gebhart/patrepeval huggingface dataset:
Distribution of incident ions and retained dose analysis for a wedge-shaped target in plasma source ion implantation (1995)

A wedge-shaped target was implanted with nitrogen ions using the plasma source ion implantation process, in order to understand the effects of the target edges on the energy and fluence distribution of incident ions. Experimental measurements and analysis of retained dose on silicon samples affixed on the surface of the target, showed results consistent with those predicted by theoretical models. Higher retained dose and greater implantation depths were observed in the vicinity of the edge contained by the normal angle as compared to the edges contained by the acute angles. The target face with smaller area accumulated, on the average, higher dose compared to the face with the larger area.
Electrocardiographic findings in <i>mdx</i> mice: A cardiac phenotype of Duchenne muscular dystrophy (2002)

The mdx mouse is a model of Duchenne muscular dystrophy (DMD). As many DMD patients die of cardiac failure, we investigated whether mdx mice exhibited clinically relevant cardiac phenotypes. We applied a recently developed method for noninvasively recording electrocardiograms (ECGs) to study male mdx mice (n = 15) and control mice (n = 15). The mdx mice had significant tachycardia and decreased heart rate variability, consistent with observations in DMD patients. Heart rate was nearly 15% faster in mdx mice than control mice (P < 0.05). The rate-corrected QT interval duration and PR interval were shorter in mdx compared to control mice (P < 0.05). The muscarinic antagonist atropine significantly increased heart rate and decreased PR interval in C57 mice. In contrast, atropine significantly decreased heart rate and increased PR interval in all mdx mice. Pharmacological autonomic blockade and baroreflex sensitivity testing demonstrated an imbalance in autonomic nervous system modulation of heart rate, with decreased parasympathetic activity and increased sympathetic activity in mdx mice. Baseline ECGs and contrary responses to muscarinic blockade by atropine in mice deficient in neuronal nitric oxide synthase (nNOS) suggest that the autonomic dysfunction in mdx mice may be independent of decreased myocardial nNOS. These electrocardiographic findings in dystrophin-deficient mice may provide new bases for diagnosing, understanding, and treating DMD patients.
A Short and Efficient Synthesis of Mono‐substituted 1,4,7‐Triazacyclononanes. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Substituted Tetrahydroisoquinolines as Microtubule-destabilizing Agents in Triple Νegative Human Breast Cancer Cells (2016)

Triple-negative breast cancer (TNBC) occurs at greater frequency amongst African-Americans, being characterized by the absence of estrogen receptor (ER), progesterone receptor (PR) and human epidermal receptor 2 (HER2). TNBC is often invasive and typically treated with cytostatic agents such as taxanes in combination with anthracyclines or platinum-based drugs. In this study, we synthesized a number of tetrahydroisoquinoline moieties by N-amination of substituted isoquinolines by O-mesytelene sulfonylhydroxylamine followed by ylide formation and reduction, which yielded the desired, substituted tetrahydroisoquinolines (THIQs) in moderate to good yield. Using a differential scatter plot to identify potential selective ER-modulating drugs in ER-positive control cells (MCF-7) driven by estradiol vs. TNBC (MDA-MB-231) cells, the in vitro data showed an absence of effects on the ER (compared to 4-hydroxytamoxifen and raloxifene). In contrast, two lead compounds halted proliferation (cytostatic) in MDA-MB-231 TNBC cells at a potency level below 2.5 μM concomitant with mitotic arrest, attenuated replicative DNA synthesis, halted microtubule nucleation/stunted tubulin polymerization, abnormal expansive cytoskeletal tubulin and actin morphologies with multinucleation of cells. The most effective cytostatic compounds GM-4-53 and GM-3-121 blocked replicative processes at the G<sub>2</sub> growth phase. These findings suggest that specific THIQs work independently of the ER, by holding static the microtubule network thereby preventing mitosis. Future work is required to establish the safety and efficacy of these drugs and their potential adjunct therapeutic gain in the presence of taxanes in TNBC.
D-103 Conformational dynamics of single HIV-1 Env trimers on the surface of native virions (2014)

The HIV-1 envelope (Env) mediates viral entry into host cells. While static images of Env define distinct conformations, direct observations of Env dynamics have yet to be realized. To enable real-time imaging of conformational events in Env, we introduced fluorophores into the variable regions of the Env gp120 subunit and measured single-molecule fluorescence resonance energy transfer (smFRET) within the context of native trimers on the surface of HIV-1 virions. We observed unliganded HIV-1 Env to be intrinsically dynamic, transitioning between 3 distinct pre-fusion conformations, and receptor CD4 and co-receptor surrogate antibody 17b to remodel the conformational landscape of Env. Differences in conformational dynamics and ligand responsiveness of neutralization-sensitive and neutralization-resistant HIV-1 isolates delineated the dynamics-based mechanism of immune evasion. smFRET also revealed neutralizing antibodies VRC01, PG16, PGT128, PGT145, and 2G12, and the entry inhibitor, BMS-626529, to stabilize the ground state of Env, thereby providing dynamics-based strategies for therapeutic intervention.
Near Field Imaging at Microwave and Millimeter Wave Frequencies (2007)

Near field imaging at microwave and millimeter wave frequencies is useful for a wide variety of applications including concealed weapon detection, through-wall and inner-wall imaging, ground penetrating radar imaging, radar cross section analysis, and non-destructive evaluation of materials. A variety of novel imaging techniques have been developed for many of these applications at the Pacific Northwest National Laboratory (PNNL) . These techniques make use of wideband holographic wavefront reconstruction methods, and have been developed to optimize the image quality and resolution. This paper will summarize several of these techniques and show imaging results for several interesting application areas.
Phytase activity of anaerobic ruminal bacteria (1998)

Phytase catalyses the release of phosphate from phytate (myo-inositol hexakisphosphate), the predominant form of phosphorus in cereal grains, oilseeds and legumes. The presence of phytase activity was investigated in 334 strains of 22 species of obligately anaerobic ruminal bacteria. Measurable activities were demonstrated in strains of Selenomonas ruminantium, Megasphaera elsdenii, Prevotella ruminicola, Mitsuokella multiacidus and Treponema spp. Strains isolated from fermentations with cereal grains proved to have high activity, and activity was particularly prevalent in S. ruminantium, with over 96% of the tested strains being positive. The measured phytase activity was found exclusively associated with the bacterial cells and was produced in the presence of approximately 14 mM phosphate. The most highly active strains were all S. ruminantium, with the exception of the one Mitsuokella multiacidus strain examined. Phytase activity varied greatly among positive strains but activities as high as 703 nmol phosphate released (ml culture)-1 were measured for a S. ruminantium strain and 387 nmol phosphate released (ml culture)-1 for the Mitsuokella multiacidus strain.
Cytochrome P450 Biodiversity and Plant Protection (1999)

チトクロームP450モノオキシゲナーゼは農薬などの外来性化合物の解毒または活性化に, 並びに, 殺菌剤, 植物成長調節剤, 殺虫共力剤, 除草剤セイフナーなどの作用点として重要である.最近のゲノムプロジェクトの成果により, P450遺伝子は生物界のバクテリア, プロトゾア, 植物, 動物, 糸状菌のすべてに分布しており, 動物や植物の種には多くの遺伝子が存在することが明らかになった. 特に, モデル植物であるシロイヌナズナには約400の遺伝子が存在すると推定されている.これらP450酵素の生化学的性質を明らかにすることが, 生理学的な役割の解明に重要である. 高等植物では, シロイヌナズナT-DNA変異株を用いた研究が生理学的な役割の解明に有効であり, また, 酵母を用いた遺伝子発現系は実際に酵素機能の解明に広く用いられている. さらに, 薬物代謝に係わるP450分子種を発現したトランスジェニク植物の作出は, 除草剤選択性植物やファイトレメディエーション用植物の育成に重要である.
Current research activities on holographic video displays (2010)

"True 3D" display technologies target replication of physical volume light distributions. Holography is a promising true 3D technique. Widespread utilization of holographic 3D video displays is hindered by current technological limits; research activities are targeted to overcome such difficulties. Rising interest in 3D video in general, and current developments in holographic 3D video and underlying technologies increase the momentum of research activities in this field. Prototypes and recent satisfactory laboratory results indicate that holographic displays are strong candidates for future 3D displays.
Design of a Multi-Color Plenoptic Camera for Snapshot Hyperspectral Imaging (2018)

The design of a custom camera lens including: a two-lens optical system, filter array, and iris has been developed enabling a greyscale plenoptic camera to acquire full field-of-view, 2D, instantaneous hyperspectral measurements. This work focuses on the use of 7 discrete color filters and their effect on the image quality. It was determined that the placement of the filters inside the aperture plane of the camera was paramount to mitigating image artifacts. In addition, design rules were developed such that the optimal optical parameters (image distance, working distance, and focal length) can be easily determined from a few charts.\n\n\n
Large Field, High Resolution Full Field Optical Coherence Tomography: A\n Pre-clinical study of human breast tissue and cancer assessment (2012)

We present a benchmark pilot study in which high-resolution Full-Field\nOptical Coherence Tomography (FF-OCT) is used to image human breast tissue and\nis evaluated to assess its ability to aid the pathologist's management of\nintra-operative diagnoses. Our aim included evaluating the safety of FF-OCT on\nhuman tissue and determining the concordance between the images obtained with\nroutinely prepared histopathological material. The compact device used for this\nstudy provides a 2 {\\mu}m-lateral and a 1 {\\mu}m-axial resolution, and is able\nto scan a 1.5cm^2 specimen in about 7 minutes. 75 breast specimens obtained\nfrom 22 patients have been imaged. Because the contrast in the images is\ngenerated by endogenous tissue components, no biological, contrast agents or\nspecimen preparation is required. We characterized the major architectural\nfeatures and tissue structures of benign breast tissue, including adipocytes,\nfibrous stroma, lobules and ducts. We subsequently characterized features\nresulting from their pathological modification and developed a decision tree\nfor diagnosis. Two breast pathologists applied these criteria, resulting in a\ndemonstrable ability to distinguish between normal or benign tissue, in situ\nand invasive carcinomas using FF-OCT images, with a sensitivity of 97% and 90%,\nrespectively, and specificity of 74% and 77% respectfully. FF-OCT shows great\npotential for the evaluation of human tissue and its characterization as\nnormal/benign vs. lesional, for numerous ex-vivo clinical use-cases. Its high\nimaging accuracy for in-situ and invasive carcinoma paves the way for\napplications where a fast architectural assessment could improve the core\nneedle biopsy workflow, tumor margin assessments, and provides quality\nassurance for tissue acquired for clinical care and research.\n
Impact of nuclear data on fast neutron therapy (1994)

By combining a new, all-particle Monte Carlo radiation transport code, PEREGRINE, with the Lawrence Livermore National Laboratory (LLNL) nuclear data base, we have studied the importance of various neutron reactions on dose distributions in biological materials. Monte Carlo calculations have been performed for 5--20 MeV neutron pencil beams incident on biologically relevant materials arranged in several simple geometries. Results highlight the importance of nuclear data used for calculating dose distributions resulting from fast neutron therapy.
A simple neutron microscope using a compound refractive lens (2002)

Images obtained with a high-magnification simple neutron microscope using a compound refractive lens are presented in this letter. The short focal length of the stack of Al biconcave lenses facilitated the setup of a simple neutron microscope at the D22 small angle scattering beam line at the Institut Laue Langevin, Grenoble, France that achieved a 35× magnification and a 214 μm resolution. Higher-resolution images could be obtained using improved neutron lens systems that enhance beam delivery from neutron sources and produce high-quality images in combination with higher resolution two-dimensional neutron detectors.
A photonic wideband analog-to-digital converter (2002)

This paper provides a comprehensive understanding of a novel photonic high-speed analog-to-digital converter (ADC) approach and its anticipated performance. Compelling analytic models, experimental data, and simulation results will convince the reader that the system will achieve the goal of developing an ADC with a resolution on the order of 12-bits and with conversion speeds in excess of 10 Gsps.
Host-Directed Inhibitors of Myxoviruses: Synthesis and in Vitro Biochemical Evaluation (2011)

Drugs targeted to viral proteins are highly vulnerable to the development of viral resistance. One little explored approach to the treatment of viral diseases is the development of agents that target host factors required for virus replication. Myxoviruses are predominantly associated with acute disease and, thus, ideally suited for this approach since the necessary treatment time is anticipated to be limited. High-throughput screening previously identified benzimidazole 22407448 with broad anti-viral activity against different influenza virus and paramyxovirus strains. Hit to lead chemistry has generated 6p (JMN3-003) with potent antiviral activity against a panel of myxovirus family members exhibiting EC(50) values in the low nanomolar range.
An Engineered Human Fc‐Mannose‐Binding‐Lectin Captures Circulating Tumor Cells (2017)

Tumor cells circulating throughout the body have shown great potential for providing new diagnostic or therapeutic strategies for treating cancer patients. However, isolating circulating tumor cells (CTCs) is still challenging due to the lack of broad spectrum reagents that bind specifically to these cells. This study shows that an engineered human blood opsonin that mimics the innate immune mechanism for opsonizing complex mannan carbohydrates, Fc-mannose binding lectin (FcMBL), exhibits a broad spectrum of CTC binding activity. Using FcMBL-coated magnetic beads, this study is able to specifically capture and isolate a broad range of tumor cells spiked into buffer or blood. FcMBL is bound preferentially to human and mouse breast cancer cells relative to normal breast epithelium, and this study demonstrates the capture of seven different types of cancer cells with greater than 90% capture efficiency, whereas two of these same cancer cells bound poorly to anti epithelial cell adhesion molecule antibodies. It is also confirmed that FcMBL-coated magnetic beads can be used to capture CTCs from the blood of mice bearing metastatic tumors. The FcMBL capture technology may therefore provide a new tool for harvesting a broad range of CTCs with high efficiency as it targets tumor cell specific surface markers that are expressed across diverse cell types and retained throughout the metastatic process.
Evaluation of Planar Elongational Viscosity by Drag Force Acting on a Bullet Bob (2008)

A simple technique to evaluate planar elongational viscosity for various fluids including low viscous fluids is examined. A bullet shaped bob is pushed into a sample fluid held in a cylindrical cup. The gap between the bob and the cup forms an annular convergent channel to produce the planar elongational flow. The drag force acting on the bob is measured while the bob moves with a certain constant speed. This technique is carried out by adding the bullet bob to the commercial rotational rheometer.
A layered approach to artifact rejection for improved neural recording (2015)

Small biological signals can be resolved in presence of large artifacts using various methods. A layered approach to artifact rejection is presented here, using multiple techniques in a cascade fashion including blanking on the second gain stage. Results show superior performance of a layered approach including fast-settle blanking compared to other methods of rejection.
<title>Instrument For Simultaneously Measuring Intensity, Time, And Wavelength: The Temporal Spectral Photometer</title> (1983)

The design, performance and characteristics of a compact instrument for measuring the intensity as a function of time and wavelength emitted from luminous events is described. The instrument enables the user to display luminous kinetics on a picosecond time scale over a wide spectral range from 200 to 850nm. To demonstrate the instrument's capabilities, data will be presented on the temporal and spectral profiles emitted from photo excited dyes.
Continuous, Low Overhead, Run-Time Validation of Program Executions (2014)

The construction of trustworthy systems demands that the execution of every piece of code is validated as genuine, that is, the executed codes do exactly what they are supposed to do. Pre-execution validations of code integrity fail to detect run time compromises like code injection, return and jump-oriented programming, and illegal dynamic linking of program modules. We propose and evaluate a generalized mechanism called REV (for Run-time Execution Validator) that can be easily integrated into a contemporary out-of-order processor to validate, as the program executes, the control flow path and instructions executed along the control flow path. To prevent memory from being tainted by compromised code, REV also prevents updates to the memory from a basic block until its execution has been authenticated. Although control flow signature based authentication of an execution has been suggested before for software testing and for restricted cases of embedded systems, their extensions to out-of-order cores is a non-incremental effort from a micro architectural standpoint. Unlike REV, the existing solutions do not scale with binary sizes, require binaries to be altered or require new ISA support and also fail to contain errors and, in general, impose a heavy performance penalty. We show, using a detailed cycle-accurate micro architectural simulator for an out-of-order pipeline implementing the X86 ISA that the performance overhead of REV is limited to 1.87% on the average across the SPEC 2006 benchmarks.
Nonlinear predictive rate control for constant bit rate MPEG video coders (2002)

A nonlinear predictive approach has been employed in MPEG (Moving Picture Experts Group) video transmission in order to improve the rate control performance of the video encoder. A nonlinear prediction and quantisation technique has been applied to the video rate control which employs a transmission buffer for constant bit rate video transmission. A radial basis function (RBF) network has been adopted as a video rate estimator to predict the rate value of a picture in advance of encoding. The quantiser control surfaces based on nonlinear equations, which map both estimated and current buffer occupancies to a suitable quantisation step size, have also been used to achieve quicker responses to dramatic video rate variation. This scheme aims to adequately accommodate non-stationary video in the limited capacity of the buffer. Performance has been evaluated in comparison to the MPEG2 Test Model 5 (TM5) in terms of the buffer occupancy and picture quality.
Perspective of Future Potent Therapies for Fuchs Endothelial Corneal Dystrophy (2018)

This article reviews the current knowledge of the genetics and pathophysiology of FECD, and it introduces some potent therapeutic modalities that show promise as new treatments for this disorder.
Comparison of ESD protection capability of lateral BJT, SCR and bidirectional. SCR for hi-voltage BiCMOS circuits (2003)

Triggering structures BJT, SCR and bi-directional SCR for high voltage BiCMOS process onchip ESD protection have been developed and analyzed using physical process and device simulation and pulse measurements. A ten-fold increase in the protection levels compared to the reference BJT structures have been demonstrated using a cylindrical lateral SCR and bidirectional SCR.
Discovery and validation of a 30-gene expression signature to identify prostate cancer patients who are candidates for active surveillance. (2015)

10 Background: Considerable attention has been devoted to the search for biomarkers of aggressive prostate cancer. While many promising markers have been proposed, it is often unclear whether their ability to risk classify is adequate to reduce overtreatment of indolent cancers. We present and validate a gene expression signature that is highly specific for indolent disease and that, when combined with Gleason, improves upon the prognostic power of Gleason alone. Methods: A 30-gene signature of indolent disease was derived from a case-control sample of men (n=254) from the Health Professionals Follow-Up Study (HPFS) who were followed prospectively from cancer diagnosis for a median of 13.7 years. Cases were defined as men with prostate cancer who experienced a metastatic event or died of cancer during follow-up, while indolent controls survived at least 8 years without metastases. Whole-transcriptome gene expression was quantified from archival formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens acquired at prostatectomy. Genes were selected by a novel analytic strategy that maximizes a partial area under the curve (pAUC) to accurately identify indolent tumors. We validated the signature in two independent cohorts: the Physicians’ Health Study (PHS; n=150) and a Swedish Watchful Waiting cohort (WW; n=253) with respective median follow-up times of 14.4 and 9.0 years. Results: When compared to a model with Gleason alone, application of the signature to both validation data sets significantly improved prognostic accuracy as measured by pAUC (p=0.003 in PHS and p<0.001 in WW). Performance was particularly strong among men diagnosed with Gleason 7, where unit standard deviation increases in the signature score were associated with odds ratios of indolence of 5.24 (95% CI 2.21-15.75; p<0.001) and 2.37 (95% CI 1.45-4.19; p=0.001) in the PHS and WW cohorts, respectively. Conclusions: We present a signature of indolent prostate cancer that adds prognostic information beyond Gleason and has the potential to guide men to active surveillance and avoid overtreatment. Validation across both treated and untreated cohorts supports the discovery of a robust signature.
Towards robust color recovery for high-capacity color QR codes (2016)

Color brings extra data capacity for QR codes, but it also brings tremendous challenges to the decoding because of color interference and illumination variation, especially for high-density QR codes. In this paper, we put forth a framework for high-capacity QR codes, HiQ, which optimizes the decoding algorithm for high-density QR codes to achieve robust and fast decoding on mobile devices, and adopts a learning-based approach for color recovery. Moreover, we propose a robust geometric transformation algorithm to correct the geometric distortion. We also provide a challenging color QR code dataset, CUHK-CQRC, which consists of 5390 high-density color QR code samples captured by different smartphones under different lighting conditions. Experimental results show that HiQ outperforms the baseline [1] by 286% in decoding success rate and 60% in bit error rate.
Identification of four antibody-binding sites in the envelope proteins of simian immunodeficiency virus, SIVsm (1993)

The majority of antigenic sites identified in the envelope proteins of SIV correspond to sites identified in HIV-1 and HIV-2, which further supports the use of the simian model in vaccine development. The pattern of reactivity to the V2 region suggests that absence of antibodies directed to this site might correlate with disease progression.