gebhart/patrepeval huggingface dataset:
Robust design of slow-light tapers in periodic waveguides (2009)

This article concerns the design of tapers for coupling power between uniform and slow-light periodic waveguides. New optimization methods are described for designing robust tapers, which not only perform well under nominal conditions, but also over a given set of parameter variations. When the set of parameter variations models the inevitable variations typical in the manufacture or operation of the coupler, a robust design is one that will have a high yield, despite these parameter variations. The ideas of successive refinement, and robust optimization based on multi-scenario optimization with iterative sampling of uncertain parameters, using a fast method for approximately evaluating the reflection coefficient, are introduced. Robust design results are compared to a linear taper, and to optimized tapers that do not take parameter variation into account. Finally, robust performance of the resulting designs is verified using an accurate, but much more expensive, method for evaluating the reflection coefficient.
A Framework for Multicast in NVO3 (2015)

This document discusses a framework of supporting multicast traffic, ,
in a network that uses Network Virtualization using Overlays over
Layer 3 (NVO3). Both infrastructure multicast and application-
specific multicast are discussed. It describes the various mechanisms
and considerations that can be used for delivering such traffic as
well as the data plane and control plane considerations for each of
the mechanisms.
A Backside-Illuminated Image Sensor With 200 000 Pixels Operating at 250 000 Frames per Second (2009)

In this paper, a high-speed image sensor with very high sensitivity is developed. The high sensitivity is achieved by introduction of backside illumination and charge-carrier multiplication (CCM). The high frame rate is guaranteed by installing the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in situ</i> storage image sensor (ISIS) structure on the front side. A test sensor of the BSI-ISIS has been developed and evaluated. It is shown that an image with a very low signal level embedded under the noise floor is recognizable by activating the CCM.
RETRACTED: Robust expansion of HIV CAR T cells following antigen boosting in ART-suppressed nonhuman primates (2020)

Chimeric antigen receptor (CAR) T cells targeting CD19+ hematologic malignancies have rapidly emerged as a promising, novel therapy. In contrast, results from the few CAR T-cell studies for infectious diseases such as HIV-1 have been less convincing. These challenges are likely due to the low level of antigen present in antiretroviral therapy (ART)-suppressed patients in contrast to those with hematologic malignancies. Using our well-established nonhuman primate model of ART-suppressed HIV-1 infection, we tested strategies to overcome these limitations and challenges. We first optimized CAR T-cell production to maintain central memory subsets, consistent with current clinical paradigms. We hypothesized that additional exogenous antigen might be required in an ART-suppressed setting to aid expansion and persistence of CAR T cells. Thus, we studied 4 simian/HIV-infected, ART-suppressed rhesus macaques infused with virus-specific CD4CAR T cells, followed by supplemental infusion of cell-associated HIV-1 envelope (Env). Env boosting led to significant and unprecedented expansion of virus-specific CAR+ T cells in vivo; after ART treatment interruption, viral rebound was significantly delayed compared with controls (P = .014). In 2 animals with declining CAR T cells, rhesusized anti-programmed cell death protein 1 (PD-1) antibody was administered to reverse PD-1-dependent immune exhaustion. Immune checkpoint blockade triggered expansion of exhausted CAR T cells and concordantly lowered viral loads to undetectable levels. These results show that supplemental cell-associated antigen enables robust expansion of CAR T cells in an antigen-sparse environment. To our knowledge, this is the first study to show expansion of virus-specific CAR T cells in infected, suppressed hosts, and delay/control of viral recrudescence.
High-performance single-mode fiber-optic switch (1994)

A piezoelectrically actuated four-port Mach-Zehnder switch with 30-micros switching time and 0.25-dB insertion loss is demonstrated at a wavelength of 1.3 microm. The worst-case cross talk is below -21 dB for an arbitrary input polarization. The process of fabricating the switch from commercial fiber couplers with length matching of the interferometer arms is described.
Structural deformation of single-walled carbon nanotubes and fullerene encapsulation due to magnetized-plasma ion irradiation (2001)

Positive and negative bias-voltages are applied to single-walled carbon nanotubes (SWNTs) in magnetized alkali–metal and alkali–fullerene plasmas. When accelerated ions are irradiated to the SWNTs through plasma sheaths, drastic structural deformations such as deflection and tube cutting of the SWNTs are observed to take place. Furthermore, this phenomenon is found to be accompanied by the fullerene encapsulation inside the SWNTs in the case of the positive-bias application in the alkali–fullerene plasma, giving the possibility that various kinds of atoms and molecules can effectively be intercalated by our plasma method.
Protective effect of bilberry (Vaccinium myrtillus) against doxorubicin-induced oxidative cardiotoxicity in rats (2011)

Background:Doxorubicin (DOX) is a commonly used chemotherapeutic agent. It is associated with serious dose-limiting cardiotoxicity, which is at least partly caused by generation of reactive oxygen species (ROS). Supplementations with bilberries were effective in reducing oxidative stress in many tissue injuries due their high content of antioxidants. The present study investigated the potential protective effect of bilberry extract against DOX-induced cardiotoxicity in rats.Material/Methods:Rats were treated orally with a methanolic extract of bilberry for 10 days. DOX was injected intraperitoneally on day 7. Twenty-four hours after the last bilberry administration, rats were subjected to ECG study. Blood was then withdrawn and cardiac tissues were dissected for assessment of oxidative stress and cardiac tissue injury. Cardiac tissues were also subjected to histopathological examination.Results:Bilberry extract significantly inhibited DOX-provoked reduced glutathione depletion and accumulation of oxidized glutathione, malondialdehyde and protein carbonyls in cardiac tissues. This was accompanied by significant amelioration of reduced cardiac catalase, superoxide dismutase, and glutathione peroxidase activities; and increased cardiac myeloperoxidase activity in response to DOX challenge. Pretreatment with bilberry significantly guarded against DOX-induced increase in serum activities of lactate dehydrogenase, creatine phosphokinase and creatine kinase-MB, as well as the level of troponin I. Bilberry alleviated ECG changes in rats treated with DOX and attenuated its pathological changes.Conclusions:Bilberry protects against DOX-induced cardiotoxicity in rats. This can be attributed, at least in part, to its antioxidant activity.
Plasma‐based biomaterials for the treatment of cutaneous radiation injury (2018)

Cutaneous wounds caused by an exposure to high doses of ionizing radiation remain a therapeutic challenge. While new experimental strategies for treatment are being developed, there are currently no off-the-shelf therapies for the treatment of cutaneous radiation injury that have been proven to promote repair of the damaged tissues. Plasma-based biomaterials are biologically active biomaterials made from platelet enriched plasma, which can be made into both solid and semi-solid forms, are inexpensive, and are available as off-the-shelf, nonrefrigerated products. In this study, the use of plasma-based biomaterials for the mitigation of acute and late toxicity for cutaneous radiation injury was investigated using a mouse model. A 2-cm diameter circle of the dorsal skin was irradiated with a single dose of 35 Gy followed by topical treatment with plasma-based biomaterial or vehicle once daily for 5 weeks postirradiation. Weekly imaging demonstrated more complete wound resolution in the plasma-based biomaterial vs. vehicle group which became statistically significant (p < 0.05) at weeks 12, 13, and 14 postmaximum wound area. Despite more complete wound healing, at 9 and 17 weeks postirradiation, there was no statistically significant difference in collagen deposition or skin thickness between the plasma-based biomaterial and vehicle groups based on Masson trichrome staining nor was there a statistically significant difference in inflammatory or fibrosis-related gene expression between the groups. Although significant improvement was not observed for late toxicity, plasma-based biomaterials were effective at promoting wound closure, thus helping to mitigate acute toxicity.
ChemInform Abstract: Epoxy Pyranoses, Chiral Synthons for Versatile Regio- and Stereocontrolled Functionalizations (2010)

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Direct observation of G-protein binding to the human δ-opioid receptor using plasmon-waveguide resonance spectroscopy. VOLUME 278 (2003) PAGES 48890-48897 (2005)

PAGE 48891: In the right column, under the heading “Lipid Bilayer Formation, hDOR Incorporation, and G-protein Addition,” “methanol (0.05:0.95: 0.5, v/v)” should read “methanol (0.05:9.5:0.5, v/v).”
Microstructure and Rheology of Nonionic Trisiloxane Surfactant Solutions (1994)

The nonionic trisiloxane surfactant, M(D'E12)M (=((Me)3SiO)2Si(Me)-(CH2)3(OCH2CH2)12OH), forms clear isotropic solutions in water at all concentrations between 10 and 43 °C. Both water-rich and surfactant-rich solutions are low viscosity Newtonian liquids. However, at intermediate concentrations, the solutions are non-Newtonian and viscoelastic. This rheological behavior along with supporting data from small-angle X-ray and neutron scattering, and pulse-gradient NMR measurements points to a progressive change in surfactant microstructure across the concentration range. This change is parallel to the progression of liquid crystal phase behavior at lower temperatures. The results are interpreted in terms of a model in which small spherical micelles formed at low concentrations transform progressively to entangled worm-like micelles, branched interconnected worm-like micelles, and then a random bilayer structure which persists to 100 % surfactant.
Alteration of Stress Distribution Patterns in Symptomatic Valgus Instability of the Elbow in Baseball Players (2016)

The information obtained from the CT images can useful for early detection of overstress conditions of the elbow joint.
Sparse Factor Analysis for Learning and Content Analytics (2013)

We develop a new model and algorithms for machine learning-based learning analytics, which estimate a learner's knowledge of the concepts underlying a domain, and content analytics, which estimate the relationships among a collection of questions and those concepts. Our model represents the probability that a learner provides the correct response to a question in terms of three factors: their understanding of a set of underlying concepts, the concepts involved in each question, and each question's intrinsic difficulty. We estimate these factors given the graded responses to a collection of questions. The underlying estimation problem is ill-posed in general, especially when only a subset of the questions are answered. The key observation that enables a well-posed solution is the fact that typical educational domains of interest involve only a small number of key concepts. Leveraging this observation, we develop both a bi-convex maximum-likelihood and a Bayesian solution to the resulting SPARse Factor Analysis (SPARFA) problem. We also incorporate user-defined tags on questions to facilitate the interpretability of the estimated factors. Experiments with synthetic and real-world data demonstrate the efficacy of our approach. Finally, we make a connection between SPARFA and noisy, binary-valued (1-bit) dictionary learning that is of independent interest.
Supplemental Table 2 from <i>KRAS</i> Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine (2023)

&lt;p&gt;The differential mutual information score (Ic, methods) is used in this table to correlate pathways with activity of decitabine in solid tumor cell lines.&lt;/p&gt;
Abstract 1005: Tamoxifen treatment induces the epigenetic changes in breast cancer stem cells (2019)

Purpose: Breast cancer is diagnosed in younger women population and is the leading cause of cancer-related deaths in India. Tamoxifen (TOM) is one of the most effective and widely used first-line endocrine therapy for ER+ breast cancer. However, breast cancer patients often develop TOM resistance and enhanced with caner stem cell (CSC)-like phenotypes. These TOM-resistance (TR) breast cancer phenotypes are highly aggressive and they do not respond to most of the chemotherapies. It is therefore essential to understand the mechanism that resulted in the development of TR in breast cancer. The current study was designed to investigate the epigenetic changes associated mechanism that induces the development of hormone-resistance in breast CSCs.Experimental Procedure: In this study, we used ALDEFLOUR assay, flow cytometry, mammosphere culture, western blot, Chromatin-immunoprecipitation, and RT-PCR analyses.Results: Our study showed that breast CSC-like population possesses higher TR cancer cell phenotypes than non-CSCs. We generated MCF7-derived mammospheres (CSCs) utilizing MammoCult media. However, when treated with TOM (1µM)-we observed an increased number of mammospheres (CSCs) than vehicle control. We found a strong interplay between TR and epigenetic changes, in particular, the changes observed in histone demethylase, which is believed to be one of the crucial links that involved in the development of therapy resistance and enhanced CSC population. Furthermore, TR breast CSCs derived from MCF7 cells display an increased expression of the NOTCH-1 protein. Induced overexpression of NOTCH in MCF7 cells increased the number of mammosphere formation ability than control cells. Finally, overexpression of NOTCH-1 also led to transcriptional up-regulation of cyclin genes A, B, and D.Conclusion: We observed a crucial interplay between TR and breast CSCs. TR associated epigenetic alteration enhanced the expression of NOTCH1, which resulted in increased mitotic signals in the tumor cells including CSCs. Thus, these new phenotypes of breast CSCs with TR characteristics need more understanding for the development of effective combinatorial and adjuvant therapies.Note: This abstract was not presented at the meeting.Citation Format: Kanagarj Palaniyandi, Dhanavathy Gnasampandapandian, Ilangovan Ramachandran, Yuvaraj Sambandam, Parthasarathy Chandrakesan. Tamoxifen treatment induces the epigenetic changes in breast cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1005.
Antenna Placement and Performance Tradeoffs With Hand Blockage in Millimeter Wave Systems (2019)

The ongoing commercial deployment of millimeter wave systems brings into focus a number of practical issues in form factor user equipment (UE) design. With wavelengths becoming smaller, antenna gain patterns becoming directional, and link budgets critically dependent on beamforming, it becomes imperative to use a number of antenna modules at different locations of the UE for good performance. While more antennas/modules can enhance beamforming array gains, it comes with the trade-off of higher component cost, power consumption of the associated radio frequency circuitry, and a beam management overhead in learning the appropriate beam weights. Thus, the goal of a good UE design is to provide robust spherical coverage corresponding to good array gains over the entire sphere around the UE with a low beam management overhead, complexity, and cost. The scope of this paper is to study the implications of two popular commercial millimeter-wave UE designs (a face and an edge design) on spherical coverage. We show that the analog beam codebooks can result in good performance for both the designs, and the edge design provides a better trade-off in terms of robust performance (with hand blockage), beam management overhead, implementation complexity from an antenna placement standpoint, and cost.
Purkinje triggers of ventricular fibrillation in patients with hypertrophic cardiomyopathy (2021)

In our study of patients with HCM and recurrent VF, VF was not initiated from the myocardium but rather from Purkinje arborization. These sources colocalized with the hypertrophic substrate, suggesting electromechanical interaction. Focal ablation at these sites was associated with a marked reduction in VF burden.
Characterization of Brain Sulfatide Molecular Species in Arylsulfatase A Deficient Mice Using Electrospray Ionization Tandem Mass Spectrometry (2005)

This thesis covers a wide range of analytical method development for lipid analysis in complex biological samples; from sample preparation using pressurized fluid extraction (PFE) and separation with reversed phase capillary liquid chromatography (RP-LC) to detection by electrospray ionization mass spectrometry (ESI/MS) and tandem MS.The requirements for fast, reliable and selective extraction methods with minimal usage of solvents have accelerated the development of new extraction techniques. PFE is one of the new automated, fast and efficient liquid extraction techniques which use elevated temperature and pressure with standard liquid solvents. In this thesis the reliability and efficiency of the PFE technique was investigated for the extraction of total lipid content from cod, herring muscle and human brain tissue as well as for pesticides from fatty foodstuffs. Improved or comparable efficiencies were achieved with reduced time and solvent consumption as compared to traditional methods. A RP-LC coupled online to ESI/MS for the analysis of phosphatidylcholine (PC) and sphingomyelin (SM) molecular species was developed and used for the analysis of brain lipids from eight groups of mice treated with vehicle and various neuroleptics. The effect of postnatal iron administration in lipid composition and behavior was investigated. Whether or not these effects could be altered by subchronic administration of the neuroleptics (clozapine and haloperidol) were examined. The results support the hypothesis that an association between psychiatric disorders, behavior abnormalities and lipid membrane constitution in the brain exists.Finally, a tandem MS precursor ion scan was used to analyze the developmental profile of brain sulfatide accumulation in arylsulfatase A (ASA) deficient (ASA -/-) as compared to wild type control (ASA +/+) mice. The ASA -/- mice were developed as a model of the monogenic disease metachromatic leukodystrophy with an established deficiency of the lysosomal enzyme ASA. The results showed that an alteration in the composition of sulfatide molecular species was observed between the ASA -/- and ASA +/+ mice.This thesis shows that modern analytical methods can provide new insights in the extraction and analysis of lipids from complex biological samples.
The optical design and performance of TolTEC: a millimeter-wave imaging polarimeter (2020)

TolTEC is an imaging polarimeter that will be mounted on the 50m diameter Large Millimeter Telescope (LMT) in Mexico. This camera simultaneously images the focal plane at three wavebands centered at 1.1, 1.4, and 2.0mm. TolTEC combines polarization-sensitive Kinetic Inductance Detectors (KIDs) with the LMT to produce 5-10 arcmin resolution maps of the sky in both total intensity and polarization. The light from the telescope is coupled to the TolTEC instrument using three room temperature mirrors. Before entering the cryostat, the light passes through a rapid-spinning achromatic half-wave plate, and once inside it passes through a 1 K Lyot stop that controls the telescope illumination. Inside the cryostat, a series of aluminum mirrors, silicon lenses, and dichroic filters split the light into three wavelength bands and direct each band to a different detector array. We will describe the design, and performance of the optics before installation at the telescope.
Numerical Modeling of Anisotropic Fiber Bundle Behavior in Oxygenators (2011)

Prediction of flow patterns through oxygenator fiber bundles can allow shape optimization so that efficient gas exchange occurs with minimal thrombus formation and hemolysis. Computational fluid dynamics (CFD) simulations can be used to predict three-dimensional flow velocities and flow distribution from spatially dependent variables and they allow estimations of erythrocyte residence time within the fiber bundle. This study builds upon previous work to develop an accurate numerical model for oxygenators, which would allow for accelerated iterations in oxygenator shape and diffuser plate design optimization. Hollow fiber flow channels were developed to permit experimental calculation of fluid permeability in two directions: main flow along the hollow fiber and perpendicular to the hollow fibers. Commercial software was used to develop three-dimensional CFD models of the experimental flow channels and an anisotropic porous media model for oxygenators from these experimental results. The oxygenator model was used to predict pressure loss throughout the device, visualize blood distribution within the fiber bundle, and estimate erythrocyte residence time within the bundle. Experimental flow channels measurements produced a streamwise permeability of 1.143e(-8) m(2) and transverse permeability of 2.385e(-9) m(2) . These permeabilities, coupled with previous work with volume porosity, were used to develop the numerical model of anisotropic behavior through porous fiber bundles, which indicated a more uniform flow field throughout the oxygenator. Incorporation of known anisotropic fiber bundle behavior in previous numerical models more accurately represents fluid behavior through an oxygenator fiber bundle. CFD coupled with experimental validation can produce a powerful tool for oxygenator design and development.
AMITIES (2013)

This paper presents an architecture to control avatars and virtual characters in remote interaction environments. A human-in-the-loop (interactor) metaphor provides remote control of multiple virtual characters, with support for multiple interactors and multiple observers. Custom animation blending routines and a gesture-based interface provide interactors with an intuitive digital puppetry paradigm. This paradigm reduces the cognitive and physical loads on the interactor while supporting natural bi-directional conversation between a user and the virtual characters or avatar counterparts. A multi-server-client architecture, based on a low-demand network protocol, connects the user environment, interactor station(s) and observer station(s). The associated system affords the delivery of personalized experiences that adapt to the actions and interactions of individual users, while staying true to each virtual character's personality and backstory. This approach has been used to create experiences designed for training, education, rehabilitation, remote presence and other-related applications.
Topics in Biomedical Optics: introduction to the feature issue (2009)

This Applied Optics feature issue on Topics in Biomedical Optics highlights papers presented at the 2008 Biomedical Topical meeting sponsored by the Optical Society.