gebhart/patrepeval huggingface dataset:
In vivo increase of the human lens equatorial diameter during accommodation (1996)

The movement of the human lens equator during accommodation was examined in vivo. High-resolution ultrasound images of the lens equator were obtained from young human subjects whose amplitude of accommodation was controlled with 1% tropicamide and 2% pilocarpine. To avoid errors that otherwise arise from eye rotation or other movement, the cornea and sclera were used as positional references in comparative studies of the video images obtained from the unaccommodated and accommodated states. During accommodation, the movement at the lens equator involved small displacement; i.e., < 100 microns, and the equator did not move anteriorly or posteriorly but peripherally toward the sclera. These results indicate that the lens equator is under increased zonular tension during accommodation, in contradiction to Helmholtz's widely accepted theory of accommodation.
Software platform dedicated for in-memory computing circuit evaluation (2017)

This paper presents a new software platform, co-developed by research teams with expertises in memory design, and software engineering and compilation aspects, to dimension and evaluate a novel In-Memory Power Aware CompuTing (IMPACT) system for IoT. IMPACT circuit is an emerging memory that promises to save execution time and power consumption by embedding computing abilities. The proposed platform permits to manually convert a software application from conventional to IMPACT implementation using vector representation. The two implementations are then compiled on the Low Level Virtual Machine (LLVM) and traced in order to evaluate their performance in terms of timing and energy consumption. The results of emulating image-processing and secure applications on IMPACT system show a significant gain in the execution time and the energy consumption compared to a conventional system with an ARM Cortex®-M7 processor. The execution time can be reduced from 50x to 6145x, depending on the application and the workload size. Furthermore, the gain of the energy consumption is about 12.6x.
DNA nanoparticle-mediated ABCA4 delivery rescues Stargardt dystrophy in mice (2012)

Mutations in the photoreceptor-specific flippase ABCA4 are associated with Stargardt disease and many other forms of retinal degeneration that currently lack curative therapies. Gene replacement is a logical strategy for ABCA4-associated disease, particularly given the current success of traditional viral-mediated gene delivery, such as with adeno-associated viral (AAV) vectors. However, the large size of the ABCA4 cDNA (6.8 kbp) has hampered progress in the development of genetic treatments. Nonviral DNA nanoparticles (NPs) can accommodate large genes, unlike traditional viral vectors, which have capacity limitations. We utilized an optimized DNA NP technology to subretinally deliver ABCA4 to Abca4-deficient mice. We detected persistent ABCA4 transgene expression for up to 8 months after injection and found marked correction of functional and structural Stargardt phenotypes, such as improved recovery of dark adaptation and reduced lipofuscin granules. These data suggest that DNA NPs may be an excellent, clinically relevant gene delivery approach for genes too large for traditional viral vectors.
Abstract 4421: SY-5609, an orally available selective CDK7 inhibitor demonstrates broad anti-tumor activity<i>in vivo</i> (2019)

Previously, we reported on a series of highly potent, selective, and non-covalent CDK7 inhibitors that demonstrated antiproliferative activity against triple-negative breast cancer (TNBC) and ovarian cancer (OVA) cell lines and tumor growth inhibition in cell line-derived (CDX) and patient-derived (PDX) mouse xenograft models. Here, we report on the in vitro and in vivo profile of our development candidate, SY-5609. Methods: Kinase inhibition assays at both Km and 2 mM [ATP] were used to assess inhibition of CDK2, CDK7, CDK9, and CDK12. SPR was used to determine the Kd, kon, and koff binding characteristics of SY-5609 to immobilized CDK7/Cyclin H dimer. CDK7 compound occupancy was determined using a biotinylated small molecule probe to pull down free CDK7 following incubating of HL60 cells with SY-5609. Inhibition of tumor cell line growth was assessed following 72 hrs of incubation with SY-5609. Flow cytometry was used to assess apoptosis and cell cycle modulation after 48 hrs of treatment. Effects on DNA damage and repair were assessed by immunofluorescence staining for γH2AX and RAD51 proteins. To assess in vivo effects, mice were implanted subcutaneously and randomized for treatment when tumors reached 150-200 mm3 and dosed orally for 3 weeks by both QD and BID dosing regimens. Collected tumor tissue samples were analyzed for protein levels of MCL1, pCDK2, MYC, and RNA Pol II CTD pSer5 by western blot. Results: SY-5609 bound CDK7/Cyclin H with a Kd of 0.059 nM and occupied CDK7 in HL60 cells with an EC50 of 33 nM. Cell growth inhibition EC50 values were 6-17 nM in a panel of solid tumor cell lines. Selectivity of SY-5609 over CDK12, CDK9, and CDK2 was 2492-, 2508-, and 8068-fold, respectively. SY-5609 led to induction of apoptosis, cell cycle arrest, and inhibition of DNA damage repair in tumor cell lines. Dose-dependent tumor growth inhibition was observed in a panel of CDX and PDX solid tumor models with both QD and BID dosing of SY-5609 with resulting decreases in direct (pCDK2, RNA Pol II CTD pSer5) and indirect (MCL1, MYC) protein biomarkers. In summary, we describe SY-5609, an orally available, potent, and selective CDK7 inhibitor that drives strong responses in CDX and PDX tumor models. These data support the rationale for advancing SY-5609 into IND-enabling studies.Citation Format: Shanhu Hu, Jason Marineau, Kristin Hamman, Michael Bradley, Anneli Savinainen, Sydney Alnemy, Nisha Rajagopal, David Orlando, Claudio Chuaqui, Eric Olson. SY-5609, an orally available selective CDK7 inhibitor demonstrates broad anti-tumor activity in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4421.
Prototype of a Software-Defined Broadcast Media Indexing Engine (2007)

The paper describes the prototype of a broadcast media indexing engine based on a 64-point weighted-overlap-add DFT filter bank implemented in an FPGA. In its present configuration, the device simultaneously demodulates and displays a speech/music flag for 5 FM radio stations, with audio output routed to a loudspeaker via a user-operated switch. Extension to the full FM radio band will be possible using a larger FPGA.
A Novel Synthesis of 4H-1,4-Benzoxazines. (1996)

The reaction of methyl 2-chloro-5-ethoxycarbonylamino-4-fluorobenzoate (4a) and 1-bromo-3,3-dimethyl-2-butanone (2) in the presence of 2.2 eq of lithium bis(trimethylsilyl)amide afforded the 4H-1,4-benzoxazine (6a) in good yield instead of the expected 4-oxazolin-2-one (5a). The generality of the reaction and the mechanism are discussed.
CD4<sup>+</sup>CD25<sup>−</sup>LAG3<sup>+</sup>regulatory T cells controlled by the transcription factor Egr-2 (2009)

Regulatory T cells (Tregs) are engaged in the maintenance of immunological self-tolerance and immune homeostasis. IL-10 has an important role in maintaining the normal immune state. Here, we show that IL-10-secreting Tregs can be delineated in normal mice as CD4(+)CD25(-)Foxp3(-) T cells that express lymphocyte activation gene 3 (LAG-3), an MHC-class-II-binding CD4 homolog. Although approximately 2% of the CD4(+)CD25(-) T cell population consisted of CD4(+)CD25(-)LAG3(+) T cells in the spleen, CD4(+)CD25(-)LAG3(+) T cells are enriched to approximately 8% in the Peyer's patch. They are hypoproliferative upon in vitro antigenic stimulation and suppress in vivo development of colitis. Gene expression analysis reveals that CD4(+)CD25(-)LAG3(+) Tregs characteristically express early growth response gene 2 (Egr-2), a key molecule for anergy induction. Retroviral gene transfer of Egr-2 converts naïve CD4(+) T cells into the IL-10-secreting and LAG-3-expressing phenotype, and Egr-2-transduced CD4(+) T cells exhibit antigen-specific immunosuppressive capacity in vivo. Unlike Foxp3(+) natural Tregs, high-affinity interactions with selecting peptide/MHC ligands expressed in the thymus do not induce the development of CD4(+)CD25(-)LAG3(+) Tregs. In contrast, the number of CD4(+)CD25(-)LAG3(+) Tregs is influenced by the presence of environmental microbiota. Thus, IL-10-secreting Egr-2(+)LAG3(+)CD4(+) Tregs can be exploited for the control of peripheral immunity.
Membrane versus centrifuge-based therapeutic plasma exchange: a randomized prospective crossover study (2015)

Although the centrifugal procedures were conducted using flow rates that could easily be obtained using peripheral access, plasma removal efficiency was significantly higher and treatment time was significantly lower in cTPE as compared to mTPE. Despite this lower treatment time, the decline in markers of procedure efficacy was comparable. Especially in centers performing many procedures per year, cTPE in contrast to mTPE can reduce treatment time without compromising treatment efficacy.
Parallel Programming with MatlabMPI (2001)

MatlabMPI is a Matlab implementation of the Message Passing Interface (MPI) standard and allows any Matlab program to exploit multiple processors. MatlabMPI currently implements the basic six functions that are the core of the MPI point-to-point communications standard. The key technical innovation of MatlabMPI is that it implements the widely used MPI ``look and feel'' on top of standard Matlab file I/O, resulting in an extremely compact (~100 lines) and ``pure'' implementation which runs anywhere Matlab runs. The performance has been tested on both shared and distributed memory parallel computers. MatlabMPI can match the bandwidth of C based MPI at large message sizes. A test image filtering application using MatlabMPI achieved a speedup of ~70 on a parallel computer.
Application of Cre/lox Site-specific Recombination System in Transgenic Plants (2010)

Site-specific recombination system, which consists of recombinase and the related-recombinase recognizing short DNA sequences, has been developed into genetic manipulation tool by two-component interaction for the goal of targeted integration and precise excision of DNA fragment. Cre/lox recombination system, which belongs to the family of site-specific recombination system including Cre/lox, FLP/frt, R/RS and Gin/gix, is one of the best characterized and most widely used system. Cre/lox system consists of Cre recombinase and 34 bp lox sites, which initially was applied in basic transgenic animal research such as gene knockout, gene activation and gene translocation. With the rapid development of biotechnology, Cre/lox system has been investigated to transgenic plants and makes impressive progress in recent years. In this paper, the advances of Cre-lox system are reviewed, providing insight of site-specific integration, site-specific excision and plant chloroplast transformation to construct environmental friendly plant genetic transformation system with high-level foreign gene expression.
Control of Nucleation Rate for Tetragonal Hen-Egg White Lysozyme Crystals by Application of an Electric Field with Variable Frequencies (2009)

Control of the nucleation rate is important for the growth of high quality protein crystals; therefore, the development of improved growth methods is required. Crystal growth with an external electric field is an attractive method for control of the nucleation rate. However, mainly a decrease in nucleation rate was observed when an external electric field was applied using DC voltage. By focusing on the chemical potential of the liquid and solid, control of both the increase and the decrease in nucleation rate was successfully achieved by applying an AC electric field. Control of nucleation rate in terms of enhancement and retardation is reported for hen-egg white lysozyme crystals by imposition of an electric field with varying frequencies, which was determined by the electrical permittivity of both the hen-egg white lysozyme solution and crystals.
Second harmonic generation in field poled, quasi-phase-matched, bulk LiNbO/sub 3/ (1994)

Field induced periodic poling is used to create >10 micron period structures in /spl sim/250 micron thick slabs of LiNbO/sub 3/. Third order quasi-phase-matched second harmonic blue light generation is demonstrated by free propagation of a 937 nm fundamental Gaussian beam in periodically poled LiNbO/sub 3/, with a conversion efficiency of 0.2%/W cm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structure-preserving model reduction for nonlinear port-Hamiltonian systems (2011)

Port-Hamiltonian systems result from port-based network modeling of physical systems and constitute an important class of passive nonlinear state-space systems. In this paper, we develop a framework for model reduction of large-scale multi-input/multi-output nonlinear port-Hamiltonian systems that retains the port-Hamiltonian structure in the reduced order models. Within this framework, reduced order models are determined by the selection of two families of approximating subspaces. We consider two approaches deriving from a) a POD-based selection of subspaces, and b) an an ℋ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -based quasi-optimal selection of subspaces. We compare performance of the reduced order models on a nonlinear lossy LC ladder network.
Altered spontaneous brain activity in patients with strabismic amblyopia: A resting‑state fMRI study using regional homogeneity analysis (2019)

The present study aimed to compare the regional homogeneity (ReHo) of resting-state brain function between subjects with strabismic amblyopia and normal controls. A total of 12 adult patients with strabismic amblyopia and 34 age- and gender-matched normal controls were enrolled in the present study. All patients were subjected to resting-state magnetic resonance imaging using a Siemens Trio 3.0T magnetic resonance scanner. ReHo values of the whole brain were calculated and standardized. An independent-samples t-test was used to analyze the differences in ReHo values between the two groups. Patients with strabismic amblyopia exhibited reduced ReHo values in certain parts of the occipital lobe, including the lingual gyrus, cuneus and superior occipital gyrus. Increased ReHo values were observed in the precuneus and certain parts of the prefrontal cortex of patients with strabismic amblyopia, including the superior frontal gyrus and middle frontal gyrus. The ReHo index of the precuneus was negatively correlated with age. However, there was no correlation between the ReHo values and the visual acuity of patients with strabismic amblyopia. ROC curve analysis demonstrated that the greatest area under curve (AUC) value was in the medial prefrontal cortex (AUC=0.864). The results of the present study suggested that visual information processing may be impaired in visual areas V1 and V2. Furthermore, adult patients with strabismic amblyopia exhibited brain plasticity that compensated for visuomotor coordination and visuospatial imagery deficits.
Link Buffer Sizing: A New Look at the Old Problem (2005)

We revisit the question of how much buffer an IP router should allocate for its droptail FIFO link. For a long time, setting the buffer size to the bitrate-delay product has been regarded as reasonable. Recent studies of interaction between queueing at IP routers and TCP congestion control offered alternative guidelines. First, we explore and reconcile contradictions between the existing rules. Then, we argue that the problem of link buffer sizing needs a new formulation: design a buffer sizing algorithm that accommodates needs of all Internet applications without engaging IP routers in any additional signaling. Our solution keeps network queues short: set the buffer size to 2L datagrams, where L is the number of input links. We also explain how end systems can utilize the network effectively despite such small buffering at routers.
Porphyrin–Silicon Hybrid Field-Effect Transistor with Individually Addressable Top-gate Structure (2011)

A conductance-controllable hybrid device that utilizes the photoinduced charge transfer behavior of a porphyrin in a field-effect transistor (FET) with a nanogap is proposed and analyzed. A conventional metal-oxide-semiconductor (MOS) structure is modified to form a nanogap in which the porphyrin can be embedded. The conductance of an inversion channel is controlled by the negatively charged, optically activated porphyrin molecules. The proposed nanogap-formed MOSFET structure solves the conventional dilemma that a top-gate cannot be used for an organic-inorganic hybrid device because the top-gate blocks an entire area of a channel where organic material should be immobilized. The top-gate structure has much practicality compared with the back-gate structure because each device can be controlled individually. Furthermore, the device is highly compatible with the chip-based integrated system because the fabrication process follows the standard complementary metal-oxide-semiconductor (CMOS) technology. The charge transfer mechanisms between silicon and porphyrin are analyzed using devices with different doping polarities and geometrical parameters. The results show that the influence of the negative charge of the porphyrin in the device is reversed when opposite doping polarities are used. The device characteristics can be comprehensively evaluated using the energy band diagram analysis and simulation. The possible application of the proposed device for nonvolatile memory is demonstrated using the optical charging and electrical discharging behavior of the porphyrins.
Simulation of supersymmetric quantum mechanics in a Cooper-pair box shunted by a Josephson rhombus (2015)

Supersymmetries in quantum mechanics offer a way to obtain degeneracies in the excitation spectrum which do not originate from selection rules. The mechanism behind the degeneracies is the same as the one that leads to the miraculous cancellations of divergences in supersymmetric field theories found in the high energy physics context. There is up to now no realistic proposal of nonintegrable systems that show level degeneracies due to a supersymmetric structure. Here, we propose an implementation of a quantum-mechanical supersymmetry in a Cooper-pair box shunted by a Josephson junction rhombus which is effectively $\ensuremath{\pi}$ periodic in the superconducting phase difference. For a characteristic ratio between the strength of the $2\ensuremath{\pi}$- and the $\ensuremath{\pi}$-periodic junction, we find a twofold degeneracy of all the energy levels all the way from the weak junction/charge qubit limit to the strong junction/transmon regime. We provide explicit experimental values for the parameters of the system and show that tuning in and out of the supersymmetric point is easily achieved by varying an external gate voltage. We furthermore discuss a microwave experiment to detect the supersymmetry and conclude that it can indeed be implemented with currently existing Josephson junction technology.
Color-Based Signal Light Tracking in Real-Time Video (2006)

Tracking or detecting the position and color of signal lights has an important role in transport industry. Auto detection of signal light colors and their position using computer vision techniques provides or acts as a proof against a fraudulent claim losses. The current technology, such as vehicle mounted recording system, provides event recognition videos and the cause behind an accident. But it does not provide the complete information about color associated with signal lights. The detection of the color of a signal light under different illuminations is a critical issue. In this research, an intelligent method for tracking color of signal lights using La*b* color model combined with contour tracking is proposed. This research finds application in transportation, law enforcement and insurance claims. The system increases the efficiency of the accident investigation process and reduces the economic loss associated with automobile accidents of all types.
EGFP and DsRed expressing cultures of <i>Escherichia coli</i> imaged by confocal, two‐photon and fluorescence lifetime microscopy (2000)

The green fluorescent protein (GFP) has become an invaluable marker for monitoring protein localization and gene expression in vivo. Recently a new red fluorescent protein (drFP583 or DsRed), isolated from tropical corals, has been described [Matz, M.V. et al. (1999) Nature Biotech. 17, 969-973]. With emission maxima at 509 and 583 nm respectively, EGFP and DsRed are suited for almost crossover free dual color labeling upon simultaneous excitation. We imaged mixed populations of Escherichia coli expressing either EGFP or DsRed by one-photon confocal and by two-photon microscopy. Both excitation modes proved to be suitable for imaging cells expressing either of the fluorescent proteins. DsRed had an extended maturation time and E. coli expressing this fluorescent protein were significantly smaller than those expressing EGFP. In aging bacterial cultures DsRed appeared to aggregate within the cells, accompanied by a strong reduction in its fluorescence lifetime as determined by fluorescence lifetime imaging microscopy.
Fully textured growth of Y1Ba2Cu3O7−δ films by sputtering on LiNbO3 substrates (1989)

We present details about the deposition of thin Y1Ba2Cu3O7−δ films on single-crystal LiNbO3 substrates by planar dc magnetron sputtering. Among other data, results of transition temperature (Tc(R=0) =88 K) and critical current density (jc &gt;2×109 A/m2 at 77 K) plus some details about film-to-substrate orientation which is present in all three crystallographic directions are reported.
Robust statistical registration of 3D ultrasound images using texture information (2004)

A new registration method for ultrasound volumes relying on on a statistical texture-based similarity measure is investigated. Texture information is given by spatial Gabor filters and represented by statistical kernel-based distributions. The registration similarity measure is then defined as a probabilistic distance, derived from Bhattacharyya coefficient, between two statistical distributions. Given this similarity measure, parametric ultrasound image registration is stated as a robust minimization issue. We also exploit frequency properties of spatial Gabor filters to propose a multiresolution approach to perform this minimization. We provide a preliminary evaluation of the new registration technique on clinical data.
Synthesis of 1,4‐dihydro‐4‐oxopyridazino[1,6‐<i>a</i>]indole‐3‐carboxylic acids and 1,4‐dihydro‐4‐oxopyrido[3′,2′:4,5]pyrrolo[1,2‐<i>b</i>]‐pyridazine‐3‐carboxylic acids as potential antibacterial agents (1994)

Abstract A few aza analogues of the quinolones have been prepared in the two families of the 1,4‐dihydro‐4‐oxopyridazino[1,6‐ a ]indole‐3‐carboxylic acids and the 1,4‐dihydro‐4‐oxopyrido[3′,2′:4,5]pyrrolo[1,2‐ b ]‐pyridazine‐3‐carboxylic acids to check their antibacterial potential. One compound 6c shows antibacterial activities of the level of nalidixic acid and represents a new lead structure differing from the classical quinolones.
Lead-free high-strain single-crystal piezoelectrics in the alkaline–bismuth–titanate perovskite family (1998)

Doped alkaline–bismuth–titanate perovskite single crystals have been grown in ferroelectric phases with high piezoelectric actuation. Rhombohedral-phase Na1/2Bi1/2TiO3–BaTiO3 crystals exhibit up to 0.25% free strain with low hysteresis along the cubic 〈001〉 direction (d33∼450 pC/N). Tetragonal phase crystals exhibit free strains as high as 0.85% with greater hysteresis characteristic of domain switching; low field d33 exceeds 500 pC/N. Strain energy densities exceed those of optimized polycrystalline lead perovskites, and actuation capability is retained at compressive stresses &gt;100 MPa.