gebhart/patrepeval huggingface dataset:
The Discovery of Pyrano[3,4‐b]indole‐Based Allosteric Inhibitors of HCV NS5B Polymerase with In Vivo Activity (2008)

Antiviral agents against hepatitis C: The discovery and synthesis of pyrano[3,4-b]indole based inhibitors of HCV NS5B polymerase is described. These compounds effectively inhibit HCV NS5B polymerase and display potent activities in a subgenomic HCV replicon assay. In particular, a sec-butyl-analogue of HCV-371 demonstrates in vivo antiviral activity in the chimeric mouse model of HCV infection. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2452/2008/z800168_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Supplementary Tables 1-2, Figures 1-4 from Antibody-Maytansinoid Conjugates Designed to Bypass Multidrug Resistance (2023)

Supplementary Tables 1-2, Figures 1-4 from Antibody-Maytansinoid Conjugates Designed to Bypass Multidrug Resistance
The Shanghai-Hongkong Team at MediaEval2012: Violent Scene Detection Using Trajectory-based Features (2012)

The Violent Scene Detection task offers a very practical challenge in detecting complex and diverse violent video clips in movies. In this working note paper, we will briefly describe our system and discuss the results, which achieved top performance in
Selective Formation of Cyclic Dimers in Solutions of Reversible Supramolecular Polymers (2001)

Communication to the Editor - No Abstract
Structural Segmentation of Multitrack Audio (2012)

Structural segmentation of musical audio signals is one of many active areas of Music Information Retrieval (MIR) research. One aspect of this important topic which has so far received little attention though is the potential advantage to be gained by utilizing multitrack audio. This paper gives an overview of current segmentation techniques, and demonstrates that by applying a particular segmentation algorithm to multitrack data, rather than the usual case of fully mixed audio, we achieve a significant and quantifiable increase in accuracy when locating segment boundaries. Additionally, we provide details of a structurally annotated multitrack test set available for use by other researchers.
Both Low and High Responder Myoglobin-Specific T Cells, Tolerant to F1 Help High But Not Low Responder B Cells (1983)

T cells, B cells, and antigen-presenting cells (APC) have all been implicated in the site and mechanism of action of immune response (Ir) genes (1, 2). We have studied the antibody and T cell proliferative responses to the model natural globular protein antigen, sperm whale myoglobin (Mb), and have previously found these responses to be controlled by two H-2-linked Ir genes, one mapping in I-A and one in I-C, in addition to one or more non-H-2-linked genes (3–8). Moreover, each of the two (or more) H-2-linked Ir genes appears to control the response to a different set of antigenic determinants on the Mb molecule (4, 7). Interestingly, only strains which have T cells which proliferate in response to a given part of the molecule make antibodies to that part of the Mb molecule (4). Since we have been interested in the mechanism by which Ir genes function, especially with such exquisite antigen-specificity, this relation between T cell and B cell specificity under Ir gene control was particularly intriguing.
Supplementary Table 1 from Identification of Promiscuous KIF20A Long Peptides Bearing Both CD4<sup>+</sup> and CD8<sup>+</sup> T-cell Epitopes: KIF20A-Specific CD4<sup>+</sup> T-cell Immunity in Patients with Malignant Tumor (2023)

&lt;p&gt;Supplementary Table 1 - PDF file 19K, Binding algorithm scores of KIF20A-derived peptides for HLA-class II molecules&lt;/p&gt;
Supplementary Data from IRE1α Disruption in Triple-Negative Breast Cancer Cooperates with Antiangiogenic Therapy by Reversing ER Stress Adaptation and Remodeling the Tumor Microenvironment (2023)

&lt;p&gt;Supplementary Data, including Supplementary Materials and Methods, References for Supplementary Data, and Figs. S1 to S5 including Figure Legends&lt;/p&gt;
Flexible Fiberoptic and Rigid-Rod Lens Endoscopy of the Lower Urinary Tract: A Prospective Controlled Comparison (1984)

Cystourethroscopy was performed on 80 men by separate examiners with a rigid-rod lens instrument and a flexible fiberoptic choledochonephroscope. Findings with the flexible system were equivalent to or more accurate than those with the rigid endoscope in 94 per cent of the cases. With the flexible instrument the duration of the examination was unchanged, patient comfort was improved, the amount of irrigation fluid was reduced, and patient preparation and positioning were simpler and quicker.
Brownfield Redevelopment In Toronto, Ontario: An Examination Of Sustainability And The Toronto Portlands (2021)

Brownfields are "abandoned, vacant, derelict or underutilized commercial and industrial properties where past actions have resulted in actual or perceived contamination" (NRTEE, 2003, p.1). Brownfield redevelopment, because of its contributions to urban sustainability, intensification and environmental quality, has become a critical issue in urban development literature of late. Through case-study research this paper aims to evaluate the relative sustainability of four Port Lands brownfield redevelopments that involve converting brownfields into green space in the City of Toronto. This study has shown how brownfield redevelopment and more specifically, turning brownfields into green space represent an application of all three pillars of sustainability. However, the exact extent of how this type of redevelopment represents an application of sustainable development cannot be truly measured or quantified. It has also highlighted the need to develop a comprehensive set of sustainability indicators that can be specifically applied to projects that aim to convert brownfields into green space.
Inhibitory Effect of Pyrophosphate, Citrate, Magnesium and Chondroitin Sulphate in Calcium Oxalate Urolithiasis (1989)

The inhibitory capacity of pyrophosphate, citrate, magnesium and chondroitin sulphate was investigated, using the urine of 21 calcium oxalate stone-forming patients without metabolic alterations. The inhibitory effect of these substances was assessed by a combination of nephelometry (light scattering) and optical microscopy. The results showed that citrate and magnesium had an inhibitory effect in a significant number of cases. Pyrophosphate and chondroitin sulphate had a less marked effect. The main urinary lithogenic biochemical parameters of the patients were also studied to see if there was a relationship between them and the inhibitory capacity of the compounds.
NL-Augmenter 🦎 → 🐍 A Framework for Task-Sensitive Natural Language Augmentation (2023)

Data augmentation is an important method for evaluating the robustness of and enhancing the diversity of training data for natural language processing (NLP) models. In this paper, we present NL-Augmenter, a new participatory Python-based natural language (NL) augmentation framework which supports the creation of transformations (modifications to the data) and filters (data splits according to specific features). We describe the framework and an initial set of 117 transformations and 23 filters for a variety of NL tasks annotated with noisy descriptive tags. The transformations incorporate noise, intentional and accidental human mistakes, socio-linguistic variation, semantically-valid style, syntax changes, as well as artificial constructs that are unambiguous to humans. We demonstrate the efficacy of NL-Augmenter by using its transformations to analyze the robustness of popular language models. We find different models to be differently challenged on different tasks, with quasi-systematic score decreases. The infrastructure, datacards, and robustness evaluation results are publicly available on GitHub for the benefit of researchers working on paraphrase generation, robustness analysis, and low-resource NLP. El aumento de datos es un método importante para evaluar la solidez y mejorar la diversidad del entrenamiento datos para modelos de procesamiento de lenguaje natural (NLP). इस लेख में, हम एनएल-ऑगमेंटर का प्रस्ताव करते हैं - एक नया भागी- दारी पूर्वक, पायथन में बनाया गया, लैंग्वेज (एनएल) ऑग्मेंटेशन फ्रेमवर्क जो ट्रांसफॉर्मेशन (डेटा में बदलाव करना) और फीलटर (फीचर्स के अनुसार डेटा का भाग करना) के नीरमान का समर्थन करता है।. 我们描述了NL-Augmenter框架及其初步包含的117种转换和23个过滤器，并 大致标注分类了一系列可适配的自然语言任务. این دگرگونی ها شامل نویز، اشتباهات عمدی و تصادفی انسانی، تنوع اجتماعی-زبانی، سبک معنایی معتبر، تغییرات نحوی و همچنین ساختارهای مصنوعی است که برای انسان ها مبهم است. NL-Augmenterpa allin kaynintam qawachiyku, tikrakuyninku- nata servichikuspayku, chaywanmi qawariyku modelos de lenguaje popular nisqapa allin takyasqa kayninta. Kami menemukan model yang berbeda ditantang secara berbeda pada tugas yang berbeda, dengan penurunan skor kuasi-sistematis. Infrastruktur, kartu data, dan hasil evaluasi ketahanan dipublikasikan tersedia secara gratis di GitHub untuk kepentingan para peneliti yang mengerjakan pembuatan parafrase, analisis ketahanan, dan NLP sumber daya rendah.
Lasing boosted with plasmonic nanostructures (2016)

Plasmonics, a technique to tightly concentrate light down to the nanoscaleby coupling photons to surface plasmons,has been employed to downscalelasersto sub-wavelength dimensions. The resultant device is called a spaser, short for surface plasmon amplification by stimulated emission of radiation, or more generally plasmonic nanolaser, which is being explored for applicationsin areas such as sensing and biomedical imaging. In this talk we will first make an overview of the major advances achieved thus far in this emerging field. Then, we will present our work addressing two major challenges regarding wavelength tunablility and lasing directionality of plasmonic nanolasers. To this date, single plasmonic nanoparticles, two-dimensional arrays of nanoapertures in plasmonic metasurfaces, and bulk plasmonic metamaterials have been designed and utilized as plasmonicnanocavities. Lasing wavelength tunability and directionality have been achieved with these nanocavities. Interesting effects have been also observed in other geometries. For instance, the 3-D random nanostructures bring in a possibility to control the lasing resonance by simply tuning the polarization of the pump laser, which is out of reach of conventional dielectric-cavity based lasers. By engineering the absorption and scattering properties, the laser can operate without degradation of lasing performance in the presence of densely packed metal nanostructures; consequently, spatial confinement of lasing modes at micron-scales has been obtained. We also present our two approaches to numerically model realistic spasers and nanolaser arrays. In the frequency domain, the spasers that utilize plasmonic modes of metallic nano-particles are modeled within the classical electrodynamics scattering framework using an intensity-dependent Lorentzian dielectric function, which rigorously accounts for quantum-mechanical saturation effects. In the time domain, we have developed a systematic approach to study lasing in plasmonic nanostructures using a finite difference model coupled to the rate equations of a multi-level gain system (4- and 6-level system). The modeling results show good agreement with experimental data.
Magnetic Vector-field of Optical Antennas from Electromagnetic Duality (2012)

Combining scattering-scanning near-field optical microscopy (s-SNOM) with infrared synchrotron micro-spectroscopy we determine the magnetic near-field modes of an infrared linear antenna by measuring the electric field of its electro-magnetic dual, the linear slot antenna.
Gut microbiota-associated compounds increase lethal prostate cancer risk. (2021)

147 Background: Gut-microbiota-mediated metabolism of trimethylamine-associated nutrients and amino acids has been linked to altered cholesterol metabolism and endothelial inflammation. However, the association between these compounds and lethal prostate cancer (PCa) remains unknown. Methods: A nested case-control study was performed using samples from the Prostate, Lung, Colorectal, and Ovarian (PLCO) cancer screening trial to evaluate the association between baseline serum levels of target metabolites (choline, carnitine, betaine, γ-butyrobetaine, crotonobetaine, trimethylamine N-oxide, phenylacetylglutamine, hippuric acid, and p-cresol sulfate) and lethal PCa risk. Lethal cases were randomly matched to controls at a 1:3 ratio on the basis of age, race, and enrollment date. Multivariable logistic regression, conditioned on case status and adjusted for PSA and BMI, was performed to assess the association between analyte quartile (Q) with lethal PCa. Trend of increasing odd ratios (OR) was evaluated using the Cochran-Armitage test. Results: 173 lethal PCa cases and 519 controls were analyzed. Relative to those in Q1, cases with baseline levels of choline and betaine above the median exhibited increased odds of developing lethal PCa after adjusting for BMI and PSA (Table). Lethal PCa risk increased across quartiles of choline in a dose-dependent fashion ( P-trend: 0.005), but not for betaine (P-trend: 0.08). Higher serum levels of other trimethylamine-associated compounds including γ-butyrobetaine, crotonobetaine, trimethylamine N-oxide were not consistently associated with PCa mortality. Baseline serum levels of phenylacetylglutamine, a gut-microbiota metabolite of phenylalanine, were associated with incident lethal PCa, with risk increasing across quantiles (P-trend: 0.003). Elevations in hippuric acid and p-cresol sulfate levels were not consistently associated with greater lethal PCa risk. Conclusions: Serum levels choline, betaine, and phenylacetylglutamine are associated with PCa mortality, underscoring the potential role of gut-microbiota-mediated metabolism in the biology of lethal PCa. Clinical trial information: NCT00002540. [Table: see text]
New heterogeneous multi-chip module integration technology using self-assembly method (2008)

We have newly proposed heterogeneous multi-chip module integration technologies in which MEMS and LSI chips are mounted on Si or flexible substrates using a self-assembly method. A large numbers of chips were precisely and simultaneously self-assembled and bonded onto the substrates with high alignment accuracy of approximately 400 nm. Thick MEMS and LSI chips with a thickness of more than 100 mum were electrically connected by unique lateral interconnections formed crossing over chip edges with large step height. We evaluated fundamental electrical characteristics using daisy chains formed crossing over test chips which were face-up bonded onto the substrates by the self-assembly. We obtained excellent characteristics in these daisy chains. In addition, RF test chips with amplitude shift keying (ASK) demodulator and signal processing circuits were self-assembled onto the substrates and electrically connected by the lateral interconnections. We confirmed that these test chips work well.
Evaluation of Decay Ratio of BWRs using Singular Value Decomposition Method (2005)

A new method for evaluating the decay ratio of boiling water reactors (BWR) using the singular value decomposition (SVD) method was proposed. In the SVD method, time-series data are decomposed into uncorrelated signal components and the auto-correlation functions (ACF) of these decomposed components are calculated. The ACF having a form of damping oscillation is related to the complex conjugate dominant poles of the frequency transfer function of BWR dynamics. The decay ratio and the natural frequency can be determined by applying a least square fitting to the ACF. The proposed method was applied to LPRM and APRM signals measured during stability experiments performed in Ringhals-1 at BOC-14. It was found that LPRM signals that were measured under 9 operating conditions were consistently decomposed into three type components whose ACFs had the forms of slow attenuation, fast attenuation and damping oscillation. Under the respective operating conditions, LPRM signals measured at various positions were decomposed into the ACFs with almost the same values of the decay ratio and the natural frequency. In virtue of this high decomposition performance, the decay ratios can be estimated with small standard deviations compared with conventional methods. Some guidelines for an accurate determination of decay ratios are also presented.
Telomere length and telomerase activity in T cells are biomarkers of high‐performing centenarians (2018)

It is generally recognized that the function of the immune system declines with increased age and one of the major immune changes is impaired T-cell responses upon antigen presentation/stimulation. Some "high-performing" centenarians (100+ years old) are remarkably successful in escaping, or largely postponing, major age-related diseases. However, the majority of centenarians ("low-performing") have experienced these pathologies and are forced to reside in long-term nursing facilities. Previous studies have pooled all centenarians examining heterogeneous populations of resting/unstimulated peripheral blood mononuclear cells (PBMCs). T cells represent around 60% of PBMC and are in a quiescence state when unstimulated. However, upon stimulation, T cells rapidly divide and exhibit dramatic changes in gene expression. We have compared stimulated T-cell responses and identified a set of transcripts expressed in vitro that are dramatically different in high- vs. low-performing centenarians. We have also identified several other measurements that are different between high- and low-performing centenarians: (a) The amount of proliferation following in vitro stimulation is dramatically greater in high-performing centenarians compared to 67- to 83-year-old controls and low-performing centenarians; (b) telomere length is greater in the high-performing centenarians; and (c) telomerase activity following stimulation is greater in the high-performing centenarians. In addition, we have validated a number of genes whose expression is directly related to telomere length and these are potential fundamental biomarkers of aging that may influence the risk and progression of multiple aging conditions.
IBM PowerNP network processor: Hardware, software, and applications (2003)

Deep packet processing is migrating to the edges of service provider networks to simplify and speed up core functions. On the other hand, the cores of such networks are migrating to the switching of high-speed traffic aggregates. As a result, more services will have to be performed at the edges, on behalf of both the core and the end users. Associated network equipment will therefore require high flexibility to support evolving high-level services as well as extraordinary performance to deal with the high packet rates. Whereas, in the past, network equipment was based either on general-purpose processors (GPPs) or application-specific integrated circuits (ASICs), favoring flexibility over speed or vice versa, the network processor approach achieves both flexibility and performance. The key advantage of network processors is that hardware-level performance is complemented by flexible software architecture. This paper provides an overview of the IBM PowerNP™ NP4GS3 network processor and how it addresses these issues. Its hardware and software design characteristics and its comprehensive base operating software make it well suited for a wide range of networking applications.
A Framework for Energy-Based Kinetostatic Modeling of Compliant Mechanisms (2017)

Although energy-based methods have advantages over the Newtonian methods for kinetostatic modeling, the geometric nonlinearities inherent in deflections of compliant mechanisms preclude most of the energy-based theorems. Castigliano’s first theorem and the Crotti-Engesser theorem, which don’t require the problem being solved to be linear, are selected to construct the energy-based kinetostatic modeling framework for compliant mechanisms in this work. Utilization of these two theorems requires explicitly formulating the strain energy in terms of deflections and the complementary strain energy in terms of loads, which are derived based on the beam constraint model. The kinetostatic modeling of two compliant mechanisms are provided to demonstrate the effectiveness of using Castigliano’s first theorem and the Crotti-Engesser theorem with the explicit formulations in this framework. Future work will be focused on incorporating use of the principle of minimum strain energy and the principle of minimum complementary strain energy.
A non-homogeneous MRF model for multiresolution Bayesian estimation (2002)

The popularity of Bayesian methods in image processing applications has generated great interest in image modeling. A good image model needs to be non-homogeneous to be able to adapt to the local characteristics of the different regions in an image. In the past however, such a formulation was difficult since it was not clear as to how to choose the parameters of the non-homogeneous model. But now motivated by results in maximum likelihood parameter estimation of MRF models, we formulate in this paper a non-homogeneous Markov random field (MRF) image model in the multiresolution framework. The advantage of the multiresolution framework is two fold: first, it makes it possible to estimate the parameters of the nonhomogeneous MRF at any resolution by using the image at the coarser resolution. Second, it yields multiresolution algorithms which are computationally efficient and more robust than their single resolution counterparts. Experimental results in tomographic image reconstruction and optical flow computation problems verify the superior modeling provided by the new model.
Thermocapillary Actuation of Millimeter-Scale Rotary Structures (2013)

In this paper, we describe the rotary motion, by Marangoni flow, of a millimeter-scale rotary structure immersed in a thin layer of liquid. A 16 × 8 array of 1 × 0.8 × 0.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> surface-mount resistors is suspended ≈ 500 μm above the liquid to serve as a programmable heat source. The continuous operation of resistor elements is used to impose a spatially-defined temperature gradient on the surface of the liquid. With a maximum temperature gradient of 36.6 K/mm at the surface of a 2 mm-thick film of liquid with viscosity 5 cSt, a stainless steel rotary structure with a weight of ≈ 10 mg, a diameter of 4.1 mm, and blade angle of 34° takes 28 s to make a 360° rotation. In general, the angular velocity of the rotary structure is affected by the temperature gradient of the liquid surface and liquid viscosity among several factors.
New stacked microstrip antenna with large bandwidth and high gain (1994)

A new radiating element is presented, which can provide simultaneously a large bandwidth and high gain. It consists of four identical patches uniformly displayed within a rectangular aperture (2*2) and fed electromagnetically by a driven patch etched on a lower substrate. It is shown that a good coupling with the parasitic patches is obtained, causing a large bandwidth, and the resonance modes of each patch are excited in phase, giving a high gain.