gebhart/patrepeval huggingface dataset:
Human beta-globin locus control region: analysis of the 5' DNase I hypersensitive site HS 2 in transgenic mice. (1991)

The human beta-globin locus control region (LCR) is essential for high-level expression of human epsilon-, gamma-, and beta-globin genes. Developmentally stable DNase I hypersensitive sites (designated HS) mark sequences within this region that are important for LCR activity. A 1.9-kilobase (kb) fragment containing the 5' HS 2 site enhances human beta-globin gene expression 100-fold in transgenic mice and also confers position-independent expression. To further define important sequences within this region, deletion mutations of the 1.9-kb fragment were introduced upstream of the human beta-globin gene, and the constructs were tested for activity in transgenic mice. Although enhancer activity was gradually lost with deletions of both 5' and 3' sequences, a 373-base-pair (bp) fragment retained the ability to confer relative position-independent expression. Three prominent DNase I footprints were observed in this region with extracts from the human erythroleukemia cell line K-562, one of which contained duplicated binding sites for transcription factor AP-1 (activator protein 1). When the 1.9-kb fragment containing an 18-bp deletion of the AP-1 binding sites was tested in transgenic mice, enhancer activity decreased 20-fold but position-independent expression was retained.
Ozone Degradation of Polycyclic Aromatic Hydrocarbons Adsorbed on Asbestos (1986)

Abstract The polycyclic aromatic hydrocarbons (PAH) represent a major source of pollution. The adsorption properties of chrysotile give us a good application as an asbestos filter and the regeneration can be made by ozonolysis for a complete destruction to non toxic compounds.
Photoreceptor cells are major contributors to diabetes-induced oxidative stress and local inflammation in the retina (2013)

Accumulating evidence suggests that photoreceptor cells play a previously unappreciated role in the development of early stages of diabetic retinopathy, but the mechanism by which this occurs is not clear. Inhibition of oxidative stress is known to inhibit the vascular lesions of early diabetic retinopathy, and we investigated whether the diabetes-induced oxidative stress in the retina emanates from photoreceptors. Superoxide generation was assessed in retinas of male C57BL/6J mice made diabetic for 2 mo (4 mo of age when killed) using histochemical (dichlorofluorescein and dihydroethidine) and bioluminescence (lucigenin) methods. Photoreceptors were eliminated in vivo by genetic (opsin(-/-)) and chemical (iodoacetic acid) techniques. Immunoblots were used to measure expression of intercellular adhesion molecule 1 and the inducible form of nitric oxide synthase. Diabetes increased the generation of superoxide by diabetic mouse retina more at night than during the day. Photoreceptors were the major source of reactive oxygen species in the retina, and their deletion (either genetically in opsin(-/-) mice or acutely with iodoacetic acid) inhibited the expected diabetes-induced increase in superoxide and inflammatory proteins in the remaining retina. Both mitochondria and NADPH oxidase contributed to the observed retinal superoxide generation, which could be inhibited in vivo with either methylene blue or apocynin. Photoreceptors are the major source of superoxide generated by retinas of diabetic mice. Pharmaceuticals targeting photoreceptor oxidative stress could offer a unique therapy for diabetic retinopathy.
PBS NSLP: Network Traffic Authorization (2013)

This document describes the NSIS Signaling Layer protocol (NSLP) for
network traffic authorization on the Internet, the Permission-Based
Sending (PBS) NSLP. This NSLP aims to prevent Denial-of-Service (DoS)
attacks and other forms of unauthorized traffic. PBS NSLP is based on
a hybrid approach: a proactive approach of explicitly granting
permissions and a reactive approach of monitoring and countering
attacks. Signaling installs and maintains the permission state of
routers for a data flow. A monitoring mechanism provides a second line
of defense against attacks. PBS NSLP uses two security mechanisms:
message security for protecting the integrity of the message on end-
to-end traffic and channel security for protecting the integrity and
confidentiality between adjacent nodes. To authenticate data packets,
the PBS NSLP requests a sender to use an existing security protocol,
the IPsec Authentication Header (AH).
Recurrent Fusion of <i>TMPRSS2</i> and ETS Transcription Factor Genes in Prostate Cancer (2005)

Recurrent chromosomal rearrangements have not been well characterized in common carcinomas. We used a bioinformatics approach to discover candidate oncogenic chromosomal aberrations on the basis of outlier gene expression. Two ETS transcription factors, ERG and ETV1, were identified as outliers in prostate cancer. We identified recurrent gene fusions of the 5' untranslated region of TMPRSS2 to ERG or ETV1 in prostate cancer tissues with outlier expression. By using fluorescence in situ hybridization, we demonstrated that 23 of 29 prostate cancer samples harbor rearrangements in ERG or ETV1. Cell line experiments suggest that the androgen-responsive promoter elements of TMPRSS2 mediate the overexpression of ETS family members in prostate cancer. These results have implications in the development of carcinomas and the molecular diagnosis and treatment of prostate cancer.
Selection and Characterization of HIV-1 with a Novel S68 Deletion in Reverse Transcriptase (2011)

Resistance to human immunodeficiency virus type 1 (HIV-1) represents a significant problem in the design of novel therapeutics and the management of treatment regimens in infected persons. Resistance profiles can be elucidated by defining modifications to the viral genome conferred upon exposure to novel nucleoside reverse transcriptase (RT) inhibitors (NRTI). In vitro testing of HIV-1LAI-infected primary human lymphocytes treated with β-D-2',3'-dideoxy-2',3'-didehydro-5-fluorocytidine (DFC; Dexelvucitabine; Reverset) produced a novel deletion of AGT at codon 68 (S68Δ) alone and in combination with K65R that differentially affects drug response. Dual-approach clone techniques utilizing TOPO cloning and pyrosequencing confirmed the novel S68Δ in the HIV-1 genome. The S68Δ HIV-1 RT was phenotyped against various antiviral agents in a heteropolymeric DNA polymerase assay and in human lymphocytes. Drug susceptibility results indicate that the S68Δ displayed a 10- to 30-fold increase in resistance to DFC, lamivudine, emtricitabine, tenofovir, abacavir, and amdoxovir and modest resistance to stavudine, β-d-2',3'-oxa-5-fluorocytidine, or 9-(β-D-1,3-dioxolan-4-yl)guanine and remained susceptible to 3'-azido-3'-deoxythymidine, 2',3'-dideoxyinosine (ddI), 1-(β-D-dioxolane)thymine (DOT) and lopinavir. Modeling revealed a central role for S68 in affecting conformation of the β3-β4 finger region and provides a rational for the selective resistance. These data indicate that the novel S68Δ is a previously unrecognized deletion that may represent an important factor in NRTI multidrug resistance treatment strategies.
Bit-depth extension using spatiotemporal microdither based on models of the equivalent input noise of the visual system (2003)

Continuous tone, or “contone”, imagery usually has 24 bits/pixel as a minimum, with eight bits each for the three primaries in typical displays. However, lower-cost displays constrain this number because of various system limitations. Conversely, high quality displays seek to achieve 9-10 bits/pixel/color, though there may be system bottlenecks limited at 8. The two main artifacts from reduced bit-depth are contouring and loss of amplitude detail; these can be prevented by dithering the image prior to these bit-depth losses. Early work in this area includes Roberts’ noise modulation technique, Mista’s blue noise mask, Tyler’s technique of bit-stealing, and Mulligan’s use of the visual system’s spatiotemporal properties for spatiotemporal dithering. However, most halftoning/dithering work was primarily directed to displays at the lower end of bits/pixel (e.g., 1 bit as in halftoning) and higher ppi. Like Tyler, we approach the problem from the higher end of bits/pixel/color, say 6-8, and use available high frequency color content to generate even higher luminance amplitude resolution. Bit-depth extension with a high starting bit-depth (and often lower spatial resolution) changes the game substantially from halftoning experience. For example, complex algorithms like error diffusion and annealing are not needed, just the simple addition of noise. Instead of a spatial dither, it is better to use an amplitude dither, termed <i>microdither</i> by Pappas. We have looked at methods of generating the highest invisible opponent color spatiotemporal noise and other patterns, and have used Ahumada’s concept of equivalent input noise to guide our work. This paper will report on techniques and observations made in achieving contone quality on ~100 ppi 6 bits/pixel/color LCD displays with no visible dither patterns, noise, contours, or loss of amplitude detail at viewing distances as close as the near focus limit (~120 mm). These include the interaction of display nonlinearities and their role of generating a low-spatial frequency flicker from mutually high-pass spatial and temporal noise, as well as the temporal response symmetries.
An investigation into different masking behaviours resulting from estimation of tonality index (2003)

A psychoacoustics model that approximates the masking threshold is presented. The significance of the tonality index is highlighted by comparing two well-known methods used in its estimation: unpredictability and spectral flatness measure. The first method has a tendency to give a lower threshold in the low frequency (below 3 kHz) region whereas the second one tends to be lower in the high frequency range. A new method is proposed which combines both techniques to achieve better results. This technique moderates the complexity of the two earlier methods and increases the compression ratio considerably without compromising the audio quality.
Galactosylsphingamides: new α-GalCer analogues to probe the F’-pocket of CD1d (2017)

Invariant Natural Killer T-cells (iNKT-cells) are an attractive target for immune response modulation, as upon CD1d-mediated stimulation with KRN7000, a synthetic α-galactosylceramide, they produce a vast amount of cytokines. Here we present a synthesis that allows swift modification of the phytosphingosine side chain by amidation of an advanced methyl ester precursor. The resulting KRN7000 derivatives, termed α-galactosylsphingamides, were evaluated for their capacity to stimulate iNKT-cells. While introduction of the amide-motif in the phytosphingosine chain is tolerated for CD1d binding and TCR recognition, the studied α-galactosylsphingamides showed compromised antigenic properties.
Development of Thermally and Chemically Stable Large-Hydrophobe Alkoxy Carboxylate Surfactants (2012)

Abstract The Guerbet reaction produces large, branched hydrophobes through the dimerization of linear alcohols. High-performance, low-cost enhanced oil recovery (EOR) surfactants are produced by carboxylation (carboxymethylation) of large Guerbet alkoxylates. Alkoxy groups such as propylene oxide (PO) and ethylene oxide (EO) are incorporated as extenders to the Guerbet alcohol, followed by carboxylation to make the anionic surfactant. Previously, the use of low-cost Guerbet alkoxy sulfate surfactants for EOR applications at high temperatures was established by enhancing their thermal stability when the pH is maintained at 10–11. Alternative thermally and chemically stable anionic surfactant structures are highly desired, especially for application under conditions where alkali usage is prohibitive. These novel large-hydrophobe carboxylate surfactants meet this need. In addition, the Guerbet alkoxy carboxylate structure can be tailored to fit the specific EOR requirements. These surfactants are stable at elevated temperatures both with and without alkali, and furthermore they can be used in environments of high salinity and high hardness (high concentration of divalent ions). Carboxylate surfactants have been used in formulations to produce ultra-low interfacial tensions with low microemulsion viscosities for a wide variety of crude oils under a large range of reservoir conditions. A parallel paper titled "Novel Large-Hydrophobe Alkoxy Carboxylate Surfactants for Enhanced Oil Recovery" will discuss the application of these surfactants. Thus, the advent of this class of cost-effective surfactants greatly broadens the application of chemical EOR.
Resistive and reactive loads’ influences on highly coupled piezoelectric generators for wideband vibrations energy harvesting (2018)

One of the main challenges in energy harvesting from ambient vibrations is to find efficient ways to scavenge the energy, not only at the mechanical system resonance but also on a wider frequency band. Instead of tuning the mechanical part of the system, as usually proposed in the state of the art, this article develops extensively the possibility to tune the properties of the harvester using the electrical interface. Due to the progress in materials, piezoelectric harvesters can exhibit relatively high electromechanical coupling: hence, the electrical part can now have a substantial influence on the global parameters of the piezoelectric system. In order to harness the energy efficiently from this kind of generator on a wide frequency band, not only the electrical load’s effect on the harvester’s damping should be tuned but also its effect on the harvester’s stiffness. In this article, we present an analytical analysis of the influences of the resistive and reactive behavior of the electrical interface on highly coupled piezoelectric harvesters. We develop a normalized study of the multiphysics interactions, reducing the number of parameters of the problem to a few physically meaningful variables. The respective influence of each of these variables on the harvesting power has been studied and led us to the optimal electrical damping expression and the influences of the damping and of the coupling on the equivalent admittance of the piezoelectric energy harvester. Finally, we linked these normalized variables with real reactive load expressions, in order to study how a resistive, capacitive, and inductive behavior could affect the global performances of the system. The theoretical analysis and results are supported by experimental tests on a highly coupled piezoelectric system [Formula: see text]. Using an adequate tuning of a RC load at each frequency, the maximum harvested power [Formula: see text] under a small acceleration amplitude of [Formula: see text] is reached over a 14 Hz large frequency band around 105 Hz which has been predicted by the model with less than 5% error.
Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems (2019)

Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag system to engineer targeted gene activation and DNA methylation in Arabidopsis. We demonstrate that a dCas9-SunTag system utilizing the transcriptional activator VP64 drives robust and specific activation of several loci, including protein coding genes and transposable elements, in diverse chromatin contexts. In addition, we present a CRISPR-based methylation targeting system for plants, utilizing a SunTag system with the catalytic domain of the Nicotiana tabacum DRM methyltransferase, which efficiently targets DNA methylation to specific loci, including the FWA promoter, triggering a developmental phenotype, and the SUPERMAN promoter. These SunTag systems represent valuable tools for the site-specific manipulation of plant epigenomes.
Dynamic DMD-driven optoelectronics tweezers for microscopic particle manipulation (2004)

We demonstrate dynamic manipulation of microscopic particles using a DMD-produced projection image in an optoelectronics tweezers system. Single-particle trapping and movement (up to 40 /spl mu/m/sec) via optically-induced dielectrophoresis were observed.
Augmenting Computer-Aided Design Software With Multi-Functional Capabilities to Automate Multi-Process Additive Manufacturing (2017)

The ability to access individual layers of a part as they are being printed has allowed additive manufacturing (AM) researchers to experiment with the in situ placement of components, thereby creating multi-process parts with additional functionality, such as customized printed electronics. As AM has evolved to become an established method for creating end-use parts, this interest in multi-process printing has increased. Although progress has been made in developing multi-process hardware, which can combine AM with other technologies, holistic design software, capable of readily integrating these processes, is developing at a slower rate. In this paper, an integrated software solution capable of supporting multi-process 3D printing from design through manufacture is described, featuring the integration of electronic components and circuits interconnected by copper wires. This solution features automated generation of the cavities that accommodate electronic components as well as toolpath generation for a multi-process 3D printer capable of automated wire embedding. As a case study of the developed technology, a hexagonal 3D printed body, which included a microcontroller, four LEDs, a USB connector, two resistors, and a Zener diode, all interconnected by embedded copper wires, was fabricated within a short cycle time: 5.75 h from design to fabricated part. Short cycle times allow multiple design iterations to be realized and printed within the same day.
A Class of Non-binary Regular Girth-8 LDPC Codes for Optical Communication Channels (2009)

We investigate the feasibility of non-binary, regular LDPC codes for optical transmission. Our results indicate that non-binary codes not only beat their bit-length-matched binary counterparts in performance but also admit 3.26 times less complex decoders.
Field testing for toxic algae with a microarray: initial results from the MIDTAL project (2010)

In: Pagou, P. and Hallegraeff, G. (eds). Proceedings of the 14th International Conference on Harmful Algae. International Society for the Study of Harmful Algae and Intergovernmental Oceanographic Commission of UNESCO 2012 ISBN 978-87-990827-3-5\n\nArchived in DUO with permission from ISSHA.
An Ergonomic Wireless Charging System for Integration With Daily Life Activities (2020)

In this article, we present a clothing-integrated wireless power transfer and harvesting system that uses a novel class of anchor-shaped antennas for wireless power transfer up to the 4-ft distance. Notably, the system allows wireless charging during daily life activities, such as sitting on a chair or while lying on a fabric surface. Owning to up to a 4-ft power transfer, a user may also walk around during the wireless charging. The proposed system features a novel anchor-shaped antenna, which is miniaturized than a loop antenna and extends the range of fringing fields. Furthermore, a textile-based rectifying circuit with RF-to-dc conversion efficiency of 77.23% at 22.5 dBm is proposed. The efficiency remains better than 60% for an input power from 2 dBm to 24 dBm. For garment integration, a system consisting of a rectifier and an antenna were prototyped by using embroidered conductive thread on denim fabric. To understand the effectiveness, wireless power transfer tests are conducted under mechanical deformations and misalignments. The resulting prototype was tested for power transfer of several mW power over an area of 4 ft × 4 ft and by using a 1-W transmitter. This textile power harvesting system can be used as an ergonomic charging platform to supply power to a wide range of wearable medical, Internet of Things, and portable devices.
Bonding soft rubber or plasticized elastomers to metal (1980)

Approach using bond-cover coat of unplasticized rubber between soft rubber and adhesive eliminates diffusion problem. Approach is useful in making improved seals in automobile engines, industrial and public plumbing, and in other areas using soft-rubber-to-metal bonds. Seals and gaskets made this way would not have to be replaced very often, reducing cost of maintenance.
LVS check for photonic integrated circuits: curvilinear feature extraction and validation (2015)

This work is motivated by the demand of an electronic design automation (EDA) approach for the emerging ecosystem of the photonic integrated circuit (PIC) technology. A reliable physical verification flow cannot be achieved without the adaption of the traditional EDA tools to the photonic design verification needs. We analyze how layout versus schematic (LVS) checking is performed differently for photonic designs, and propose an LVS flow that addresses the particular need of curvilinear feature validation (curved path length and bend curvature extraction). We show that it is possible to reuse and extend the current LVS tools to perform such critical but non-traditional checks, which ensures a more reliable photonic layout implementation in term of functionality and circuit yield. Going forward, we propose possible future studies that can further improve the flows.
Pattern Recognition and Logic with Optical Gates (1985)

Threshold logic has traditionally been reserved for purely academic considerations related to the theory of switching functions. Modern VLSI circuitry is ill-suited to the implementation of threshold logic devices and relies exclusively on simple gates for its computational power. Recent developments in integrated optics have shown 1 that it is possible to optically implement a threshold function.
Examination of New Vector Control System of Permanent Magnet Synchronous Motor for High-Speed Drives (2009)

A new vector control system for permanent magnet synchronous motor drives has been developed. To stabilize the current control loop in the high rotating speed region, a novel configuration of current controller is introduced.The unique characteristic of the proposed current controller is that the current regulator is connected to the conventional motor model in a series. By analyzing the transfer characteristics of the control, it became clear that the influence of the coupling component between d-q axes can be deleted theoretically if the control parameters are set properly. Stability and torque response of the proposed vector control system were improved. Effectiveness of the proposed controller was demonstrated by a time domain simulation and, some experiments.In addition, the robustness of the controlling system was investigated in some experiments.
The Insulin-like Growth Factor I Receptor/Insulin Receptor Tyrosine Kinase Inhibitor PQIP Exhibits Enhanced Antitumor Effects in Combination with Chemotherapy Against Colorectal Cancer Models (2010)

Combination treatment with PQIP, the dual IGF-IR/insulin receptor tyrosine kinase inhibitor, and standard colorectal cancer chemotherapy resulted in enhanced antiproliferative effects against colorectal cancer cell line models, providing a scientific rationale for the testing of OSI-906 and standard colorectal cancer treatment regimens.