gebhart/patrepeval huggingface dataset:
Interleukin-6 in two-stage revision arthroplasty (2015)

The purpose of this study was to evaluate whether the serum level of interleukin 6 (IL-6) could be used to identify the persistence of infection after the first stage of a two-stage revision for periprosthetic joint infection. Between 2010 and 2011, we prospectively studied 55 patients (23 men, 32 women; mean age 69.5 years; 36 to 86) with a periprosthetic joint infection. Bacteria were identified in two intra-operative tissue samples during re-implantation in 16 patients. These cases were classified as representing persistent infection. To calculate a precise cut-off value which could be used in everyday clinical practice, a 3 x 2 contingency table was constructed and manually defined. We found that a serum IL-6 ≥ 13 pg/mL can be regarded as indicating infection: its positive-predictive value is 90.9%. A serum IL-6 ≤ 8 pg/mL can be regarded as indicating an absence of infection: its negative predictive value is 92.1%. The serum IL-6 level seems to be a reasonable marker for identifying persistent infection after the first stage of a revision joint arthroplasty and before attempting re-implantation.
Inhibition of Histone Deacetylase Protects the Retina from Ischemic Injury (2010)

PURPOSE. The pathogenesis of retinal ischemia results from a series of events involving changes in gene expression and inflammatory cytokines. Protein acetylation is an essential mechanism in regulating transcriptional and inflammatory events. The purpose of this study was to investigate the neuroprotective action of the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) in a retinal ischemic model. METHODS. To investigate whether HDAC inhibition can reduce ischemic injury, rats were treated with TSA (2.5 mg/kg intraperitoneally) twice daily on days 0, 1, 2, and 3. Seven days after ischemic injury, morphometric and electroretinographic (ERG) analyses were used to assess retinal structure and function. Western blot and immunohistochemical analyses were used to evaluate TSA-induced changes in histone-H3 acetylation and MMP secretion. RESULTS. In vehicle-treated animals, ERG a- and b-waves from ischemic eyes were significantly reduced compared with contralateral responses. In addition, histologic examination of these eyes revealed significant degeneration of inner retinal layers. In rats treated with TSA, amplitudes of ERG a- and b-waves from ischemic eyes were significantly increased, and normal inner retina morphology was preserved. Ischemia also increased the levels of retinal TNF-alpha, which was blocked by TSA treatment. In astrocyte cultures, the addition of TNF-alpha (10 ng/mL) stimulated the secretion of MMP-1 and MMP-3, which were blocked by TSA (100 nM). CONCLUSIONS. These studies provide the first evidence that suppressing HDAC activity can protect the retina from ischemic injury. This neuroprotective response is associated with the suppression of retinal TNF-alpha expression and signaling. The use of HDAC inhibitors may provide a novel treatment for ischemic retinal injury.
Abstract 5501: Reduced Coronary Reserve as a Mechanism in Beta-Adrenergic Receptor Mediated Cardiomyopathy and its Rescue by Adenylyl Cyclase Type 5 Knockout (2008)

Reduced coronary reserve (CR) is a cardinal feature of human cardiomyopathy, but it has not been studied extensively in mouse models of cardiomyopathy, potentially because of difficulties inherent to measuring CR in such a small heart. The first goal of this study was to determine if reduced CR is a potential mechanism involved in a transgenic (Tg) mouse model of cardiomyopathy, induced by cardiac overexpression of beta 2 -adrenergic receptors (beta 2 -AR Tg). Older beta 2 -AR Tg mice (16–17 months, n=7) developed cardiomyopathy, as reflected by decreased LV ejection fraction (LVEF, 50±7%), and increased fibrosis (5.2±0.4%) and apoptosis (3.8±0.6%). CR was obtained by measuring LV coronary blood flow at baseline and with adenosine (160 microg/kg/min) induced hyperemia using high resolution ultrasound (Vevo 770). CR was significantly decreased in beta 2 -AR Tg (1.8±0.2) compared with wild type (WT) (3.0±0.3, n=6). The next goal was to determine if the rescue of the beta 2 -AR Tg cardiomyopathy resulted in a rescue of reduced CR. Since adenylyl cyclase type 5 knockout (AC5 KO) mice are protected against catecholamine stress and the development of heart failure (HF), and exhibit enhanced CR (3.7±0.4, n=5), we hypothesized that mating these mice with beta 2 -AR Tg might rescue the cardiomyopathy. Older (16–17 months, n=4) bigenic mice (beta 2 -AR Tg x AC5 KO) demonstrated a rescue of cardiomyopathy, as reflected by normalized LVEF (71±1%) and levels of apoptosis (0.11±0.01%) and fibrosis (1.09±0.33%), similar to WT. In these mice, CR was also normalized (3.4±0.6). Reduced CR in beta 2 -AR Tg cardiomyopathy is similar to that observed in large mammalian models, and in patients with cardiomyopathy. Thus, this mechanism is important to consider in mouse models of cardiomyopathy, in general, and also in particular for the mechanism of the rescue of the beta 2 -AR Tg cardiomyopathy by AC5 KO.
Mechanisms Involved in the Immunotoxicity Induced by Dermal Application of JP-8 Jet Fuel (2000)

Dermal application of JP-8 jet fuel induces immune suppression. Classic delayed-type hypersensitivity as well as the induction of contact hypersensitivity to allergens applied to the shaved skin of JP-8-treated mice is suppressed. In addition, the ability of T cells isolated from JP-8-treated mice to proliferate in vitro is suppressed. Here we focused on further characterizing the immunotoxicity induced by JP-8 exposure and determining the mechanism involved. Suppression of T-cell proliferation was first noted 3 to 4 days after a single JP-8 treatment and lasted for approximately 3 weeks, at which time T-cell proliferation returned to normal. Cellular immune reactions appear to be more susceptible to the immunosuppressive effects of JP-8, as antibody production in JP-8-treated mice was identical to that found in normal controls. The mechanism through which dermal application of JP-8 suppresses cell-mediated immune reactions appears to be via the release of immune biological-response modifiers. Blocking the production of prostaglandin E(2) with a selective cyclooxygenase-2 inhibitor abrogated JP-8-induced immune suppression. Neutralizing the activity of interleukin-10 with a highly specific monoclonal antibody also blocked JP-8-induced immune suppression. Furthermore, injecting JP-8-treated mice with recombinant interleukin-12, a cytokine that drives cell-mediated immune reactions in vivo, overcame the immunotoxic effects of JP-8 and restored immune function. These data indicate that immune suppressive cytokines, presumably produced by JP-8-treated epidermal cells, are responsible for immune suppression in JP-8-treated mice and that blocking and/or neutralizing their production in vivo overcomes the immunotoxic effects of JP-8.
The Stabilizing Effect of Pre-Equilibria: A Trifluoromethyl Complex as CF2 Reservoir in Catalytic Olefin Difluorocarbenation (2020)

A new, efficient, catalytic difluorocarbenation of olefins to give 1,1-difluorocyclopropanes is presented. The catalyst, an organobismuth complex, uses TMSCF&lt;sub&gt;3&lt;/sub&gt; as a stoichiometric difluorocarbene source. We demonstrate both the viability and robustness of this reaction over a wide range of alkenes and alkynes, including electron-poor alkenes, to generate the corresponding 1,1-difluorocyclopropanes and 1,1-difluorocyclopropenes. Ease of catalyst recovery from the reaction mixture is another attractive feature of this method. In depth experimental and theoretical studies showed that the key difluorocarbene-generating step proceeds through a bismuth non-redox synchronous mechanism generating a highly reactive free CF&lt;sub&gt;2&lt;/sub&gt; in an endergonic pre-equilibrium. It is the reversibility when generating the difluorocarbene that accounts for the high selectivity, while minimizing CF&lt;sub&gt;2&lt;/sub&gt;-recombination side-reactions.
High Numerical Aperture Reflection Mode Coherent Diffractive Imaging of Nano-Patterned Surfaces using a Tabletop Extreme Ultraviolet Source (2015)

Using an extreme-ultraviolet tabletop diffraction microscope, we demonstrate unprecedented resolution by imaging structures in an extended reflection mode. Titanium nano-patterns are reconstructed with a 40nm transverse resolution; surface variations are imaged with sub-nanometer axial resolution.
Innovative thrombolytic strategy using a heterodimer diabody against TAFI and PAI-1 in mouse models of thrombosis and stroke (2014)

Circulating thrombin-activatable fibrinolysis inhibitor (TAFI) and plasminogen activator inhibitor-1 (PAI-1) are causal factors for thrombolytic failure. Therefore, we evaluated an antibody-engineered bispecific inhibitor against TAFI and PAI-1 (heterodimer diabody, Db-TCK26D6x33H1F7) in several mouse models of thrombosis and stroke. Prophylactic administration of the diabody (0.8 mg/kg) in a thromboplastin-induced model of thromboembolism led to decreased lung fibrin deposition. In a model of cerebral ischemia and reperfusion, diabody administration (0.8 mg/kg, 1 hour postocclusion) led to a mitigated cerebral injury with a 2.3-fold reduced lesion and improved functional outcomes. In a mouse model of thrombin-induced middle cerebral artery occlusion, the efficacy of the diabody was compared to the standard thrombolytic treatment with recombinant tissue-type plasminogen activator (tPA). Early administration of diabody (0.8 mg/kg) caused a twofold decrease in brain lesion size, whereas that of tPA (10 mg/kg) had a much smaller effect. Delayed administration of diabody or tPA had no effect on lesion size, whereas the combined administration of diabody with tPA caused a 1.7-fold decrease in lesion size. In contrast to tPA, the diabody did not increase accumulative bleeding. In conclusion, administration of a bispecific inhibitor against TAFI and PAI-1 results in a prominent profibrinolytic effect in mice without increased bleeding.
The hippocampus as a predictive map (2016)

ABSTRACT A cognitive map has long been the dominant metaphor for hippocampal function, embracing the idea that place cells encode a geometric representation of space. However, evidence for predictive coding, reward sensitivity, and policy dependence in place cells suggests that the representation is not purely spatial. We approach this puzzle from a reinforcement learning perspective: what kind of spatial representation is most useful for maximizing future reward? We show that the answer takes the form of a predictive representation. This representation captures many aspects of place cell responses that fall outside the traditional view of a cognitive map. Furthermore, we argue that entorhinal grid cells encode a low-dimensional basis set for the predictive representation, useful for suppressing noise in predictions and extracting multiscale structure for hierarchical planning.
Geology; its principles, practice and potential for Geotechnics (2009)

Abstract Three themes are developed in this paper. The first deals with those principles basic to the science of geology and thus to the use of geology in geotechnical engineering; namely, the principles of superposition and uniformitarianism; their use is illustrated with reference to commonly occurring geotechnical situations. Then the application of these principles in practice is explained, together with the difficulties that follow if little thought is given to the demands they make for their proper use. Two common causes for difficulty are considered; namely, using an inappropriate description and working at an inappropriate scale. Finally, the potential geology has to open new areas of research is illustrated with examples, ranging in dimension over almost 14 orders of magnitude, the largest involving regional structure, the London Basin. The examples that follow are of progressively smaller volume: displacements in landslides, the failure of crystalline rock, the response of mineral surfaces to contact with water, the possible effects of strain energy stored in minerals, and the characters of silica gel, a material that could influence and possibly govern the geomechanical and geochemical response of silicate particles. Each of these subjects could lead to an understanding of geological materials that changes the development of geotechnical engineering. Each is capable of becoming a scientific area to which engineers refer for solutions to problems in ground engineering and guidance in the use of soils as a construction material. In developing these themes mention is also made of the roots of engineering geology in Britain, as these throw light onto the similarities and differences between engineering geology and geology for engineers, and between engineering geology used in practice and that needed to develop the subject. The greatest danger at present comes from the lack of education in practical and theoretical geology for many who enter engineering geology; it is that which will do most to limit the extraordinary potential for advances in geotechnical engineering that can be provided by geology.
Silorane-based Dental Composite: Behavior and Abilities (2006)

The purpose of this study was to examine the characteristics of an innovative composite material for dental restorations based on silorane--a monomer with a new chemical composition, and thereby compare the examined characteristics against those of well-known methacrylate-based composites. Degree of conversion at 2-mm and 6-mm depths as well as hardness, modulus of elasticity, and creep resistance through the middle of 6-mm high samples were measured. It was observed that up to 20 minutes after curing, curing time--and not irradiance--played the determinant role for a high degree of cure. No differences were registered between the two categories of material in terms of hardness. However, modulus of elasticity of the silorane-based material was slightly lower and the creep resistance higher than a methacrylate composite (Tetric EvoCeram). In conclusion, siloranes exhibited good mechanical properties comparable to those of clinically successful methacrylate-based composite materials.
The ADNP Syndrome and CP201 (NAP) Potential and Hope (2020)

Activity-dependent neuroprotective protein (<i>ADNP</i>) syndrome, also known as Helsmoortel-Van Der Aa syndrome, is a rare condition, which is diagnosed in children exhibiting signs of autism. Specifically, the disease is suspected when a child is suffering from developmental delay and/or intellectual disability. The syndrome occurs when one of the two copies of the <i>ADNP</i> gene carries a pathogenic sequence variant, mostly a <i>de novo</i> mutation resulting in loss of normal functions. Original data showed that <i>Adnp</i> <sup>+/-</sup> mice suffer from learning and memory deficiencies, muscle weakness, and communication problems. Further studies showed that the ADNP microtubule-interacting fragment NAP (called here CP201) resolves, in part, <i>Adnp</i> deficiencies and protects against <i>ADNP</i> pathogenic sequence variant abnormalities. With a clean toxicology and positive human adult experience, CP201 is planned for future clinical trials in the <i>ADNP</i> syndrome.
Studies onDalbergia sissoo(Roxb.)leaves: Possible mechanism(s) of action in infectious diarrhoea (2006)

<b>Objective</b> : Several medicinal plants have been evaluated for their antidiarrhoeal activity. Most studies evaluated their effect on intestinal motility and antimicrobial activity and, therefore, did not take into account the pathogenesis of infectious diarrhoea. Features of infectious diarrhoea like abdominal pain, cramps, inflammation, and passage of blood/mucus in the stools are the combined effect of one or more virulence factors of the infecting organism. The effect of medicinal plants on the microbial virulent features can serve as marker(s) for testing their efficacy. In this study, we evaluated the effect of a decoction of dried leaves of <i> Dalbergia sissoo</i> on aspects of pathogenicity, that is, colonisation to intestinal epithelial cells and production/action of enterotoxins. This was done to define its possible mechanism(s) of action in infectious diarrhoea.<br><b> Materials and Methods</b> : Antibacterial, antiprotozoal, and antiviral activities of the plant decoction were checked by agar dilution method, tube dilution method, and neutral red uptake assay, respectively. Cholera toxin (CT) and <i> Escherichia coli</i> labile toxin (LT) were assayed by ganglioside monosialic acid receptor ELISA. Suckling mouse assay was used to assess <i> E. coli</i> stable toxin (ST). As a measure of colonisation, the effect against adherence of <i> E. coli</i> and invasion of <i> E. coli</i> and <i> Shigella flexneri</i> to HEp-2 cells were studied.<i> <br></i> Results: The decoction had no antibacterial, antiprotozoal, and antiviral activity. It reduced the production and the binding of CT and bacterial adherence and invasion.<br><b> Conclusion</b> : This study showed that <i> D</i> . <i> sissoo</i> is antidiarrhoeal as it affects bacterial virulence. However, it has no antimicrobial activity.
Additive Manufacturing and Characterization of Ultem Polymers and Composites (2015)

The objective of this project was to conduct additive manufacturing to produce aircraft engine components by Fused Deposition Modeling (FDM), using commercially available polyetherimides - Ultem 9085 and experimental Ultem 1000 mixed with 10 percent chopped carbon fiber. A property comparison between FDM-printed and injection-molded coupons for Ultem 9085, Ultem 1000 resin and the fiber-filled composite Ultem 1000 was carried out. Furthermore, an acoustic liner was printed from Ultem 9085 simulating conventional honeycomb structured liners and tested in a wind tunnel. Composite compressor inlet guide vanes were also printed using fiber-filled Ultem 1000 filaments and tested in a cascade rig. The fiber-filled Ultem 1000 filaments and composite vanes were characterized by scanning electron microscope (SEM) and acid digestion to determine the porosity of FDM-printed articles which ranged from 25-31 percent. Coupons of Ultem 9085 and experimental Ultem 1000 composites were tested at room temperature and 400 degrees Fahrenheit to evaluate their corresponding mechanical properties.
Molecular Design of Squaraine Dyes for Efficient Far-red and Near-IR Sensitization of Solar Cells (2005)

Abstract The introduction of short carboxyl anchoring groups into anilino-squaraines resulted in a much improved photosensitization on nanocrystalline TiO2 electrode over far-red/near-IR region, yielding a maximum monochromatic incident photon-to-current conversion efficiency of 73% at 670 nm.
Geohazard Prediction and Real-time Updates with Uncertainties (2012)

Large-scale capital assets and human life are all at risk in exploration for oil and gas. Pre-drill assessment of geohazards has, therefore, become an essential component of well planning. No well is drilled without such an assessment. Quality seismic data hold the key to accurate pre-drill pressure prediction. The behavior of rock velocities with depth is related to the state of shale dewatering and compaction, and consequently, the pore pressure that can be expected at depth. Clearly, seismic velocity is the key to pore-pressure prediction. However, as velocity estimation from seismic data is not unique, incorporation of velocity uncertainty in drilling risk analysis can yield a better understanding of the range of potential costs. Therefore, quantification of velocity and correspondingly geohazard uncertainties is essential in decision-making during drilling operations, and, thus, managing these uncertainties generates business value. In particular, decisions for casing points should take into account the geohazard risk associated with the uncertainty in our knowledge of the velocity model. This paper introduces workflows for pore-pressure and fracture-pressure prediction that account for seismic and related uncertainties associated with the ambiguity of tomographic velocity model building. Also, we demonstrate how the geohazard uncertainty can be updated in real drilling time.
Evolutionarily Conserved Roles For Blood-Brain Barrier Xenobiotic Transporters In Endogenous Steroid Partitioning And Behavior (2017)

Optimal brain function depends upon efficient control over the brain entry of blood components; this is provided by the blood-brain barrier (BBB). Curiously, some brain-impermeable drugs can still cause behavioral side effects. To investigate this phenomenon, we asked whether the promiscuous drug efflux transporter Mdr1 has dual functions in transporting drugs and endogenous molecules. If this is true, brain-impermeable drugs may cause behavioral side effects by affecting brain levels of endogenous molecules. Using computational, genetic and pharmacologic approaches across diverse organisms we demonstrate that BBB-localized efflux transporters are critical for regulating brain levels of endogenous steroids, and steroid-regulated behaviors (sleep in Drosophila and anxiety in mice). Furthermore, we show that Mdr1-interacting drugs are associated with anxiety-related behaviors in humans. We propose a general mechanism for common behavioral side effects of prescription drugs: pharmacologically challenging BBB efflux transporters disrupts brain levels of endogenous substrates, and implicates the BBB in behavioral regulation.
Low-jitter clock multiplication: a comparison between PLLs and DLLs (2002)

This paper shows that, for a given power budget, a practical phase-locked loop (PLL)-based clock multiplier generates less jitter than a delay-locked loop (DLL) equivalent. This is due to the fact that the delay cells in a PLL ring-oscillator can consume more power per cell than their counterparts in the DLL. We can show that this effect is stronger than the notorious jitter accumulation effect that occurs in the voltage-controlled oscillator (VCO) of a PLL. First, an analysis of the stochastic-output jitter of the architectures, due to the most important noise sources, is presented. Then, another important source of jitter in a DLL-based clock multiplier is treated, namely the stochastic mismatch in the delay cells which compose the DLL voltage-controlled delay line (VCDL). An analysis is presented that relates the stochastic spread of the delay of the cells to the output jitter of the clock multiplier. A circuit design technique, called impedance level scaling, is then presented which allows the designer to optimize the noise and mismatch behavior of a circuit, independently from other specifications such as speed and linearity. Applying this technique on a delay cell design yields a direct tradeoff between noise induced jitter and power usage, and between stochastic mismatch induced jitter and power usage.
Dissociation of multiple protein ion charge states following a single gas-phase purification and concentration procedure (2002)

The formation of a range of precursor ion charge states from a single concentrated and purified charge state, followed by activation of each charge state, is introduced as a means to obtain more protein structural information than is available from dissociation of a single charge state alone. This approach is illustrated using off-resonance collisional activation of the [M + 8H]8+ to [M + 6H]6+ precursor ions of the bacteriophage MS2 viral coat protein following concentration and purification of the [M + 8H]8+ charge state. This range of charge states was selected on the basis of an ion trap collisional activation study of the effects of precursor ion charge state on the dissociation of the [M + 12H]12+ to [M + 5H]5+ ions. Gas-phase ion/ion proton-transfer reactions and the ion parking technique were applied to purify and concentrate selected precursor ion charge states as well as to simplify the product ion spectra. The high-charge-state ions fragment preferentially at the N-terminal side of proline residues while the product ion spectra of the lowest charge states investigated are dominated by C-terminal aspartic acid cleavages. Maximum structural information is obtained by fragmentation of the intermediate-charge states.