gebhart/patrepeval huggingface dataset:
Enhanced Antiretroviral Therapy in Rhesus Macaques Improves RT-SHIV Viral Decay Kinetics (2014)

Using an established nonhuman primate model, rhesus macaques were infected intravenously with a chimeric simian immunodeficiency virus (SIV) consisting of SIVmac239 with the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase from clone HXBc2 (RT-SHIV). The impacts of two enhanced (four- and five-drug) highly active antiretroviral therapies (HAART) on early viral decay and rebound were determined. The four-drug combination consisted of an integrase inhibitor, L-870-812 (L-812), together with a three-drug regimen comprising emtricitabine [(-)-FTC], tenofovir (TFV), and efavirenz (EFV). The five-drug combination consisted of one analog for each of the four DNA precursors {using TFV, (-)-FTC, (-)-β-D-(2R,4R)-1,3-dioxolane-2,6-diaminopurine (amdoxovir [DAPD]), and zidovudine (AZT)}, together with EFV. A cohort treated with a three-drug combination of (-)-FTC, TFV, and EFV served as treated controls. Daily administration of a three-, four-, or five-drug combination of antiretroviral agents was initiated at week 6 or 8 after inoculation and continued up to week 50, followed by a rebound period. Plasma samples were collected routinely, and drug levels were monitored using liquid chromatography-tandem mass spectrometry (LC-MS-MS). Viral loads were monitored with a standard TaqMan quantitative reverse transcriptase PCR (qRT-PCR) assay. Comprehensive analyses of replication dynamics were performed. RT-SHIV infection in rhesus macaques produced typical viral infection kinetics, with untreated controls establishing persistent viral loads of >10(4) copies of RNA/ml. RT-SHIV loads at the start of treatment (V0) were similar in all treated cohorts (P > 0.5). All antiretroviral drug levels were measureable in plasma. The four-drug and five-drug combination regimens (enhanced HAART) improved suppression of the viral load (within 1 week; P < 0.01) and had overall greater potency (P < 0.02) than the three-drug regimen (HAART). Moreover, rebound viremia occurred rapidly following cessation of any treatment. The enhanced HAART (four- or five-drug combination) showed significant improvement in viral suppression compared to the three-drug combination, but no combination was sufficient to eliminate viral reservoirs.
Comparison of Pathological Outcomes of Active Surveillance Candidates Who Underwent Radical Prostatectomy Using Contemporary Protocols at a High-volume Korean Center (2012)

The contemporary active surveillance protocols showed similar pathological characteristics in patients who had undergone radical prostatectomy. However, we concluded that the Prostate Cancer Research International: Active Surveillance protocol would be most helpful to Korean populations in choosing candidates for active surveillance considering the balance between sensitivity and specificity and the accuracy of diagnosis.
Integration and electrical characterization of photosensitive polyimide (2001)

A base line process of photosensitive polyimide was developed to significantly reduce cycle time in backend polyimide processes as compared to the use of conventional nonphotosensitive polyimide. A 6 μm resolution was obtained by the use of a wet etch process of photosensitive polyimide (PSPI) in aqueous tetramethylammonium hydroxide developer. The feasibility of the polyimide as a passivation stress-buffer layer and passivation-etch mask was also demonstrated. Electrical characterization was performed to measure the surface resistance and the intralevel leakage current along the interface between the polyimide and tetraethylorthosilicate. These findings suggested that reduction of the moisture content of the polymer films is critical to ensure electrical isolation during the integration of PSPI into multilevel structures.
Supplementary Data from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer (2023)

&lt;p&gt;Supplementary methods and tables&lt;/p&gt;
Learning-Based Dimensionality Reduction for Computing Compact and Effective Local Feature Descriptors (2023)

A distinctive representation of image patches in form of features is a key component of many computer vision and robotics tasks, such as image matching, image retrieval, and visual localization. State-of-the-art descriptors, from hand-crafted descriptors such as SIFT to learned ones such as HardNet, are usually high-dimensional; 128 dimensions or even more. The higher the dimensionality, the larger the memory consumption and computational time for approaches using such descriptors. In this paper, we investigate multi-layer perceptrons (MLPs) to extract low-dimensional but high-quality descriptors. We thoroughly analyze our method in unsuper-vised, self-supervised, and supervised settings, and evaluate the dimensionality reduction results on four representative descriptors. We consider different applications, including visual localization, patch verification, image matching and retrieval. The experiments show that our lightweight MLPs trained using supervised method achieve better dimensionality reduction than PCA. The lower-dimensional descriptors generated by our approach outperform the original higher-dimensional descriptors in downstream tasks, especially for the hand-crafted ones. The code is available at https://github.com/PRBonn/descriptor-dr.
Changes in gene transcription during a beta-mediated cell death. (1996)

The a beta peptide induces cell death in neurons grown in cell culture. Previous studies have shown that the mechanism of a beta-mediated cell death of central nervous system neurons appears to be via apoptosis. Apoptosis is an active process that involves both gene transcription and translation. Using semi-quantitative polymerase chain reaction, we have analyzed the levels of a variety of transcripts in primary neuronal cultures treated with a beta that are likely to play important roles in apoptosis. Following addition of 10 microM a beta 1-42 the immediate early response gene, c-fos, shows a rapid and sustained increase in transcript level while c-jun levels increase at a slower rate. Bcl-2 and its homologues, bcl-X and bax, also increase in amount with bcl-2 and bcl-X increasing more rapidly than bax. These data provide support indicating that a beta-mediated cell death in central nervous system neurons is an active process similar to that seen in apoptosis.
Polypoidal choroidal vasculopathy and treatments (2008)

Although the polypoidal choroidal vasculopathy and age-related macular degeneration have been known to share common genetic factors, its clinical characteristics including the different responses to photodynamic therapy suggest that polypoidal choroidal vasculopathy is a separate clinical entity from age-related macular degeneration. The results of photodynamic therapy for polypoidal choroidal vasculopathy are encouraging; however, recurrence may affect vision over time. Therapeutic modalities to inhibit development of the exudative choroidal vasculature of polypoidal choroidal vasculopathy are desirable.
Development and Validation of HealthImpact: An Incident Diabetes Prediction Model Based on Administrative Data (2016)

HealthImpact is an efficient and effective method of risk stratification for incident diabetes that is not predicated on patient-provided information or laboratory tests.
A 3D interconnect system for large biosensor array and CMOS signal-processing IC integration (2010)

In this paper, two new interconnect technologies designed for integration of a large biosensor array and a signal processing CMOS IC are presented; a TSV technology that can be fabricated in wafers that cannot be aggressively thinned down or have sensitive sensors fabricated in prior processes, and a compliant interconnect technology that enables minimal stress permanent interconnections or low-force temporary interconnections to allow reuse of CMOS ICs. In addition, integration of TSV to a silicon nanowire label-free biosensor is demonstrated.
Nonlinear refractive index measurements of glasses and crystals (1987)

We have measured the nonlinear index for numerous glasses and crystals with the goal of determining the material properties that contribute to the magnitude and dispersion of n2. We have found that a nearly‐degenerate three‐wave‐mixing (TWM) process, similar to that first used by Maker and Terhune, is the most useful method since it can provide both rapid and accurate n2 measurements.
Impermeable Graphene Oxide Protects Silicon from Oxidation (2021)

The presence of a natural silicon oxide (SiO<i><sub>x</sub></i>) layer over the surface of silicon (Si) has been a roadblock for hybrid semiconductor and organic electronics technology. The presence of an insulating oxide layer is a limiting operational factor, which blocks charge transfer and therefore electrical signals for a range of applications. Etching the SiO<i><sub>x</sub></i> layer by fluoride solutions leaves a reactive Si-H surface that is only stable for few hours before it starts reoxidizing under ambient conditions. Controlled passivation of silicon is also of key importance for improving Si photovoltaic efficiency. Here, we show that a thin layer of graphene oxide (GO<i><sub>x</sub></i>) prevents Si surfaces from oxidation under ambient conditions for more than 30 days. In addition, we show that the protective GO<i><sub>x</sub></i> layer can be modified with molecules enabling a functional surface that allows for further chemical conjugation or connections with upper electrodes, while preserving the underneath Si in a nonoxidized form. The GO<i><sub>x</sub></i> layer can be switched electrochemically to reduced graphene oxide, allowing the development of a dynamic material for molecular electronics technologies. These findings demonstrate that 2D materials are alternatives to organic self-assembled monolayers that are typically used to protect and tune the properties of Si and open a realm of possibilities that combine Si and 2D materials technologies.
Model Driven Therapy (2003)

Model Driven Therapy emerges as the way to perform optimal medical and surgical interventions, providing physicians and surgeons with the possibility to augment their capacities of sensing multi-modal information, of combining them to define optimal strategies, and of performing accurate and safe actions.
High-Viscosity Electronic Materials Printing Using Ultrasonic Inkjet System (2007)

The nozzle-less structure of the ultrasonic inkjet system is advantageous leading to printability of inks of a wide range of viscosities without clogging. In the ultrasonic inkjet head, dot placement accuracy of high-viscosity ink was as same as that of standard viscosity ink. The shape of meniscus changes as the viscosity increases. Using the printability of high-viscosity inks, the ultrasonic inkjet printing was applied for LED packaging by depositing silicone resin and fabrication of solution-processed organic thin-film transistors by printing high-viscosity organic conducting ink, PEDOT:PSS.
Seabed Properties Derived from Ambient Noise (2006)

An extensive study of low-frequency ambient noise wavefields in the seabed has resulted in a new approach to determine the near-surface shear velocity. 33 minutes of continuous ambient noise recorded by an ocean-bottom cable (OBC) system without using an active source were analyzed for seafloor compliance and Scholte waves. Seafloor compliance was not observed and requires longer recording time. Scholte waves were observed in the frequency-wavenumber spectrum. The Scholte wave phase-velocity was modeled with a realistic one-dimensional near-surface model. The horizontal over vertical spectral ratio of the Scholte waves was also modeled and shown to be very sensitive to the near-surface shear velocity model. Applications of the method include shear-wave statics estimation and geohazard prediction.
Endothelial CFTR dysfunction and its involvement in the pathogenesis of pulmonary arterial hypertension (2021)

F. Antigny and co-workers raise interesting points in their comment on the transcriptomic analysis of cystic fibrosis transmembrane conductance regulator (CFTR)-impaired endothelial cells (ECs) revealing a pro-inflammatory phenotype [1]. Indeed, CFTR impairment in different endothelial models and organisms, and in the absence of concomitant infection, suggests that ECs are an overlooked mediator in the exaggerated pro-inflammatory phenotype observed in cystic fibrosis (CF). Whether endothelial CFTR is involved in other vascular diseases is an intriguing question. Indeed, a recent report indicates a pivotal role of CFTR in pulmonary arterial hypertension (PAH) [2]. The role of endothelial CFTR dysfunction goes beyond cystic fibrosis by playing a role in pulmonary arterial hypertension <https://bit.ly/2UnC7IF>
Coherence of Spin-Polarized Fermions Interacting with a Clock Laser in a Stark-Shift-Free Optical Lattice (2008)

We investigated the coherence of spin-polarized ^{87}Sr atoms trapped in a light-shift-free one-dimensional optical lattice during their interaction with a clock laser on the ^1S_0-^3P_0 transition. Collapses and revivals appeared for more than 50 Rabi cycles, attributed to the thermal distribution of discrete vibrational states in the lattice potential. The population oscillation in the clock states lasted more than 1s, demonstrating high immunity from decoherence. This long atomic coherence suggests the feasibility of Pauli blocking of collisions in optical clock excitation.
A miniature electrothermal thruster using microwave-excited microplasmas: Thrust measurement and its comparison with numerical analysis (2007)

A microplasma thruster has been developed, consisting of a cylindrical microplasma source 10mm long and 1.5mm in inner diameter and a conical micronozzle 1.0–1.4mm long with a throat of 0.12–0.2mm in diameter. The feed or propellant gas employed is Ar at pressures of 10–100kPa, and the surface-wave-excited plasma is established by 4.0GHz microwaves at powers of &amp;lt;10W. The thrust has been measured by a combination of target and pendulum methods, exhibiting the performance improved by discharging the plasma. The thrust obtained is 1.4mN at an Ar gas flow rate of 60SCCM (1.8mg∕s) and a microwave power of 6W, giving a specific impulse of 79s and a thrust efficiency of 8.7%. The thrust and specific impulse are 0.9mN and 51s, respectively, in cold-gas operation. A comparison with numerical analysis indicates that the pressure thrust contributes significantly to the total thrust at low gas flow rates, and that the micronozzle tends to have an isothermal wall rather than an adiabatic.
A Real-Time Millimeter Wave V2V Channel Sounder (2022)

Wireless communication in millimeter wave spectrum is poised to provide the latency and bandwidth needed for advanced use cases unfeasible at lower frequencies. Despite the market potential of vehicular communication networks, investigations into the millimeter wave vehicular channel are lacking. In this paper, we present a detailed overview of a novel 1 GHz wide, multi-antenna vehicle to vehicle directional channel sounding and measurement platform operating at 28 GHz. The channel sounder uses two 256-element phased arrays at the transmitter vehicle and four 64-element arrays at the receiver vehicle, with the receiver measuring 116 different directional beams in less than 1 millisecond. By measuring the full multi-beam channel impulse response at large bandwidths, our system provides unprecedented insight in instantaneous mobile vehicle to vehicle channels. The system also uses centimeter-level global position tracking and 360 degree video capture to provide additional contextual information for joint communication and sensing applications. An initial measurement campaign was conducted on highway and surface streets in Austin, Texas. We show example data that highlights the sensing capability of the system. Preliminary results from the measurement campaign show that bumper mounted mmWave arrays provide rich scattering in traffic as well a provide significant directional diversity aiding towards high reliability vehicular communication. Additionally, potential waveguide effects from high traffic in lanes can also extend the range of mmWave signals significantly.
Software Resolved Networks (2018)

Enterprise networks often need to implement complex policies that match business objectives. They will embrace IPv6 like ISP networks in the coming years. Among the benefits of IPv6, the recently proposed IPv6 Segment Routing (SRv6) architecture supports richer policies in a clean manner. This matches very well the requirements of enterprise networks.
Single-Electron Transport in Ropes of Carbon Nanotubes (1997)

The electrical properties of individual bundles, or "ropes," of single-walled carbon nanotubes have been measured. Below about 10 kelvin, the low-bias conductance was suppressed for voltages less than a few millivolts. In addition, dramatic peaks were observed in the conductance as a function of a gate voltage that modulated the number of electrons in the rope. These results are interpreted in terms of single-electron charging and resonant tunneling through the quantized energy levels of the nanotubes composing the rope.
Joule heating effects in nanoscale carbon-based memory devices (2016)

One of the emerging candidates to bridge the gap between fast but volatile DRAM and non-volatile but slow storage devices is tetrahedral amorphous carbon (ta-C) based memory [1]-[3]. This offers a very good scalability, data retention and sub-5ns switching [2], [3]. Amorphous carbon memory devices can be electrically and optically switched from a high resistance state (HRS) to a low resistance state (LRS) [4]. The electrical conduction in the LRS is thought to be through sp <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> clusters that form a conductive filament [4].
Roadmap on biological pathways for electronic nanofabrication and materials (2018)

Abstract Conventional microchip fabrication is energy and resource intensive. Thus, the discovery of new manufacturing approaches that reduce these expenditures would be highly beneficial to the semiconductor industry. In comparison, living systems construct complex nanometer-scale structures with high yields and low energy utilization. Combining the capabilities of living systems with synthetic DNA-/protein-based self-assembly may offer intriguing potential for revolutionizing the synthesis of complex sub-10 nm information processing architectures. The successful discovery of new biologically based paradigms would not only help extend the current semiconductor technology roadmap, but also offer additional potential growth areas in biology, medicine, agriculture and sustainability for the semiconductor industry. This article summarizes discussions surrounding key emerging technologies explored at the Workshop on Biological Pathways for Electronic Nanofabrication and Materials that was held on 16–17 November 2016 at the IBM Almaden Research Center in San Jose, CA.
Optical Imaging and Spectroscopy (2008)

Preface. Acknowledgments. 1. Past, present and future. 1.1 Three revolutions. 1.2 Computational imaging. 1.3 Overview. 1.4 The fourth revolution. Problems. 2. Geometric imaging. 2.1 Visibility. 2.2 Optical elements. 2.3 Focal imaging. 2.4 Imaging systems. 2.5 Pinhole and coded aperture imaging. 2.6 Projection tomography. 2.7 Reference structure tomography. Problems. 3. Analysis. 3.1 Analytical tools. 3.2 Fields and transformations. 3.3 Fourier analysis. 3.4 Transfer functions and filters. 3.5 The Fresnel transformation. 3.6 The Whittaker-Shannon sampling theorem. 3.7 Discrete analysis of linear transformations. 3.8 Multiscale sampling. 3.9 B-splines. 3.10 Wavelets. Problems. 4. Wave imaging. 4.1 Waves and fields. 4.2 Wave model for optical fields. 4.3 Wave propagation. 4.4 Diffraction. 4.5 Wave analysis of optical elements. 4.6 Wave propagation through thin lenses. 4.7 Fourier analysis of wave imaging. 4.8 Holography. Problems. 5. Detection. 5.1 The Optoelectronic interface. 5.2 Quantum mechanics of optical detection. 5.3 Optoelectronic detectors. 5.3.1 Photoconductive detectors. 5.3.2 Photodiodes. 5.4 Physical characteristics of optical detectors. 5.5 Noise. 5.6 Charge coupled devices. 5.7 Active pixel sensors. 5.8 Infrared focal plane arrays. Problems. 6. Coherence imaging. 6.1 Coherence and spectral fields. 6.2 Coherence propagation. 6.3 Measuring coherence. 6.4 Fourier analysis of coherence imaging. 6.5 Optical coherence tomography. 6.6 Modal analysis. 6.7 Radiometry. Problems. 7. Sampling. 7.1 Samples and pixels. 7.2 Image plane sampling on electronic detector arrays. 7.3 Color imaging. 7.4 Practical sampling models. 7.5 Generalized sampling. Problems. 8. Coding and inverse problems. 8.1 Coding taxonomy. 8.2 Pixel coding. 8.3 Convolutional coding. 8.4 Implicit coding. 8.5 Inverse problems. Problems. 9. Spectroscopy. 9.1 Spectral measurements. 9.2 Spatially dispersive spectroscopy. 9.3 Coded aperture spectroscopy. 9.4 Interferometric Spectroscopy. 9.5 Resonant spectroscopy. 9.6 Spectroscopic filters. 9.7 Tunable filters. 9.8 2D spectroscopy. Problems. 10. Computational imaging. 10.1 Imaging systems. 10.2 Depth of field. 10.3 Resolution. 10.4 Multiple aperture imaging. 10.5 Generalized sampling revisited. 10.6 Spectral imaging. Problems. References.
Progress towards a MEMS tunable infrared filter using porous silicon (2014)

The unique optical properties of porous silicon show it to be a promising material for imaging and spectroscopy in the mid-infrared and long-infrared wavelength ranges. A tunable MEMS filter using porous silicon as a high-reflectivity layer is proposed. Measurements on fabricated porous silicon-based distributed Bragg reflectors and Fabry-Perot etalons are presented.
Equalization and clock recovery for a 2.5-10-Gb/s 2-PAM/4-PAM backplane transceiver cell (2003)

A folded multitap transmitter equalizer and multitap receiver equalizer counteract the losses and reflections present in the backplane environment. A flexible 2-PAM/4-PAM clock data recovery circuit uses select transitions for receive clock recovery. Bit-error rate less than 10/sup -15/ and power equal to 40 mW/Gb/s has been measured when operating over a 20-in backplane with two connectors at 10 Gb/s.
8.1: Invited Paper : A High‐Brightness Electrofluidic Display Film (2012)

Abstract Electrofluidic displays operate by transposing a pigment between an optically hidden or revealed state. The transposition is powered by electromechanical force, and over similar distance switches ∼100X faster than electrophoresis by moving the pigment with the fluid, not through the fluid. We report on progress with our previously reported pixel structures, and on a new electrofluidic film that is the first of its kind for all fluidic displays (electrowetting, electrophoretic, electrokinetic, electrofluidic). The new structure operates without capsules or pixel walls for fluid confinement, and requires no pixel electrode alignment.