gebhart/patrepeval huggingface dataset:
Optical photon reassignment super-resolved scanning laser ophthalmoscopy (Conference Presentation) (2017)

Conventional scanning laser ophthalmoscopy (SLO) utilizes a finite collection pinhole at a retinal conjugate plane to strongly reject out-of-focus light while primarily transmitting the in-focus, retinal backscattered signal. However, to improve lateral resolution, a sub-Airy disk collection pinhole is necessary, which drastically reduces the signal-to-noise ratio (SNR) of the system and is thus not commonly employed. Recently, an all-optical, super-resolution microscopy technique known as optical photon reassignment (OPRA) microscopy (also known as re-scan confocal microscopy) has been developed to bypass this fundamental tradeoff between resolution and SNR in confocal microscopy. We present a methodology and system design for obtaining super resolution in retinal imaging by combining the concepts of SLO and OPRA microscopy. The resolution improvement of the system was quantified using a 1951 USAF target at a telecentric intermediate image plane. Retinal images from human volunteers were acquired with this system both with and without using the OPRA technique to demonstrate the resolution improvement when imaging parafoveal cone photoreceptors. Finally, we quantified the resolution improvement in the retina by analyzing the radially averaged power spectrum of the retinal images.
First‐in‐human, randomized, double‐blind, placebo‐controlled, dose escalation trial of the anti‐herpes simplex virus monoclonal antibody HDIT101 in healthy volunteers (2022)

HDIT101 is a first-in-class humanized monoclonal antibody recognizing a conserved epitope in glycoprotein B, a target present on the surface of herpes simplex virus 1 (HSV-1) and HSV-2 particles as well as on virus-infected cells. This was a first-in-human, single-center, double-blind, placebo-controlled trial in 24 healthy volunteers, randomized 3:1 (placebo:active) in each of the six dose levels with escalating doses up to 12,150 mg HDIT101. HDIT101 was administered intravenously, to study safety, pharmacokinetics (PKs), and immunogenicity. HDIT101 was well-tolerated in all recipients and no serious or severe adverse events, no infusion-related reactions, and no events suggestive of dose limiting off-target toxicity occurred. The mean serum exposure (area under the curve from zero to infinity [AUC<sub>0-∞</sub> ]) of HDIT101 showed a linear increase from 4340 h*μg/ml at a dose of 50 mg to 1,122,247 h*μg/ml at a dose of 12,150 mg. No immunogenic effects following HDIT101 exposure were observed at any of the applied doses. HDIT101 demonstrated the expected PK properties of a monoclonal antibody was well-tolerated, and could be safely administered even at excessively high doses that may be required for treatment of patients with septical HSV spread.
Wound Healing Assays in Well Plate—Coupled Microfluidic Devices with Controlled Parallel Flow (2009)

The migratory or proliferative responses mounted by wounded cell monolayers are important to drug discovery and drug safety testing, as well as to basic research across a number of disciplines, including stem-cell biology, cell biology, ophthalmology, endocrinology, microbiology, oncology, and developmental biology. Scratch wounding by mechanical means is the golden standard to achieve an appropriate model system in which to study these cellular reactions. The scratch wounding technique is plagued by wound size irregularity, release of cytosolic contents along the wound edge, and difficulty in scaling up to higher throughput screening. To address these issues, we developed a microfluidic device coupled to a well plate in which wounds were produced enzymatically using highly controlled laminar flow streams. Within the device, epithelial cells were cultivated and exposed to different compounds. Proliferation and migration were characterized by bright-field microscopy. Resulting wound size was highly uniform compared with reported variability of manual scratch wounding. The protocol for wounding was fully automated using customized software, and response to wounding was followed in real time by microscopy.
3J solar cells comprising a lattice matched epitaxial SiGeSn subcell (2016)

The performance of quad-junction Ge based III-V multi-junction solar cells depends upon successful integration of a 1.0eV sub-cell into the existing InGaP/In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.01</sub> GaAs/Ge stack. The SiGeSn ternary alloy offers a means to fabricate a lattice-matched, 1.0eV sub-cell with the advantage that SiGeSn has both a tuneable band-gap and variable lattice parameter, enabling the material to be integrated into lattice-matched multi-junction architectures. A 1eV SiGeSn junction has been grown as both a single junction device and as the third junction in a InGaP/In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.01</sub> GaAs/SiGeSn triple junction device. The SiGeSn junction produces sufficient current to almost current match the InGaP and In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.01</sub> GaAs junctions and achieves a peak external quantum efficiency > 80% is demonstrated suggesting a lower limit on the base minority hole diffusion length of 5m. However, a degradation in open-circuit voltage and fill factor are observed with the SiGeSn sub-cell. This low voltage from the SiGeSn subcell is is attributed to recombination from defect levels within the SiGeSn band gap.
Spatiotemporal mechanisms for simple image feature perception in normal and amblyopic vision (2010)

We used the method of image classification to investigate the spatiotemporal mechanisms for simple feature perception in normal and amblyopic vision. In the first experiment, we estimated the spatiotemporal mechanism for detecting a luminance increment of a bright bar embedded in spatiotemporal noise for normal and amblyopic observers. The normal template is characterized by a temporal summation zone surrounded by symmetric spatial inhibition zones and followed by a temporal inhibition zone. The abnormal amblyopic template lacks inhibition but shows normal temporal summation. Neither blurring the stimuli in space nor varying the target signal-to-noise ratios caused any significant change in the normal or amblyopic template. However, decreasing the fundamental frequency of the stimuli restored the normal template in the amblyopic eye. Furthermore, the normal periphery demonstrates a spatiotemporal template similar to that of the amblyopic eye. The second experiment mapped the spatiotemporal interaction dynamics of flankers in an orientation discrimination task. For normal peripheral vision, assimilation of the perceived target orientation into the flanker orientation (i.e., crowding) occurs at flanker locations adjacent to the target in space and around or before the target presentation in time. Cueing the target may influence the spatiotemporal interaction map, but the strongest crowding never coincides with the target presentation. The amblyopic spatiotemporal interaction map is similar to that of the normal periphery, except that in general the spatiotemporal interaction is more widely distributed around and after the target presentation. Distant flankers induced "anti-crowding" (repulsion) of perceived orientation in both normal and amblyopic vision.
The influence of composition ratio on the morphology of biomedical polyurethanes (1999)

Two series of thermoplastic polyurethane elastomers were synthesized from 4,4′-methylenediphenyl diisocyanate (MDI), 1,4-butanediol (BDO) chain extender, and each of poly(tetramethylene oxide) (PTMO) and poly(hexamethylene oxide) (PHMO) macrodiols. The PTMO and PHMO molecular weights were kept constant at 993 and 852 g/mol, respectively. In the PTMO-based series, the composition ratio was varied between 48 and 58% (w/w) of macrodiol; 2 commercially available PTMO-based polymers were also included. These were Pellethane 2363 80A® and its harder counterpart, Pellethane 2363 55D®. In the PHMO-based series, the composition ratio was varied between 50 and 60% (w/w) of macrodiol. The materials were characterized by differential scanning calorimetry (DSC), dynamic mechanical thermal analysis (DMTA), wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS). Mechanical performance was also assessed by tensile testing, stress hysteresis, and hardness testing. Altering the composition ratio had a similar effect on morphology and properties for both the PTMO and PHMO-based series. An increase in hard segment content was associated with increased hard microdomain crystallinity, hardness, and stiffness. In both series, he beginning of hard microdomain interconnectivity was observed at a composition ratio of 52% soft segment. That is to say, for the processing and annealing conditions employed, macrodiol contents of 52% and below began to produce continuous, rather than discrete, hard microdomains. Pellethane 80A® was shown to have a discrete hard microdomain morphology, while Pellethane 55D® was shown to incorporate interconnecting hard microdomains. It is suggested that the superior biostability performance of Pellethane 55D relative to Pellethane 80A may be related to its interconnecting hard microdomain texture. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 937–952, 1999
Clinical and endocrine responses to embryonic and fetal death induced by manual rupture of the amniotic vesicle during early pregnancy in cows (1987)

Pregnancy was terminated in 4 cows by manual rupture of the amniotic vesicle on day 41 (n = 1) and day 46 (n = 3) after insemination. Each cow was necropsied 36 days after vesicle rupture, by which time only one cow had come into estrus. Luteal activity, monitored daily by plasma progesterone assay, was still evident in 2 cows 35 days after fetal death; in the remaining 2 cows, regression of the corpus luteum (CL) was achieved at 28 and 32 days, respectively. Uterine release of prostaglandin F2 alpha (PGF2 alpha), measured as the 15-keto metabolite (PGFM) PGF2 alpha, was monitored by a plasma sampling schedule; specimens were obtained every 4 hours. There were no appreciable releases of PGF2 alpha associated with fetal death. The first appreciable PGF2 alpha release in episodic form was seen only in conjunction with CL regression. In all cows, a palpable membrane slip was evident for 18 days after rupture of the amniotic vesicle, although at that time, uterine resilience was diminished in the 2 cows in which the CL subsequently regressed. After 18 days, the uterus was noticeably edematous and fluid-filled in all cows; in 1 of the cows with a regressed CL, the uterus had returned to prepregnancy size and tone by day 33.(ABSTRACT TRUNCATED AT 250 WORDS)
An Electron Microscopic Study of Normal and Chronically Denervated Rat Skeletal Muscle Following Succinylcholine Challenge (1974)

The ultrastructure of normal and chronically denervated rat skeletal muscle was studied with and without succinylcholine (SCC) challenge. Conventional electron microscopy and cytochemical tracing with horseradish-peroxidase to label the sarcolemma were used. Sarcolemmal breaks did not occur in the 28 days following denervation nor were they seen in normal and denervated muscle following SCC challenge. This study does not confirm the hypothesis that abnormal efflux of muscle protein following SCC challenge results from membrane breaks in normal or denervated muscle.
Photoelectrocatalysis to Improve Cycloreversion Quantum Yields of Photochromic Dithienylethene Compounds (2012)

An open and shut case: photoirradiation of the 9-mesityl-10-methylacridinium ion, which acts as a photoredox catalyst, evoked catalytic cycloreversion of the photochromic 1,2-dithienylethene (DTE) compounds with one order of magnitude enhancement in quantum yields. Mechanistic studies revealed that the back electron transfer and electron transfer from the neutral closed form of DTE compounds to the open-form radical cation are key steps.
Dry Thermal Oxidation of Polycrystalline and Amorphous Silicon Films for Application to Thin Film Transistors (1998)

Dry thermal oxidation of polycrystalline silicon (p-Si) and amorphous silicon (a-Si) has been studied. An oxidation temperature of 1070°C is a break point, at which the oxidation time of one atomic layer is nearly equal to the stress relaxation time. Below the break point temperature, oxidation stress is not relaxed at the silicon-oxide interface, because the stress relaxation time is longer than the oxidation time of one atomic layer. The high oxidation stress, together with the presence of grains and grain-boundaries, makes the interface rough, resulting in poor electrical properties in p-Si thin film transistors (TFTs). It is, therefore, important for fabricating good TFTs that p-Si or a-Si films are oxidized under conditions such that the oxidation time of one atomic layer is longer than the stress relaxation time to relax the oxidation stress at the interface.
High-performance, robustly verified Monte Carlo simulation with FullMonte (2018)

We introduce the FullMonte tetrahedral 3-D Monte Carlo (MC) software package for simulation, visualization, and analysis of light propagation in heterogeneous turbid media including tissue. It provides the highest computational performance and richest set of input, output, and analysis facilities of any open-source tetrahedral-mesh MC light simulator. It also provides a robust framework for statistical verification. A scripting interface makes set-up of simulation runs simple, including parameter sweeps, while simultaneously providing customization options. Data formats shared with class-leading visualization tools, VTK and Paraview, facilitate interactive generation of publication-quality fluence and irradiance maps. The simulator can read and write file formats supported by other similar simulators, such as TIM-OS, MMC, COMSOL (finite-element simulations), and MCML to support comparison. Where simulator features permit, FullMonte can take a single test case, run it in multiple software packages, and load the results together for comparison. Example meshes, optical properties, set-up scripts, and output files are provided for user convenience. We demonstrate its use in several test cases, including photodynamic therapy of the brain, bioluminescence imaging (BLI) in a mouse phantom, and a comparison against MCML for layered geometries. Application domains that can benefit from use of FullMonte include photodynamic, photothermal, and photobiomodulation therapies, BLI, diffuse optical tomography, MC software development, and biophotonics education. Since MC results may be used for preclinical or even clinical experiments, a robust and rigorous verification process is essential. Being a stochastic numerical method, MC simulation has unique challenges associated with verification of output results since observed differences may be due simply to output variance or actual differences in expected output. We describe and have implemented a rigorous and statistically justified framework for comparing between simulators of the same class and for performing regression testing.
The Sagnac effect and the role of simultaneity in relativity theory (2021)

We thoroughly examine the role of absolute and relative simultaneity in the interpretation of the Sagnac effect, using an approach that allows for determining the local speed along the light path. If the local speed of light is assumed to be c over the whole closed contour, there is no agreement with the observed result. There is agreement if the local speed is c along an open section of the contour only. Thus a rigorous and coherent interpretation of the Sagnac effect favours absolute over relative simultaneity. The implications for the Lorentz transformations and synchronization by means of the Global Positioning System are considered.
3.7-GHz Multi-Bank High-Current Single-Port Cache SRAM with 0.5V-1.4V Wide Voltage Range Operation in 3nm FinFET for HPC Applications (2023)

Wordline driver sleep (WLSLP) and write driver sleep (WDSLP) circuits are introduced to reduce leakage power while keeping fast write speed. With WLSLP and WDSLP, leakage power is reduced by 71%. In our SRAM design, it demonstrates 3.7GHz at 1.4 V and wide-range operation down to 0.5 V. It achieves the best FoM defined as density × frequency.
HetPipe: Enabling Large DNN Training on (Whimpy) Heterogeneous GPU Clusters through Integration of Pipelined Model Parallelism and Data Parallelism (2020)

Deep Neural Network (DNN) models have continuously been growing in size in order to improve the accuracy and quality of the models. Moreover, for training of large DNN models, the use of heterogeneous GPUs is inevitable due to the short release cycle of new GPU architectures. In this paper, we investigate how to enable training of large DNN models on a heterogeneous GPU cluster that possibly includes whimpy GPUs that, as a standalone, could not be used for training. We present a DNN training system, HetPipe (Heterogeneous Pipeline), that integrates pipelined model parallelism (PMP) with data parallelism (DP). In HetPipe, a group of multiple GPUs, called a virtual worker, processes minibatches in a pipelined manner, and multiple such virtual workers employ data parallelism for higher performance. We also propose a novel parameter synchronization model, which we refer to as Wave Synchronous Parallel (WSP) to accommodate both PMP and DP for virtual workers, and provide convergence proof of WSP. Our experimental results on a given heterogeneous setting show that with HetPipe, DNN models converge up to 49% faster compared to the state-of-the-art DP technique.
Adenovirus-Mediated Interferon γ Gene Therapy for Allergic Asthma: Involvement of Interleukin 12 and STAT4 Signaling (2002)

Allergic asthma is associated with airway inflammation and hyperresponsiveness caused by the dysregulated production of cytokines secreted by allergen-specific helper T type 2 (Th2) cells. Allergic subjects produce relatively low amounts of interferon gamma (IFN-gamma), a pleiotropic Th1 cytokine that downregulates Th2-associated responses. In this study, we examined the possibility of modulating ovalbumin (OVA)-induced inflammation and airway hyperreactivity (AHR) by recombinant adenovirus-mediated IFN-gamma (Ad-IFN-gamma) gene transfer. OVA-sensitized mice treated with Ad-IFN-gamma exhibit significantly lower levels of Th2 cytokines interleukin 4 (IL-4) and IL-5, OVA-specific serum IgE, lung eosinophilia, and AHR in response to methacholine challenge compared with control mice. The lung sections of the treated mice show less epithelial damage, mucous plugging, and eosinophil infiltration than controls. In contrast, Ad-IFN-gamma-treated mice express significantly higher levels of IFN-gamma and IL-12 when compared with controls. Moreover, administration of Ad-IFN-gamma to mice with established AHR significantly reduced AHR, Th2 cytokines, and lung inflammation. The IFN-gamma effects were dependent on IL-12 and STAT4 (signal transducer and activator of transcription 4), as mice treated with antibodies to IL-12 and STAT4 deficient mice show attenuated Ad-IFN-gamma responses. Thus, these results demonstrate that mucosal Ad-IFN-gamma gene transfer can effectively attenuate established allergen-induced airway inflammation and AHR, predominantly through an IL-12- and STAT4-dependent mechanism.
Randomness and the reverberation time, RT<inf>60</inf>, of acoustic responses (2014)

This paper investigates an implication of the clustering, on the complex plane, of the roots of transfer function polynomials obtained from acoustic responses. These polynomials can be the high order transfer functions obtained from room impulse responses or the relatively lower order ones obtained from head related impulse responses. This clustering behavior is explained using results from the theory of the roots of random polynomials. It is demonstrated that, although they do not appear that way, the coefficients of acoustic polynomials can be modeled as random polynomials with certain constraints applied. In the case of room impulse responses, the median of their clustered roots is shown to be directly related to the reverberation time of the room. This is shown to be an accurate measure of the reverberation time by comparison with other estimation techniques.
A General Method for Suzuki–Miyaura Coupling Reactions Using Lithium Triisopropyl Borates (2012)

Conditions for the Suzuki–Miyaura coupling of lithium triisopropyl borates are reported, as well as a procedure for a one-pot lithiation, borylation, and subsequent Suzuki–Miyaura coupling of various heterocycles with aryl halides. These borate species are much more stable toward protodeboronation than the corresponding boronic acids and can conveniently be stored on benchtop at room temperature.
Contribution of the Gut Microbiome to Drug Disposition, Pharmacokinetic and Pharmacodynamic Variability (2021)

The trillions of microbes that make up the gut microbiome are an important contributor to health and disease. With respect to xenobiotics, particularly orally administered compounds, the gut microbiome interacts directly with drugs to break them down into metabolic products. In addition, microbial products such as bile acids interact with nuclear receptors on host drug-metabolizing enzyme machinery, thus indirectly influencing drug disposition and pharmacokinetics. Gut microbes also influence drugs that undergo enterohepatic recycling by reversing host enzyme metabolic processes and increasing exposure to toxic metabolites as exemplified by the chemotherapy agent irinotecan and non-steroidal anti-inflammatory drugs. Recent data with immune checkpoint inhibitors demonstrate the impact of the gut microbiome on drug pharmacodynamics. We summarize the clinical importance of gut microbe interaction with digoxin, irinotecan, immune checkpoint inhibitors, levodopa, and non-steroidal anti-inflammatory drugs. Understanding the complex interactions of the gut microbiome with xenobiotics is challenging; and highly sensitive methods such as untargeted metabolomics with molecular networking along with other in silico methods and animal and human in vivo studies will uncover mechanisms and pathways. Incorporating the contribution of the gut microbiome to drug disposition, pharmacokinetics, and pharmacodynamics is vital in this era of precision medicine.
Experimental Research on Compressible Turbulent Shear Layers, Viscous-Inviscid Interactions, and Flow Separation. (1986)

This report describes the DoD-University Research Instrumentation Program Equipment Acquisition for Pennsylvania Univ. The thrust of this effort has been to outfit and upgrade Penn State's Supersonic Wind Tunnel Laboratory with modern instrumentation so that research in support oif national defense can be conducted. The subject area of this research is viscous-inviscid interactions in supersonic flight.