, TSA or other HDIs may have therapeutic benefit in the treatment of SLE.
Tramadol versus nalbuphine in total intravenous anaesthesia for dilatation and evacuation. (2007)

Quality of analgesia was better in nalbuphine group but both drugs provide suitable analgesic supplementation to TIVA.
Fibrocytes in lung disease (2007)

Fibrocytes were first described over a decade ago as a population of cells in circulation with fibroblast-like properties, which were involved in tissue repair. Since that time, we have learned a significant amount about these bone marrow-derived cells, which contribute to wound healing and fibrosis. Fibrocytes express leukocyte markers such as CD34, CD45, and CD13 and also express mesenchymal markers such as pro-collagens I and III, vimentin, and fibronectin. In addition, they have been shown to express the chemokine receptors CXCR4 and CCR7, which appear to be important in cellular trafficking from the vascular to the extravascular compartment. Fibrocytes have been shown to contribute to a number of fibrotic disorders, and here, we review their involvement in lung diseases including pulmonary fibrosis, asthma, and vascular remodeling.
Analysis of US Hydraulic Fracturing Fluid System and Proppant Trends (2014)

Abstract Building upon the analysis contained in a related paper (SPE-163875), "Analysis of U.S. Hydraulic Fracturing Design Trends," presented at the 2013 SPE Hydraulic Fracturing Technology Conference, this paper will provide a more comprehensive and robust analysis of hydraulic fracturing fluid systems and proppant trends across major shale plays in the United States between 2011 and the first half of 2013. This paper will present key insights gleaned from the categorization and analysis of over 55,000 hydraulic fracturing treatments, collected from FracFocus.org. FracFocus.org is a website established in early 2011 with a centralized registry to provide hydraulic fracturing chemical disclosures across the United States. The website provides the data for the analysis presented in this paper, consisting of chemical disclosure records for nearly 55,000 hydraulically fractured wells. The data set includes information on all chemicals and proppants, fracture date, TVD, water volume, production type. We have collected all available data, identified key constituent materials, and classified each treatment according to a widely used set of frac type categories. This paper investigates changes in key hydraulic fracturing technical parameters at the both the aggregate US level and regional level between 2011 and the first half of 2013. The analysis identifies changes over time in frac type, using the broad categories of conventional, water frac, hybrid, energized, etc. The paper also includes analysis on proppant trends, including usage rates for key proppant types (sand, resin-coated sand, and ceramics) and proppant loading trends. To date, most knowledge of aggregate consumption trends on hydraulic fracturing chemicals and proppant is anecdotal and based on the direct experience of operators or service companies. This paper provides a more rigorous quantitative perspective on hydraulic fracturing fluid trends in the United States between 2011 and the first half of 2013.
Replacement of the P1 Amino Acid of Human Immunodeficiency Virus Type 1 Gag Processing Sites Can Inhibit or Enhance the Rate of Cleavage by the Viral Protease (2002)

Processing of the human immunodeficiency virus type 1 (HIV-1) Gag precursor is highly regulated, with differential rates of cleavage at the five major processing sites to give characteristic processing intermediates. We examined the role of the P1 amino acid in determining the rate of cleavage at each of these five sites by using libraries of mutants generated by site-directed mutagenesis. Between 12 and 17 substitution mutants were tested at each P1 position in Gag, using recombinant HIV-1 protease (PR) in an in vitro processing reaction of radiolabeled Gag substrate. There were three sites in Gag (MA/CA, CA/p2, NC/p1) where one or more substitutions mediated enhanced rates of cleavage, with an enhancement greater than 60-fold in the case of NC/p1. For the other two sites (p2/NC, p1/p6), the wild-type amino acid conferred optimal cleavage. The order of the relative rates of cleavage with the P1 amino acids Tyr, Met, and Leu suggests that processing sites can be placed into two groups and that the two groups are defined by the size of the P1' amino acid. These results point to a trans effect between the P1 and P1' amino acids that is likely to be a major determinant of the rate of cleavage at the individual sites and therefore also a determinant of the ordered cleavage of the Gag precursor.
Neurite Outgrowth in PC12 Cells (1999)

Nerve growth factor (NGF)-induced neurite outgrowth from rat PC12 cells was coincident with elevated (>/=2-fold) levels of endogenous ubiquitin (Ub) protein conjugates, elevated rates of formation of 125I-labeled Ub approximately E1 (Ub-activating enzyme) thiol esters and 125I-labeled Ub approximately E2 (Ub carrier protein) thiol esters in vitro, and enhanced capacity to synthesize 125I-labeled Ub-protein conjugates de novo. Activities of at least four E2s were increased in NGF-treated cells, including E2(14K), a component of the N-end rule pathway. Ubiquitylation of 125 I-labeled beta-lactoglobulin was up to 4-fold greater in supernatants from NGF-treated cells versus untreated cells and was selectively inhibited by the dipeptide Leu-Ala, an inhibitor of Ub isopeptide ligase (E3). However, Ub-dependent proteolysis of 125I-labeled beta-lactoglobulin was not increased in supernatants from NGF-treated cells, suggesting that neurite outgrowth is promoted by enhanced rates of synthesis (rather than degradation) of Ub-protein conjugates. Consistent with this observation, neurite outgrowth was induced by proteasome inhibitors (lactacystin and clasto-lactacystin beta-lactone) and was associated with elevated levels of ubiquitylated protein and stabilization of the Ub-dependent substrate, p53. Lactacystin-induced neurite outgrowth was blocked by the dipeptide Leu-Ala (2 mM) but not by His-Ala. These data 1) demonstrate that the enhanced pool of ubiquitylated protein observed during neuritogenesis in PC12 cells reflects coordinated up-regulation of Ub-conjugating activity, 2) suggest that Ub-dependent proteolysis is a negative regulator of neurite outgrowth in vitro, and 3) support a role for E2(14K)/E3-mediated protein ubiquitylation in PC12 cell neurite outgrowth.
Lipid Phosphate Phosphatases in Arabidopsis (2001)

An Arabidopsis thaliana gene (AtLPP1) was isolated on the basis that it was transiently induced by ionizing radiation. The putative AtLPP1 gene product showed homology to the yeast and mammalian lipid phosphate phosphatase enzymes and possessed a phosphatase signature sequence motif. Heterologous expression and biochemical characterization of the AtLPP1 gene in yeast showed that it encoded an enzyme (AtLpp1p) that exhibited both diacylglycerol pyrophosphate phosphatase and phosphatidate phosphatase activities. Kinetic analysis indicated that diacylglycerol pyrophosphate was the preferred substrate for AtLpp1p in vitro. A second Arabidopsis gene (AtLPP2) was identified based on sequence homology to AtLPP1 that was also heterologously expressed in yeast. The AtLpp2p enzyme also utilized diacylglycerol pyrophosphate and phosphatidate but with no preference for either substrate. The AtLpp1p and AtLpp2p enzymes showed differences in their apparent affinities for diacylglycerol pyrophosphate and phosphatidate as well as other enzymological properties. Northern blot analyses showed that the AtLPP1 gene was preferentially expressed in leaves and roots, whereas the AtLPP2 gene was expressed in all tissues examined. AtLPP1, but not AtLPP2, was regulated in response to various stress conditions. The AtLPP1 gene was transiently induced by genotoxic stress (gamma ray or UV-B) and elicitor treatments with mastoparan and harpin. The regulation of the AtLPP1 gene in response to stress was consistent with the hypothesis that its encoded lipid phosphate phosphatase enzyme may attenuate the signaling functions of phosphatidate and/or diacylglycerol pyrophosphate that form in response to stress in plants.
Metabolomics classifies phase of care and identifies risk for mortality in a porcine model of multiple injuries and hemorrhagic shock (2012)

The results of this study demonstrate the potential for metabolomics as a tool to classify the metabolic flux, to identify relevant biochemical pathways, and to identify clinically useful biomarkers.
Human transforming growth factor beta.alpha 2-macroglobulin complex is a latent form of transforming growth factor beta. (1988)

125I-Labeled human platelet-derived transforming growth factor beta (125I-TGF-beta) and human alpha 2-macroglobulin (alpha 2M) formed a complex as demonstrated by 5% native polyacrylamide gel electrophoresis. The 125I-TGF-beta.alpha 2M complex migrated at a position identical to that of the fast migrating form of alpha 2M. Most of the 125I-TGF-beta.alpha 2M complex could be dissociated by acid or urea treatment. When 125I-TGF-beta was incubated with serum, the high molecular weight form of 125I-TGF-beta could be immunoprecipitated by anti-human alpha 2M anti-sera as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. alpha 2M purified from platelet-rich plasma also showed the latent transforming growth factor activity and immunoreactivity of TGF-beta. These results suggest that TGF-beta.alpha 2M complex is a latent form of TGF-beta.
Low-Frequency Sonophoresis: A Noninvasive Method of Drug Delivery and Diagnostics (2000)

Transdermal drug delivery offers an attractive alternative to injections and oral medications. However, applications of transdermal drug delivery are limited to only a few drugs as a result of low skin permeability. Application of low-frequency ultrasound enhances skin permeability, a phenomenon referred to as low-frequency sonophoresis. In this method, a short application of ultrasound is used to permeabilize skin for a prolonged period of time. During this period, ultrasonically permeabilized skin may be utilized for drug delivery. In addition, a sample of interstitial fluid or its components may be extracted through permeabilized skin for diagnostic applications. In this paper, we report our in vivo studies that demonstrate the principles of both of these concepts. Detailed studies on drug delivery are performed using inulin and mannitol as model drugs. Studies on diagnostics are performed using glucose as a model analyte. Applications of this technology to drug delivery and diagnostics are discussed.
Magnetostriction effect of amorphous CoFeB thin films and application in spin-dependent tunnel junctions (2005)

CoFeB thin films and magnetic tunnel junctions using them are studied for magnetostriction effect. The single-layer films were sputter deposited with excellent soft magnetic properties including a high saturation magnetization of 1.5T, a near-zero hard axis coercivity, a low easy axis coercivity of 2.0Oe, and an induced magnetic anisotropy field of 32Oe. The saturation magnetostriction constant is measured to be 31ppm. Magnetic tunnel junctions (MTJs) were fabricated and tested for potential strain gauge applications. The gauge factor for the magnetostrictive MTJs, a measure of strain sensitivity, is many times of the best piezoresistive devices.
A high performance 1.8 V, 0.20 μm CMOS technology with copper metallization (2002)

A high performance 0.20 /spl mu/m logic technology has been developed with six levels of planarized copper interconnects. 0.15 /spl mu/m transistors (L/sub gate/=0.15/spl plusmn/0.04 /spl mu/m) are optimized for 1.8 V operation to provide high performance with low power-delay products and excellent reliability. Copper has been integrated into the back-end to provide low resistance interconnects. Critical layer pitches for the technology are summarized and enable fabrication of 7.6 /spl mu/m/sup 2/ 6T SRAM cells.
Systematic Review of Medical Treatment in Melanoma: Current Status and Future Prospects (2011)

The incidence of melanoma is increasing worldwide, and the prognosis for patients with high-risk or advanced metastatic melanoma remains poor despite advances in the field. Standard treatment for patients with thick (≥2.0 mm) primary melanoma with or without regional metastases to lymph nodes is surgery followed by adjuvant therapy or clinical trial enrollment. Adjuvant therapy with interferon-α and cancer vaccines is discussed in detail. Patients who progress to stage IV metastatic melanoma have a median survival of ≤1 year. Standard treatment with chemotherapy yields low response rates, of which few are durable. Cytokine therapy with IL-2 achieves durable benefits in a greater fraction, but it is accompanied by severe toxicities that require the patient to be hospitalized for support during treatment. A systematic literature review of treatments for advanced, metastatic disease was conducted to present the success of current treatments and the promise of those still in clinical development that may yield incremental improvements in the treatment of advanced, metastatic melanoma.
Inherited Complete Deficiency of 20-Kilodalton Homologous Restriction Factor (CD59) as a Cause of Paroxysmal Nocturnal Hemoglobinuria (1990)

PAROXYSMAL nocturnal hemoglobinuria is a rare acquired disease caused by an unusual susceptibility of erythrocytes to the lytic action of complement. The abnormal erythrocytes are thought to originate from the clonal proliferation of bone marrow progenitors altered by somatic mutation.1 Erythrocytes from patients with paroxysmal nocturnal hemoglobinuria have been shown to be deficient in membrane glycoproteins, such as decay-accelerating factor (DAF)2 , 3 and a factor called either homologous restriction factor4 (HRF) or C8-binding protein5 (C8bp). DAF can inhibit the formation and induce the dissociation of C3 convertases of the classical and alternative pathways of complement activation.6 7 8 HRF/C8bp appears to limit the . . .
Performance, carcass, cartilage calcium, sensory and collagen traits of longissimus muscles of open versus 30-month-old heifers that produced one calf. (1990)

One hundred eleven Simmental x Hereford (3/8 to 5/8 Simmental) heifers were used to determine the effects of age, parturition and implantation on performance, carcass and meat-sensory traits, muscle-collagen characteristics and thoracic-button calcification. Eighty-five heifers that calved at about 2 yr of age, designated as single-calf heifers (SCH), were either implanted (I-SCH) with Synovex-H or not implanted (NI-SCH). The remaining 26, 2-yr-old non-pregnant heifers (2-OH) served as controls. Additionally, 24, 1-yr-old open heifers (1-OH) from the same genetic source were utilized as the standard heifer-production system. The 1-OH and 2-OH were slaughtered after being fed a high-grain diet for 137 and 112 d, respectively. The SCH were fed the same high-grain diet beginning about 1 mo after calving and were fed 137 d before slaughter. The 33 I-SCH were implanted when started on the high-grain diet. Calves were weaned about 5 wk before the SCH were slaughtered. The 2-OH had the highest (P less than .05) feedlot ADG, whereas no differences (P greater than .05) occurred among other treatments. Dressing percentages were higher (P less than .01) for I-SCH than for NI-SCH. Carcass weights were lowest (P less than .05) and percentage kidney, pelvic and heart fat was highest (P less than .01) for 1-OH. Fat thickness, yield grades, marbling scores and quality grades were similar (P greater than .05) and desirable for all treatments.(ABSTRACT TRUNCATED AT 250 WORDS)
Adiponectin‐Mediated Modulation of Lymphatic Vessel Formation and Lymphedema (2013)

Adiponectin can promote lymphatic vessel formation via activation of AMPK/Akt/endothelial nitric oxide synthase signaling within LECs, thereby leading to amelioration of lymphedema.
Low cost/high volume laser modules using silicon optical bench technology (2002)

Reports on the use of SiOB technology used in the production of low cost/high volume, reliable edge emitting laser modules. The SiOB platform is designed for manufacturability, reduced parts count, reduced process steps, and ability to accept design changes to respond to a rapidly changing marketplace. For example, this SiOB technology has been used for at least four different laser designs/types without significant changes in the process. The SiOB technology is the first of its kind in that it integrates: i) silicon micromachining for the lens holder cavities and back face monitor turning mirror, ii) Ti/Pt/Au for interconnect metalization, photodiode bonding, and turning mirror iii) aluminum for AlO bonding attachment of the lens, and iv) Au/Sn solder for laser attachment. The laser and photodiode are passively aligned using a visual alignment system and fiducials on the silicon. The lens is self-aligned to the silicon during the AlO bonding process.
Optimization of Nanosized Silver Particle Synthesis via Experimental Design (2007)

Highly dispersed silver nanoparticles could be used as catalysts, as staining pigments for glasses and ceramics, as antimicrobial materials, in surface-enhanced Raman spectroscopy, as transparent conductive coatings, in electronics, etc. Consequently, the versatility of such particles provides strong incentives to the development of a systematic way to produce their dispersions. In this work, the optimization of the synthesis of nanosized silver particles by chemical reduction using formaldehyde in aqueous solution was studied. Effects of the possible processing variables such as the reaction temperature T, the mole ratio of [formaldehyde]/[AgNO3], [NaOH]/[AgNO3], the weight ratio of PVP/AgNO3, and the molecular weight (MW) of protective agent PVP (Polyvinyl−pyrrolidone) were considered. The data-driven model on the basis of the 44 designed experimental runs provided us the optimal conditions for closely achieving the product with the specified mean particle size and conversion of silver nitrate.
Noninvasive microwave measurement of respiration (1975)

A microwave technique for measuring respiratory movements of man and animal is described. The technique is noncontacting and is based on the scattering of continuous wave radiation. Preliminary results are shown for both animal and man, indicating the usefulness of the procedure.
Improved predictions of secondary structures for RNA. (1989)

The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70%. Performance is judged by comparison with structures known from phylogenetic analysis. The algorithm also generates suboptimal structures. On average, the best structure within 10% of the lowest free energy contains roughly 90% of phylogenetically known helixes. The algorithm does not include tertiary interactions or pseudoknots and employs a crude model for single-stranded regions. The only favorable interactions are base pairing and stacking of terminal unpaired nucleotides at the ends of helixes. The excellent performance is consistent with these interactions being the primary interactions determining RNA secondary structure.
A 'virtual body' model for surgical education and rehearsal (1996)

A general digital model of human anatomy is very helpful both in supporting the process of anatomical segmentation and as a reference system for simulating surgical situations or even rehearsal of interventions. This article describes the data structure and implementation of such a model. Neither superhero nor crash-test dummy, Voxel-Man is an attempt to combine in a single framework a detailed spatial model enabling realistic visualization with a symbolic model of the human body. We show that although a general model does not correspond in detail to an individual patient, it does provide a variety of novel features for surgical education and training.
Cachectin: More Than a Tumor Necrosis Factor (1987)

THE metabolic impact of infectious and neoplastic disease states has long been known to clinicians.1 2 3 4 Invasive diseases may disrupt normal homeo-static mechanisms, both locally and systemically. For example, acute gram-negative infections frequently lead to profound metabolic acidosis and to biphasic changes in plasma glucose concentration, both seen in the context of hypotension, disseminated intravascular coagulation, and widespread tissue injury.5 6 7 8 9 10 11 12 Chronic infectious diseases, as well as neoplastic diseases, may provoke a severe wasting diathesis, in which negative calorie and nitrogen balance lead to death despite the absence of a large parasite or tumor burden.It was once widely believed that invasive . . .