gebhart/patrepeval huggingface dataset:
Stability of acetazolamide, allopurinol, azathioprine, clonazepam, and flucytosine in extemporaneously compounded oral liquids (1996)

The stability of drugs commonly prescribed for use in oral liquid dosage forms but not commercially available as such was studied. Acetazolamide 25 mg/mL, allopurinol 20 mg/mL, azathioprine 50 mg/mL, clonazepam 0.1 mg/mL, and flucytosine 10 mg/mL were prepared in 1:1 mixture of Ora-Sweet and Ora-Plus (Paddock Laboratories), a 1:1 mixture of Ora-Sweet SF and Ora-Plus (Paddock Laboratories), and cherry syrup and placed in polyethylene terephthalate bottles. The sources of the drugs were capsules and tablets. Six bottles were prepared per liquid; three were stored at 5 degrees C and three at 25 degrees C, all in the dark. A sample was removed from each bottle initially and at intervals up to 60 days and analyzed for drug concentration by stability-indicating high-performance liquid chromatography. At least 94% of the initial drug concentration was retained in all the oral liquids for up to 60 days. There were no substantial changes in the appearance or odor of the liquids, or in the pH. Acetazolamide 25 mg/mL, allopurinol 20 mg/mL, azathioprine 50 mg/mL, clonazepam 0.1 mg/mL, and flucytosine 10 mg/mL were stable for up to 60 days at 5 and 25 degrees C in three extemporaneously compounded oral liquids.
Issues in the design of EHTS: a multiuser hypertext system for collaboration (1992)

The paper describes the architecture, issues from the design, and experiences from the use of EHTS (Emacs hyper text system), a multiuser hypertext system for collaboration. EHTS consists of a text editor, a graphical browser, and an active hypertext database named HyperBase. HyperBase is built on the client-server model and has been designed especially to support collaboration among its users, by providing an event mechanism and a fine-grained lock mechanism. Events from HyperBase are used to notify the editor and browser about important actions on the shared data, enabling them to monitor changes. Four categories of issues from the design and experiences from the use of EHTS are reported: architecture, collaboration, user interface, and data model. Based on experiences with the client-server model, the author suggests a new and improved architecture for the event driven multiuser hypertext system. One major lesson learned is that events and fine-grained locks can provide powerful support for data sharing among multiple users simultaneously working in the same environment. The need for a flexible data model is another lesson learned. It is difficult to predict what data model objects actually will be needed, when the data model is designed before the user interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Three Dimensional Absolute Nodal Coordinate Formulation for Beam Elements: Theory (2000)

The description of a beam element by only the displacement of its centerline leads to some difficulties in the representation of the torsion and shear effects. For instance such a representation does not capture the rotation of the beam as a rigid body about its own axis. This problem was circumvented in the literature by using a local coordinate system in the incremental finite element method or by using the multibody floating frame of reference formulation. The use of such a local element coordinate system leads to a highly nonlinear expression for the inertia forces as the result of the large element rotation. In this investigation, an absolute nodal coordinate formulation is presented for the large rotation and deformation analysis of three dimensional beam elements. This formulation leads to a constant mass matrix, and as a result, the vectors of the centrifugal and Coriolis forces are identically equal to zero. The formulation presented in this paper takes into account the effect of rotary inertia, torsion and shear, and ensures continuity of the slopes as well as the rotation of the beam cross section at the nodal points. Using the proposed formulation curved beams can be systematically modeled.
Kinetics of Langmuirian Adsorption onto Planar, Spherical, and Cylindrical Surfaces (1999)

The kinetics of adsorption processes in solution onto adsorbents having different geometric shapes have been explored theoretically. The basic assumptions were (i) the diffusion of adsorbate in quiescent homogeneous solution with no convection, (ii) simple Langmuir-type adsorption kinetics and isotherm, (iii) the bulk concentration of the adsorbate in solution being sufficiently high to stay constant during the adsorption process, and (iv) the geometric shape of the adsorption surface being planar, spherical, or cylindrical. The diffusion equation with the time-dependent boundary conditions implied by the adsorption process was shown to lead to a nonlinear Volterra-type integral equation which is common for the three adsorbent geometries with a single definitive parameter, geometric factor, varying between 0 and 1. A numerical method was developed for solving this equation, and approximate analytical solutions were derived for the very beginning and the very end of the adsorption process. Implications of the results for the analytical methods based on the use of microparticles, such as various immunoassays, are discussed.
Scalable Activation of Rare Triggers in Hardware Trojans by Repeated Maximal Clique Sampling (2020)

Hardware Trojans are serious threat to security and reliability of computing systems. It is hard to detect these malicious implants using traditional validation methods since an adversary is likely to hide them under rare trigger conditions. While existing statistical test generation methods are promising for Trojan detection, they are not suitable for activating extremely rare trigger conditions in stealthy Trojans. To address the fundamental challenge of activating rare triggers, we propose a new test generation paradigm for trigger activation by repeated maximal clique sampling (TARMAC). The basic idea is to utilize a satisfiability modulo theories (SMTs) solver to construct a test corresponding to each maximal clique. This article makes three fundamental contributions: 1) it proves that the trigger activation problem can be mapped to clique cover problem, and the test vectors generated by covering maximal cliques are complete and compact; 2) it proposes efficient test generation algorithms to activate trigger conditions by repeated maximal clique sampling; and 3) it outlines an efficient mechanism to run the clique sampling in parallel to significantly improve the scalability of our test generation framework. The experimental results demonstrate that our proposed approach is scalable and it outperforms state-of-the-art approaches by several orders-of-magnitude in detecting stealthy Trojans.
Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica (1994)

A highly repetitive composite element, Ylt1, was detected in the genome of the dimorphic fungus Yarrowia lipolytica. Ylt1 resembles retrotransposons found in other eukaryotes. It is about 9.4 kb long and can transpose in the genome. The Ylt1 element is bounded by a long terminal repeat (LTR), the zeta element. Several copies of zeta were isolated and sequenced. The sequence of this element is well conserved. It is 714 bp long and is bounded by nucleotides 5'-TG...CA-3', which are part of a short inverted repeat, a feature conserved in the LTRs of retroviruses and retrotransposons. Sequence analysis revealed motifs commonly found in LTR elements, like signals for the start and termination of transcription. The zeta element exists as part of retrotransposon Ylt1, as well as a solo element in the genome. Ylt1 and solo zeta elements are flanked by a 4-bp directly repeated genomic sequence. The copy numbers of Ylt1 and solo zeta are dependent on the strain examined, but at least 35 copies of the composite Ylt1 element and more than 30 copies of the solo zeta element per haploid genome have been observed.
Performance Comparison of Optically Pumped Type-II Mid-Infrared Lasers (Briefing Charts) (2005)

We report a comparative study on the performance of three optically pumped type-II quantum well lasers with differing quantum well confinement. One of the active regions emphasized hole confinement another emphasized electron confinement while the third incorporated both electron and hole confinement. In all cases the wells were inserted in a thick In(x)Ga(1-x)As(y)Sb(1-y) waveguide/absorber region. The lasing wavelengths at 84 K were 2.26 um 3.44 um and 2.37 um respectively. The maximum peak output powers and differential quantum efficiencies Eta, at 84 K were similar for the hole well and W lasers (= 13 W, Eta =O.55) but significantly reduced in the electron well only laser (2.3 W, Eta = 0.14). Waveguide loss measurements via the traditional quantum efficiency vs cavity length method and by a Hakki-Paoli method revealed that all three lasers had low waveguide loss that either increased slowly or not at all with increasing temperature. However the laser's internal efficiency Etai, showed a linear decline with increasing temperature with the Etai, of the electron well only laser significantly less than the other two. The data suggests that for antimonide based type-ll designs, strong hole confinement is essential for improved performance. The data further suggest that it is hole leakage from the QW and/or hole dilution that is largely responsible for the degradation in laser performance.
Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film (2002)

We developed a new technique to immobilize a set of molecular beacons on an agarose film-coated slide and found that it has the ability to identify a single nucleotide difference in label-free DNA targets. The annealing properties, specificity and hybridization dynamics of the present technique were compared with those of the conventional technique that directly immobilizes molecular beacons on a planar glass slide. It is demonstrated that the molecular beacon array on an agarose film has high quench efficiency, an excellent discrimination ratio for single nucleotide mismatches and a short detection time. We hypothesize that such a low fluorescence background and high specificity molecular beacon array will find practical applications in label-free, high-throughput mutation analysis and disease diagnosis.
Structural changes in the C‐terminus of Ca2+‐bound rat S100B(ββ) upon binding to a peptide derived from the C‐terminal regulatory domain of p53 (1999)

S100B(beta beta) is a dimeric Ca2+-binding protein that interacts with p53, inhibits its phosphorylation by protein kinase C (PKC) and promotes disassembly of the p53 tetramer. Likewise, a 22 residue peptide derived from the C-terminal regulatory domain of p53 has been shown to interact with S100B(beta beta) in a Ca2+-dependent manner and inhibits its phosphorylation by PKC. Hence, structural studies of Ca2+-loaded S100B(beta beta) bound to the p53 peptide were initiated to characterize this interaction. Analysis of nuclear Overhauser effect (NOE) correlations, amide proton exchange rates, 3J(NH-H alpha) coupling constants, and chemical shift index data show that, like apo- and Ca2+-bound S100B(beta beta), S100B remains a dimer in the p53 peptide complex, and each subunit has four helices (helix 1, Glu2-Arg20; helix 2, Lys29-Asn38; helix 3, Gln50-Asp61; helix 4, Phe70-Phe87), four loops (loop 1, Glu21-His25; loop 2, Glu39-Glu49; loop 3, Glu62-Gly66; loop 4, Phe88-Glu91), and two beta-strands (beta-strand 1, Lys26-Lys28; beta-strand 2, Glu67-Asp69), which forms a short antiparallel beta-sheet. However, in the presence of the p53 peptide helix 4 is longer by five residues than in apo- or Ca2+-bound S100B(beta beta). Furthermore, the amide proton exchange rates in helix 3 (K55, V56, E58, T59, L60, D61) are significantly slower than those of Ca2+-bound S100B(beta beta). Together, these observations plus intermolecular NOE correlations between the p53 peptide and S100B(beta beta) support the notion that the p53 peptide binds in a region of S100B(beta beta), which includes residues in helix 2, helix 3, loop 2, and the C-terminal loop, and that binding of the p53 peptide interacts with and induces the extension of helix 4.
Eliciting hyperacute xenograft response to treat human cancer: alpha(1,3) galactosyltransferase gene therapy. (1998)

Xenograft hyperacute rejection in humans occurs as a secondary response to a cellular glycosylation incompatibility with most non-human mammalian species. A key component of hyperacute rejection, alpha(1,3)galactosyl (agal) epitopes present on the surface of most non-human mammal cells, is bound by host anti-agal IgG antibodies leading to the activation of complement and, cellular lysis (1). The enzyme causing specific glycosylation patterns, alpha(1,3)galactosyltransferase [alpha(1,3)GT], directs the addition of agal to N-acetyl glucosamine residues in the trans Golgi apparatus in most mammalian species including Mus musculus, but not old world primates, apes or humans. In this report, we cloned both a truncated and full length murine alpha(1,3)GT gene into a retroviral vector backbone in order to transfer alpha(1,3)galactosyl epitopes into human A375 melanoma cells. Expression of agal epitopes on A375 cells after alpha(1,3)GT gene transfer was demonstrated using FITC-labeled ligand and FACS analysis. These cells were exposed to human serum for 30 minutes and > 90% of the agal expressing cells were killed by this treatment. These pretreated cells failed to establish tumors after implantation into athymic nude mice. This is the first report of retroviral vector transfer of the alpha(1,3)GT gene into human tumor cells in an attempt to elicit hyperacute rejection as a novel anti-cancer gene therapy strategy.
Risk of hepatobiliary disease in adults with severe ??1-antitrypsin deficiency (PiZZ): is chronic viral hepatitis B or C an additional risk factor for cirrhosis and hepatocellular carcinoma? (1996)

Although males and females with severe alpha 1-antitrypsin deficiency are not at significantly greater risk of gallstone disease, they are at greater risk of cirrhosis and HCC, the risk of HCC being more manifest in males. The risk of cirrhosis or HCC was unrelated to the presence of hepatitis B or C infection.
Promotion of IgA Immune Response in Patients with Crohn&rsquo;s Disease by Oral Bacteriotherapy with <i>Lactobacillus GG</i> (1996)

The effect of oral bacteriotherapy with human Lactobacillus casei strain GG (10(10) colony-forming units twice daily for 10 days) was investigated in Crohn's disease and in juvenile chronic arthritis which are chronic inflammatory diseases associated with impaired mucosal barrier function. During oral bacteriotherapy, the gut immune response was indirectly assessed by solid-phase enzyme-linked immunoassay in 14 children with Crohn's disease, in 9 with juvenile chronic arthritis, and in 7 controls. The immunostimulatory effect of Lactobacillus GG was specific for Crohn's disease, irrespective of its activity: the mean (95% confidence interval) number of specific antibody secreting cells in the IgA class to beta-lactoglobulin increased significantly from 0.2 (0.04-1.3) to 1.4 (0.3-6.0)/10(6) cells and to casein from 0.3 (0.1-1.4) to 1.0 (0.2-4.8)/10(6) cells. The results indicate that orally administered Lactobacillus GG has the potential to increase the gut IgA immune response and thereby to promote the gut immunological barrier. Consequently, Lactobacillus GG could provide an adjunct nutritional therapy for Crohn's disease.
Detection of ECG waveforms by neural networks (1997)

In this study, ECG waveform detection was performed by using artificial neural networks (ANNs). Initially, the R peak of the QRS complex is detected, and then feature vectors are formed by using the amplitudes of the significant frequency components of the DFT spectrum. Grow and Learn (GAL) and Kohonen networks are comparatively investigated to detect four different ECG waveforms. The comparative performance results of GAL and Kohonen networks are reported.
Granulocyte-macrophage colony-stimulating factor augments the primary antibody response by enhancing the function of antigen-presenting cells. (1987)

Purified, recombinant-derived murine granulocyte-monocyte colony-stimulating factor was found to enhance the primary in vitro immune response to SRBC by murine spleen cells. In determining the mechanism of this augmentation, it was found that only splenic adherent cells and neither resting nor activated T cells nor B cells expressed specific receptors for GM-CSF. When splenic adherent cells were pulsed briefly with GM-CSF before addition to macrophage-depleted cultures, they reconstituted the PFC response to a significantly greater degree than did control macrophages. Splenic adherent cells incubated overnight with SRBC plus GM-CSF were also more efficient antigen-presenting cells than splenic adherent cells incubated with antigen alone. The mechanism of this enhanced antigen presentation was found to be due to a GM-CSF-dependent increase in the level of IL 1 secretion and Ia antigen expression. Consistent with these data was the finding that GM-CSF augmented IL 2 production by splenic T cells in response to suboptimal concentrations of Con A. Finally, the day 5 in vivo antibody response (as measured by serum titers) of mice immunized with a low dose of SRBC was enhanced by two daily inoculations of GM-CSF. Thus, the role that GM-CSF plays in augmenting immune responses may not be solely accounted for by its ability to cause the proliferation or differentiation of macrophages, but more than likely includes its ability to enhance the function of antigen-presenting macrophages.
Effects of Anthocyanins and Other Phenolic Compounds on the Production of Tumor Necrosis Factor α in LPS/IFN-γ-Activated RAW 264.7 Macrophages (2002)

Flavonoids have been reported to demonstrate their benefits in lowering oxidative stress and beneficial effects on cardiovascular and chronic inflammatory diseases. Common phenolic compounds, including phenolic acids, flavonols, isoflavones, and anthocyanins, present in fruits, vegetables, and grains were investigated for their effects on the production of tumor necrosis factor alpha (TNF-alpha) in LPS/IFN-gamma-activated RAW 264.7 macrophages. Gallic acid and (+)-catechin showed small but significant effects, whereas chlorogenic acid had no effect on TNF-alpha production. The flavonol quercetin inhibited TNF-alpha production, but kaempferol and myricetin induced the secretion of TNF-alpha. The isoflavone genistein was an inhibitor of TNF-alpha, whereas daidzein induced TNF-alpha production. Glycosylation of genistein changed its inhibitory effects to TNF-alpha induction, and glycosylation of daidzein had no effect on its activity. Anthocyanidins/anthocyanins and anthocyanin-rich extracts induced TNF-alpha production and acted as modulators of the immune response in activated macrophages. This is the first study to report the effects of anthocyanins and berry extracts on TNF-alpha production.
The Interfacial Stability of Li with Two New Solvent‐Free Ionic Liquids: 1,2‐Dimethyl‐3‐propylimidazolium Imide and Methide (1995)

The room temperature stability of the Li interface in the presence of 1,2‐dimethyl‐3‐propylimidazolium imide and methide was followed by electrochemical impedance spectroscopy for a period of 112 days. We found that while Li foil initially reacted with both ionic liquids, the interfacial film on Li formed in the imide‐based electrolyte stabilized at an interfacial resistance of 1.5 kΩ cm2, while that for the methide‐based electrolyte rose to an interfacial resistance value exceeding 50 kΩ cm2.
An essential role for the interferon-inducible, double-stranded RNA-activated protein kinase PKR in the tumor necrosis factor-induced apoptosis in U937 cells. (1996)

Tumor necrosis factor alpha (TNF-alpha) is well-characterized for its necrotic action against tumor cells; however, it has been increasingly associated with an apoptosis-inducing potential on target cells. While the signaling events and the actual cytolytic mechanism(s) for both TNF-alpha-induced necrosis and apoptosis remain to be fully elucidated, we report here on (i) the ability of TNF-alpha to induce apoptosis in the promonocytic U937 cells, (ii) the discovery of a cross-talk between the TNF-alpha and the interferon signaling pathways, and (iii) the pivotal role of interferon-inducible, double-stranded RNA-activated protein kinase (PKR) in the induction of apoptosis by TNF-alpha. Our data from microscopy studies, trypan blue exclusion staining, and apoptotic DNA ladder electrophoresis revealed that a subclone derived from U937 and carrying a PKR antisense expression vector was resistant to TNF-alpha-induced apoptosis. Further, TNF-alpha initiated a generalized RNA degradation process in which the participation of PKR was required. Finally, the PKR gene is a candidate "death gene" since overexpression of this gene could bring about apoptosis in U937 cells.
Lip Motion Automatic Detection (1997)

An algorithm for speaker&amp;apos;s lip motion detection is presented, based on the processing of a colour video sequence of speaker&amp;apos;s face under natural lighting conditions and without any particular make-up. It is intended for applications in speech recognition, videoconferencing or speaker&amp;apos;s face synthesis and animation. The algorithm is based on a statistical approach using Markov Random Field (MRF) modelling, with a spatiotemporal neighbourhood of the pixels in the image sequence. Two kinds of observations are used : the temporal difference between successive images (motion information) and the purity of red hue in the current and past images (spatial information about lip location). The field of hidden labels, relevant for lip motion detection, is obtained by energy minimisation and proves to be robust to lighting conditions (shadows). This label field is used to extract qualitative information (mouth opening and closing) but also quantitative information by measuring some geomet...
Staphylococcus aureus α-Hemolysin Activates the NLRP3-Inflammasome in Human and Mouse Monocytic Cells (2009)

Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA) causes severe necrotizing infections of the skin, soft tissues, and lungs. Staphylococcal alpha-hemolysin is an essential virulence factor in mouse models of CA-MRSA necrotizing pneumonia. S. aureus alpha-hemolysin has long been known to induce inflammatory signaling and cell death in host organisms, however the mechanism underlying these signaling events were not well understood. Using highly purified recombinant alpha-hemolysin, we now demonstrate that alpha-hemolysin activates the Nucleotide-binding domain and leucine-rich repeat containing gene family, pyrin domain containing 3 protein (NLRP3)-inflammasome, a host inflammatory signaling complex involved in responses to pathogens and endogenous danger signals. Non-cytolytic mutant alpha-hemolysin molecules fail to elicit NLRP3-inflammasome signaling, demonstrating that the responses are not due to non-specific activation of this innate immune signaling system by bacterially derived proteins. In monocyte-derived cells from humans and mice, inflammasome assembly in response to alpha-hemolysin results in activation of the cysteine proteinase, caspase-1. We also show that inflammasome activation by alpha-hemolysin works in conjunction with signaling by other CA-MRSA-derived Pathogen Associated Molecular Patterns (PAMPs) to induce secretion of pro-inflammatory cytokines IL-1beta and IL-18. Additionally, alpha-hemolysin induces cell death in these cells through an NLRP3-dependent program of cellular necrosis, resulting in the release of endogenous pro-inflammatory molecules, like the chromatin-associated protein, High-mobility group box 1 (HMGB1). These studies link the activity of a major S. aureus virulence factor to a specific host signaling pathway. The cellular events linked to inflammasome activity have clear relevance to the disease processes associated with CA-MRSA including tissue necrosis and inflammation.