gebhart/patrepeval huggingface dataset:
Modeling biofilms with dual extracellular electron transfer mechanisms (2013)

Electrochemically active biofilms have a unique form of respiration in which they utilize solid external materials as terminal electron acceptors for their metabolism. Currently, two primary mechanisms have been identified for long-range extracellular electron transfer (EET): a diffusion- and a conduction-based mechanism. Evidence in the literature suggests that some biofilms, particularly Shewanella oneidensis, produce the requisite components for both mechanisms. In this study, a generic model is presented that incorporates the diffusion- and the conduction-based mechanisms and allows electrochemically active biofilms to utilize both simultaneously. The model was applied to S. oneidensis and Geobacter sulfurreducens biofilms using experimentally generated data found in the literature. Our simulation results show that (1) biofilms having both mechanisms available, especially if they can interact, may have a metabolic advantage over biofilms that can use only a single mechanism; (2) the thickness of G. sulfurreducens biofilms is likely not limited by conductivity; (3) accurate intrabiofilm diffusion coefficient values are critical for current generation predictions; and (4) the local biofilm potential and redox potential are two distinct parameters and cannot be assumed to have identical values. Finally, we determined that simulated cyclic and squarewave voltammetry based on our model are currently not capable of determining the specific percentages of extracellular electron transfer mechanisms in a biofilm. The developed model will be a critical tool for designing experiments to explain EET mechanisms.
An Instrument for Measuring the Modulation Transfer Functions of Low Power Telescopes and Telemicroscopes (1988)

An instrument using an electro-optical Fourier method for measuring the modulation transfer function (MTF) of low power telescopes and telemicroscopes is described. Because these devices are afocal, or nearly so, relay optics are needed to form real images at the detection section of the apparatus. The system is capable of measuring the MTF in monochromatic and white light, at any target azimuth, across the field of view, and through focus. The target system contains 14 square-wave gratings with spatial frequencies that range from 2.5 to 156 cpd. Images of these gratings are scanned across a slit. The output data are fed to a first-order recursive digital Butterworth bandpass filter for MTF analysis. The apparatus is diffraction limited at f/31.4. Therefore, it negligibly affects the measurement of the MTF of telescopes and telemicroscopes tested with exit pupils of up to 6.4 mm.
O5‐10‐03: MAPPING GENOME REPAIR HOTSPOTS IN POST‐MITOTIC HUMAN NEURONS (2019)

Neurons are the longest-living cells in our bodies and do not divide once they are terminally differentiated in early development. This lack of renewal makes neurons particularly susceptible to the age-related decline of their genomes. Genome instability is a hallmark of aging and is associated with Alzheimer's disease pathology. Despite this, we have limited knowledge of what healthy or disrupted genomic integrity looks like in neurons and how genomic instability contributes to AD progression. In order to better understand the mechanism of genome integrity in neurons, we have developed a novel next-generation sequencing method - ‘Repaired-Seq’ - that identifies frequently repaired regions of the genome in non-dividing cells. Repaired-Seq allows us to contextualize regions of the genome that are actively being surveyed for damage in neurons derived from human patients. Using Repaired-Seq, we have identified over 50,000 genome repair hotspots in neurons derived from embryonic stem cell lines. We have also found numerous genes transcribed by neurons that are either enriched or depleted for repair hotspots when accounting for gene length. Although genome repair correlates well with regions of open chromatin, many dynamic repair hotspots also exist in closed regions of neuronal genomes, indicating potential roles to regions of the genome that are not in active use. Finally, following application of DNA damaging agents, we find that new sites appear in the genome at the expense of repair hot spots that are prevalent under normal conditions. Repaired-Seq is a powerful method to understand the genomics of DNA repair in post-mitotic human neurons. The development of this method has led to the identification of a genomic feature observed for the first time in neurons – the repair hotspot. Interestingly, these sites populate the whole genome and are not exclusively limited to transcribed regions of the genome. Additionally, the stability of these sites of frequent repair suggests they are highly regulated, and that the accumulation of age-associated DNA lesions could potentially disrupt their careful maintenance. Repaired-Seq will prove to be a powerful tool in examining differences in the genome repair landscape in neurons derived from both cognitively normal and Alzheimer's disease patients.
Fluorenobenzofuran as the core structure of high triplet energy host materials for green phosphorescent organic light-emitting diodes (2012)

Thermally stable high triplet energy host materials based on a fluorenobenzofuran (BFF) core were synthesized and the device performances of green phosphorescent organic light-emitting diodes were investigated. BFF was designed as the electron transport type core with improved thermal stability. Two host materials based on the BFF core showed a high glass transition temperature over 140 °C and high triplet energy above 2.70 eV. They were used as the host materials for green phosphorescent organic light-emitting diodes and a high quantum efficiency close to 20% was achieved.
Data from Muscadine Grape Skin Extract (MPX) in Men with Biochemically Recurrent Prostate Cancer: A Randomized, Multicenter, Placebo-Controlled Clinical Trial (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; MuscadinePlus (MPX), a commercial preparation of pulverized muscadine grape skin, was evaluated as a therapeutic option for men with biochemically recurrent (BCR) prostate cancer wishing to defer androgen deprivation therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; This was a 12-month, multicenter, placebo-controlled, two-dose, double-blinded trial of MPX in 125 men with BCR prostate cancer, powered to detect a PSA doubling time (PSADT) difference of 6 months (low dose) and 12 months (high dose) relative to placebo. Participants were stratified (baseline PSADT, Gleason score) and randomly assigned 1:2:2 to receive placebo, 500 mg MPX (low), or 4,000 mg MPX (high) daily. Correlates included superoxide dismutase-2 (&lt;i&gt;SOD2&lt;/i&gt;) genotype, lipid peroxidation, and polyphenol pharmacokinetics.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The evaluable population included 112 patients, all treated for at least 6 months and 62% treated for 12 months. No significant difference was found in PSADT change between control and treatment arms (&lt;i&gt;P&lt;/i&gt; = 0.81): control 0.9 months (&lt;i&gt;n&lt;/i&gt; = 20; range, 6.7–83.1), low dose 1.5 months (&lt;i&gt;n&lt;/i&gt; = 52; range, 10.3–87.2), high dose 0.9 months (&lt;i&gt;n&lt;/i&gt; = 40; range, 27.3–88.1). One high-dose patient experienced objective response. No drug-related CTCAE grade 3–4 adverse events were seen. In a preplanned exploratory analysis, PSADT pre-to-post increase was significant in the 27 (26%) genotyped patients with &lt;i&gt;SOD2&lt;/i&gt; Alanine/Alanine genotype (rs4880 T&gt;C polymorphism) on MPX (pooled treatment arms; 6.4 months, &lt;i&gt;P&lt;/i&gt; = 0.02), but not in control (1.8 months, &lt;i&gt;P&lt;/i&gt; = 0.25).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Compared with placebo, MPX did not significantly prolong PSADT in BCR patients over two different doses. Exploratory analysis revealed a patient population with potential benefit that would require further study. &lt;i&gt;Clin Cancer Res; 24(2); 306–15. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Reconstructive ultrasound elasticity imaging for renal pathology detection (2002)

The real-time capability of ultrasound is it's major advantage for reconstructive elasticity imaging. In addition to providing important immediate feedback during patient examination, real-time data capture provides an excellent means for retrospective data processing. With retrospective processing, normal axial strain images can be optimized for highest SNR, the accuracy of lateral displacement estimates can be improved, and finally, non-linear elastic properties of tissue can be evaluated resulting in contrast enhancement of elasticity imaging. Retrospective processing requires no new data capture and adds new important features to reconstructive ultrasound elasticity imaging.
Universal Multi-Stage Precoding with Monomial Phase Rotation for Full-Diversity M2M Transmission (2014)

Machine-to-machine (M2M) communications have been considered as an important application to connect a massively large number of different devices in networks. In particular for M2M wireless networks, low latency and high reliability are of great importance. To fulfill the requirements, a diversity technique exploiting limited resources is proposed in this paper for short-message transmissions. The proposed method uses multiple stages of fast unitary transforms and diagonal phase rotations to achieve full- diversity gain. A monomial phase rotation is also proposed to facilitate an optimization of the precoding matrix. It is verified that the proposed four-stage precoding provides universal diversity gain irrespective of channel selectivity in time and frequency, without changing monomial parameters. In addition, it is shown that the four-stage precoding based on the discrete Haar transform (DHT) achieves a full diversity while the computational complexity is significantly reduced from a log- linear order to a linear order compared to the other unitary transforms such as the discrete Fourier transform (DFT).
A novel millimeter-wave channel simulator and applications for 5G wireless communications (2017)

This paper presents details and applications of a novel channel simulation software named NYUSIM, which can be used to generate realistic temporal and spatial channel responses to support realistic physical-and link-layer simulations and design for fifth-generation (5G) cellular communications. NYUSIM is built upon the statistical spatial channel model for broadband millimeter-wave (mmWave) wireless communication systems developed by researchers at New York University (NYU). The simulator is applicable for a wide range of carrier frequencies (500 MHz to 100 GHz), radio frequency (RF) bandwidths (0 to 800 MHz), antenna beamwidths (7° to 360° for azimuth and 7° to 45° for elevation), and operating scenarios (urban microcell, urban macrocell, and rural macrocell), and also incorporates multiple-input multiple-output (MIMO) antenna arrays at the transmitter and receiver. This paper also provides examples to demonstrate how to use NYUSIM for analyzing MIMO channel conditions and spectral efficiencies, which show that NYUSIM is an alternative and more realistic channel model compared to the 3rd Generation Partnership Project (3GPP) and other channel models for mmWave bands.
Measurement of the cross section for top-quark pair production in pp collisions at $\sqrt {s} = {7}\,{\text{TeV}}$ with the ATLAS detector using final states with two high-p T leptons (2012)

A bstract A measurement is reported of the production cross section of top-quark pairs ( t $\overline t$ ) in proton-proton collisions at a center-of-mass energy of 7 TeV recorded with the ATLAS detector at the LHC. Candidate events have a signature consistent with containing two isolated leptons, large missing transverse momentum, and at least two jets. Using a data sample corresponding to an integrated luminosity of 0.70 fb −1 , a t $\overline t$ production cross section ${\sigma_{t\overline t }} = {176}\pm {5}\left( {{\text{stat}}.} \right)_{ - {11}}^{ + 14}\left( {{\text{syst}}.} \right)\pm {8}\left( {{\text{lum}}.} \right)$ pb is measured for an assumed top-quark mass of m t = 172 . 5 GeV. This measurement is in good agreement with Standard Model predictions.
Improved Manufacturing Quality and Bonding of Laser Machined Microfluidic Systems (2015)

Laser micro-machining offers a versatile tool for the rapid manufacturing of polymeric microfluidics systems, with a typical turn-around-time in the order of minutes. However, the chaotic nature of the thermal evaporative ablation process can yield a significant number of defects in the surface of the manufactured microchannels, in the form of residual condensed material. In this work we have investigated the use of solvent evaporation by which to not only laminate bond the laser machined structures but to remove a significant number of the defect formed by the condensation of residual polymer. Results are presented of the surface profiling of the bonded channel structures and demonstrations of the bonding of the microchips to produce autonomous capillary microchannels.
Arctigenin Prevents Retinal Edema in a Murine Retinal Vein Occlusion Model (2023)

Macular edema causes vision loss in patients with retinal vein occlusion (RVO) and diabetic macular edema (DME). The intravitreal injection of anti-vascular endothelial growth factor (VEGF) agents is used for treatment; however, this therapy is invasive, and recurrence occurs in some cases. The establishment of a non-invasive treatment would help to solve these problems. Here, we focused on arctigenin, a lignan polyphenol found in burdock sprout, and has effects on inflammatory and microcirculatory when taken orally. We hypothesized that oral intake of arctigenin could be effective against retinal edema in RVO and DME. In this study, the degree of retinal edema by measuring the total retinal thickness using optical coherence tomography (OCT) and the thickness of the inner nuclear layer (INL) by hematoxylin-eosin (H&E) staining were investigated. Oral administration of arctigenin ameliorated retinal edema in an RVO murine model by inhibiting the decrease in occludin and vascular endothelial (VE)-cadherin. Moreover, in retinas with edema, arctigenin suppressed the induction of VEGF, tumor necrosis factor α (TNFα), and matrix metallopeptidase 9 (MMP9). Next, the effects of arctigenin on barrier function were assessed in human retinal microvascular endothelial cells (HRMECs) by measuring the trans-endothelial electrical resistance (TEER) and conducting fluorescein isothiocyanate (FITC)-dextran permeability assays. Arctigenin showed a protective effect against VEGF-induced barrier dysfunction. In addition, arctigenin inhibited the TNFα-mediated activation of the nuclear factor-kappaB (NF-κB)/p38 mitogen-activated protein kinase (MAPK) pathway. These results suggested that oral administration of arctigenin has beneficial effects on retinal edema by inhibiting vascular hyperpermeability in endothelial cells.
Label-Free Surface Enhanced Raman Scattering Approach for High-Throughput Screening of Biocatalysts (2016)

Biocatalyst discovery and directed evolution are central to many pharmaceutical research programs, yet the lack of robust high-throughput screening methods for large libraries of enzyme variants generated (typically 10(6)-10(8)) has hampered progress and slowed enzyme optimization. We have developed a label-free generally applicable approach based on Raman spectroscopy which results in significant reductions in acquisition times (>30-fold). Surface enhanced Raman scattering (SERS) is employed to monitor the enzyme-catalyzed conversion by xanthine oxidase of hypoxanthine to xanthine to uric acid. This approach measures the substrates and products directly and does not require chromogenic substrates or lengthy chromatography, was successfully benchmarked against HPLC, and shows high levels of accuracy and reproducibility. Furthermore, we demonstrate that this SERS approach has utility in monitoring enzyme inhibition illustrating additional medical significance to this high-throughput screening method.
Efficacy and Safety of Photodynamic Therapy for Recurrent, High Grade Nonmuscle Invasive Bladder Cancer Refractory or Intolerant to Bacille Calmette-Guérin Immunotherapy (2013)

Photodynamic therapy with Radachlorin is a safe, effective treatment for nonmuscle invasive bladder cancer refractory or intolerant to bacillus Calmette-Guérin therapy in select patients.
Radio frequency superconducting parametric transducer for gravitational wave antennae (1995)

We report on the design and testing of an ultrasensitive, electromechanical transducer for use on resonant mass gravitational wave antennae. The transducer is a superconducting, radio frequency resonant bridge circuit operating near 200 MHz. We have minimized several important sources of noise in this transducer system. The Johnson noise of the transducer circuit is reduced through using a superconducting niobium stripline circuit and low-loss insulating materials. At a temperature of 4.2 K we have achieved unloaded electrical quality factors of 200 000. The bridge circuit is balanced by piezoelectric actuators which control the spacing between the proof mass and capacitive segments of the stripline circuit and we have achieved a residual bridge imbalance of 3×10−7. Finally, low noise cryogenically cooled field-effect transistors are used for the first amplifier stage, enabling us to obtain an amplifier noise level which is 5400 times the quantum limit. The transducer, which has a 0.080 kg proof mass, was affixed to the end of a prototype, resonant bar, gravitational wave antenna with a mass of approximately 100 kg. The primary purpose of this small antenna was to evaluate the transducer, which is designed to be mounted on a much more massive antenna. Our theoretical analysis and measurements of the detector agree and indicate a burst noise temperature of 1.8 K using the 100 kg bar. This corresponds to a gravity wave burst sensitivity of h=1.1×10−16, in terms of relative strain amplitude. With no other improvements, if the transducer mechanically resonant frequency were tuned to and installed on a 2000 kg antenna, the antenna would reach a noise temperature of 1.3 mK, which is equivalent to a gravitational wave burst sensitivity, h≊5.7×10−19.
In vivo regeneration of murine prostate from dissociated cell populations of postnatal epithelia and urogenital sinus mesenchyme (2003)

The existence of a postnatal prostate stem cell is supported by several types of evidence. Withdrawal of androgen leads to involution of the gland, but readdition can rapidly stimulate regeneration. Tissue fragments derived from mouse or rat prostatic epithelia from midgestation embryos or adult mice, when combined with tissue fragments from urogenital sinus mesenchyme and grafted under the kidney capsule, can regenerate prostatic structures. Indirect evidence supports that the stem cell population is contained within the basal layer. Purified prostatic stem cell preparations would be useful to define the physical and functional properties required for regeneration and to compare with cells that accumulate during abnormal growth states, like prostate cancer. We have developed a regeneration system using dissociated cell populations of postnatal prostate epithelia and embryonic urogenital sinus mesenchyme. Efficient in vivo regeneration of prostatic structures in the subcapsular space of the kidney was observed within 4-8 wk with as few as 103 epithelial cells from prostates derived from donors 10 d to 6 wk of age. The regenerated structures show a branching tubular epithelial morphology, with expression of a panel of markers consistent with prostate development. Donor epithelial populations can be readily infected with GFP expressing lentiviral vectors to provide integration markers and easy visualization. The cell preparations of urogenital sinus mesenchyme can be expanded in short-term in vitro culture while their inductive capabilities are retained. Further definition of the subpopulation of prostate epithelial cells containing the regeneration activity should be possible with such technologies.
Measurement of Intraoperative Blood Loss in Pediatric Orthopaedic Patients: Evaluation of a New Method (2018)

Estimated blood loss measured using the Triton system correlated better with the reference method than with the gravimetric method. The visual estimation method was found to be inaccurate. Intraoperative use of the Triton system is convenient and precise for monitoring intraoperative blood loss.
Hot-Carrier Photoemission in Scaled CMOS Technologies: A Challenge for Emission Based Testing and Diagnostics (2006)

Optical testing of advanced CMOS circuits successfully exploits the near-infrared photon emission by hot-carriers in transistor channels (see EMMI (Ng et al., 1999) and PICA (Kash and Tsang, 1997) (Song et al., 2005) techniques). However, due to the continuous scaling of features size and supply voltage, spontaneous emission is becoming fainter and optical circuit diagnostics becomes more challenging. Here we present the experimental characterization of hot-carrier luminescence emitted by transistors in four CMOS technologies from two different manufacturers. Aim of the research is to gain a better perspective on emission trends and dependences on technological parameters. In particular, we identify luminescence changes due to short-channel effects (SCE) and we ascertain that, for each technology node, there are two operating regions, for short- and long-channels. We highlight the emission reduction of p-FETs compared to n-FETs, due to a "red-shift" (lower energy) of the hot-carrier distribution. Eventually, we give perspectives about emission trends in actual and future technology nodes, showing that luminescence dramatically decreases with voltage, but it recovers strength when moving from older to more advanced technology generations. Such results extend the applicability of optical testing techniques, based on present single-photon detectors, to future low-voltage chips