gebhart/patrepeval huggingface dataset:
Removal of N-Alkyl Modifications from N2-Alkylguanine and N4-Alkylcytosine in DNA by the Adaptive Response Protein AlkB (2013)

The AlkB enzyme is an Fe(II)- and α-ketoglutarate-dependent dioxygenase that repairs DNA alkyl lesions by a direct reversal of damage mechanism as part of the adaptive response in E. coli. The reported substrate scope of AlkB includes simple DNA alkyl adducts, such as 1-methyladenine, 3-methylcytosine, 3-ethylcytosine, 1-methylguanine, 3-methylthymine, and N(6)-methyladenine, as well as more complex DNA adducts, such as 1,N(6)-ethenoadenine, 3,N(4)-ethenocytosine, and 1,N(6)-ethanoadenine. Previous studies have revealed, in a piecemeal way, that AlkB has an impressive repertoire of substrates. The present study makes two additions to this list, showing that alkyl adducts on the N(2) position of guanine and N(4) position of cytosine are also substrates for AlkB. Using high resolution ESI-TOF mass spectrometry, we show that AlkB has the biochemical capability to repair in vitro N(2)-methylguanine, N(2)-ethylguanine, N(2)-furan-2-yl-methylguanine, N(2)-tetrahydrofuran-2-yl-methylguanine, and N(4)-methylcytosine in ssDNA but not in dsDNA. When viewed together with previous work, the experimental data herein demonstrate that AlkB is able to repair all simple N-alkyl adducts occurring at the Watson-Crick base pairing interface of the four DNA bases, confirming AlkB as a versatile gatekeeper of genomic integrity under alkylation stress.
Proapoptotic effects of ANG II in human coronary artery endothelial cells: role of AT1receptor and PKC activation (1999)

Anoxia-reoxygenation, tumor necrosis factor-alpha (TNF-alpha), and angiotensin II (ANG II) have been shown to induce apoptosis in myocytes. However, the role of these mediators in causing apoptosis of human coronary artery endothelial cells (HCAEC) is not known. This study was designed to examine the interaction of these mediators in induction of apoptosis in HCAEC. Cultured HCAEC were exposed to anoxia-reoxygenation, TNF-alpha, and ANG II. TNF-alpha enhanced apoptosis of HCAEC (determined by DNA nick-end labeling in situ and DNA laddering) caused by anoxia-reoxygenation. ANG II increased apoptosis beyond that caused by anoxia-reoxygenation and TNF-alpha. Apoptosis caused by ANG II was reduced by losartan, a specific ANG II type 1 receptor (AT1R) blocker, whereas PD-123,177, a specific ANG II type 2 receptor blocker, under identical conditions had minimal effect. The proapoptotic effects of ANG II were associated with the activation of protein kinase C (PKC). The importance of PKC activation as a signal transduction mechanism became evident in experiments wherein treatment of HCAEC with a specific inhibitor of PKC activation decreased ANG II-mediated apoptosis. Thus AT1R activation appears to be responsible for apoptosis caused by ANG II in HCAEC, and AT1R activation-mediated apoptosis involves activation of PKC.
Compact fiber laser for 589 nm laser guide star generation (2006)

In this paper, we developed an all-fiber laser system for generating a 589 nm source for laser-guided adaptive optics. The design is based on sum-frequency mixing two fiber lasers in a nonlinear material to produce a CW output at the desired wavelength. Combining an Er/Yb:doped fiber laser operating at 1583 nm with a 938 nm Nd:silica fiber laser, one can generate 589 nm via sum-frequency mixing in a periodically poled crystal. The integrated system design and performance is presented
Observation of structure in the $J /\psi$ -pair mass spectrum (2020)

Using proton-proton collision data at centre-of-mass energies of $\sqrt{s} = 7$, $8$ and $13\mathrm{\,TeV}$ recorded by the LHCb experiment at the Large Hadron Collider, corresponding to an integrated luminosity of $9\mathrm{\,fb}^{-1}$, the invariant mass spectrum of $J/\psi$ pairs is studied. A narrow structure around $6.9\mathrm{\,GeV/}c^2$ matching the lineshape of a resonance and a broad structure just above twice the $J/\psi$ mass are observed. The deviation of the data from nonresonant $J/\psi$-pair production is above five standard deviations in the mass region between $6.2$ and $7.4\mathrm{\,GeV/}c^2$, covering predicted masses of states composed of four charm quarks. The mass and natural width of the narrow $X(6900)$ structure are measured assuming a Breit--Wigner lineshape.
On Chip Sub-Wavelength Grating Fabry-Perot Cavity, toward Integrated Cavity Optomechanics Applications (2019)

Sub-Wavelength Grating (SWG) periodic media are comprised of alternative dielectric layers with a pitch Λ small enough in comparison to the wavelength to supress any diffraction or interference effect. As a good first approximation, SWG media can be considered as uniform and lossless ones, with an averaging effect over the dielectric permittivity. The use of SWG media as core and/or cladding materials of optical waveguides was first proposed and demonstrated in 2010 as a way to realize easy engineering of the refractive guided index of light with simple lithographic patterning. Since then, SWG waveguides have found various applications such as waveguide crossing, multimode interferometers, optical filters, mid-infrared waveguides, or even optical biosensing.
Liquid Crystals (2017)

Abstract This article discusses modern directions of research in liquid crystals (LCs). LCs represent one of the best studied classes of soft matter, along with colloids, polymer solutions and melts, gels, and foams. Phenomena observed in LCs and approaches developed for their description become of heuristic value in other branches of science. This article considers the basic properties of low-molecular weight thermotropic LCs, with an additional emphasis on the developments of the last decade, such as LC colloids. It begins with an overview of thermotropic and lyotropic systems, followed by a review of the concept of order parameter, elasticity, surface anchoring, and topological defects. It also evaluates hybrid systems combining LCs with polymers or colloids, along with new ways of creating mesomorphic systems and the dynamics of LCs, including anisotropic viscosity, director dynamics and the Frederiks transition, and flow induced by thermal expansion. Finally, it describes various applications of LCs.
Autonomous Planning and Control for Intelligent Vehicles in Traffic (2019)

This paper addresses the trajectory planning problem for autonomous vehicles in traffic. We build a stochastic Markov decision process (MDP) model to represent the behaviors of the vehicles. This MDP model takes into account the road geometry and is able to reproduce more diverse driving styles. We introduce a new concept, namely, the “dynamic cell,” to dynamically modify the state of the traffic according to different vehicle velocities, driver intents (signals), and the sizes of the surrounding vehicles (i.e., truck, sedan, and so on). We then use Bézier curves to plan smooth paths for lane switching. The maximum curvature of the path is enforced via certain design parameters. By designing suitable reward functions, different desired driving styles of the intelligent vehicle can be achieved by solving a reinforcement learning problem. The desired driving behaviors (i.e., autonomous highway overtaking) are demonstrated with an in-house developed traffic simulator.
LSR-BO: Local Search Region Constrained Bayesian Optimization for Performance Optimization of Vapor Compression Systems (2023)

Bayesian optimization (BO) has recently been demonstrated as a powerful tool for efficient derivative-free optimization of expensive black-box functions, such as those prevalent in performance optimization of complex energy systems. Classical BO algorithms ignore the relationship between consecutive optimizer candidates, resulting in jumps in the admissible search space which can lead to fail-safe mechanisms being triggered, or undesired transient dynamics that violate operational constraints. In this paper, we propose LSR-BO, a novel global optimization methodology that enforces local search region (LSR) constraints by design, which restricts how much the optimizer candidate can be changed at every iteration. We demonstrate that naively incorporating LSR constraints into BO causes the algorithm to get stuck in local suboptimal solutions, and overcome this challenge through the development a novel exploration strategy that can gracefully navigate the trade-off between short-term "local", and long-term "global", performance improvement. Furthermore, we provide theoretical guarantees on the convergence of LSR-BO. Finally, we verify the effectiveness of our proposed LSR-BO method on an illustrative benchmark and a real-world energy minimization problem for a commercial vapor compression system.
Host–Guest Complexation by β-Cyclodextrin Enhances the Solubility of an Esterified Protein (2022)

The carboxyl groups of a protein can be esterified by reaction with a diazo compound, 2-diazo-2-(<i>p</i>-methylphenyl)-<i>N</i>,<i>N</i>-dimethylacetamide. This esterification enables the entry of the protein into the cytosol of a mammalian cell, where the nascent ester groups are hydrolyzed by endogenous esterases. The low aqueous solubility of the ensuing esterified protein is, however, a major practical challenge. Solubility screening revealed that β-cyclodextrin (β-CD) is an optimal solubilizing agent for esterified green fluorescent protein (est-GFP). Its addition can increase the recovery of est-GFP by 10-fold. α-CD, γ-CD, and cucurbit-7-uril are less effective excipients. <sup>1</sup>H NMR titration experiments revealed that β-CD encapsulates the hydrophobic tolyl group of ester conjugates with <i>K</i><sub>a</sub> = 321 M<sup>-1</sup>. Combining l-arginine and sucrose with β-CD enables the nearly quantitative recovery of est-GFP. Thus, the insolubility of esterified proteins can be overcome with excipients.
Secondary electron yield measurements from materials with application to collectors of high-power microwave devices (2006)

An experimental test facility has been established for measuring the secondary electron yield (SEY) of materials thought to be suitable for low yield vacuum electronic applications such as collectors in high-power microwave (HPM) tubes. Experiments can be broadly divided into two energy-regimes: a high-energy (1-50 keV) and a low-energy (10 eV-1 keV) regime. Measurements of SEY at high energies are presented for the following materials: copper, titanium, and Poco graphite. Observation of time-dependent SEY behavior in these samples suggests that surface processes play an important role during measurements. In addition, SEY at low energies and as a function of the angle of incidence of primary electrons has been measured for plasma sprayed boron carbide (PSBC). The experimental results presented here are benchmarked with existing SEY data in the literature, empirically and to first principle formulae
Supplementary Figure S8 from Adiponectin Receptor Signaling on Dendritic Cells Blunts Antitumor Immunity (2023)

&lt;p&gt;Transduction of AdipoR1/R2 into murine DCs promotes antigen specific tolerance in vitro.&lt;/p&gt;
Transplantation of Autologous Peripheral Blood Progenitor Cells Procured after High-Dose Cytarabine-Based Consolidation Chemotherapy for Adults with Secondary Acute Myelogenous Leukemia in first Remission (1999)

Patients with acute myelogenous leukemia secondary to an antecedent hematologic disturbance or cytotoxic chemotherapy are considered to have a very low likelihood of leukemia-free survival regardless of the form of post-remission therapy. The purpose of this study is to evaluate, on the basis of intention to treat, the feasibility and efficacy of high-dose cytarabine/anthracycline consolidation chemotherapy followed by autologous transplantation of chemotherapy/rHuG-CSF-mobilized peripheral blood progenitor cells for seventeen adult patients (median age 63, range 27 to 68) with secondary acute myelogenous leukemia in first remission. Ten eligible patients underwent autologous transplantation of peripheral blood progenitor cells procured following high-dose cytarabine/mitoxantrone consolidation chemotherapy used as a method of in vivo purging. A median of 5 collections (range 2 to 13) were required to procure a median of 9.27 x 10(8) total mononuclear cells/kg (range 2.35 to 21.44 x 10(8) per kg). The median number of CD34-positive progenitor cells was 1.18 x 10(6) kg (range 0.34 to 30.9 x 10(6) kg). After preparative conditioning with 11.25 Gy total body radiation and cyclophosphamide (120 mg/kg) and autologous transplantation, the median time to neutrophil and platelet recovery were 18 days (range 12 to 29 days) and 25 days (range 8 to 158+ days), respectively. After a median follow-up for surviving patients of 33.4 months (range 7.5 to 54 months), 9 of 17 patients (53%) remain alive with 7 in continued first remission. The median remission duration is 13 months (3 to 53 months) and actuarial leukemia-free survival at 3 years is 51+/-25%. Toxicity of autologous peripheral blood progenitor cell transplant included serious liver and pulmonary toxicity in 2 and 1 patient, respectively. Our results demonstrate that a postremission program of high-dose cytarabine-based consolidation chemotherapy followed by autologous transplantation of chemotherapy-mobilized peripheral blood progenitor cells is feasible for patients with secondary acute myelogenous leukemia producing prolonged leukemia-free survival with minimal toxicity.
Synthesis of TiC Particle Reinforced Aluminum Composite by Reactive Infiltration Process (2002)

A new synthetic process of composite material, reactive infiltration technique, in which both combustion synthesis and spontaneous infiltration are combined, was investigated. In this research, fabrication of TiC/Al composites was attempted by the in situ synthesis of TiC particles and the subsequent spontaneous infiltration of molten aluminum. The combustion synthesis of Ti-C-Al system is triggered by a reaction between titanium and aluminum at around 933 K, which is the melting point of aluminum. In the powder blend containing the optimum amount of aluminum, (Ti:C:Al=1:0.95:0.8-1.2), the synthesized Al-Ti intermetallics melted by their heat of reaction, and TiC particles were synthesized successfully. Heating the optimum powder blend with the aluminum ingot, the TiC particle reinforced Al composite was fabricated at low temperature during a short range of time.
ChemInform Abstract: SYNTHESIS AND STRUCTURAL ANALYSIS OF SPIRO(1,3,2Λ5‐BENZOXAZA(DIAZA)PHOSPHOLE‐2,5′‐Λ5‐DIBENZOPHOSPHOLES# ) (1983)

Abstract Die 0‐Aminophenole und o‐Phenylendiamine (I) reagieren mit den Dibromdibenzophospholen (II) zu den Titelverbindungen (III).
Towards cardiovascular risk stratification using imaging data (2009)

In spite of the advancement and proliferation of cardiovascular imaging data, the rate of deaths due to unpredicted heart attack remains high. Thus, it becomes imperative to develop novel computational tools to mine quantitative parameters from imaging data for early detection and diagnosis of asymptomatic cardiovascular disease. In this paper, we present our progress towards developing a computational framework to mine cardiac imaging data and provide quantitative measures for developing a new risk assessment method. Specifically, we present computational methods developed for the detection of coronary calcification and segmentation of thoracic aorta in non-contrast cardiac computed tomography, and detection of neovessels in plaques in intravascular ultrasound imaging data.
Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map (2014)

Determining how the plethora of genomic abnormalities that exist within a given tumor cell affects drug responses remains a major challenge in oncology. Here, we develop a new mapping approach to connect cancer genotypes to drug responses using engineered isogenic cell lines and demonstrate how the resulting dataset can guide clinical interrogation.
IANA Considerations for IPv6 Neighbor Discovery Prefix Information Option Flags (2018)

The Prefix Information Option in the IPv6 Neighbor Discovery Router
Advertisement message defines an 8-bit flag field with two flags
defined and the remaining 6 bits reserved (Reserved1). RFC 6275 has
defined a new flag from this field without creating a IANA registry or
updating RFC 4861. The purpose of this document is to request a new
IANA registry for the PIO flags. This document updates RFC 4861.
Abstract 1918: Patient-derived hormone-naive prostate cancer xenograft models reveal GRB10 as an AR-repressed gene driving the development of castration-resistant prostate cancer (2018)

Abstract Prostate cancer is the most commonly diagnosed noncutaneous cancer and the leading cause of cancer-related death in North American men. Although androgen-deprivation therapy is initially effective in controlling the growth of hormone-naive prostate cancers (HNPC) in patients, currently incurable castration-resistant prostate cancer (CRPC) inevitably develops. Thus, we aim to identify CRPC driver genes that may provide new targets to enhance CRPC therapy. In this study, patient-derived xenografts (PDXs) of HNPCs that develop CRPC following host castration were examined for changes in expression of genes at various time points after castration using transcriptome profiling analysis; particular attention was given to pre-CRPC changes in expression indicative of genes acting as potential CRPC drivers. Eighty genes were found to be significantly upregulated at the CRPC stage while 7 of them also showed elevated expression prior to CRPC development. Among the latter, Growth Factor Receptor Bound Protein 10 (GRB10) was the most significantly and consistently upregulated gene. Moreover, we found GRB10 expression was elevated in clinical CRPC compared to HNPC in several clinical cohorts. Further investigation suggests that GRB10 is transcriptionally regulated by androgen receptor through an androgen-responsive element located in GRB10's intron. Functionally, we found that GRB10 knockdown markedly reduced prostate cancer cell proliferation and activity of AKT, a well-established CRPC mediator. Also, a positive correlation between AKT activity and GRB10 expression was found in clinical cohorts. In conclusion, GRB10 acts as a driver of CRPC and sensitizes AR pathway inhibitors, and hence GRB10-targeting provides a novel therapeutic strategy for the disease. Citation Format: Jun Hao, Xinpei Ci, Hui Xue, Rebecca Wu, Xin Dong, Fang Zhang, Sifeng Qu, Fan Zhang, Anne M. Haegert, Peter W. Gout, Colin Collins, Martin E. Gleave, Dong Lin, Yuzhuo Wang. Patient-derived hormone-naive prostate cancer xenograft models reveal GRB10 as an AR-repressed gene driving the development of castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1918.
Accelerometer-based estimation of the elongation speed in a motorcycle suspension via Kalman-filter techniques (2010)

This paper is about the estimation of the elongation speed in a motorcycle electro-hydraulic suspension using a couple of accelerometers or a single sensor at wheel side. A Kalman filtering approach allows to successfully solve the estimation problem in both the cases, overcoming the vibrational disturbances which heavily affect the accelerometers on a sport motorbike. To be implemented on an off-the-shelf ECU, the Kalman observers need a low computational cost estimator of force. Therefore the secondary aim of the paper is to present a simplified model of the semi-active damper and compare it with a Neural Network based benchmark. Experimental results show that both velocity and force can be correctly estimated, also in the case of a single accelerometer with just a slight loss of performances.
Control of DeDosition and Surface ProDerties of CuInSe2 Thin Films for Solar Cells (1988)

The surface characteristics of CuInSeg films deposited in two layers by vacuum evaporation using elemental sources are controlled by deposition conditions or modified by postdeposition etching. With the first layer substrate temperature less than 350°C the height of growth defects is reduced to less than 3 pm. For composite films where the Cu content exceeds 2 6% , the surf ace morphology has an angular faceted structure which may be associated with the onset of a second, Cu2Se, phase. CuInSe2/ (CdZn) S devices fabricated on these films have poor diode characteristics. Specular CuInSe2 films can be produced by etching in a bromine in water solution. CuInSe2/ (CdZn)S devices where up to 60% of the CuInSe2 film was removed, show that through-film properties are uniform.
Diadem Firewall: Web Server Overload Attack Detection and Response (2005)

High-profile web servers often become the victim of web server overload Distributed Denial-of-Service (DDoS) attacks. Motivations of such attacks range from technical challenge (e.g. script kiddies) to financial profit (e.g. blackmailing the web server’s owner). This paper presents the DIADEM Firewall architecture that allows an ISP to protect its customers from being the target of a DDoS attack. Additionally, it provides protection against usage of customer hosts for attacks. Furthermore, the use-case of the web server overload attack detection and response mechanism will be explained in more details. Finally, we outline the integration an FPGA based highspeed classifier engine integrated into the Linux Netfilter firewall as well as its deployment during a response action against the DDoS attack. 1.
In Vivo Rapid Assessment of Compound Exposure (RACE) for Profiling the Pharmacokinetics of Novel Chemical Probes (2012)

The Rapid Assessment of Compound Exposure (RACE) assay is an easy and efficient method for estimating the pharmacokinetic parameter of exposure (AUC: area under the curve) of novel chemical probe compounds in mice. RACE is a truncated and compressed version of a traditional comprehensive in vivo pharmacokinetics study. The method uses a single standard formulation, dose, route of administration, and a small cohort of mice (n = 4). Standardized protocols and an abbreviated sample collection scheme reduce the labor needed to perform both the in-life and bioanalytical phases of the study. The procedure reduces the complexity of data analysis by eliminating all but one calculated pharmacokinetic parameter; estimated exposure (eAUC20-120), a parameter that is sufficient to rank order compounds based on exposure, but is also easily determined by most software using the simple trapezoidal rule. The RACE assay protocol is readily applicable to early/exploratory studies of most compounds, and is intended to be employed by laboratories with limited expertise in pharmacology and pharmacokinetics. Curr. Protoc. Chem. Biol. 4:299-309 © 2012 by John Wiley & Sons, Inc.