gebhart/patrepeval huggingface dataset:
Endoscopic optical coherence tomography of the retina at 1310 nm using paired-angle rotating scanning (2007)

Vitrectomy (removal of the vitreous humor) is an ophthalmic surgery required as a precursor to several posterior chamber procedures. Vitrectomy is commonly performed using an endoscopic vitreous cutter and fiber based light delivery for observation through a surgical microscope. Cross-sectional visualization of the retina and remnant vitreous layers during surgery using an external optical coherence tomography (OCT) scanner is impractical due to deformation in the shape of the eye and the cornea. We present a forward imaging probe with 820 &mgr;m outer diameter (21 gauge needle) for cross-sectional endoscopic OCT imaging during ophthalmic surgeries. The Paired-Angle-Rotating Scanner (PARS) OCT probe is based on angle polished gradient index (GRIN) lenses which are rotated about the optical axis. The scan pattern is determined by the angle between the GRIN lenses and the relative angular velocity. Endoscopic placement of the PARS-OCT probe tip near the retinal surface permits use of a longer wavelength light, in particular 1310 nm, which would otherwise suffer significant attenuation traversing the vitreous humor. The prototype endoscopic PARS-OCT probe is coupled to a commercially available 1310 nm swept laser source, and uses commercial software for data acquisition, processing, and display of retinal images in real time at an A-scan rate of 16 kHz. We present an analysis of aberrations due to off axis use of GRIN lenses and measure the scan pattern of the PARS probe. Images acquired on an ex vivo porcine retina are presented, motivating development of the endoscopic PARS-OCT probe for clinical evaluation.
W-band Power Amplifier in 0.15μm InGaAs pHEMT Technology with Microstrip Transmission Lines (2013)

In this paper, the existing feasibility of microstrip transmission lines (MTL) in RF applications has been asserted with the design of a novel 2 stage common source power amplifier (PA). The novel inductorless MTL based PA is designed in 0.15μm InGaAs pHEMT. The PA achieves a gain of 10 dB, operating 3-dB bandwidth of 3 GHz, in the W band at 82 GHz center frequency. The PAE and P1dB are 9.1 % and 9.2 dBm respectively. The power consumed by the PA is 38 mW for a source voltage of 2.5 V. At microwave frequencies, the conventional lumped components cannot work as their desired performance as an inductor or capacitor is significantly dwarfed by the undesired device parasitics. In today’s wireless communication we need to operate at those very high frequencies and therefore the need of MTL is very much essential. The simulation of the PA is conducted with 0.15μm InGaAs pHEMT process technology. As we know, at microwave frequencies III-V semiconductors such as the InGaAs pHEMT are used in spite of their high power consumption because they have significantly higher fT and breakdown voltage and importantly very high electron mobility when compared to CMOS. The MTL is transmission line geometry with a single conductor trace on one side of a dielectric substrate and a single ground plane on the opposite side. The MTL achieves inductance with the flow of current in the conductor, whereas the capacitance is associated with the conducting strip separated from the ground plane by the dielectric substrate [1]. In Fig. 1 Inset, a typical MTL device is illustrated. The dielectric substrate considered in this paper is GaAs. The microstrip characteristic impedance, Z, and the inductance, L, are computed as follows:
A Route to 5,5-Dithiospiroketals and to Long-Chain Monomers from the Biomass (2022)

5,5-Dithiospiroketals are prepared by a double radical addition of α,α'-bisxanthyl acetone to an alkene followed by ionic or thermal cleavage of the xanthate groups and acid-catalyzed ring closure. A modification employs α-chloro-α'-xanthyl acetone to give unsymmetrical derivatives. Reductive removal of the sulfur atoms with Raney nickel furnishes long-chain α,ω-diacids, diols, and diamines. Using biosourced alkenes, monomers and polymers can be obtained where essentially all the carbons are derived from the biomass.
Pregnancy outcome in women with polycystic ovary syndrome in relation to second-trimester testosterone levels (2020)

Women with PCOS have higher levels of total testosterone and free androgen index during pregnancy than women without PCOS matched for body mass index. Preliminary evidence shows that women with PCOS and the highest maternal testosterone levels in early second trimester had the highest risk of developing preeclampsia. This finding, however, is driven by a limited number of cases and should be interpreted with caution.
Demonstration of 40-km-reach WDM-PON with Capacity of 40-Gb/s Based on Wavelength-locked F-P LD (2009)

We demonstrate 40-km-reach 32-channel gigabit wavelength division multiplexing-passive optical network (WDM-PON) based on Fabry-Perot laser diode with external ASE injection. The dispersion, back-reflection and crosstalk effects in WDM-PON are also investigated.
On the design of a decision engine for connected vehicles with an application to congestion management (2018)

Vehicles are becoming connected entities. As a result, a likely scenario is that such entities might be literally bombarded with information from a multitude of devices. In this context, a key challenging requirement for both connected and autonomous vehicles is that they will need to become cognitive bodies, able to parse information and use only the pieces of information that are relevant to the vehicle in the context of a given journey. In order to address this fundamental requirement, a decision engine is presented in this paper. The engine makes it possible for the vehicle to understand which pieces of information are really relevant, and subsequently to process only those pieces of information. In order to illustrate the key features of our system, we show that it is possible to build upon the engine to develop a distributed traffic management system, and then we validate such a system via both conventional (numerical and SUMO-based) simulations and a Hardware-in-the-Loop (HIL) platform. Both the conventional simulations and the HIL validation showed that the engine can be effectively used to design a distributed traffic management system.
Upper limits on the strength of periodic gravitational waves from PSR J1939+2134 (2004)

The first science run of the LIGO and GEO gravitational wave detectors presented the opportunity to test methods of searching for gravitational waves from known pulsars. Here we present new direct upper limits on the strength of waves from the pulsar PSR J1939+2134 using two independent analysis methods, one in the frequency domain using frequentist statistics and one in the time domain using Bayesian inference. Both methods show that the strain amplitude at Earth from this pulsar is less than a few times 10-22.
Electronic States of Perovskite-Type Oxides and Ferroelectricity (2000)

A relation between B -site transition metal and ferroelectricity is investigated in A B O 3 perovskite-type oxides. We focus on intensity of the covalent bonds between the B-site atom and the oxygen octahedron and evaluate Harrison's covalency parameter α. The density functional theory within the local density approximation is adopted to obtain the valence electron energy levels of free atoms from which the covalency α is calculated. Strong correlation between the covalency α and the Curie temperature ( T C ) is found. As the covalency α increases, T C of ferroelectricity arises. It is also noted that the hybridization between Pb 6 p and O 2 p is crucial for the high ferroelectricity of PbTiO 3 .
Fibroblasts—a key host cell type in tumor initiation, progression, and metastasis (2012)

Tumor initiation, growth, invasion, and metastasis occur as a consequence of a complex interplay between the host environment and cancer cells. Fibroblasts are now recognized as a key host cell type involved in host-cancer signaling. This review discusses some recent studies that highlight the roles of fibroblasts in tumor initiation, early progression, invasion, and metastasis. Some clinical studies describing the prognostic significance of fibroblast-derived markers and signatures are also discussed.
Spectral analysis of ultrasound radiofrequency backscatter for the identification of five tissue types found in and around the paravertebral space (2018)

In a pilot study, radiofrequency backscatter data was collected in the paravertebral (PV) spaces of 4 healthy individuals. Using the associated gray scale ultrasound and Doppler data as guidance, regions-of-interest (ROIs) were chosen to represent five tissue types found in and around the PV space – rib shadow, pleura, superior costotransverse ligament, intercostal vessel (artery or vein), and the PV space away from the vessel. ROI sizes of 1.0 mm, 1.5 mm, and 2.0 mm square were examined for auto-regressive (AR) orders of 10, 20, 30, and 40 and bandwidths of 3dB, 6dB, 20dB. Spectral estimations were performed for each ROI size, AR order, and bandwidth over the A-lines of the ultrasound radiofrequency data. The spectra were averaged and normalized using data collected from a tissue phantom. Eight spectral parameters &ndash; Y-intercept, slope, and mid-band fit of the regression line, maximum dB of the spectra, frequency at maximum dB, minimum dB of the spectra, frequency at minimum dB, and integrated backscatter were calculated for each spectral estimate and used to create ensembles of bagged tree classifiers. An ROI size of 2.0 mm, bandwidth of 20 dB, and AR order 10 had the lowest out-of-bag error at 0.315, and averaged across all tissue types, an accuracy of 89.15&percnt;, sensitivity of 0.70, specificity of 0.93, and Youden’s Index (YI) of 0.62. These results show that the identification of the five tissues types in radiofrequency backscatter from intercostal ultrasound is feasible.
Multiview Photometric Stereo Using Planar Mesh Parameterization (2013)

We propose a method for accurate 3D shape reconstruction using uncalibrated multiview photometric stereo. A coarse mesh reconstructed using multiview stereo is first parameterized using a planar mesh parameterization technique. Subsequently, multiview photometric stereo is performed in the 2D parameter domain of the mesh, where all geometric and photometric cues from multiple images can be treated uniformly. Unlike traditional methods, there is no need for merging view-dependent surface normal maps. Our key contribution is a new photometric stereo based mesh refinement technique that can efficiently reconstruct meshes with extremely fine geometric details by directly estimating a displacement texture map in the 2D parameter domain. We demonstrate that intricate surface geometry can be reconstructed using several challenging datasets containing surfaces with specular reflections, multiple albedos and complex topologies.
ChemInform Abstract: A Practical Entry to β‐Aryl‐β‐alkyl Amino Alcohols: Application to the Synthesis of a Potent BACE1 Inhibitor. (2013)

Abstract The presented reaction is amenable to being carried out on a multigram scale.
Data from BAD Phosphorylation Determines Ovarian Cancer Chemosensitivity and Patient Survival (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Despite initial sensitivity to chemotherapy, ovarian cancers (OVCA) often develop drug resistance, which limits patient survival. Using specimens and/or genomic data from 289 patients and a panel of cancer cell lines, we explored genome-wide expression changes that underlie the evolution of OVCA chemoresistance and characterized the BCL2 antagonist of cell death (BAD) apoptosis pathway as a determinant of chemosensitivity and patient survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Serial OVCA cell cisplatin treatments were performed in parallel with measurements of genome-wide expression changes. Pathway analysis was carried out on genes associated with increasing cisplatin resistance (EC&lt;sub&gt;50&lt;/sub&gt;). BAD-pathway expression and BAD protein phosphorylation were evaluated in patient samples and cell lines as determinants of chemosensitivity and/or clinical outcome and as therapeutic targets.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Induced &lt;i&gt;in vitro&lt;/i&gt; OVCA cisplatin resistance was associated with BAD-pathway expression (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). In OVCA cell lines and primary specimens, BAD protein phosphorylation was associated with platinum resistance (&lt;i&gt;n&lt;/i&gt; = 147, &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and also with overall patient survival (&lt;i&gt;n&lt;/i&gt; = 134, &lt;i&gt;P&lt;/i&gt; = 0.0007). Targeted modulation of BAD-phosphorylation levels influenced cisplatin sensitivity. A 47-gene BAD-pathway score was associated with &lt;i&gt;in vitro&lt;/i&gt; phosphorylated BAD levels and with survival in 142 patients with advanced-stage (III/IV) serous OVCA. Integration of BAD-phosphorylation or BAD-pathway score with OVCA surgical cytoreductive status was significantly associated with overall survival by log-rank test (&lt;i&gt;P&lt;/i&gt; = 0.004 and &lt;i&gt;P&lt;/i&gt; &lt; 0.0001, respectively).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; The BAD apoptosis pathway influences OVCA chemosensitivity and overall survival, likely via modulation of BAD phosphorylation. The pathway has clinical relevance as a biomarker of therapeutic response, patient survival, and as a promising therapeutic target. &lt;i&gt;Clin Cancer Res; 17(19); 6356–66. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Fabrication and DC characteristics of vertically stacked SIS-type structures for use as low-temperature detectors (1995)

We discuss the fabrication and current-voltage characteristics (IVC) of Sn-(I-Sn)5 and Nb/(Al-AlOx-Nb)12 multilayer devices consisting of tunnel junctions stacked on top of one another. Three-terminal devices including a phonon and quasiparticle generator and both a single-junction (SJ) and multijunction (MJ) detector based on tin structures have been fabricated. The MJ detector showed better sensitivity to the same phonon irradiation level compared with the SJ detector. The result shows that the multijunction approach to low-temperature detector design is promising and might improve the energy resolution and sensitivity of detectors. For niobium-based structures, we have successfully employed a timed ion milling to define the area of devices.
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses (2018)

The human interferon (IFN)-induced MxA protein is a key antiviral host restriction factor exhibiting broad antiviral activity against many RNA viruses, including highly pathogenic avian influenza A viruses (IAV) of the H5N1 and H7N7 subtype. To date the mechanism for how MxA exerts its antiviral activity is unclear, however, additional cellular factors are believed to be essential for this activity. To identify MxA cofactors we performed a genome-wide siRNA-based screen in human airway epithelial cells (A549) constitutively expressing MxA using an H5N1 reporter virus. These data were complemented with a proteomic screen to identify MxA-interacting proteins. The combined data identified SMARCA2, the ATPase subunit of the BAF chromatin remodeling complex, as a crucial factor required for the antiviral activity of MxA against IAV. Intriguingly, our data demonstrate that although SMARCA2 is essential for expression of some IFN-stimulated genes (ISGs), and the establishment of an antiviral state, it is not required for expression of MxA, suggesting an indirect effect on MxA activity. Transcriptome analysis of SMARCA2-depleted A549-MxA cells identified a small set of SMARCA2-regulated factors required for activity of MxA, in particular IFITM2 and IGFBP3. These findings reveal that several virus-inducible factors work in concert to enable MxA restriction of IAV.
[Results of a series of 104 consecutive bilateral bone marrow biopsy specimens in lymphoproliferative disorders]. (1995)

On the basis of these data, the use of bilateral bone marrow biopsy specimens may be justified in lymphoproliferative disorders, both at the time of diagnosis and in reassessment prior to ABMT--when the bone marrow was initially infiltrated.
IC‐P‐061: PERSISTENT HIPPOCAMPAL PREDOMINANT ATROPHY IN PRE‐DEMENTIA AS A MARKER FOR SLOWER FUNCTIONAL DECLINE (2014)

Striking differences between patients in their age of onset, clinical symptoms and clinical trajectories are well documented in Alzheimer's disease (AD). Among AD dementia subtypes, the patterns of regional neurodegeneration in its clinical variants are expected to be highly correlated with the clinical phenotype. However, it is unclear if predominant regional atrophy patterns: a) change over time in the pre-dementia stages (Cognitively normal (CN) and Mild cognitive impairment (MCI)) and b) if they relate to differing rates of functional decline. We compute one and two-year hippocampal atrophy and cortical atrophy in CN and MCI subjects in the Alzheimer 's disease Neuroimaging Initiative (ADNI) using a registration-based cube propagation method. Among 504 subjects with 234 MCI, and 169 CN, we defined apriori a group with predominant hippocampal atrophy at year one (>1 standard deviation of the hippocampal atrophy of the population and <1 standard deviation of the cortical atrophy). We tested two hypotheses 1) Subjects meeting criteria at year one are consistent in their atrophy pattern at year two. 2) Subjects with stable hippocampal predominant atrophy have slower functional decline on (Clinical Dementia Rating Scale: Sum of Boxes (CDR-SB). .110 subjects met criteria for hippocampal predominant atrophy. Among these 52% (57 subjects) meeting criteria at year one remain in the same group at year two i.e., with persistent hippocampal predominant atrophy. At baseline, persistent hippocampal atrophy group had a lower CDR SB mean than the non-persistent hippocampal atrophy group (1.1 vs. 1.9, p<0.001). In a linear regression with CDR-SB scores as outcome and controlling for age, sex, education and APOE, persistent hippocampal atrophy group had a slower decline in the CDR SB scores over a year than the non-persistent group (F (1,80) = 28.6, p < .0001). Among the unstable ones (in hippocampal predominant atrophy group at year one and not in the same group at year two), 32% go on to develop both hippocampal and cortical atrophy Identifying the groups with persisting hippocampal predominant atrophy patterns in the pre-dementia stages could help delineate the future clinical trajectories of clinical phenotypes very early in the disease course. This could have direct implications for diagnosis, patient counseling, management and design of clinical trials in AD.
Network‐based identification of critical transcription regulators in the metabolic syndrome in mice (2008)

Systematic approaches that integrate genetic and gene expression data have been employed to elucidate gene interactions underlying traits. In this study, 53 transcription factors and 460 of their know target genes are analyzed by employing network component analysis (NCA) method to infer transcription factor activities (TFAs). Linkage analysis was applied with the TFA data to map the genetic determinates that regulate the activity of individual transcription factors. Chromosome regions controlling the level of activity of a particular transcription factor are mapped as TFA quantitative trait loci (tQTLs). In this study, we report the sexually dimorphic TFAs in somatic tissues of mice. These transcription factors exhibited highly tissue‐specific patterns of activity and most of them have varying activity levels that are significantly correlated with clinical traits involved in the metabolic syndrome. Genetic analysis provided evidence of the reuglators of sexually dimorphic transcription factors, as the activities of certain transcription factors were controlled by tQTL hotspots that exhibited tissue‐/sex‐specific pattern. Several transcription factors (Myb, Bcl6, Ets2, Fli1, Cebpa, Rarb and Sfpi1) are found to be associated with metabolic traits and investigation of their biological roles in metabolism may reveal molecular mechanism involved in metabolic syndrome in mouse.
Comparison of Nonlinear Compensation Techniques for 400-Gb/s Coherent Multi-Band OFDM Super-Channels (2018)

The last few years, many studies have been published on the 3rd-order inverse Volterra series transfer function nonlinear equalizer (IVSTF-NLE) in long-haul optical communication systems. Nonetheless, no experimental work has been published on investigating the potential of the 3rd-order IVSTF-NLE for the compensation of Kerr nonlinearities in a long-haul wavelength division multiplexing (WDM) system consisting of high-bit rate super-channels, as high as 400 Gb/s. In this paper, we study experimentally the performance of a 3rd-order IVSTF-NLE in a coherent optical WDM system, with a central, 400-Gb/s, 4-band, dual-polarization (DP), 16-ary quadrature amplitude modulation (QAM) orthogonal frequency division multiplexing (OFDM) super-channel. We compare its performance against the performance of the digital back-propagation split-step Fourier (DBP-SSF) method for the compensation of nonlinearities after 10 × 100 km of ITU-T G.652 standard single mode fiber (SSMF). In the second part of this paper, we compare, via Monte Carlo simulations, the performance of the 3rd-order IVSTF-NLE and the DBP-SSF method, in terms of reach extension and computational complexity, after propagation through ITU-T G.652 SSMF and a ITU-T G.655 large effective area fiber (LEAF). By means of both experimental evaluation and simulations, we show that, in the presence of strong nonlinear effects, the 3rd-order IVSTF-NLE, which uses a single step per span, performs similarly with the two-steps-per-span DBP-SSF, whereas the eight-steps-per-span DBP-SSF is only marginally better but at the vast expense of computational complexity.
Gain Characterization and Parameter Extraction of 1.3 μm InAs Quantum Dot Lasers on Silicon (2018)

We report the current and wavelength dependence of gain and transparency current for a variety of quantum dot laser structures. The dependence on number of quantum dot layers and templates for growth are reported.
SpaceCuts: Making Room for Visualizations on Maps (2016)

Visual map features like streets, rail tracks, or rivers do not provide enough space to visualize multiple attributes on them. Related approaches to solve space issues distort the map with lenses, apply distortion techniques to the map geometry, or employ three dimensional visualizations. All these techniques come at the cost of distortion or overlapping of relevant map features or they even produce overlap of visualized data. In this paper, we present SpaceCuts, a technique to generate additional space for data visualization on maps that does not distort the map and introduces only minimal overlap by cutting the map along a geographic structure and pulling the resulting areas apart. Besides introducing the basic technique, we discuss possible interactions, further extensions, application scenarios, and outline potential future research.
Adiabatically tapered periodic segmentation of channel waveguides for mode-size transformation and fundamental mode excitation (1996)

We report modeling, fabrication, and characterization of tapered waveguides, using periodically segmented annealed proton exchange in LiNbO(3). For a taper transforming the 1/e full width (intensity) mode size from 6.0 microm x 4.4 microm to 2.0 microm x 1.3 microm, 0.4-dB excess loss was observed. The large, slightly elliptical mode can ease coupling to single-mode fibers and circular free-space beams. The same taper structure was used to excite a highly multimoded (13 modes) waveguide with more than 95% of the power stably launched into the lowest-order mode. This function is useful for nonlinear waveguide devices, such as difference-frequency generators, in which modes at highly disparate wavelengths interact.