gebhart/patrepeval huggingface dataset:
Morphine and HIV‐Tat increase microglial‐free radical production and oxidative stress: possible role in cytokine regulation (2008)

Opiate abuse alters the progression of human immunodeficiency virus and may increase the risk of neuroAIDS. As neuroAIDS is associated with altered microglial reactivity, the combined effects of human immunodeficiency virus-Tat and morphine were determined in cultured microglia. Specifically, experiments determined the effects of Tat and morphine on microglial-free radical production and oxidative stress, and on cytokine release. Data show that combined Tat and morphine cause early and synergistic increases in reactive oxygen species, with concomitant increases in protein oxidation. Furthermore, combined Tat and morphine, but not Tat or morphine alone, cause reversible decreases in proteasome activity. The effects of morphine on free radical production and oxidative stress are prevented by pre-treatment with naloxone, illustrating the important role of opioid receptor activation in these phenomena. While Tat is well known to induce cytokine release from cultured microglia, morphine decreases Tat-induced release of the cytokines tumor necrosis factor-alpha and interleukin-6, as well as the chemokine monocyte chemoattractant protein-1 (MCP-1). Finally, experiments using the reversible proteasome inhibitor MG115 show that temporary, non-cytotoxic decreases in proteasome activity increase protein oxidation and decrease tumor necrosis factor-alpha, interleukin-6, and MCP-1 release from microglia. Taken together, these data suggest that oxidative stress and proteasome inhibition may be involved in the immunomodulatory properties of opioid receptor activation in microglia.
Energy-Efficient Building Ventilation Control Using the Finite Element Modeling of SRC (2012)

Significant amounts of energy can be saved every year by appropriate building opening ventilation control. Towards this direction, SRC (System of Resistances and Capacitances), a finite element based hydro-thermal building simulation program can be used in order to define the operation schedules of building openings, which achieve energy savings, while preserving thermal comfort in building interiors. SRCmodels buildings as a collection of thermal circuit elements, which when assembled together form a global system. This systemic point of view, allows real time simulations to be performed, temperatures at the building zones to be calculated and thermal effects of the openings' ventilation to be estimated at every simulation time step. These zone temperature calculations and thermal effect estimations are repeated in an iterative algorithm in order to derive the opening operation schedules which comply with imposed energy and comfort constrains. Essentially the operation schedules of the openings are obtained by defining and solving a convex optimization problem at every iteration step. At the end of the iteration process, the schedules which satisfy the energy and comfort criteria, are finally selected. The examined method is tested ona simple one-zone model building. Extensions to multiple zonebuildings of higher complexity are straightforward.
Extraction efficiency of highly confined surface plasmon-polaritons to far-field radiation: an upper limit (2008)

We propose a unique method determining an upper limit of extraction efficiency of the surface plasmon-polaritons (SPPs), E(SP), which are highly confined on a corrugated metal surface. The method is based on measurement of the spectral bandwidth of a grating-induced absorption spectrum as a function of metal dielectric constant. After finding the fact that E(SP) exhibits an extremely linear relationship with the collision frequency Gamma of metal over a SPP band below the surface plasmon frequency, an upper limit of E(SP) can be determined by an asymptotic estimation as Gamma-->0 for total decay rates of the confined SPPs. Our method based on the bandwidth measurement is inherently free from the ambiguity and underestimation difficulties pertaining to the previous prism-coupling approaches for E(SP) estimation. It will also be quite applicable for evaluating SPP-mediated light-emitting diodes (LEDs) of which total external efficiency is dominantly restricted by the upper limit of E(SP). Especially for the case when SPP excitation probability approaches unity, the proposed method would excellently figure out the maximum realizable external efficiency of SPP-mediated LEDs.
Muscle Flap Closures in Spine Surgery (2021)

Study Design: Retrospective cohort study using the National Surgical Quality Improvement Program. Objective: The objective of this study was to identify preoperative factors that impact the decision to perform prophylactic muscle flap closure and assess risk factors for wound healing complications in patients undergoing spinal procedures with and without muscle flap closure. Summary of Background Data: Prior studies suggest that muscle flap closure following complex spine surgery results in a lower risk of wound healing complications. However, these studies have been limited to single institutions and/or surgeons. Methods: The National Surgical Quality Improvement Program database was queried for all patients undergoing spine surgery between 2005 and 2017 with and without concomitant muscle flaps. Preoperative and perioperative variables were extracted. Univariate and multivariate analyses were performed to assess risk factors influencing surgical site infection (SSI) and wound disruption, as well as to delineate which preoperative factors increased the likelihood of patients receiving flap closures a priori . Results: Concomitant muscle flaps were performed on 758 patients; 301,670 patients did not receive a flap. Overall 29 (3.83%) patients in the flap group experienced SSI compared to 5154 (1.71%) in the nonflap group ( P &lt;0.0001). Preoperative steroid use [odds ratio (OR) 0.5; P &lt;0.0001], wound infection (OR 0.24; P &lt;0.0001), elevated white blood cell count (OR 1.034; P &lt;0.0001), low hematocrit (OR 0.94; P &lt;0.0001), preoperative transfusion (OR 0.22; P =0.0068) were significantly associated with utilization of muscle flaps. Perioperative factors including a contaminated wound (OR 4.72; P &lt;0.0001), the American Society of Anesthesiologists classification of severe disease (OR 1.92; P =0.024), and longer operative time (OR 1.001; P =0.0024) were significantly associated with postoperative wound disruption. In addition, after propensity score matching for these factors that increase risk of wound complications, there was no difference in the rates of SSI between the flap and nonflap group. Conclusion: Our results suggest that patients with a higher burden of illness preoperatively are more likely to receive prophylactic paraspinal flaps which can reduce the rates of wound-related complications.
599Rapid rises in antibody titers observed following single dose administration of a novel 4-antigen Staphylococcus aureus vaccine (SA4Ag) to healthy adults (2014)

Background. Staphylococcus aureus is a leading cause of serious healthcareassociated infections, resulting in substantial healthcare system burden. To date, there is no licensed vaccine to prevent invasive S. aureus disease. In this first-in-human study, we evaluated the safety, tolerability and immunogenicity of a single-dose of a 4-antigen S. aureus vaccine (SA4Ag) containing capsular polysaccharide serotypes 5 and 8 (CP5 and CP8) individually conjugated to CRM 197 , a recombinant surface protein clumping factor A (rmClfA), and a recombinant manganese transporter protein C (rP305A).
Autosensitization as a Pathomechanism in Asthma (2007)

Recent observations indicate that autoimmune disorders and allergies are more closely connected to each other than traditionally considered. Both diseases are characterized by a break of immunological tolerance and in both Th1- and Th2-driven mechanisms may be involved. Moreover, patients suffering from severe chronic atopic diseases have been shown to develop autoreactive antibodies and vice versa autoreactive IgE antibodies may contribute to the perpetuation of allergic immune responses. However, animal models for the investigation of the underlying mechanisms have not been available so far. Here we demonstrate that allergic sensitization and subsequent airway aerosol challenge of mice to a potential autoantigen leads to an allergic airway inflammation and chronic exposure of sensitized mice to a foreign allergen induces autoreactive antibodies. Thus, autoreactive immune mechanisms may be induced either by molecular mimicry or as a consequence of chronic allergic inflammatory processes and these reactivities may then possibly contribute to the perpetuation of allergic immune responses even in the absence of exogenous allergens and to the development of autoimmune diseases.
Robust Variable Step-Sise Affine Projection Algorithm Suitable For Acoustic Echo Cancellation (2008)

Publication in the conference proceedings of EUSIPCO, Lausanne, Switzerland, 2008
Renaissance in tumor immunotherapy: possible combination with phototherapy (Conference Presentation) (2016)

Photodynamic therapy (PDT) uses the combination of non-toxic dyes and harmless visible light to produce highly toxic reactive oxygen species that destroy tumors. The ideal cancer treatment should target both the primary tumor and the metastases with minimal toxicity. This is best accomplished by educating the body's immune system to recognize the tumor as foreign so that after the primary tumor is destroyed, distant metastases will also be eradicated. PDT may accomplish this feat and stimulate long-term, specific anti-tumor immunity. PDT causes an acute inflammatory response, the rapid induction of large amounts of necrotic and apoptotic tumor cells, induction of damage-associated molecular patterns (DAMPS) including heat-shock proteins, stimulates tumor antigen presentation to naïve T-cells, and generation of cytotoxic T-cells that can destroy distant tumor metastases. By using various syngeneic mouse tumors in immunocompetent mice, we have studied specific PDT regimens related to tumor type as well as mouse genotype and phenotype. We have investigated the role of tumor-associated antigens in PDT-induced immune response by choosing mouse tumors that express: model defined antigen, naturally-occurring cancer testis antigen, and oncogenic virus-derived antigen. We studied the synergistic combination of low-dose cyclophosphamide and PDT that unmasks the PDT-induced immune response by depleting the immunosuppressive T-regulatory cells. PDT combined with immunostimulants (toll-like receptor ligands) can synergistically maximize the generation of anti-tumor immunity by activating dendritic cells and switching immunosuppressive macrophages to a tumor rejection phenotype. Tumors expressing defined tumor-associated antigens with known MHC class I peptides allows anti-tumor immunity to be quantitatively compared.
Telescope polarization and image quality: Lyot coronagraph performance (2016)

In this paper we apply a vector representation of physical optics, sometimes called polarization aberration theory to study image formation in astronomical telescopes and instruments. We describe image formation in-terms of interferometry and use the Fresnel polarization equations to show how light, upon propagation through an optical system become partially polarized. We make the observation that orthogonally polarized light does not interfere to form an intensity image. We show how the two polarization aberrations (diattenuation and and retardance) distort the system PSF, decrease transmittance, and increase unwanted background above that predicted using the nonphysical scalar models. We apply the polarization aberration theory (PolAbT) described earlier (Breckinridge, Lam and Chipman, 2015, PASP 127, 445-468) to the fore-optics of the system designed for AFTA-WFIRST– CGI to obtain a performance estimate. Analysis of the open-literature design using PolAbT leads us to estimate that the WFIRST-CGI contrast will be in the 10<sup>-5</sup> regime at the occulting mask. Much above the levels predicted by others (Krist, Nemati and Mennesson, 2016, JATIS 2, 011003). Remind the reader: 1. Polarizers are operators, not filters in the same sense as colored filters, 2. Adaptive optics does not correct polarization aberrations, 3. Calculations of both diattenuation and retardance are needed to model real-world telescope/coronagraph systems.
NMR imaging of changes in vascular morphology due to tumor angiogenesis (1998)

Tumor-sprouted vessels are greater in both number and diameter in comparison to their healthy counterparts. A novel technique based on magnetic susceptibility contrast mechanisms that are sensitive to varying sizes of blood vessels is presented to measure differences between the relaxation rates (1/T2 and 1/T2*) in a rat glioma model and normal cerebral cortex. deltaR2 and deltaR2*, the differences between relaxation rates precontrast and postcontrast agent injection, were measured for an intravascular equilibrium contrast agent (MION) at various echo times. Since deltaR2*/deltaR2 increases as vessel size increases, this ratio can be used as a measure of the average vessel size within an ROI or a voxel. The stability and longevity of the contrast agent within the vasculature were verified (n = 2 trials), and the ratio of deltaR2*/deltaR2 between the tumor and normal cortex was measured to be 1.9+/-0.2 (n = 4, echo time = 20 ms, and susceptibility difference (deltachi) approximately 10(-6)). This ratio compared favorably to a predicted ratio determined using histologically determined vessel sizes and theoretical Monte Carlo modeling results (1.9+/-0.1). Maps of the ratio of deltaR2*/deltaR2 were also made on a pixel-by-pixel basis. These techniques support the hypothesis that susceptibility contrast MRI can provide useful quantitative metrics of in vivo tumor vascular morphology.
Evaluation of allowable time and histopathological changes in warm ischemia of the uterus in cynomolgus monkey as a model for uterus transplantation (2016)

The uterus of the cynomolgus monkey tolerates warm ischemia for up to 4 h.
Portable thin layer chromatography for field detection of explosives and propellants (2012)

A field deployable detection kit for explosives and propellants using thin layer chromatography (TLC) has been developed at Lawrence Livermore National Laboratory (LLNL). The chemistry of the kit has been modified to allow for field detection of propellants (through propellant stabilizers), military explosives, peroxide explosives, nitrates and inorganic oxidizer precursors. For many of these target analytes, the detection limit is in the &#956;g to pg range. A new miniaturized, bench prototype, field portable TLC (Micro TLC) kit has also been developed for the detection and identification of common military explosives. It has been demonstrated in a laboratory environment and is ready for field-testing. The kit is comprised of a low cost set of commercially available components specifically assembled for rapid identification needed in the field and identifies the common military explosives: HMX, RDX, Tetryl, Explosive D or picric acid, and TNT all on one plate. Additional modifications of the Micro TLC system have been made with fluorescent organosilicon co-polymer coatings to detect a large suite of explosives.
Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis (2020)

Artificial intelligence and machine learning have demonstrated their potential role in predictive chemistry and synthetic planning of small molecules; there are at least a few reports of companies employing <i>in silico</i> synthetic planning into their overall approach to accessing target molecules. A data-driven synthesis planning program is one component being developed and evaluated by the Machine Learning for Pharmaceutical Discovery and Synthesis (MLPDS) consortium, comprising MIT and 13 chemical and pharmaceutical company members. Together, we wrote this perspective to share how we think predictive models can be integrated into medicinal chemistry synthesis workflows, how they are currently used within MLPDS member companies, and the outlook for this field.
Complete characterization of channel-resistant DMT with cyclic prefix (2003)

We provide a complete characterization of discrete multitone transmission (DMT) systems that employ a cyclic prefix redundancy and that can be equalized by a bank of one-tap equalizers in each subchannel, for almost all values of channel parameters. We show that among all possible finite-impulse response transmitting and receiving filters of arbitrary order, such channel-resistant transmission requires 1) that the receive filters be matched to the transmit filters and 2) that to within a scaling and delay, the transmit and receive filters have inverse discrete Fourier transform and discrete Fourier transform (DFT) coefficients. Thus, we prove that, should cyclic prefix be applied, only trivial variants of traditional DFT-based DMT systems are channel resistant.
Low on-Resistance SOI Dual-Trench-Gate MOSFET (2011)

A low specific on-resistance <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX"> $(R_{{\rm on}, {\rm sp}})$</tex></formula> integrable silicon-on-insulator (SOI) MOSFET is proposed, and its mechanism is investigated by simulation. The SOI MOSFET features double trenches and dual gates (DTDG SOI): an oxide trench in the drift region, a buried gate inset in the oxide trench, and another trench gate (TG) extended to a buried oxide layer. First, the dual gates form dual conduction channels, and the extended gate widens the vertical conduction area; both of which sharply reduce <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$R_{{\rm on}, {\rm sp}}$</tex> </formula> . Second, the oxide trench folds the drift region in the vertical direction, resulting in a reduced device pitch and <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$R_{{\rm on}, {\rm sp}}$</tex></formula> . Third, the oxide trench causes multidirectional depletion. This not only enhances the reduced surface field effect and thus reshapes the electric field distribution but also increases the drift doping concentration, leading to a reduced <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$R_{{\rm on}, {\rm sp}}$</tex></formula> and an improved breakdown voltage (BV). Compared with a conventional SOI lateral Double-diffused metal oxide semiconductor (LDMOS), the DTDG MOSFET increases BV from 39 to 92 V at the same cell pitch or decreases <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$R_{{\rm on}, { \rm sp}}$</tex></formula> by 77% at the same BV by simulation. Finally, the TG extended synchronously acts as an isolation trench between the high/low-voltage regions in a high-voltage integrated circuit, saving the chip area and simplifying the isolation process.
Development and Demonstration of a Soot Generator Integrated Bench Reactor (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Experimental evaluation of soot trapping and oxidation behaviors of various diesel particulate filters (DPF) has been traditionally hampered by several experimental difficulties, such as the deposition of soot particles with well-characterized and consistent properties, and the tracking of the soot oxidation rate in real time. In the present study, an integrated bench flow-reactor system with a soot generator has been developed and its capabilities were demonstrated with regards to: &lt;ul class="list disc"&gt;&lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;Consistently and controllably loading soot on DPF samples;&lt;/div&gt;&lt;/li&gt;&lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;Monitoring the exhaust gas composition by FTIR, including quantification of the soot oxidation rate using CO and CO&lt;sub&gt;2&lt;/sub&gt;;&lt;/div&gt;&lt;/li&gt;&lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;Measuring soot oxidation characteristics of various DPF samples.&lt;/div&gt;&lt;/li&gt;&lt;/ul&gt;&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Soot particles were produced from a laminar propane co-flow diffusion flame. The production rate of particulate matter (PM) of the soot generator, which is tunable by adjusting the air to fuel ratio of the propane flame, can be set within a range from tens of mg to 400 mg per hour. Properties of collected soot samples, such as the BET surface area and the oxidation activity, were analyzed.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The capabilities of this reactor were demonstrated by conducting tests to evaluate the soot oxidation activity of three types of cordierite DPF samples with variations in the washcoat, including bare, platinum group metals (PGMs) washcoat and non-PGM washcoat. The non-PGM washcoat shows promising performance on enhancing soot oxidation by oxygen.&lt;/div&gt;&lt;/div&gt;
Quantification of the microvascular blood flow of the ovine corpus luteum with contrast ultrasound (2009)

The ovine corpus luteum is an ideal model for the development of methodologies for angiogenesis monitoring with contrast enhanced ultrasound. We employ three indicator dilution models, namely, the lognormal function, the gamma variate function, and the local density random walk model to fit contrast ultrasound time-intensity curves from ovine corpora lutea at the peak of the estrus cycle. We extract hemodynamic-related parameters such as the mean transit time, the wash-in time, the area under the curve and the peak intensity and measure inter- and intra-animal reproducibility. The mean transit time and the wash-in time are reproducible with acceptable relative dispersions whereas the peak intensity and the area under the curve have large variabilities.
Propagation over Clutter: Physical Stochastic Model (2006)

Propagation of radio signals from a base above clutter, such as buildings and trees to a mobile immersed in clutter, is treated theoretically by accounting for random diffuse scattering at the mobile. Closed form expressions are derived for path gain as well as for angular spectrum at the base. The resulting predictions are in close agreement with widely accepted models and empirical results. The angular spectrum at the base is found to be Lorentzian of width close to that reported for urban measurements in Aarhus. Small-scale fading and distance-depedent loss are treated in a unified way, as opposed to the heuristic methodologies, which formulate them as separate factors.
Polysaccharide Pharmacokinetics: Amphotericin B Arabinogalactan Conjugate—A Drug Delivery System or a New Pharmaceutical Entity? (2010)

Conjugation of poorly soluble drugs to polysaccharides affects their solubility, pharmacokinetics (PK), and pharmacodynamics. The need for amphotericin B (AmB) analog with improved solubility and reduced toxicity is immense. Conjugation of AmB to arabinogalactan (AG) produced a highly soluble AmB-AG conjugate, with high and low molecular weight (H-M(w) and L-M(w)) fractions. Its similar antifungal activity to AmB poses the question whether AmB-AG is a prodrug of AmB or a novel pharmaceutical entity. We compared the PK of AmB-AG and AmB in rats. Upon AmB-AG administration, no free AmB was released. The half-lives and the volumes of distribution of AmB, H-M(w) and L-M(w) were 10.9, 8.8, and 1.5 h and 1630, 217, and 133 mL/kg, respectively. We conclude that PK of small molecules conjugated to polysaccharides is mainly dictated by the macromolecular moiety and shows molecular weight dependency. Our findings define AmB-AG as a novel pharmaceutical entity with high clinical potential.