gebhart/patrepeval huggingface dataset:
Cytochrome P450 monooxygenase lipid metabolites are significant second messengers in the resolution of choroidal neovascularization (2017)

Age-related macular degeneration (AMD) is the most common cause of blindness for individuals age 50 and above in the developed world. Abnormal growth of choroidal blood vessels, or choroidal neovascularization (CNV), is a hallmark of the neovascular (wet) form of advanced AMD and leads to significant vision loss. A growing body of evidence supports a strong link between neovascular disease and inflammation. Metabolites of long-chain polyunsaturated fatty acids derived from the cytochrome P450 (CYP) monooxygenase pathway serve as vital second messengers that regulate a number of hormones and growth factors involved in inflammation and vascular function. Using transgenic mice with altered CYP lipid biosynthetic pathways in a mouse model of laser-induced CNV, we characterized the role of these lipid metabolites in regulating neovascular disease. We discovered that the CYP-derived lipid metabolites epoxydocosapentaenoic acids (EDPs) and epoxyeicosatetraenoic acids (EEQs) are vital in dampening CNV severity. Specifically, overexpression of the monooxygenase CYP2C8 or genetic ablation or inhibition of the soluble epoxide hydrolase (sEH) enzyme led to increased levels of EDP and EEQ with attenuated CNV development. In contrast, when we promoted the degradation of these CYP-derived metabolites by transgenic overexpression of sEH, the protective effect against CNV was lost. We found that these molecules work in part through their ability to regulate the expression of key leukocyte adhesion molecules, on both leukocytes and endothelial cells, thereby mediating leukocyte recruitment. These results suggest that CYP lipid signaling molecules and their regulators are potential therapeutic targets in neovascular diseases.
CSpace high-resolution volumetric 3D display (2013)

We are currently in the process of developing a static-volume 3D display, CSpace® display, that has the capability to produce images of much larger size than any other static-volume display currently under development, with up to nearly 800 million voxel resolution. A key component in achieving the size and resolution of the display is the optical system that transfers the pixel data from a standard DMD projection unit to the voxel size required by the display with high contrast and minimal distortion. The current optical system is capable of such performance for only small image sizes, and thus new designs of the optical system must be developed. We report here on the design and testing of a new optical projection system with the intent of achieving performance close to that of a telecentric lens. Theoretical analysis with Zemax allowed selection of appropriate lens size, spacing, and focal length, and identified the need for tilting the assembly to produce the desired beam properties. Experimental analysis using the CSpace® prototype showed that the improved beam parameters allowed for higher resolution and brighter images than those previously achieved, though their remains room for further improvement of the design. Heating of the DMD and its housing components were also addressed to minimize heating effects on the optical system. A combination of a thermo-electric cooler and a small fan produced sufficient cooling to stabilize the temperature of the system to acceptable levels.
Designing a resource broker for heterogeneous grids (2007)

Abstract Grids provide uniform access to aggregations of heterogeneous resources and services such as computers, networks and storage owned by multiple organizations. However, such a dynamic environment poses many challenges for application composition and deployment. In this paper, we present the design of the Gridbus Grid resource broker that allows users to create applications and specify different objectives through different interfaces without having to deal with the complexity of Grid infrastructure. We present the unique requirements that motivated our design and discuss how these provide flexibility in extending the functionality of the broker to support different low‐level middlewares and user interfaces. We evaluate the broker with different job profiles and Grid middleware and conclude with the lessons learnt from our development experience. Copyright © 2007 John Wiley & Sons, Ltd.
Efficient and Non-Interactive Non-Malleable Commitment. (2001)

. We present new constructions of non-malleable commitment schemes, in the public parameter model (where a trusted party makes parameters available to all parties), based on the discrete logarithm or RSA assumptions. The main features of our schemes are: they achieve near-optimal communication for arbitrarily-large messages and are noninteractive. Previous schemes either required (several rounds of) interaction or focused on achieving non-malleable commitment based on general assumptions and were thus efficient only when committing to a single bit. Although our main constructions are for the case of perfectly-hiding commitment, we also present a communication-efficient, non-interactive commitment scheme (based on general assumptions) that is perfectly binding. 1
Homogeneous Charge Compression Ignition Operation With Natural Gas: Fuel Composition Implications (2003)

Homogeneous charge compression ignition (HCCI) is a potentially attractive operating mode for stationary natural gas engines. Increasing demand for efficient, clean burning engines for electrical power generation provides an opportunity to utilize HCCI combustion if several inherent difficulties can be overcome. Fuel composition, particularly the higher hydrocarbon content (ethane, propane, and butane) of the fuel is of primary concern. Fuel composition influences HCCI operation both in terms of design, via compression ratio and initial charge temperature, and in terms of engine control. It has been demonstrated that greater concentrations of higher hydrocarbons tend to lower the ignition temperature of the mixture significantly. The purpose of this paper is to demonstrate, through simulation, the effect of fuel composition on combustion in HCCI engines. Engine performance over a range of fuels from pure methane to more typical natural gas blends is investigated. This includes both the impact of various fuels and the sensitivity of engine operation for any given fuel. Results are presented at a fixed equivalence ratio, compression ratio, and engine speed to isolate the effect of fuel composition. Conclusions are drawn as to how the difficulties arising from gas composition variations may affect the future marketability of these engines.
Elucidating the Function of Complex‐Type Oligosaccharides by Use of Chemical Synthesis of Homogeneous Glycoproteins (2011)

Abstract Protein glycosylation is a major post‐translational modification. To elucidate the effect of this modification on protein function, homogeneous glycoproteins are required. Because glycoproteins isolated from biological sources contain glycoforms, a mixture of a single protein chain with several different oligosaccharides appended, homogeneous glycoproteins obtained through chemical synthesis offer a better solution. In this review, several methods used by our group for the chemical synthesis of homogeneous glycoproteins are addressed. First, preparation of sufficient amounts of oligosaccharides with the desired structures was achieved using a combination of chemical protection and enzymatic digestion. Then glycopeptide‐ α thioesters were prepared by incorporation of oligosaccharides onto the side chains of cysteine residues in peptide‐ α thioesters. Finally, biologically active homogeneous glycoproteins were prepared through native chemical ligation of glycopeptide‐ α thioesters and subsequent oxidative folding.
Detailed study of macrobending effects in a wide transmission bandwidth hollow-core photonic bandgap fiber (2016)

We study in detail the macrobending effects in a wide transmission bandwidth (~200nm) 19 cell hollow-core photonic bandgap fiber operating at 1550nm. Our results indicate low bend sensitivity over a ~130nm wide interval within the transmission window, with negligible loss (<0.1dB) for bending radii down to 5mm. The “red shift” and “blue shift” of the bandgap edge have been observed at the short and long wavelength edges, respectively. The cutoff wavelengths where air-guiding modes stop guiding can be extracted from the bending loss spectra, which matches well with the simulated effective refractive index map of such fiber.
Optical high radix switch design (2012)

Networking consumes up to 33 percent of modern data center power. Network switches are the key source of inefficiency: a switch traversal costs an order of magnitude more than a link traversal. The authors propose a new high-radix switch architecture that uses emerging integrated optical interconnect technology to reduce switch power. They tailor every component of a switch to best exploit optical technology and improve switch scalability and energy efficiency.
Parallel-kinematics mems stages for high precision nanopositioning and manipulation (2008)

INTRODUCTION Micro Electro Mechanical Systems (MEMS) based micro-positioning stages are critically important in many micro/nano manipulation and manufacturing applications. Such stages have been extensively used in micro-force sensors, scanning probe microscopy and micro optical lens scanners [1-4]. While there is no unique definition for a micro-positioning stage, it generally refers to a system which can automatically move an end effector with certain degrees of freedom (DOF) in its work zone and maintain submicron positioning resolution. For a micropositioning stage, it is desirable to have a large work zone, high resolution, and high bandwidth simultaneously.
Infection of Baboons with Simian/Human Immunodeficiency Viruses (1995)

Baboons were evaluated for their utility to serve as a model for testing envelope-based vaccines against human immunodeficiency virus type 1 (HIV-1). The ability of HIV-1 strains IIIB, RF, and SF2 to infect baboons was compared with that of simian/human immunodeficiency virus (SHIV) recombinant viruses comprised of either HXB2 or SF2 env, tat, rev, and vpu genes inserted into the SIVmac239 backbone. Both SHIV recombinants replicated in baboon PBMC in vitro, while no evidence of replication was noted for HIV-1 strains (MN, IIIB, SF2). Infection of baboons in vivo correlated with the restriction of infection in vitro. Virus was recovered by cocultivation methods early after SHIV (HXBc2) infection of two baboons with seroconversion profiles that parallel those observed in simian immunodeficiency virus (SIV)mac-infected rhesus monkeys. One of two baboons inoculated with SHIV(SF2) also seroconverted within 4 weeks; however, the kinetics of infection in a second animal appeared much later, with seroconversion to gp120 not evident until 20 weeks and no virus recovery during 32 weeks following infection. Viral DNA was detected in the lymph nodes of the SHIV-inoculated animals by nested polymerase chain reaction (PCR) amplification. Histopathologic changes were evident in lymph nodes, yet no overt clinical disease was observed. When HIV-1 strains (IIIB, RF, and SF2) were inoculated into baboons, virus was not recovered and no seroconversion to the major HIV-1 antigens was observed. However, viral DNA from the lymph nodes of four animals inoculated with HIV-1 strains could be detected by nested PCR, indicating a persistent but diminutive infection of HIV-1. The baboon thus represents a new animal model for testing HIV-1 envelope-based vaccines including the evaluation of new immunogens, dosages, routes, and adjuvants that act in eliciting protective responses.
Is two-photon absorption a limitation to dark soliton switching? (1994)

It is shown that two-photon absorption does not always place a fundamental limitation on soliton devices: The steering angle, the key characteristic of switching devices based on the propagation of dark spatial solitons, is almost preserved as the intensity of the background wave decays in the presence of weak two-photon absorption.
Cathodic Oxygen Consumption and Electrically Induced Osteogenesis (1975)

Small amounts of electric current stimulate bone formation in the region of a cathode. The purpose of this experiment is to compare changes in oxygen and hydroxyl ion concentration that occur at the cathode at current levels known to be capable of inducing osteogenesis (10-20 muamps) with those changes that occur at current levels known to be toxic to bone (100 muamps). An oxygen consumption chamber containing an oxygen electrode is fitted with two stainless steel electrodes which are connected to a constant current source. At the cathode, with a current of 100 muamps, oxygen is consumed at nearly stoichiometric rates. At higher current (100 muamps) levels, cathodic oxygen consumption gives way to hydrogen evolution. Cathodic hydroxyl ion production is directly proportional to current. It is concluded from these in vitro experiments that at 10-20 muamps the oxygen tension in the vicinity of the cathode is lowered and the pH is moderately increased. At 100 muamps the oxygen tension is not lowered, but the pH is increased dramatically. If these same changes occur in the vicinity of a cathode in vivo, then lowering the local tissue oxygen tension and raising the local pH may be mechanisms operative in electrically induced bone formation.
Improvement of the Linearity of Optical Magnetic Field Sensors. (1995)

Optical magnetic field sensors with high linearity and low harmonic distortion were developed. Bi-substituted rare earth iron garnets were prepared by the LPE method for use as the Faraday rotators of these sensors. The linearity error of the sensor output was obtained within ±1.0% for alternating magnetic fields of up to 300 Oe. The sensor optical system has a new converged beam optical system using ball lenses. The linearity of these sensors is very much better than that of sensors using a collimated beam optical system, on account of the use of graded index (GRIN) lenses. Sensors using GRIN lenses have non-linearity, since only the zeroth-order beam diffracted by garnet maze domains is detected. Sensors using ball lenses have high linearity bacause of the detection of diffracted beams up to the second-order. These experimental results agree well with the calculated results.
TCP congestion avoidance for selective flows in SDN (2018)

We propose a system and a method for network-based flow-control to avoid Transmission Control Protocol (TCP) congestion for “selective flows” in Software Defined Networks (SDN). In the proposed system, the controller, which has a global visibility of the network state uses switch data such as queue fullness and packet sojourn times, to enforce TCP flow control on certain flows, called “ordinary flows,” unbeknown to end hosts. The objective is to prevent important or delay-sensitive so called selective flows to suffer from congestion collapse, which causes them to significantly reduce rate, and hence, the quality of experience for end-users. Our method achieves network-based TCP acknowledgment (ACK) pacing without modifying end-host TCP stack. To this effect, the controller sends new OpenFlow commands to request certain switches to modify some ACK header parameters and/or behavior of ACK packets of ordinary flows that share the same switch queues with the selective flows. Results of the experiments performed on a real testbed are provided to demonstrate the feasibility of the proposed method.
Haplotype analysis of the estrogen receptor 1 gene in male genital and reproductive abnormalities (2007)

Our results support the hypothesis that homozygosity for the specific ESR1 'AGATA' haplotype may increase the susceptibility to the development of male genital abnormalities in response to estrogenic EEDs.
Recent Advances in the Synthesis and Applications of Benzo[<i>b</i>]thiophenes (1999)

Abstract Recent developments in the application and synthesis of benzo[b]thiophenes are reviewed, with an emphasis on various cyclization methodologies leading to the heterocyclic core structure. Key Words: Applicationsbenzothiophenesbenzo[b]thiophenescyclizationsynthesissynthetic methodology
Stability of far fields in double heterostructure and multiple quantum well InAsSb/InPAsSb/InAs midinfrared lasers (1997)

Far fields in perpendicular direction to the junction are investigated in double heterostructure (DH) and multiple quantum well (MQW) midwave-infrared InAsSb/InPAsSb/InAs lasers (λ=3.2–3.6 μm). Strong broadening of the far fields in the DH lasers was observed with increases in temperature and/or current. On the contrary, MQW lasers with otherwise identical structure exhibit very stable far fields as narrow as 23° for all the operating conditions investigated. Our experiment and theoretical modeling suggest that these different behaviors of far fields in DH and MQW lasers are attributed to the refractive index fluctuation in the InAsSb laser active region.
X-ray tube in parallel magnetic fields (2003)

Our hybrid x-ray/MR system (a fixed-anode x-ray fluoroscopic system in an interventional MR system) provides the high spatial and temporal resolution of x-ray fluoroscopy with the soft-tissue contrast, 3D visualization and physiological information of MRI. X-rays are produced in an x-ray tube by bombarding a target with high-energy electrons, ionized from the cathode, then accelerated by the electric field between the cathode and anode. In the hybrid system, the x-ray tube is placed in a high magnetic field, aligned to be parallel to the cathode-anode axis of the tube. A finite-element program was used to simulate the electron trajectories in a geometry similar to our fixed anode tube. External magnetic fields parallel to the cathode-anode axis, ranging from 0 to 0.5T, were simulated. Experimentally, focal spot images were acquired using a 30μm pinhole at a magnification of 8.9 in magnetic fields ranging from 0 to 0.5T. No lateral deflection of the focal spot was observed in either the simulation or the experiment, if the magnetic field and the cathode-anode axis were aligned, regardless of the field strength. However, the field strength affected the size and the current density distribution of the focal spot. We conclude that fixed anode x-ray tubes can be used in a magnetic field although its desired electron optics must be fairly “straight” and the cathode-anode axis must be well aligned with the field. Further issues arising from the focal spot size change, such as overheating of the target, and to a lesser extent the system spatial resolution, should be carefully considered.
Probability mass function distance approach for fast speaker diarization (2017)

In this paper, a new method for speaker diarization is presented. Using spectral features, vector quantization is applied over all audio data. Frames are labelled with the id of the closest codeword. Based on the histogram of frame ids, a probability mass function is estimated for each speech segment. Sequential clustering is implemented based on the distances between probability mass functions. Prosodic parameters are incorporated in order to determine whether there is speaker change within each segment. When applied to real life call center conversations, proposed system achieves 17% relative improvement in terms of diarization error rate compared to a standard open source toolkit. Besides, in terms of processing times, 7 times faster processing is achieved with respect to reference toolkit.
Abstract 4076: A novel prodrug of indoximod with enhanced pharmacokinetic properties (2017)

Abstract IDO1 catalyzes degradation of tryptophan (Trp) into kynurenines, which plays an important role in the regulation of immune responses by triggering anergy on reactive effector T cells and by modulating differentiation and activation of regulatory T cells (Treg). Indoximod has been demonstrated to relieve IDO-mediated immunosuppression in vitro and in vivo, by creation of an artificial Trp-sufficiency signal that bypasses activation of GCN2 and inhibition of mTOR in conditions of Trp deprivation. Inhibition of the IDO pathway by indoximod in combination with immune-stimulatory treatments leads to increased T cell proliferation, Treg reprogramming and antitumor effect. Indoximod has demonstrated an excellent safety profile in human clinical trials and is being dosed orally at 1200 mg bid. Increases in doses above this level do not generally result in increased plasma concentration or drug exposure due to limiting dose-dependent oral bioavailability. Animal models suggest that increased therapeutic benefit could be achieved at higher levels of exposure. For this reason, we synthesized and tested the pharmacokinetic profile of several indoximod prodrugs in mice, rat and monkeys in both liquid and capsule formulations. We selected clinical development drug candidate NLG802, which increases indoximod exposure and plasma concentration ~ 2-fold in rats and ~ 5-fold in monkeys dosed with capsules of comparable formulation to that being used in clinical trials. NLG802 is rapidly absorbed and metabolized in vivo to indoximod. NLG802 DMPK profile and GLP toxicology studies have been carried out in rats and monkeys suggesting a safe toxicological profile at predicted therapeutic doses. In a preclinical tumor model of mice bearing established B16F10 tumors, administration of NLG802 markedly enhanced the anti-tumor responses of naïve, resting pmel-1 cells to vaccination with cognate hgp100 peptide plus CpG-1826 in IFA. In this tumor model, NLG802 plus pmel-1/vaccine produced significant tumor size reduction within 4 days of vaccination. Moreover, the tumor response was achieved at lower doses than equivalent molar doses of indoximod. In conclusion, NLG802 is a prodrug of indoximod predicted to increase clinical drug exposure to indoximod above the current achievable levels and will soon enter Phase 1 safety testing in oncology clinical trials. Citation Format: Mario R. Mautino, Sanjeev Kumar, Hong Zhuang, Jesse Waldo, Firoz Jaipuri, Hima Potturi, Erik Brincks, James Adams, Agnieszka Marcinowicz, Clarissa Van Allen, Nicholas Vahanian, Charles J. Link. A novel prodrug of indoximod with enhanced pharmacokinetic properties [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4076. doi:10.1158/1538-7445.AM2017-4076
Enhanced Catalysis of Ribonuclease B Folding by the Interaction of Calnexin or Calreticulin with ERp57 (1998)

The endoplasmic reticulum is the site of folding, disulfide bond formation, and N-glycosylation of secretory proteins. Correctly folded proteins are exported from the endoplasmic reticulum, whereas incorrectly folded proteins are retained by a quality control system. The type I membrane-protein calnexin and its soluble homologue calreticulin are constituents of this system that recognize monoglucosylated N-linked glycans that are present on unfolded glycoproteins. Although several components of the quality control apparatus are well characterized, it is not known whether and how they interact with enzymes that catalyze protein folding. The endoplasmic reticulum protein ERp57 is homologous to protein-disulfide isomerase and can be cross-linked to the same monoglucosylated glycoproteins that bind to calnexin and calreticulin. The present study demonstrates that the disulfide isomerase activity of ERp57 on the refolding of monoglucosylated ribonuclease B is much greater when this glycoprotein is associated with calnexin or calreticulin. This result is in contrast to protein-disulfide isomerase, whose activity on monoglucosylated ribonuclease B is decreased in the presence of these lectins. No direct binding of monoglucosylated ribonuclease B or monoglucosylated glycans to ERp57 could be detected, but we show that ERp57 interacts directly with calnexin.