gebhart/patrepeval huggingface dataset:
Association between disorganization of retinal inner layers and visual acuity after proliferative diabetic retinopathy surgery (2019)

We report to evaluate if disorganization of the retinal inner layers (DRIL) obtained by swept-source optical coherence tomography (SS-OCT) predicts the postoperative best-corrected visual acuity (BCVA) to treat proliferative diabetic retinopathy (PDR). Twenty-one eyes of 21 patients who underwent vitrectomy for PDR were studied retrospectively. BCVA and SS-OCT images were obtained until 6 months postoperatively. The associations between BCVA and SS-OCT parameters measured in a 1-mm central foveal area were evaluated. The DRIL length, external limiting membrane disruption, and ellipsoid zone (EZ) disruption 1 month postoperatively were associated positively with the postoperative logarithm of the minimum angle of resolution (logMAR) BCVA at 1, 3, and 6 months (1 month, p = 0.009, p = 0.013, p = 0.001; 3 months, p = 0.03, p = 0.021, p = 0.002; and 6 months, p = 0.021, p = 0.013, and p = 0.005, respectively). The eyes with a 500-µm or longer DRIL 1 month postoperatively (19%, 4/21 eyes) had significantly worse VA at 1, 3, and 6 months postoperatively (p = 0.007, p = 0.008, and p = 0.020, respectively). Multilinear regression analysis of all visits until 6 months postoperatively showed that the DRIL was correlated more significantly (p = 0.0004) with logMAR BCVA than the disrupted EZ length. The DRIL in the early postoperative period may predict the visual outcomes after treating PDR.
Output stabilization technology with chemical impurity control on ArF excimer laser (2000)

Based on accurate gas analysis technology it has been found that both gas purity and gas control are key factors in optimizing the performance of ArF excimer lasers. The study of the behavior of gas impurities inside the laser chamber showed that impurities built up not only during laser operation but also during rest periods. In-situ gas analysis and controlled impurity gas addition clarified that hydrogen fluoride and oxygen impurities, are the main causes for the decrease of laser output energy. Based on our experiments, a modified gas composition was chosen for the ArF laser that significantly improved its output characteristics.
Quantitative measurement of ultrasound pressure field by optical phase contrast method and acoustic holography (2016)

Abstract A fast and accurate measurement of an ultrasound field with various exposure sequences is necessary to ensure the efficacy and safety of various ultrasound applications in medicine. The most common method used to measure an ultrasound pressure field, that is, hydrophone scanning, requires a long scanning time and potentially disturbs the field. This may limit the efficiency of developing applications of ultrasound. In this study, an optical phase contrast method enabling fast and noninterfering measurements is proposed. In this method, the modulated phase of light caused by the focused ultrasound pressure field is measured. Then, a computed tomography (CT) algorithm used to quantitatively reconstruct a three-dimensional (3D) pressure field is applied. For a high-intensity focused ultrasound field, a new approach that combines the optical phase contrast method and acoustic holography was attempted. First, the optical measurement of focused ultrasound was rapidly performed over the field near a transducer. Second, the nonlinear propagation of the measured ultrasound was simulated. The result of the new approach agreed well with that of the measurement using a hydrophone and was improved from that of the phase contrast method alone with phase unwrapping.
Mobile cardiorespiratory and metabolic laboratory: diagnosis of chronic obstructive pulmonary disease, cardiovascular and metabolic diseases (2016)

The aim of this study was to determine risk factors of chronic non-infectious diseases and early diagnosis of cardiovascular, respiratory and endocrine functional disorders in industrial workers using a mobile cardiorespiratory and metabolic laboratory. Methods. This was a prospective non-comparative observational study in a non-selected population. All participants underwent the following measurements: weight and height, wrist and thigh circumferences, pulse oxymetry, exhaled nitric oxide (NO) and exhaled carbon monooxide (CO), spirometry before and after bronchodilator inhalation, electrocardiogram, arterial stiffness and endothelial dysfunction, blood glucose and blood total cholesterol. Indirect calorimetry with energy expenditure calculation was used in several patients. Validated questionnaires were also used. Results. The study involved 194 industrial workers. High prevalence of risk factors, such as tobacco smoking (45% of active smokers, 31% of ex-smokers), obesity (BMI ≥ 30 kg x m –2 in 37%), hypercholesterolemia (34%), and endothelial dysfunction (57%), was found. Vascular biomechanics correlated with bronchial patency, systemic arterial pressure and exhaled CO concentration. Bronchial obstruction was found in 56% of subjects, of them, COPD was diagnosed in 13%. Conclusion. Mobile cardiorespiratory and metabolic laboratory allows medical care delivery directly to a working place, and effective detection of risk factors and chronic lung disease.
Routing Single Photons from a Trapped Ion Using a Photonic Integrated Circuit (2023)

Trapped ions are promising candidates for nodes of a scalable quantum network due to their long-lived qubit coherence times and high-fidelity single- and two-qubit gates. Future quantum networks based on trapped ions will require a scalable way to route photons between different nodes. Photonic integrated circuits from fabrication foundries provide a compact solution to this problem. However, these circuits typically operate at telecommunication wavelengths that are incompatible with the strong dipole emissions of trapped ions. In this work, we demonstrate the routing of single photons from a trapped ion using a photonic integrated circuit. We employ quantum frequency conversion to match the emission of the ion to the operating wavelength of a foundry-fabricated silicon nitride photonic integrated circuit, achieving a total transmission of 31.0% \ifmmode\pm\else\textpm\fi{} 0.9% through the device. Using programmable phase shifters, we switch the single photons between the output channels of the circuit and demonstrate a 50:50 beam splitting condition. These results constitute an important step towards programmable routing and entanglement distribution in large-scale quantum networks and distributed quantum computers.
Data from Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Advanced-stage ovarian clear cell carcinoma (OCCC) is unresponsive to conventional platinum-based chemotherapy. Frequent alterations in OCCC include deleterious mutations in the tumor suppressor &lt;i&gt;ARID1A&lt;/i&gt; and activating mutations in the PI3K subunit &lt;i&gt;PIK3CA&lt;/i&gt;. In this study, we aimed to identify currently unknown mutated kinases in patients with OCCC and test druggability of downstream affected pathways in OCCC models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; In a large set of patients with OCCC (&lt;i&gt;n&lt;/i&gt; = 124), the human kinome (518 kinases) and additional cancer-related genes were sequenced, and copy-number alterations were determined. Genetically characterized OCCC cell lines (&lt;i&gt;n&lt;/i&gt; = 17) and OCCC patient–derived xenografts (&lt;i&gt;n&lt;/i&gt; = 3) were used for drug testing of ERBB tyrosine kinase inhibitors erlotinib and lapatinib, the PARP inhibitor olaparib, and the mTORC1/2 inhibitor AZD8055.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We identified several putative driver mutations in kinases at low frequency that were not previously annotated in OCCC. Combining mutations and copy-number alterations, 91% of all tumors are affected in the PI3K/AKT/mTOR pathway, the MAPK pathway, or the ERBB family of receptor tyrosine kinases, and 82% in the DNA repair pathway. Strong p-S6 staining in patients with OCCC suggests high mTORC1/2 activity. We consistently found that the majority of OCCC cell lines are especially sensitive to mTORC1/2 inhibition by AZD8055 and not toward drugs targeting ERBB family of receptor tyrosine kinases or DNA repair signaling. We subsequently demonstrated the efficacy of mTORC1/2 inhibition in all our unique OCCC patient–derived xenograft models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These results propose mTORC1/2 inhibition as an effective treatment strategy in OCCC. &lt;i&gt;Clin Cancer Res; 24(16); 3928–40. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Conopressin-T from Conus tulipa Reveals an Antagonist Switch in Vasopressin-like Peptides (2008)

We report the discovery of conopressin-T, a novel bioactive peptide isolated from Conus tulipa venom. Conopressin-T belongs to the vasopressin-like peptide family and displays high sequence homology to the mammalian hormone oxytocin (OT) and to vasotocin, the endogenous vasopressin analogue found in teleost fish, the cone snail's prey. Conopressin-T was found to act as a selective antagonist at the human V 1a receptor. All peptides in this family contain two conserved amino acids within the exocyclic tripeptide (Pro7 and Gly9), which are replaced with Leu7 and Val9 in conopressin-T. Whereas conopressin-T binds only to OT and V 1a receptors, an L7P analogue had increased affinity for the V 1a receptor and weak V2 receptor binding. Surprisingly, replacing Gly9 with Val9 in OT and vasopressin revealed that this position can function as an agonist/antagonist switch at the V 1a receptor. NMR structures of both conopressin-T and L7P analogue revealed a marked difference in the orientation of the exocyclic tripeptide that may serve as templates for the design of novel ligands with enhanced affinity for the V 1a receptor.
BASIC—LIVER, PANCREAS, AND BILIARY TRACT Brain Region-Selective Mechanisms Contribute to the Progression of Cerebral Alterations in Acute Liver Failure in Rats (2011)

BACKGROUND & AIMS: Patients with acute liver failure (ALF) often die of intracranial pressure (IP) and cerebral herniation. Main contributors to increased IP are ammonia, glutamine, edema, and blood flow. The sequence of events and underlying mechanisms, as well as the temporal pattern, regional distribution, and contribution of each parameter to the progression of neurologic deterioration and IP, are unclear. We studied rats with ALF to follow the progression of changes in ammonia, glutamine, grade and type (vasogenic or cytotoxic) of edema, blood-brain barrier permeability, cerebral blood flow, and IP. We assessed whether the changes in these parameters were similar between frontal cortex and cerebellum and evaluated the presence, type, and progression of edema in 12 brain areas. METHODS: ALF was induced by injection of galactosamine. The grade and type of edema was assessed by measuring the apparent diffusion coefficient by magnetic resonance imaging. Cerebral blood flow was measured by magnetic resonance and blood-brain barrier permeability by Evans blue‐albumin extravasation. RESULTS: Increased IP arises from an early increase of blood‐brain barrier permeability in certain areas (including cerebellum but not frontal cortex) followed by vasogenic edema. Ammonia and glutamine then increase progressively, leading to cytotoxic edema in many areas. Alterations in lactate and cerebral blood flow are later events that further increase IP. CONCLUSIONS: Different mechanisms in specific regions of the brain contribute, with different temporal patterns, to the progression of cerebral alterations and IP in ALF.
<title>Single molecule fluorescence burst detection of DNA separated by capillary electrophoresis</title> (1996)

A method has been developed for detecting DNA separated by capillary gel electrophoresis using single molecule photon burst counting. A confocal fluorescence microscope was used to observe the fluorescence bursts from single molecules of DNA multiply labeled with a thiazole orange derivative as they passed through the approximately 2 micrometer diameter focused laser beam. Amplified photoelectron pulses from the photomultiplier are grouped into bins of from 360 - 450 microseconds in duration, and the resulting histogram stored in a computer for analysis. Solutions of M13 DNA were first flowed through the capillary at various concentrations, and the resulting data were used to optimize the parameters for digital filtering using a low-pass Fourier filter, selecting a discriminator level for peak detection, and applying a peak-calling algorithm. The optimized single molecule counting method was then used to detect a separation of pBR 322 DNA from pRL 277 DNA. Clusters of discrete fluorescence bursts were observed at the expected appearance time of each DNA band. These separations were easily detected when only 50 to 100 molecules of DNA per band traveled through the detection region. This new detection technology should lead to the routine analysis of DNA in capillary columns with an on-column sensitivity of approximately 100 DNA molecules per band or better.
BINDING OF AGGREGATED IgG TO NEPHRITOGENIC TYPE 12 STREPTOCOCCI: INFLUENCE OF SERUM, C1 AND C4 (1977)

The uptake of aggregated IgG by type 12, M protein positive (M + ve) streptococci was high in the presence of fresh serum, while the uptake by type 12, M-ve, type 1 and type 2, M + ve or M-ve streptococci was inhibited. Serum heated to 56 degrees C for 30 min inhibited the uptake of aggregated IgG by all strains tested. Purified C1q or macromolecular C1 added to heat-treated serum restituted the uptake of aggregated IgG. It was shown that C1 and C4 in fresh serum influenced the uptake of aggregated IgG by streptococci, resulting in the distinct reaction patterns observed.
A quad-channel 112&#x2013;128 Gb/s coherent transmitter in 40 nm CMOS (2014)

A quad-channel, 112–128 Gb/s coherent DP-QPSK transmitter in 40 nm CMOS is presented. The 27.9–32.1 Gb/s TX features a half-rate architecture with a 2-tap FIR. The measured output has an amplitude of 1.2V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp-diff</inf> with 1.3 ps deterministic jitter (DJ). The DP-QPSK TX's precoded data alignment is maintained through the quad-lane transmitter by the use of an automatic synchronous feedback loop, removing the need for a master global reset. The PLL outputs the full-rate and half-rate clock with ±0.5 UI skew adjustment relative to the data. The power consumption of the transmitter and PLL is 712 mW.
444.9 nm semipolar (112¯2) laser diode grown on an intentionally stress relaxed InGaN waveguiding layer (2012)

We demonstrate an electrically injected semipolar (112¯2) laser diode (LD) grown on an intentionally stress relaxed n-In0.09Ga0.91N waveguiding layer. Detrimental effects of misfit dislocations (MDs) in the proximity of the active region were effectively suppressed by utilizing a p/n-Al0.2Ga0.8N electron/hole blocking layer between the dislocated heterointerfaces and the active region. The threshold current density of the LD was ∼20.3 kA/cm2 with a lasing wavelength of 444.9 nm. This LD demonstrates an alternative approach in semipolar AlInGaN LD waveguide design where the thickness and composition of the waveguiding and/or cladding layers are not limited by the critical thickness for MD formation.
Networked Illumination Control With Distributed Light-Harvesting Wireless Sensors (2014)

We consider networked control of luminaires to adapt illumination in an indoor environment to occupancy and daylight based on distributed light-harvesting wireless sensing modules. Each light-harvesting wireless sensing module consists of an occupancy sensor, a light sensor, a wireless radio, a microcontroller unit, and a photovoltaic cell. The occupancy sensor and light sensor, respectively, determine presence and illumination level within their fields-of-view. This local sensor information, along with control information from neighboring sensing modules, is used by a local controller to determine the dimming level of its luminaire so as to achieve its reference setpoint. To realize this system, we propose a low-power wireless sensing protocol and a neighbor-aided illumination control method considering the harvesting constraints of the sensors. The proposed methods are implemented in an indoor lighting system testbed and the performance is shown to meet desired illumination conditions.
Theoretical Study of Bimolecular Reactions between Carbenium Ions and Paraffins:  The Proposal of a Common Intermediate for Hydride Transfer, Disproportionation, Dehydrogenation, and Alkylation (1999)

The mechanism of the bimolecular reactions of ethyl cation with ethane and propane and of s-propyl cation with ethane, propane, and isopentane is theoretically investigated by means of the B3PW91 density functional method. The study includes complete geometry optimization and characterization of the reactants, products, reaction intermediates, and transition states involved, calculation of the reaction enthalpies and activation energies for the different elemental steps, and obtainment of the equilibrium constants and relative reaction rate constants by means of transition state theory. It is found that the interaction of a carbenium ion with a saturated alkane always results in formation of a stable carbonium ion intermediate and that different intramolecular rearrangements of this common intermediate can explain the mechanism of acid-catalyzed hydrocarbon reactions, such as hydride transfer, disproportionation, dehydrogenation, and alkylation.
Tumor cell lysis and tumor growth inhibition by the isotype variants of MAb BR55-2 directed against Y oligosaccharide. (1992)

IgG3 murine MAb BR55-2 is directed against adenocarcinoma associated Y oligosaccharide. Isotype IgG1, IgG2b and IgG2a switch variants of the BR55-2 antibody were compared in antibody dependent-cell mediated cytotoxicity (ADCC) and complement mediated cytotoxicity (CDC) assays in the murine system. IgG3, IgG2a and IgG2b isotypes mediated ADCC with murine macrophages. Murine splenocytes mediated low levels of ADCC, with IgG3 and IgG2a being always more effective than IgG1 and IgG2b isotypes. All four isotypes were ineffective in CDC with murine serum as a source of complement. In the in vivo experiments, growth of human tumors xenotransplanted into nude mice was best inhibited by both IgG3 and IgG2a isotypes while IgG1 protein was the least effective. Thus, IgG3 and IgG2a isotypes are the most efficient proteins for cancer immunotherapy since they mediate the highest tumoricidal activities in vitro and in vivo.
Magnetic Viscosity of Fine Maghemite Clusters Prepared by Electrochemical Method (1998)

γ-Fe2O3 nanometric clusters have been synthesized in aqueous solution under 1,10-phenanthroline and/or PVA by an electrochemical method with dc current. Transmission electron microphotographs show that the particles are roughly spherical and their sizes are about 5 to 10 nm. The magnetic properties have been measured by a SQUID magnetometer. The magnetic clusters in the polymer behave as independent monodomains at room temperature, however, at low temperature the energy barrier increases dramatically with decreasing temperature below TB ≈︂ 150 to 200 K as there are interparticle interactions being suppressed by thermal fluctuations.
Demonstration of an Optoelectronic Dual-Diode Optically Controlled Optical Gate with a 20 Picosecond Repetition Period (2000)

Using surface-normal pulses, a low-power, optically controlled optical gate incorporating two stacked AlGaAs diodes opens and closes within 20 picoseconds with a 30% reflectivity change. Repeated gating with 20 picosecond periods is demonstrated, matching simulations.
Investigating (Pseudo)-Heterogeneous Pd-Catalysts for Kraft Lignin Depolymerization under Mild Aqueous Basic Conditions (2021)

Lignin is one of the main components of lignocellulosic biomass and corresponds to the first renewable source of aromatic compounds. It is obtained as a by-product in 100 million tons per year, mainly from the paper industry, from which only 2–3% is upgraded for chemistry purposes, with the rest being used as an energy source. The richness of the functional groups in lignin makes it an attractive precursor for a wide variety of aromatic compounds. With this aim, we investigated the Pd-catalyzed depolymerization of lignin under mild oxidizing conditions (air, 150 °C, and aqueous NaOH) producing oxygenated aromatic compounds, such as vanillin, vanillic acid, and acetovanillone. Palladium catalysts were implemented following different strategies, involving nanoparticles stabilized in water, and nanoparticles were supported on TiO2. Significant conversion of lignin was observed in all cases; however, depending on the catalyst nature and the synthetic methods, differences were observed in terms of selectivity in aromatic monomers, mainly vanillin. All these aspects are discussed in detail in this report, which also provides new insights into the role that Pd-catalysts can play for the lignin depolymerization mechanism.
Non-Hermitian physics for optical manipulation uncovers inherent instability of large clusters (2021)

Intense light traps and binds small particles, offering unique control to the microscopic world. With incoming illumination and radiative losses, optical forces are inherently nonconservative, thus non-Hermitian. Contrary to conventional systems, the operator governing time evolution is real and asymmetric (i.e., non-Hermitian), which inevitably yield complex eigenvalues when driven beyond the exceptional points, where light pumps in energy that eventually "melts" the light-bound structures. Surprisingly, unstable complex eigenvalues are prevalent for clusters with ~10 or more particles, and in the many-particle limit, their presence is inevitable. As such, optical forces alone fail to bind a large cluster. Our conclusion does not contradict with the observation of large optically-bound cluster in a fluid, where the ambient damping can take away the excess energy and restore the stability. The non-Hermitian theory overturns the understanding of optical trapping and binding, and unveils the critical role played by non-Hermiticity and exceptional points, paving the way for large-scale manipulation.
Assessing Mechanical Properties and Microstructure of Fire-Damaged Engineered Cementitious Composites (2010)

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Enhancement and suppression of surface plasmon resonance in Ag aggregate by optical gain and absorption in surrounding dielectric medium (2005)

We have observed the compensation of loss in metal by gain in interfacing dielectric in the mixture of aggregated silver nanoparticles and rhodamine 6G dye. The demonstrated six-fold enhancement of the Rayleigh scattering is the evidence of the increase of the quality factor of the surface plasmon (SP) resonance. The reported experimental observation paves the road to many practical applications of nanoplasmonics. We have also predicted and experimentally observed a suppression of the surface SP resonance in metallic nanoparticles embedded in a dielectric host with absorption.