gebhart/patrepeval huggingface dataset:
Glycerolysis of Fat by Lipase (1986)

Glycerolysis reactions of corn oil by Pseudomonas fluorescens lipase were studied batchwise in a small agitated vessel. The sampled reaction mixture was extracted with chloroform and the relative content of triglyceride (TG), 1, 2-diglyceride (1, 2-DG), 1, 3-diglyceride (1, 3-DG), 1-monoglyceride (1-MG), 2-monoglyceride (2-MG) and free fatty acid (FFA) of the condensed chloroform sample was determined using a TLC/FID analyzer. The effects of agitation speed on the initial rate of conversion were examined. Above 350rpm, the rate was maximum and constant. The time course of glycerolysis showed that at the beginning, the content of 1, 2-DG exceeded that of 1, 3-DG, but later, this was reversed. In two isomers of MG, 1-MG was detected almost exclusively, 2-MG being formed very little. The initial rates of conversion and formation of the products were proportional to enzyme concentration. No appreciable glycerolysis took place at very low water concentrations. No FFA was formed below 4% water concentration in glycerol. Above 4%, the initial FFA formation was proportional to water concentration to the 2.7th power. The dependence of the initial rate of conversion on the temperature obeyed the Arrhenius equation, giving 6.13kcal/mol of activation energy.No variation in equilibrium composition was observed in the range of 1535% of the weight proportion of the oil to the total reaction mixture. The equilibrium composition did not change with variation in enzyme concentration or temperature from 2565°C. The equilibrium composition was significantly influenced by water concentration. Below 4% water in glycerol, no FFA was present in the product mixture. The composition of the product at 3.7% water concentration in glycerol was : 20.1% 1-MG, 0.3% 2-MG, 12.3% 1, 2-DG, 29.5% 1, 3-DG, 0.0% FFA, and 37.3% unreacted TG.
Adipsin, a Biomarker of Gastrointestinal Toxicity Mediated by a Functional γ-Secretase Inhibitor (2003)

Functional gamma-secretase inhibitors (FGSIs) can block the cleavage of several transmembrane proteins including amyloid precursor protein (APP), and the cell fate regulator Notch-1. FGSIs, by inhibiting APP processing, block the generation of amyloid beta (Abeta) peptides and may slow the development of Alzheimer's disease. FGSIs used to inhibit APP processing may disrupt Notch processing, thus interfering with cell fate determination. Described herein is a FGSI-mediated gastrointestinal toxicity characterized by cell population changes in the ileum of rats, which are indicative of Notch signaling disruption. Microarray analysis of ileum from FGSI-treated rats revealed differential expression responses in a number of genes indicative of Notch signaling perturbation, including the serine protease adipsin. We were able to show that FGSI-treated rats had elevated levels of adipsin protein in gastrointestinal contents and feces, and by immunohistochemistry demonstrated that adipsin containing ileum crypt cells were increased in FGSI-treated rats. The mouse Adipsin proximal promoter contains a putative binding site for the Notch-induced transcriptional regulator Hes-1, which we demonstrate is able to bind Hes-1. Additional studies in 3T3-L1 preadipocytes demonstrate that this FGSI inhibits Hes-1 expression while up-regulating adipsin expression. Overexpression of Hes-1 was able to down-regulate adipsin expression and block pre-adipocyte differentiation. We propose that adipsin is a Hes-1-regulated gene that is de-repressed during FGSI-mediated disruption of Notch/Hes-1 signaling. Additionally, the aberrant expression of adipsin, and its presence in feces may serve as a noninvasive biomarker of gastrointestinal toxicity associated with perturbed Notch signaling.
Cardiac Myocytes Produce Interleukin-6 in Culture and in Viable Border Zone of Reperfused Infarctions (1999)

Isolated cardiac myocytes produce IL-6 mRNA in response to several cytokines as well as postischemic cardiac lymph. In addition to its production by inflammatory cells, we demonstrate that IL-6 mRNA is induced in myocytes in the viable border zone of a myocardial infarct. The potential roles of IL-6 in cardiac myocytes in an infarct border are discussed.
Electrical detection of single viruses (2004)

We report direct, real-time electrical detection of single virus particles with high selectivity by using nanowire field effect transistors. Measurements made with nanowire arrays modified with antibodies for influenza A showed discrete conductance changes characteristic of binding and unbinding in the presence of influenza A but not paramyxovirus or adenovirus. Simultaneous electrical and optical measurements using fluorescently labeled influenza A were used to demonstrate conclusively that the conductance changes correspond to binding/unbinding of single viruses at the surface of nanowire devices. pH-dependent studies further show that the detection mechanism is caused by a field effect, and that the nanowire devices can be used to determine rapidly isoelectric points and variations in receptor-virus binding kinetics for different conditions. Lastly, studies of nanowire devices modified with antibodies specific for either influenza or adenovirus show that multiple viruses can be selectively detected in parallel. The possibility of large-scale integration of these nanowire devices suggests potential for simultaneous detection of a large number of distinct viral threats at the single virus level.
Genome Sequencing of 15 Clinical Vibrio Isolates, Including 13 Non-O1/Non-O139 Serogroup Strains (2014)

We present draft genome sequences of 15 clinical Vibrio isolates of various serogroups. These are valuable data for use in studying Vibrio cholerae genetic diversity, epidemic potential, and strain attribution.
Force and Geometry Determine Structure and Function of Glaucoma Filtration Capsules (2007)

The corollary is true. Geometry can be used to manage the amount, distribution and orientation of collagen and thus control hydraulic conductivity and surface area of the filtration capsule.
A Geminivirus Induces Expression of a Host DNA Synthesis Protein in Terminally Differentiated Plant Cells (1995)

Steven Nagar, Thomas J. Pedersen, Kevin M. Carrick, Linda Hanley-Bowdoin, Dominique Robertson, A Geminivirus Induces Expression of a Host DNA Synthesis Protein in Terminally Differentiated Plant Cells, The Plant Cell, Vol. 7, No. 6 (Jun., 1995), pp. 705-719
Effects of Starvation on Survival and Maintenance of Soldier Proportion in Laboratory Groups of the Formosan Subterranean Termite, Coptotermes formosanus (Isoptera: Rhinotermitidae) (1986)

Laboratory groups of the Formosan subterranean termite, Coptotermes formosanus Shiraki, had ca. 2% soldier proportions under starvation conditions and ca. 11% when food was provided, regardless of initial soldier proportions. In the absence of food, soldiers were starved or cannibalized before workers were sacrificed. Data suggest that soldiers may represent an emergency food ration for colony survival under starvation conditions.
Specific inhibitors of tyrosine-specific protein kinases: properties of 4-hydroxycinnamamide derivatives in vitro. (1989)

Inhibition by seven synthetic 4-hydroxycinnamamide derivatives, ST 271, ST 280, ST 458, ST 494, ST 633, ST 638, and ST 642, of tyrosine-specific protein kinases (tyrosine kinase) of oncogene or proto-oncogene products (p130gag-v-fps, p70gag-actin-v-fgr, pp60v-src, pp60c-src) and epidermal growth factor (EGF) receptor kinase were investigated. ST 638 (alpha-cyano-3-ethoxy-4-hydroxy-5-phenylthiomethylcinnamamide) strongly inhibited more of the tyrosine kinases than any of the other compounds. The susceptibilities of these tyrosine kinases to ST 638 increased in the following order: EGF receptor greater than p70gag-actin-v-fgr greater than pp60c-src greater than p130gag-v-fps, pp60v-src, with 50% inhibitory concentration values of 1.1, 4.2, 18, 70, and 87 microM, respectively. The phosphorylation of the tyrosine residues in particulate fractions from RR1022 cells expressing pp60v-src was inhibited by ST 638 in a dose-dependent way, while it had a negligible effect on the phosphorylations of threonine and serine residues. Kinetic analysis showed that ST 638 competitively inhibited the phosphorylation of an exogenous substrate by the EGF receptor kinase with a Ki of 2.1 microM. ST 638 noncompetitively inhibited autophosphorylation by EGF receptor kinase. These results indicate that ST 638 is a potent and specific inhibitor of tyrosine kinases in vitro, and that its inhibitory activity is caused by competing with the substrate protein for the tyrosine kinase binding site.
Quantitative structure-activity relationship studies of inhibitors of gastric (H+/K+)-ATPase. (1991)

The (H+/K+)-ATPase enzyme inhibitory activity of omeprazole analogues (Figure 1) and 1-aryl-4-methyl-2,3-dihydropyrrolo[3,2-c]quinolines (Figure 2) was found to be significantly correlated with electronic (sigma) or pKa parameter that governs the basicity of the molecules. The former compounds are representative of irreversible blockers, and the latter of reversible blockers. Inclusion of hydrophobic (pi) and/or steric (Es) parameters sometimes led to improvement in the correlations, suggesting that these parameters may play a role in the formation of a cyclic intermediate. The derived significant correlation equations strongly support a mechanism of action, first proposed by Lindberg et al., involving such a cyclic intermediate.
Effects of Aspirin and Lipopolysaccharide on Microglia Activation after Focal Cerebral Ischemia/ Reperfusion in Rats (2013)

Aim To investigate the microglial activation after focal cerebral ischemia/reperfusion(CI/RP) in rats and the effect of aspirin(ASA) and lipopolysaccharide(LPS) on the microglial cells.Methods 114 healthy male SD rats were randomly divided into sham-operation group,control group,ASA(80 mg.kg-1) group,LPS(1 mg.kg-1) group,and ASA+LPS group.The middle cerebral artery occlusion model in rats were made by suture-occluded method with 2 hour ischemia and reperfusion of 6 h,24 h,3 d,5 d and 7 d respectively.The lectin GSI-B 4 marked activated microglias were detected by immunohistochemistry.Results The activated microglias were not detected in the sham-operation group,only detected in the infarction side of the control group and ASA group,and detected in both infarction and contralateral side in LPS group.The different morphologies of the activated microglias such as highly ramified,rod-shaped,round and amoeba-like cells as well as and foam cells were observed in the infarction core zone and border zone after CI/RP.The activated microglias in the infarction area increased significantly(P0.05) after intraperitoneal injection of LPS.The ASA intervention could significantly reduce the activated microglias regardless of CI/RP or LPS induction(P0.01 or P0.05).Conclusion ASA could inhibit early microglial activation after CI/RP or induced by LPS,and improve neurological function in rats.
REMOVAL OF ANTI-PORCINE NATURAL ANTIBODIES FROM HUMAN AND NONHUMAN PRIMATE PLASMA IN VITRO AND IN VIVO BY A Gal??1-3Gal??1-4??Glc-X IMMUNOAFFINITY COLUMN (1998)

Both methods reduced the level of anti-pig IgM and IgG xenoreactive antibodies to nearly background, but column perfusion caused less hypotension and reduction in platelets than liver perfusion. Four pig kidneys transplanted into monkeys after column perfusion did not undergo hyperacute rejection, remaining functional for 2-10 days, with a mean functional period of 7 days, demonstrating that a pig kidney can support renal function in a primate.
Cable-Based Metro Area Networks (1983)

This paper examines the system design considerations of metropolitan area networks utilizing cable television networks for the delivery of a variety of services to residential customers. Specifically, this paper focuses on the technology, marketplace, and regulatory aspects of this new and expanding market.
A Nonparametric Approach to Detect Nonlinear Correlation in Gene Expression (2010)

We propose a distribution-free approach to detect nonlinear relationships by reporting local correlation. The effect of our proposed method is analogous to piece-wise linear approximation although the method does not utilize any linear dependency. The proposed metric, maximum local correlation, was applied to both simulated cases and expression microarray data comparing the rd mouse with age-matched control animals. The rd mouse is an animal model (with a mutation for the gene Pde6b) for photoreceptor degeneration. Using simulated data, we show that maximum local correlation detects nonlinear association, which could not be detected using other correlation measures. In the microarray study, our proposed method detects nonlinear association between the expression levels of different genes, which could not be detected using the conventional linear methods. The simulation dataset, microarray expression data, and the Nonparametric Nonlinear Correlation (NNC) software library, implemented in Matlab, are included as part of the online supplemental materials.
A phase I pharmacokinetics trial comparing PF‐05280586 (a potential biosimilar) and rituximab in patients with active rheumatoid arthritis (2016)

The study demonstrated PK similarity among PF-05280586, rituximab-EU and rituximab-US. In addition, all treatments showed comparable CD19+ B cell depletion PD responses, as well as safety and immunogenicity profiles.
TINA: a natural language system for spoken language applications (1992)

A new natural language system, TINA, has been developed for applications involving spoken language tasks. TINA integrates key ideas from context free grammars, Augmented Transition Networks (ATN's), and the unification concept. TINA provides a seamless interface between syntactic and semantic analysis, and also produces a highly constraining probabilistic language model to improve recognition performance. An initial set of context-free rewrite rules provided by hand is first converted to a network structure. Probability assignments on all arcs in the network are obtained automatically from a set of example sentences. The parser uses a stack decoding search strategy, with a top-down control flow, and includes a feature-passing mechanism to deal with long-distance movement, agreement, and semantic constraints. TINA provides an automatic sentence generation capability that has been effective for identifying overgeneralization problems as well as in producing a word-pair language model for a recognizer. The parser is currently integrated with MIT's SUMMIT recognizer for use in two application domains, with the parser screening recognizer outputs either at the sentential level or to filter partial theories during the active search process.
Effect of Sediment Density on Bed‐Load Transport (1989)

Experiments on transport by water of synthetic lightweight sediments of specific gravities, 1.0<s<2.5, and uniform grain size, D=3.5mm, are described. The results confirm the dimensional reasoning that the volumetric specific sediment transport rate, qs, is proportional to a simple power relation of the quotient, shear velocity/grain fall velocity (V*/w). The sediment transport rate, qs, is found to be proportional to the sixth power of the shear velocity, V*, and inversely proportional to the fifth power of the grain fall velocity, w. An empirical formula based on the dimensional reasoning and the results above is found to be equivalent to the Einstein‐Brown bed load formula. A comparison of the experimental data with the predictions of several common bed load formulas shows the behavior of these formulas with lightweight sediments. The Einstein‐Brown formula and a modified version of Smart's formula provide good predictions.
Emerging Principles for the Recognition of Peptide Antigens by MHC Class I Molecules (1992)

Class I major histocompatibility complex (MHC) molecules interact with self and foreign peptides of diverse amino acid sequences yet exhibit distinct allele-specific selectivity for peptide binding. The structures of the peptide-binding specificity pockets (subsites) in the groove of murine H-2Kb as well as human histocompatibility antigen class I molecules have been analyzed. Deep but highly conserved pockets at each end of the groove bind the amino and carboxyl termini of peptide through extensive hydrogen bonding and, hence, dictate the orientation of peptide binding. A deep polymorphic pocket in the middle of the groove provides the chemical and structural complementarity for one of the peptide's anchor residues, thereby playing a major role in allele-specific peptide binding. Although one or two shallow pockets in the groove may also interact with specific peptide side chains, their role in the selection of peptide is minor. Thus, usage of a limited number of both deep and shallow pockets in multiple combinations appears to allow the binding of a broad range of peptides. This binding occurs with high affinity, primarily because of extensive interactions with the peptide backbone and the conserved hydrogen bonding network at both termini of the peptide. Interactions between the anchor residue (or residues) and the corresponding allele-specific pocket provide sufficient extra binding affinity not only to enhance specificity but also to endure the presentation of the peptide at the cell surface for recognition by T cells.
CLICK-IT: interactive television highlighter for sports action replay (2002)

CLICK-IT (CSIRO Laboratory for Imaging by Content and Knowledge-Interactive Television) is a PC-based system which provides the user with an intelligent highlighter pen for sports action replay. It is intended as a truly interactive improvement on the drawing pad technology currently used for video annotation in sports broadcasting. The system uses computer vision techniques to focus attention and track particular objects, e.g. player(s) or ball, and semiautomatically annotate the dynamic scene. This paper describes the system including the user interface, the tracking technology based on colour and motion information, and system performance evaluation in applications to running rugby league football, basketball and soccer.
Renal Angina (2010)

Small elevations in serum creatinine may reflect significant kidney damage and be associated with poor patient outcomes, thus rendering creatinine to be a late marker of acute kidney injury (AKI). AKI researchers refer to the AKI biomarker quest as the "search for the renal troponin I," implying that such putative earlier AKI biomarker use could allow for earlier intervention. We consider the analogy to troponin I and its acceptance to prompt evaluation and therapeutic intervention to treat myocardial ischemia and prevent myocardial infarction an informative and potentially applicable model to the AKI field. Because AKI does not hurt, there is no validated equivalent of chest pain or anginal equivalent to increase suspicion for AKI presence on the part of the clinician. So, although biomarkers may ultimately be validated to detect AKI early, unless nephrologists and intensivists can define "renal angina" to initiate "renal troponin I" assessments, AKI biomarkers may never realize their full potential to improve patient care and outcomes. The purpose of this article is to review both adult and pediatric AKI literature to devise a definition for a renal anginal syndrome equivalent.
Identification of a Novel Family of BRAFV600E Inhibitors (2012)

The BRAF oncoprotein is mutated in about half of malignant melanomas and other cancers, and a kinase activating single valine to glutamate substitution at residue 600 (BRAF(V600E)) accounts for over 90% of BRAF-mediated cancers. Several BRAF(V600E) inhibitors have been developed, although they harbor some liabilities, thus motivating the development of other BRAF(V600E) inhibitor options. We report here the use of an ELISA based high-throughput screen to identify a family of related quinolol/naphthol compounds that preferentially inhibit BRAF(V600E) over BRAF(WT) and other kinases. We also report the X-ray crystal structure of a BRAF/quinolol complex revealing the mode of inhibition, employ structure-based medicinal chemistry efforts to prepare naphthol analogues that inhibit BRAF(V600E) in vitro with IC(50) values in the 80-200 nM range under saturating ATP concentrations, and demonstrate that these compounds inhibit MAPK signaling in melanoma cells. Prospects for improving the potency and selectivity of these inhibitors are discussed.
Midbrain injection of recombinant adeno-associated virus encoding rat glial cell line-derived neurotrophic factor protects nigral neurons in a progressive 6-hydroxydopamine-induced degeneration model of Parkinson’s disease in rats (1997)

A recombinant adeno-associated virus (rAAV) vector capable of infecting cells and expressing rat glial cell line-derived neurotrophic factor (rGDNF), a putative central nervous system dopaminergic survival factor, under the control of a potent cytomegalovirus (CMV) immediate/early promoter (AAV-MD-rGDNF) was constructed. Two experiments were performed to evaluate the time course of expression of rAAV-mediated GDNF protein expression and to test the vector in an animal model of Parkinson's disease. To evaluate the ability of rAAV-rGDNF to protect nigral dopaminergic neurons in the progressive Sauer and Oertel 6-hydroxydopamine (6-OHDA) lesion model, rats received perinigral injections of either rAAV-rGDNF virus or rAAV-lacZ control virus 3 weeks prior to a striatal 6-OHDA lesion and were sacrificed 4 weeks after 6-OHDA. Cell counts of back-labeled fluorogold-positive neurons in the substantia nigra revealed that rAAV-MD-rGDNF protected a significant number of cells when compared with cell counts of rAAV-CMV-lacZ-injected rats (94% vs. 51%, respectively). In close agreement, 85% of tyrosine hydroxylase-positive cells remained in the nigral rAAV-MD-rGDNF group vs. only 49% in the lacZ group. A separate group of rats were given identical perinigral virus injections and were sacrificed at 3 and 10 weeks after surgery. Nigral GDNF protein expression remained relatively stable over the 10 weeks investigated. These data indicate that the use of rAAV, a noncytopathic viral vector, can promote delivery of functional levels of GDNF in a degenerative model of Parkinson's disease.
Prospectively randomized trial of adjuvant active‐specific immunotherapy for human colorectal cancer (1985)

Over the last four years a guinea pig model of active-specific immunotherapy (ASI) with a syngeneic tumor cell:bacillus calmette-Guerin (BCG) vaccine was translated into a prospectively randomized, controlled clinical trial in patients with colorectal cancer. Primary tumors from patients undergoing standard surgical resection were dissociated enzymatically and cryopreserved by techniques that maintain cell viability. Patients with transmural extension of tumor or nodal metastases were randomized into groups treated by resection alone (control) or resection plus ASI. With a mean follow-up of 28 months (range, 14-24), only 3 of 20 treatment patients had recurrences and none have died, whereas 9 of 20 control patients had recurrences and 4 died. These differences are statistically significant and are sufficiently encouraging to warrant expansion of these studies into other research centers.
Efficient bloch‐siegert B1+ mapping using spiral and echo‐planar readouts (2013)

The Bloch-Siegert (B-S) B1 (+) mapping technique is a fast, phase-based method that is highly SAR limited especially at 7T, necessitating the use of long repetition times. Spiral and echo-planar readouts were incorporated in a gradient-echo based B-S sequence to reduce specific absoprtion rate (SAR) and improve its scan efficiency. A novel, numerically optimized 4 ms B-S off-resonant pulse at + 1960 Hz was used to increase sensitivity and further reduce SAR compared with the conventional 6 ms Fermi B-S pulse. Using echo-planar and spiral readouts, scan time reductions of 8-16 were achieved. By reducing the B-S pulse width by a factor of 1.5, SAR was reduced by a factor of 1.5 and overall sensitivity was increased by a factor of 1.33 due to the nearly halved resonance offset of the new B-S pulse. This was validated on phantoms and volunteers at 7 T.