gebhart/patrepeval huggingface dataset:
Toward the Development of a Virus-Cell-Based Assay for the Discovery of Novel Compounds against Human Immunodeficiency Virus Type 1 (2003)

The emergence of human immunodeficiency virus type 1 (HIV-1) strains resistant to highly active antiretroviral therapy necessitates continued drug discovery for the treatment of HIV-1 infection. Most current drug discovery strategies focus upon a single aspect of HIV-1 replication. A virus-cell-based assay, which can be adapted to high-throughput screening, would allow the screening of multiple targets simultaneously. HIV-1-based vector systems mimic the HIV-1 life cycle without yielding replication-competent virus, making them potentially important tools for the development of safe, wide-ranging, rapid, and cost-effective assays amenable to high-throughput screening. Since replication of vector virus is typically restricted to a single cycle, a crucial question is whether such an assay provides the needed sensitivity to detect potential HIV-1 inhibitors. With a stable, inducible vector virus-producing cell line, the inhibitory effects of four reverse transcriptase inhibitors (zidovudine, stavudine, lamivudine, and didanosine) and one protease inhibitor (indinavir) were assessed. It was found that HIV-1 vector virus titer was inhibited in a single cycle of replication up to 300-fold without affecting cell viability, indicating that the assay provides the necessary sensitivity for identifying antiviral molecules. Thus, it seems likely that HIV-1-derived vector systems can be utilized in a novel fashion to facilitate the development of a safe, efficient method for screening compound libraries for anti-HIV-1 activity.
Using Proteomics to Understand Alzheimer’s Disease Pathogenesis (2019)

&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Our current understanding of the molecular changes that drive Alzheimer’s disease (AD) pathogenesis is incomplete. Unbiased, mass spectrometry-based proteomic studies provide an efficient and comprehensive way to quantitatively examine thousands of proteins at once using microscopic amounts of human brain tissue. Recently, the number of proteomic studies that examine protein changes in AD brain tissue has been increasing. This chapter reviews the different proteomic approaches currently being used to identify pathological protein changes in AD brain tissue including bulk tissue studies that examine protein changes throughout the progression of AD, studies of the insoluble proteome in AD, studies using proteomics to examine selective vulnerability in AD, studies of the amyloid plaque and neurofibrillary tangle proteome, studies of the synaptic proteome, and studies of the interactome of beta amyloid and tau. Combined, these complementary proteomic approaches provide increased understanding about the protein changes that occur in the AD brain. Results from these proteomic studies provide an excellent resource for future hypothesis-driven targeted studies and will help identify new biomarkers of disease and new drug targets for AD.
Optoelectronic oscillator using an ultra-high finesse Fabry-Perot etalon as a photonic filter for low phase noise at high oscillating frequencies (2013)

A 100,000 finesse Fabry-Perot etalon with a 1.5 GHz free spectral range is used as a photonic filter in an optoelectorinc oscillator. The etalon acts as a ~15 kHz microwave filter to suppress spurious modes in a single loop OEO configuration. The etalon maintains its narrow filtering capability at harmonics of the FSR. Phase noise of the 10.5 GHz tone with 2 km of delay is measured at -120 dBc/Hz at 10 kHz offset. Oscillation as high as 54 GHz with 3 km of fiber delay is achieved while maintaining suppression of spurious modes below the noise floor of the measurement. Pound-Drever-Hall frequency stabilization of the laser frequency is used to reduce optical frequency noise and keep the laser frequency centered within the etalon resonance for long term operation of the OEO.
Nanosized Amorphous Calcium Carbonate Stabilized by Poly(ethylene oxide)-b-poly(acrylic acid) Block Copolymers (2006)

Particles of amorphous calcium carbonate (ACC), formed in situ from calcium chloride by the slow release of carbon dioxide by alkaline hydrolysis of dimethyl carbonate in water, are stabilized against coalescence in the presence of very small amounts of double hydrophilic block copolymers (DHBCs) composed of poly(ethylene oxide) (PEO) and poly(acrylic acid) (PAA) blocks. Under optimized conditions, spherical particles of ACC with diameters less than 100 nm and narrow size distribution are obtained at a concentration of only 3 ppm of PEO-b-PAA as additive. Equivalent triblock or star DHBCs are compared to diblock copolymers. The results are interpreted assuming an interaction of the PAA blocks with the surface of the liquid droplets of the concentrated CaCO3 phase, formed by phase separation from the initially homogeneous reaction mixture. The adsorption layer of the block copolymer protects the liquid precursor of ACC from coalescence and/or coagulation.
Distributed Remote Vector Gaussian Source Coding for Wireless Acoustic Sensor Networks (2014)

In this paper, we consider the problem of remote vector Gaussian source coding for a wireless acoustic sensor network. Each node receives messages from multiple nodes in the network and decodes these messages using its own measurement of the sound field as side information. The node's measurement and the estimates of the source resulting from decoding the received messages are then jointly encoded and transmitted to a neighbouring node in the network. We show that for this distributed source coding scenario, one can encode a so-called conditional sufficient statistic of the sources instead of jointly encoding multiple sources. We focus on the case where node measurements are in form of noisy linearly mixed combinations of the sources and the acoustic channel mixing matrices are invertible. For this problem, we derive the rate-distortion function for vector Gaussian sources and under covariance distortion constraints.
Parametric and Optimal Design in Electronic Packaging Using DSC: Computational, Geometrical, and Material Aspects (2006)

Abstract The disturbed state concept (DSC) with the hierarchical single surface (HISS) plasticity model have been proposed and validated previously for a wide range of problems in electronic packaging. In this paper, detailed analyses are performed with the DSC∕HISS model to study the effect of various factors, such as computational and geometrical aspects and material parameters, on the failure life of chip substrate systems. The results and the methodology can be used for parametric analyses and optimal design of problems in electronic packaging.
Polycrystalline heterojunction solar cells: A device perspective (1996)

Abstract Analysis of high efficiency, thin film, small grain, polycrystalline, heterojunction CdTe and CuInSe 2 based solar cells can help explain the high quantum efficiencies and the resulting short circuit current (Jsc) as well as the forward diode current that controls the open circuit voltage (Voc). This analysis shows that minority carrier recombination at the metallurgical interface and at grain boundaries is greatly reduced by the proper “doping” of the window and absorber layers thereby increasing Jsc. Additional analysis and measurements show that the Voc in present state of the art solar cells is controlled by the magnitude of the forward diode current which appears to be caused by recombination in the space charge region of the absorber layer. This also shows that any quantitative modeling of these devices which relates the device performance to the bulk electronic properties of the material should consider the additional geometric dimension introduced by the polycrystallinity because of grain boundary effects.
Control Channel Design Trade-Offs for Ultra-Reliable and Low-Latency Communication System (2015)

Future generation of wireless networks, i.e. 5G, is envisioned to support several new use-cases demanding transmission reliability and latency that cannot be achieved by the current cellular networks such as long-term evolution (LTE). This paper looks at different design aspects of the control channel(s) to support ultra-reliable low-latency communication considering factory automation as an example scenario. In particular, we show that a fairly balanced design for both the uplink and the downlink control channels can be made given an appropriate selection of modulation, coding, diversity scheme, and time/frequency resources. By means of link-level simulations, we also show that the proposed control channel design supports a block-error rate of 10-9 under Rayleigh fading conditions at a signal-to-interference-plus-noise ratio comparable to that supported by current 4G systems (e.g. LTE). Furthermore, a radio frame structure is proposed to support the user plane end-to-end latency of 1 ms.
Experimental Study of Uniform-Shear Flow Past a Rotating Cylinder (1995)

An experimental study is made of two-dimensional uniform-shear flow (U = Uc + Gy) past a rotating cylinder of diameter D. A water-tunnel, equipped with a shear generator, was constructed. Laser-Doppler velocity measurements were undertaken to describe the wake characteristics. Data are compiled over the ranges of 600≤Re≤1,200, the shear parameter K[≡GD/Uc] up to 0.15, and the value of the cylinder rotation parameter α[≡ωD/2Uc], – 2.0≤α≤2.0. The power spectra of velocity measurements at downstream locations were analyzed to examine the vortex shedding patterns. In general, the dominant shedding frequency is shifted to a higher value as |α| and K increase. When |α| increases beyond a certain threshold value, the dominant frequency becomes less distinct. If |α| takes a value larger than around 1.5, the velocity field becomes randomized and diffuse, and the organized Karman vortex street activity weakens. The variations of the Strouhal number with K and α are described. The evolution of mean velocity profiles in the wake field is depicted. Characterizations of the velocity profiles, as K and α vary, are made based on the measurement data.
Measurement of Slow Diffusion Coefficients of Molecules with Arbitrary Scalar Couplings via Long‐Lived Spin States (2008)

New experiments are described for the determination of very slow diffusion constants by nuclear magnetic resonance (NMR) using long-lived (singlet) states. These experiments are suitable for molecules or conformations featuring a wide range of J-couplings.
Proton NMR study of bis(tetramethylammonium) tetrachlorozincate at high pressures and low temperatures (1987)

Wide-line proton NMR studies on polycryst. bis(tetramethylammonium) tetrachlorozincate were carried out at high hydrostatic pressures up to 15 kbar at 77-300 K and at ambient pressure down to 4.2 K. A 2nd-moment transition is obsd. to occur starting around 161 K, the temp. for the V-VI phase transition. This transition temp. has a neg. pressure coeff. up to 2 kbar, beyond which it changes sign. At 77 K, the 2nd moment decreases to 4 kbar and then increases again as a function of pressure. The results are explained in terms of the dynamics of the $N(CH_3)_4$ groups.
Contribution from 11th World Congress on Controversies in Obstetrics, Gynecology and Infertility (COGI) 'Celebration - 30 years of IVF' and Serono Symposia International Foundation Characterization of human PGD blastocysts with unbalanced chromosomal translocations and human embryonic stem cell line derivation (2009)

Novel embryonic stem cell lines derived from embryos carrying structural chromosomal abnormalities obtained after preimplantation genetic diagnosis (PGD) are of interest to study in terms of the influence of abnormalities on further development. A total of 22 unbalanced blastocysts obtained after PGD were analysed for structural chromosomal defects. Morphological description and chromosomal status of these blastocysts was established and they were used to derive human embryonic stem cell (ESC) lines. An outgrowth of cells was observed for six blastocysts (6/22; 27%). For two blastocysts, the exact morphology was unknown since they were at early stage, and for four blastocysts, the inner cell mass was clearly visible. Fifteen blastocysts carried an unbalanced chromosomal defect linked to a reciprocal translocation,
Identification of novel EGFR ectodomain mutations based on a large database of clinical circulating cell-free DNA sequencing tests. (2016)

e23167 Identification of novel EGFR ectodomain (ECD) mutations based on a database of clinical circulating cell-free DNA sequencing testsBackground: The Cancer Genome Atlas primarily sequenced early stage, treatment-naïve cancers, whereas our laboratory primarily sequences treatment refractory metastatic solid tumors. Circulating cell-free DNA (cfDNA) next generation sequencing (NGS) has enhanced sensitivity, which may aid in the detection of emerging resistant clones. In patients with RAS wild-type metastatic colorectal cancer (mCRC) EGFRECD mutations are associated with acquired resistance to anti-EGFR therapies. Here we report the frequencies of ECD mutations in patients with mCRC. Methods: Guardant360 is a cfDNA NGS test targeting 70 genes with complete exon sequencing for single nucleotide variants (SNVs), including all 28 exons in EGFR. Analytical sensitivity ranges to 0.05% mutant allele fraction (MAF) with analytic specificity for SNVs > 99.9999%. The 25th, 50th and 75thpercentile MAF for all 13,987 patients tested from June 2014 through January 2016 were 0.2%, 0.4% and 2.5%. Results: From 2014-2016 1,347 tests were performed on 1,257 patients with mCRC. Exon 12 EGFR SNVs [median MAF(range)] with > 3 recurrences were: 8 S464X [0.9%(0.1-3.1)]; 18 G465X [0.5%(.1-3.1); 3 K467X [0.3%(.2-1.0)]; 4 I491X [0.9%(0.3-1.6)]; 11 S492X [2.1%(0.3-5.1)]. Two novel EGFR SNVs were: 20 V441X [1.3%(0.1-2.8)]; and 5 S442X [0.2%(.1-2.7)]. Range of EGFR SNVs per case was 1-6, with a single hypermutated case demonstrating many resistance sub-clones: 6 EGFR exon 12 SNVs, and 4 KRAS and 3 NRAS SNVs in codons 12 and 61, and an STRN-ALKfusion at 0.1% MAF. Conclusions: A database of cfDNA NGS results in patients with mCRC revealed EGFR ECD SNVs known to drive anti-EGFR therapy resistance. Two spatially co-located SNVs of unknown significance were discovered, and these occurred in some cases at the highest MAF of EGFR SNVs. This analysis suggests that these two novel SNVs may function as major drivers of clonal resistance.
OSA Proceedings of the International Topical Meeting on Photonic Switching, Held in Salt Lake City, Utah on 6 - 8 March, 1992. Volume 8 (1992)

The papers in this book stem from the Third Topical Meeting on Photonic Switching organized by the Optical Society of America and held in Salt Lake City in March of 1991. The papers in this book consist of extended and enhanced submissions from authors who participated at the meeting. The papers have been grouped into eight sections: Space-Division Switching (guided-wave), Space-Division Switching (freespace), Time-Division Switching, Wavelength- Division Switching, Multi-Divisional Switching, Logic and Control, Optical Interconnection, and Novel Devices. Finally, the papers contained within this volume represent the leading edge of research in photonic switching, therefore, the reader should gain a reasonably balanced overview of the current state of photonic switching.
Production of Cybrids in Brassicaceae Species (2005)

This chapter describes a method of cytoplasm transfer within the brassicaceae family through Ca-PEG-mediated protoplast fusion. The method includes a protocol of nonmutagenic albinism induction based on spectinomycin-induced plastid ribosome deficiency (PRD). The proposed application of spectinomycin-mediated albinism allows speeding up creation of albino lines, as well as of hybrid production with substituted cytoplasm. According to described method cybrids between Orychophragmus violaceus and Brassica napus, O. violaceus and Lesquerella fendleri have been produced. Methods of further molecular analysis are also presented. The time-scale and reliability of described methods are indicated.
Noninvasive Molecular Neuroimaging Using Reporter Genes: Part II, Experimental, Current, and Future Applications (2008)

In this second article, we review the various strategies and applications that make use of reporter genes for molecular imaging of the brain in living subjects. These approaches are emerging as valuable tools for monitoring gene expression in diverse applications in laboratory animals, including the study of gene-targeted and trafficking cells, gene therapies, transgenic animals, and more complex molecular interactions within the central nervous system. Further development of more sensitive and selective reporters, combined with improvements in detection technology, will consolidate the position of in vivo reporter gene imaging as a versatile technique for greater understanding of intracellular biologic processes and underlying molecular neuropathology and will potentially establish a future role in the clinical management of patients with neurologic diseases.
An Electrooptic Feedforward System for Dynamic Control of a Quasi-Continuous-Wave Chirped Laser Source (2009)

In this letter, a feedforward system is developed for control of a quasi-continuous-wave (CW) chirped source. The goal of this study is to improve the uniformity of the temporal profile of a quasi-CW chirped laser source. The chirped spectrum input to the system is dynamically flattened using a feedforward scheme having bandwidth in excess of 1 GHz, resulting in more than three times reduction on the contrast of the input spectrum. A uniform chirped spectrum laser source can be used in time-stretched photonic analog-to-digital conversion, as part of laser radar system, or for optical coherence tomography.
Degenerate optomechanical parametric oscillators: Cooling in the vicinity of a critical point (2016)

Degenerate optomechanical parametric oscillators are optical resonators in which a mechanical degree of freedom is coupled to a cavity mode that is nonlinearly amplified via parametric down-conversion of an external pumping laser. Below a critical pumping power the down-converted field is purely quantum mechanical, making the theoretical description of such systems very challenging. Here we introduce a theoretical approach that is capable of describing this regime, even at the critical point itself. We find that the down-converted field can induce significant mechanical cooling and identify the process responsible of this as a cooling-by-heating mechanism. Moreover, we show that, contrary to naive expectations and semiclassical predictions, cooling is not optimal at the critical point, where the photon number is largest. Our approach opens the possibility of analyzing further hybrid dissipative quantum systems in the vicinity of critical points.
Supplementary Figure 1 from Reversal of NK-Cell Exhaustion in Advanced Melanoma by Tim-3 Blockade (2023)

&lt;p&gt;PDF file - 172K, Fig. S1. NK cells from melanoma patients up-regulate inhibitory receptors and down-regulate activating receptors.&lt;/p&gt;
The role of bubbles in the atomization of liquids and tissues (2014)

Ultrasonic atomization, or the emission of droplets from a liquid exposed to air, has been studied for many decades. The most accepted theory of atomization, the cavitation-wave hypothesis, states that droplets are emitted by a combination of capillary wave instabilities and cavitation bubble collapses. Recently, it was shown that tissues could also be atomized and that the result of atomization was surface erosion. Using a high static pressure chamber, we investigated the role of bubbles in the atomization of tissues and liquids. A 2-MHz, aluminum-lensed transducer was focused at the surface of either water or ex vivo bovine liver. In water at 1200 W/cm2 (p + = 6.8 MPa, p- = 5.3 MPa), we found that atomization ceased at an overpressure of 6.9 MPa, yet droplets were again released when the static pressure was increased to 13.8 MPa. In tissue at a linear in situ intensity of 22 000 W/cm2 (p + = 67 MPa, p- = 16 MPa), we found that a small increase in the static pressure (1.4 MPa) produced a qualitative change in atomization and caused thermal denaturation of the fractionated tissue rather than ejection from the surface. [Work supported by NIH EB007643, NIH DK043881, and NSBRI through NASA NCC 9-58.]
An unsupervised service annotation by review analysis (2017)

With the increase in popularity of review sites, users can write reviews on services that they have used in addition to reading reviews by other users. However, a number of reviews make it almost impossible for users to read all the reviews in detail. It is even more burdensome to compare multiple services. Thus, useful tools for extracting the unique features of services are necessary so that users can easily and intuitively understand the quality of services and compare them. In this study, we present an unsupervised method for extracting the unique and detailed features of services and the users' opinions on these features. By using the term frequency and inverse document frequency (TF-IDF) algorithm, our method can also extract in particular the praised or criticised features of a specific service. We conducted evaluations to show the validity of our method. In addition, we implemented an intuitive graphical user interface.
Supplementary Table S3 from Devimistat in Combination with Gemcitabine and Cisplatin in Biliary Tract Cancer: Preclinical Evaluation and Phase Ib Multicenter Clinical Trial (BilT-04) (2023)

&lt;p&gt;Prior and Posterior Estimates for Probability of Dose-Limiting Toxicity&lt;/p&gt;
WE‐DE‐BRA‐04: A Cost‐Effective Pixelated EPID Scintillator for Enhanced Contrast and DQE (2016)

Purpose: Beams‐eye‐view imaging applications such as real‐time soft‐tissue motion estimation and MV‐CBCT are hindered by the inherently low image contrast of electronic portal imaging devices (EPID) currently in clinical use. We investigate a cost effective scintillating glass that provides substantially increased detective quantum efficiency (DQE) and contrast to noise ratio (CNR). Methods: A pixelated scintillator prototype was built from LKH‐5 glass. The array is 12mm thick; 42.4×42.4cm2 wide and features 1.51mm pixel pitch with 20µm separation (glue+septa). The LKH‐5 array was mounted on the active matrix flat panel imager (AMPFI) of an AS‐1200 (Varian) with the GdO2S2:Tb removed. A second AS‐1200 was utilized as reference detector. The prototype EPID was characterized in terms of CNR, modulation transfer function (MTF) and DQE. Additionally, the visibility of various fiducial markers typically used in the clinic as well as a realistic 3D‐printed lung tumor model was assessed. All items were placed in a 12cm thick solid water phantom. CNR is estimated using a Las Vegas contrast phantom, presampled MTF is estimated using a slanted slit technique and the DQE is calculated from measured normalized noise power spectra (NPS) and the MTF. Results: DQE(0) for the LKH‐5 prototype increased by a factor of 8× to about 10%, compared to the AS‐1200 equipped with its standard GdO2S2:Tb scintillator. CNR increased by a factor of 5.3×. Due to the pixel size the MTF50 decreased by about 55% to 0.23lp/mm. The visibility of all fiducial markers as well as the tumor model were however markedly improved in comparison to an acquisition with the same parameters using the GdO2S2:Tb scintillator. Conclusion: LKH‐5 scintillating glasses allow the cost effective construction of thick pixelated scintillators for portal imaging which can yield a substantial increase in DQE and CNR. Soft tissue and fiducial marker visibility was found to be markedly improved. The project was supported in part by NIH grant R01CA188446‐01 and a grant from Varian Medical Systems.