gebhart/patrepeval huggingface dataset:
Administration of reduced glutathione in FOLFOX4 adjuvant treatment for colorectal cancer: effect on oxaliplatin pharmacokinetics, Pt-DNA adduct formation, and neurotoxicity (2009)

Oxaliplatin is a promising drug for cancer therapy and the oxaliplatin/5-fluorouracil/leucovorin (FOLFOX) regimen has become the standard adjuvant treatment for colorectal cancer. However, the oxaliplatin-induced neurotoxicity still represents a clinical problem leading to a discontinuation of the therapy. Many strategies have been proposed in order to manage the neurotoxicity, but their effect on antitumoral efficacy is still unclear. In this study, we investigated the effect of reduced glutathione administration on neurotoxicity, oxaliplatin pharmacokinetics, and platinum-DNA (Pt-DNA) adduct formation in patients affected by colorectal cancer treated with FOLFOX4 adjuvant regimen. Twenty-seven patients were randomized to receive GSH 1500 mg/m or saline solution before oxaliplatin infusion. Evaluation of neurotoxicity, pharmacokinetics of plasmatic total and ultrafiltered Pt, and determination of Pt-DNA adduct formation on white blood cells was performed during the 5th, 9th, and 12th cycles. At the end of all cycles of therapy, the patients in the GSH arm showed a statistically significant reduction of neurotoxicity (P=0.0037) compared with the placebo arm. There were no significant differences in the main pharmacokinetic parameters between the two arms except a lower area under the plasma concentration-time curve and a smaller apparent steady-state volume of distribution (Vss) when GSH was coadministered. This difference can be explained by the natural function of GSH in the detoxification of oxaliplatin and by its ability to remove the Pt bound to plasma proteins. The determination of Pt-DNA adduct formation shows no statistically significant differences between the two arms. In conclusion, this study indicates that coadministration of GSH is an effective strategy to reduce the oxaliplatin-induced neurotoxicity without impairing neither the pharmacokinetics of oxaliplatin, nor the Pt-DNA adduct formation.
Repositioning of an existing drug for the neglected tropical disease Onchocerciasis (2010)

Onchocerciasis, or river blindness, is a neglected tropical disease caused by the filarial nematode Onchocerca volvulus that affects more than 37 million people, mainly in third world countries. Currently, the only approved drug available for mass treatment is ivermectin, however, drug resistance is beginning to emerge, thus, new therapeutic targets and agents are desperately needed to treat and cure this devastating disease. Chitin metabolism plays a central role in invertebrate biology due to the critical structural function of chitin for the organism. Taken together with its absence in mammals, targeting chitin is an appealing therapeutic avenue. Importantly, the chitinase OvCHT1 from O. volvulus was recently discovered, however, its exact role in the worm's metabolism remains unknown. A screening effort against OvCHT1 was conducted using the Johns Hopkins Clinical Compound Library that contains over 1,500 existing drugs. Closantel, a veterinary anthelmintic with known proton ionophore activities, was identified as a potent and specific inhibitor of filarial chitinases, an activity not previously reported for this compound. Notably, closantel was found also to completely inhibit molting of O. volvulus infective L3 stage larvae. Closantel appears to target two important biochemical processes essential to filarial parasites. To begin to unravel closantel's effects, a retro-fragment-based study was used to define structural elements critical for closantel's chitinase inhibitor function. As resources towards the development of new agents that target neglected tropical diseases are scant, the finding of an existing drug with impact against O. volvulus provides promise in the hunt for new therapies against river blindness.
Optimum Vehicle Suspensions Minimizing RMS Rattlespace, Sprung-Mass Acceleration and Jerk (1981)

The optimal suspension structure for a simple one-degree-of-freedom vehicle model is derived using Linear-Quadratic regulator theory. In addition to rms rattlespace and acceleration, rms jerk is included in the performance index. The suspension structure contains a skyhook spring as well as the more well known skyhook damper to inertial ground and must be mechanized actively except for the shock isolation problem with no ground motion. When jerk weighting is predominant, the damping ratio ζ of the complex roots shifts from 0.707 to 0.5. Charts are presented which enable preliminary design calculations to be done graphically. Using frequency response and time response techniques, performance is compared to that of optimal suspensions disregarding jerk.
A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife (2015)

We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each individual reservoir, with subsequent derivation of bacterial prevalence in host populations, and generation of intra-reservoir patterns of bacterial interactions. Lastly, the number of bacterial reads obtained with the 16S-MiSeq could be a good proxy for bacterial prevalence.
5-(2′-Oxoheptadecyl)-resorcinol and 5-(2′-Oxononadecyl)-resorcinol, Cytotoxic Metabolites from a Wood-Inhabiting Basidiomycete (2002)

5-(2'-oxoheptadecyl)-resorcinol [structure: see text] and 5-(2'-oxononadecyl)-resorcinol [structure: see text] were isolated from fermentations of an imperfect basidiomycete. The structures of the compounds were determined by spectroscopic techniques. Both compounds exhibit cytotoxic effects against the human colon tumor cell lines COLO-320, DLD-1 and HT-29 and the human promyeloid leukemia cell line HL-60, the human leukemia T cell JURKAT, the human hepatocellular carcinoma cell line HEP-G2 as well as the J774 mouse macrophage cell line. The compounds induce morphological and physiological differentiation of HL-60 cells into granulocytes, which subsequently die by apoptosis. Both compounds show no antibacterial and antifungal activity.
On-site Coulomb repulsion in the small polaron systemLa1−xCaxMnO3 (1998)

Conductivity measurements from 300 to 1200 K of ${\mathrm{La}}_{1\ensuremath{-}x}{\mathrm{Ca}}_{x}{\mathrm{MnO}}_{3}$ thin films, with doping from $x=0$ to $x=1,$ show that the entire doping range fits the adiabatic small polaron model $\ensuremath{\sigma}=(A/T)\mathrm{exp}(\ensuremath{-}{E}_{a}/kT).$ Furthermore the $x$ dependence of $A$ explicitly shows the effects of on-site Coulomb repulsion, i.e., a polaron cannot hop into an occupied site. Instead of increasing monotonically as more carriers are introduced, $A$ starts to decrease at $x=0.2$ and, as expected for Hubbard band splitting, is reduced to almost zero when the lattice is full.
Dynamics of the reaction of C(+) with HCl (1988)

This paper presents the results of crossed ion-molecular beam studies of energy and angular distributions for the reaction of C<SUP>+</SUP> with HCl at relative collision energies of 0.51 and 0.88 eV. The reaction appears to be direct, proceeding on a time scale short compared to the rotational period of the transient intermediate complex. The widths of the product kinetic energy distributions are at least 6 eV, indicating that the reaction enthalpy is approximately 5.1 eV. This result is consistent with a bond dissociation energy and heat of formation for the CCl<SUP>+</SUP> product between 219 and 228 kCal mol<SUP>-1</SUP> and 230 - 239 kCal mol<SUP>-1</SUP>, respectively.
Nonlinearities in hyperbolic plasmonic metamaterials (Presentation Recording) (2015)

We will present experimental studies and numerical modeling of nonlinear optical processes in plasmonic metamaterials based on assemblies of metallic nanorods and other complex geometries. Second- and third-order nonlinear optical response originating from a plasmonic component of the metamaterial will be discussed. Such plasmonic metamaterials can be used for engineering enhanced nonlinear optical properties with the required spectral and temporal response. We will also discuss a novel concept of an on-chip ultrafast all-optical modulator based on a hyperbolic metamaterial integrated in a silicon waveguide.
DyNAVacS: an integrative tool for optimized DNA vaccine design (2006)

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.
Supplementary material: Online Updating of Computer Model Output Using Real-Time Sensor Data (2016)

Supplementary material to Online Updating of Computer Model Output Using Real-Time Sensor Data
Learning with the Weighted Trace-norm under Arbitrary Sampling Distributions (2011)

We provide rigorous guarantees on learning with the weighted trace-norm under arbitrary sampling distributions. We show that the standard weighted trace-norm might fail when the sampling distribution is not a product distribution (i.e. when row and column indexes are not selected independently), present a corrected variant for which we establish strong learning guarantees, and demonstrate that it works better in practice. We provide guarantees when weighting by either the true or empirical sampling distribution, and suggest that even if the true distribution is known (or is uniform), weighting by the empirical distribution may be beneficial.
Image processing device for automotive vision systems (2003)

Only three-chips vision system prototype "FAVIS" has been developed in order to be low cost and highly reliable processing for practical automotive applications. Prototype FAVIS has three main components, a CMOS image sensor chip, an image processing LSI chip and an single chip equipped with an RISC engine. The feature of FAVIS architecture is a tiny memory which does not have enough capacity to store even one field image data. A new image processing LSI has been designed to overcome the memory restriction and to accelerate process speed of the system. In this paper, the architecture and capabilities of prototype FAVIS are described as a platform for automotive vision systems.
Formation of Oxygen Radicals in 12CaO·7Al2O3:  Instability of Extraframework Oxide Ions and Uptake of Oxygen Gas (2004)

The thermodynamics and kinetics of oxygen radical formation in cages of a nanoporous crystal, 12CaO·7Al2O3, were examined during isothermal annealing in a dry oxygen atmosphere. The formation of oxygen radicals, O2- and O-, involves the outward diffusion of extraframework oxide ions, their oxidation by absorbed oxygen molecules to form O- and O2- at the surface, and subsequent inward diffusion of the oxygen radicals. The instability of the extraframework oxide ions provides the driving force for this process. Evaluating the radical formation enthalpy and entropy enabled us to determine the temperature and oxygen partial pressure dependences of equilibrium oxygen radical concentration. The rate-limiting process for the radical formation is not the surface reaction, but the total ionic diffusion process, in which the smaller diffusivity of O2- likely dominates the process.
Pd(ii) conjugated chitosan nanofibre mats for application in Heck cross-coupling reactions (2011)

Pd(II)-chitosan composite nanofibres of 62 ± 9 nm diameter are efficient catalysts for Heck cross-coupling reactions. Using a model reaction of iodo-benzene and n-butyl acrylate, we demonstrate that this material can be used as a recyclable catalytic support with a very low loading of palladium (0.17 mol% Pd).
Wheel-Shaped Cu20-Tungstophosphate [Cu20X(OH)24(H2O)12(P8W48O184)]25− Ion (X = Cl, Br, I) and the Role of the Halide Guest (2009)

We have synthesized the known [Cu(20)Cl(OH)(24)(H(2)O)(12)(P(8)W(48)O(184))](25-) (1) and report here its bromide and iodide analogues, [Cu(20)Br(OH)(24)(H(2)O)(12)(P(8)W(48)O(184))](25-) (2) and [Cu(20)I(OH)(24)(H(2)O)(12)(P(8)W(48)O(184))](25-) (3). These polyanions were characterized in the solid state by IR spectroscopy and single-crystal X-ray diffraction. Magnetic susceptibility and magnetization data over 1.8-300 K show that the Cu(2+) ions in 1-2 are antiferromagnetically coupled, leading to a diamagnetic ground state. The effective exchange coupling constant J(eff) was estimated as approximately -3 K for both 1 and 2. Electron paramagnetic resonance measurements were made on 1 and 2 over 5-295 K at microwave frequencies of 9.5, 34, and 220 GHz. The observed (weak) signals were characteristic of randomly distributed Cu(2+) ions only, with g values and hyperfine constants typical of the unpaired electron in a 3d(x(2)-y(2)) orbital of Cu(2+). No signals attributable to the copper-hydroxo cluster were detected, supporting the conclusions from the magnetization measurements. DFT calculations were performed as well to obtain additional information on the anionic guest inside the cavity created by the copper-hydroxo cage related to electronic structure and energies of encapsulation. The polyanions 2 and 3 were also characterized by cyclic voltammetry (CV) in a pH 5 medium. Their CVs are composed by an initial two-step reduction of the Cu(2+) centers to Cu(0) through Cu(+), followed at more negative potential by the redox processes of the W centers. A comparison with the CV characteristics of the previously studied compound 1 indicates that the potential locations of the Cu or W waves of the three analogues do not depend significantly upon the identity of the central halide X. This observation is in accordance with conclusions of DFT calculations. The modified electrodes based on 2 and the room-temperature ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate triggers an efficient reduction of nitrate. To our knowledge, this is the first example of electrocatalytic nitrate reduction by a polyanion entrapped in room-temperature ionic liquid films.
AudiSDN: Automated Detection of Network Policy Inconsistencies in Software-Defined Networks (2020)

At the foundation of every network security architecture lies the premise that formulated network flow policies are reliably deployed and enforced by the network infrastructure. However, software-defined networks (SDNs) add a particular challenge to satisfying this premise, as for SDNs the flow pol-icy implementation spans multiple applications and abstraction layers across the SDN stack. In this paper, we focus on the question of how to automatically identify cases in which the SDN stack fails to prevent policy inconsistencies from arising among these components. This question is rather essential, as when such inconsistencies arise the implications to the security and reliability of the network are devastating. We present AudiSDN, an automated fuzz-testing framework designed to formulate test cases in which policy inconsistencies can arise in OpenFlow networks, the most prevalent SDN protocol used today. We also present results from applying AudiSDN to two widely used SDN controllers, Floodlight and ONOS. In fact, our test results have led to the filing of 3 separate CVE reports. We believe that the approach presented in this paper is applicable to the breadth of OpenFlow platforms used today, and that its broader usage will help to address a serious but yet understudied pragmatic concern.
Mechanism of Formation of Highly Dispersed Metallic Ruthenium Particles on Ceria Support by Heating and Reduction (2019)

The structural change of Ru/CeO2 and Ru/SiO2 catalysts during pretreatments was investigated by in situ Ru K edge quick-scanning X-ray absorption fine structure (XAFS) combined with temperature-programmed reduction with H2 and X-ray diffraction (XRD). After impregnation and drying, two pretreatment sequences were applied: (i) calcination in air at 573 K and reduction with H2 and (ii) heating in inert gas at 573 K and reduction with H2. In sequence (i) of Ru/CeO2, the extended XAFS (EXAFS) spectra showed the formation of crystalline RuO2 during calcination. On the other hand, in sequence (ii) of Ru/CeO2 and Ru/SiO2, the EXAFS results indicated that the Ru oxide was still noncrystalline after heating. The size of Ru metal particle during reduction was determined by Ru–Ru coordination number in EXAFS (CNRu–Ru) and reduction degree. The size was almost constant for Ru/CeO2 (CNRu–Ru: about 4) or Ru/SiO2 (CNRu–Ru: about 8) in sequence (ii), indicating the absence of aggregation. The size was increased for Ru/CeO2 in sequence (i); however, the XRD results suggested that each RuO2 crystallite was slowly reduced to one Ru particle. After all, aggregation during reduction was not significant for all Ru/CeO2 and Ru/SiO2 catalysts.
Operation of a coplanar-electrode plasma display panel cell (1999)

Plasma display panels (PDPs) are composed of miniature gas discharge devices sustained in noble gas mixtures. In this paper, the dynamics of a coplanar-electrode PDP cell are described using results from a two-dimensional computer simulation. During the first voltage pulse, the discharge takes place between the top and bottom electrodes. Due to charging of the bottom dielectric during the first discharge pulse, a surface discharge takes place between the top coplanar electrodes on successive pulses.
Myelodysplastic Syndrome: A Review of Current Care (2011)

Myelodysplastic syndrome (MDS) is a heterogenous group of hematopoietic stem cell malignancies characterized by cytopenias, dysplastic hematopoiesis, increased proliferation, recurrent cytogenetic anomalies, and increased risk for transformation to acute myeloid leukemia. The expansion in our understanding of MDS biology has facilitated a new era in treatment of this disorder. This awareness has led to improved categorization of disease entities, as well as the development and validation of prognostic models for risk stratification. Moreover, progress has fostered the development of active disease-specific treatment modalities in addition to supportive care. Currently, three major treatment modalities are FDA-approved for the treatment of MDS. Within this chapter we will summarize the current classification system(s), prognostic stratification, and therapeutic modalities for this complex group of diseases including novel therapeutics.
Comparison of estimated glomerular filtration rate (eGFR) using the MDRD and CKD-EPI equations for CKD screening in a large population (2010)

the use of the CKD-EPI equation results in a lower estimated prevalence of CKD, compared to the MDRD equation. This may have important implications for public health and clinical practice, as well as for future modification of guidelines for laboratories.
Turbulent Dynamics and Heat Transfer in Transcritical Channel Flow (2017)

We present direct numerical simulations (DNS) of turbulent channel flow to study turbulent dynamics and heat transfer effects at a transcritical temperature and supercritical pressure regime. The fully compressible Navier–Stokes equations in conservative form are closed with the Peng–Robinson (PR) equation of state and the Chung's model for the thermophysical and transport properties. To quantify the turbulent heat transfer effect, the bottom and top walls of the channel are maintained at different isothermal temperatures, Ttop/bot = Tpb±ΔT/2, where Tpb is the pseudoboiling temperature of working fluid and ΔT = 20 K. The bulk pressure and velocity are 1.1pc and 36 m/s, respectively, where pc is the critical pressure. The statistical mean profiles shows significant thermophysical variation in the regime having large thermodynamic gradient near the walls compared to the ideal gas case and the average pseudoboiling location is observed at y/h = 0.92. The root mean square (RMS) profiles of fluctuating velocity are attenuated in the pseudogas region, whereas the thermodynamic fluctuations are greater in that region than the pseudoliquid region. One-dimensional energy spectra fall off steeply at high wavenumber showing the adequacy of the DNS resolution. Instantaneous visualizations of near-wall turbulent structures reveal that the dense fluid ejection from the bottom wall reaches to the channel center region resulting in the large fluctuation in the thermodynamic properties across the channel.
Latency hiding for caches (2023)

A technique for accessing a memory having a high latency portion and a low latency portion is provided. The technique includes detecting a promotion trigger to promote data from the high latency portion to the low latency portion, in response to the promotion trigger, copying cache lines associated with the promotion trigger from the high latency portion to the low latency portion, and in response to a read request, providing data from either or both of the high latency portion or the low latency portion, based on a state associated with data in the high latency portion and the low latency portion.
Crystallization and X-ray diffraction analysis of a novel surface-adhesin protein: protein E fromHaemophilus influenzae (2012)

Protein E (PE) is a ubiquitous multifunctional surface protein of Haemophilus spp. and other bacterial pathogens of the Pasteurellaceae family. H. influenzae utilizes PE for attachment to respiratory epithelial cells. In addition, PE interacts directly with plasminogen and the extracellular matrix (ECM) components vitronectin and laminin. Vitronectin is a complement regulator that inhibits the formation of the membrane-attack complex (MAC). PE-mediated vitronectin recruitment at the H. influenzae surface thus inhibits MAC and protects against serum bactericidal activity. Laminin is an abundant ECM protein and is present in the basement membrane that helps in adherence of H. influenzae during colonization. Here, the expression, purification and crystallization of and the collection of high-resolution data for this important H. influenzae adhesin are reported. To solve the phase problem for PE, Met residues were introduced and an SeMet variant was expressed and crystallized. Both native and SeMet-containing PE gave plate-like crystals in space group P2(1), with unit-cell parameters a = 44, b = 57, c = 61 Å, β = 96°. Diffraction data collected from native and SeMet-derivative crystals extended to resolutions of 1.8 and 2.6 Å, respectively.