gebhart/patrepeval huggingface dataset:
Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques (2020)

Summary The HIV-1 envelope (Env) is comprised by mass of over 50% glycans. A goal of HIV-1 vaccine development is the induction of Env glycan-reactive broadly neutralizing antibodies (bnAbs). The 2G12 bnAb recognizes an Env glycan cluster using a unique variable heavy (V H ) domain-swapped conformation that results in fragment antigen-binding (Fab) dimerization. Here we describe Fab-dimerized glycan (FDG)-reactive antibodies without V H -swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques that neutralized heterologous HIV-1 isolates. FDG precursors were boosted by vaccination in macaques, and were present in HIV-1-naïve humans with an average estimated frequency of one per 340,000 B cells. These data demonstrate frequent HIV-1 Env glycan-reactive bnAb B cell precursors in macaques and humans and reveal a novel strategy for their induction by vaccination. Highlights Discovery of Fab-dimerized HIV-1 glycan-reactive antibodies with a non-domain-swapped architecture Fab-dimerized antibodies neutralize heterologous HIV-1 isolates. Antibodies with this architecture can be elicited by vaccination in macaques. Fab-dimerized antibodies are found in HIV-1 naïve humans.
Achieving high spectral efficiency in long-haul transmission with pre-filtering and multi-symbol detection (2010)

We investigate a high spectral efficiency transmission approach employing aggressive pre-filtering and multi-symbol detection. We show that pre-filtering induces symbol correlation thus enabling a higher spectral-efficiency limit than that of the original modulation format. We demonstrate 100 G transoceanic transmission at 419% spectral efficiency using this approach.
Mechanism of Vortex Perturbation via Unsteady Pitching (2018)

Experiments indicate that vortices trailing finite wings can be perturbed by periodic wing pitching, leading to rapid dissipation and bursting. To illustrate the perturbation mechanism, Betz vortex rollup relations are combined with the Theodorsen theory for unsteady lift response. A sinusoidal pitch motion on a rigid elliptic planform wing is computed in this study as one example. Pitching modifies the instantaneous lift due to the planform variations, via the reduced frequency, and the rollup relations are applied to low-frequency experimental conditions. The combined Betz–Theodorsen theory shows that relatively large spanwise perturbations of the vortex centers can be achieved and may accelerate the exponential growth associated with the Crow instability. In fact, 84.2% of the displacement of the unsteady trailing vortices due to unsteady pitching is oriented in the direction of the Crow instability. Furthermore, the axial velocity in the vortex center, calculated based on the Batchelor method, varies on the order of the flight speed. This forms two types of stagnation points produced by approaching and retreating axial core velocities; in the former case, conservation of mass leads to observations of “bursting.” This observation can be explained adequately on the basis of quasi-steady considerations.
Dictionary learning from phaseless measurements (2016)

We propose a new algorithm to learn a dictionary along with sparse representations from signal measurements without phase. Specifically, we consider the task of reconstructing a two-dimensional image from squared-magnitude measurements of a complex-valued linear transformation of the original image. Several recent phase retrieval algorithms exploit underlying sparsity of the unknown signal in order to improve recovery performance. In this work, we consider sparse phase retrieval when the sparsifying dictionary is not known in advance, and we learn a dictionary such that each patch of the reconstructed image can be sparsely represented. Our numerical experiments demonstrate that our proposed scheme can obtain significantly better reconstructions for noisy phase retrieval problems than methods that cannot exploit such "hidden" sparsity.
Concordance of ETS fusion status of matched metastatic castration-resistant prostate cancer and primary prostate cancer: Data from NCI 9012, a randomized ETS fusion-stratified phase II trial. (2014)

5019 Background: Fusions of androgen-regulated genes with ETS transcription family members have been reported in 50% of localized pPCa patients (pts), with TMPRSS2-ERG fusions being the most common. ETS fusion products functionally depend upon Poly (ADP-ribose) polymerase 1 (PARP1), and its inhibition is preferentially cytotoxic to ETS translocation positive disease in preclinical models. We hypothesized that targeting ETS gene fusions will improve response rate in pts with these molecular subtypes and in pts with ETS fusion positive tumors, targeting the promoter and transcription factor of ETS fusion is more effective than targeting a single aspect of the fusion. Methods: Eligible mCRPC pts undergo a metastatic site biopsy to determine ETS fusion status by immunohistochemistry (ERG), fluorescent in-situ hybridization and/or RNA in-situ hybridization (ETV1) and sequencing (ETV4). Pts are stratified by ETS status and randomized to abiraterone (ABI) +/- the PARP inhibitor veliparib. Soft tissue biopsies are done using 18-gauge needle: 1-cm core (≥ 6 specimens), 2-cm core (≥4 specimens). For bone biopsy: 2-8 cores. We report interim results on rates of positive biopsy, ETS status/type and concordance between primary PCa and metastasis. Results: To date, 86 pts (Caucasians: 80%, African Americans 14%) with a median age 70 years and a median PSA 36.3 ng/ml have been enrolled. Of the 86 pts, 1 had an unreachable bone lesion, 36 had soft tissue and 49 had bone biopsies; all soft tissue and 36/49 (73%) bone biopsies were evaluable for analysis (13 had no tumor), ETS fusion status is positive in 36% pts: ERG positive (31%), ETV1 positive (4%), ETV4 positive (1%). Concordance of ETS status between primary PCa and metastatic site was found in 30/31 pts (97 % [95% CI: 83-99.9%]. Conclusions: This trial represents one of the first prospective predictive biomarker-driven trials in mCRPC. Results indicate feasibility of real time biopsy (adequate tissue yield including from bone) and biomarker determination, and demonstrates significant concordance of ETS status between primary PCa and metastasis in the subset analyzed to date. Clinical trial information: NCT01576172.
Asel, a restriction endonuclease fromAquaspirillum serpenswhich recognizes 5′AT TAAT3′ (1988)

Journal Article Asel , a restriction endonuclease from Aquaspirillum serpens which recognizes 5′AT TAAT3′ Get access Carol Polisson, Carol Polisson New England Biolabs32 Tozer Road, Beverly, MA 01915, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard D. Morgan Richard D. Morgan New England Biolabs32 Tozer Road, Beverly, MA 01915, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 21, 11 November 1988, Page 10365, https://doi.org/10.1093/nar/16.21.10365 Published: 11 November 1988 Article history Received: 03 October 1988 Published: 11 November 1988
Effect of the Chemical Composition and Double-cold-reducing on the DI Canmaking Properties (1997)

The DI (Drawn and Ironed) canmaking properties (the effect of the load of DI canmaking, the dome inversion pressure and the load of neck forming) was measured in the 350ml 211 (66mm) diameter size DI canmaking with many kinds of steels prepared in the laboratory. The chemical composition, especially carbon content, was widely varied from 0.05 to 0.0010wt%. The following points were clarified.1) The DR (double-cold-reduced) ultra-low carbon steel tinplate is advantageous for preventing the wrinkles at the necking by reducing the strength of the expected necking part.2) The bottom reverse pressure depends on both thickness and YS of the tinplate. The pressure increment is evaluated experimentally to be 0.074MPa/0.02mm in thickness and 1.7MPa/10MPa in YS, respectively. As the results, the application of the-ultra-low carbon steel, adequately hardened by the cold reducing after annealing, may be advantageous for reducing tinplate thickness without deterioration of necking formability.
Abstract 111: Tumor microenvironment derived NRG1 promotes antiandrogen resistance in prostate cancer (2019)

Despite the improved clinical outcomes for patients with advanced prostate cancer due to the use of second generation antiandrogens, acquired drug resistance inevitably occurs and remains the major challenge for prostate cancer therapy. While several cell-autonomous mechanisms of drug resistance have been elucidated previously, for a large number of patients the mechanism of resistance remains unclear. Recent studies point to the importance of the tumor microenvironment (TME), and cancer associated fibroblasts (CAF) in the TME, in mediating tumor progression and resistance to therapy, but whether CAFs specifically contribute to antiandrogen resistance in prostate cancer is not known. Using a preclinical model that faithfully mimics the typical progression of patients on antiandrogen therapy, we found that antiandrogen resistance develops significantly faster when cells are grown in the presence of their cognate CAFs. By carrying out biochemical purification and mass spectrometry analysis, we identified NRG1 as a CAF secreted factor, and found that it can promote antiandrogen resistance in tumor cells, via activation of HER3 in the tumor. Importantly, blocking either NRG1 or HER3 can re-sensitize tumors to antiandrogen treatment in this model. Moreover, NRG1 expression is up-regulated in CAFs after antiandrogen exposure or in androgen deprivation condition. Clinically, increased stroma-NRG1 expression was observed in patients post androgen deprivation therapy but not in hormonally intact men. Taken together, this work has revealed a novel, NRG1-mediated non-cell autonomous mechanism of antiandrogen resistance in prostate cancer, and suggests that therapeutically targeting NRG1 in the setting of metastatic, antiandrogen-resistant prostate cancer with elevated NRG1 could provide significant benefit to patients.Note: This abstract was not presented at the meeting.Citation Format: Zeda Zhang, Wouter Karthaus, Jose Mauricio Mota, Ping Mu, Chao Wu, Wassim Abida, Eliot Linton, Young Sun Lee, Eugine Lee, Ninghui Mao, Elizabeth Adams, Danielle Choi, Dana E. Rathkopf, Brett Carver, Anuradha Gopalan, Xuejun Jiang, Philip Watson, Charles Sawyers. Tumor microenvironment derived NRG1 promotes antiandrogen resistance in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 111.
Laser Generation of coherent photon state carrying orbital angular momentum with charge and handedness control using flat-photonics (2015)

International audience
Critical Behavior of Binary Liquid Mixtures of Deuterated and Protonated Polymers (1985)

Binary mixtures of protonated and perdeuterated 1,4-polybutadiene have been examined by small-angle neutron scattering and are shown to exhibit an upper critical solution temperature. The scattering results above the critical temperature are described by the mean-field theory of de Gennes for homogeneous binary polymer mixtures. These results contradict the universally held assumption that mixtures of deuterated and protonated polymers of otherwise identical chemical structure form ideal solutions.
Two-Stage GaN HEMT Amplifier With Gate–Source Voltage Shaping for Efficiency Versus Bandwidth Enhancements (2010)

In this paper a two-stage 2-GHz GaN HEMT amplifier with 15-W output power, 28-dB power gain, and 70% power-added efficiency (PAE) is presented. The power stage is designed to operate under class F conditions. The driver stage operates under class F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> conditions and feeds the power stage with both fundamental and second harmonic components. The inter stage matching is designed to target a quasi-half sine voltage shape at the intrinsic gate port of the power stage. The goal is to reduce aperture angle of the power stage and get PAE improvements over a wide frequency bandwidth. In addition to the amplifier design description, this paper reports original time-domain waveform measurements at internal nodes of the designed two-stage power amplifier using calibrated high-impedance probes and large signal network analyzer. Furthermore, waveform measurements recorded at different frequencies show that aperture angle remains reduced over large frequency bandwidth. In this study, a PAE greater than 60% is reached over 20% frequency bandwidth.
A High Frequency Inverter for Variable Load Operation (2018)

Inverters operating at high frequency (HF, 3-30MHz) are important to numerous industrial and commercial applications such as induction heating, plasma generation, and wireless power transfer. A major challenge in these applications is that the load impedance can vary dynamically in both real and complex components over a wide range, making it difficult to maintain high-efficiency soft-switched operation. The constraints that a variable load impedance place on high frequency inverter design results in systems that are often bulky, expensive, and inefficient. This paper presents the design, physical prototype, controller, and experimental results of a high-frequency variable load inverter that is able to directly drive widely variable loads with high efficiency. The prototype can deliver 1kW into a 22 ohm load at 95.4% efficiency as well as deliver significant power to a wide range of both capacitive and inductive loads.
Metamorphic solar cell having improved current generation (2023)

A semiconductor device structure having increased photogenerated current density, and increased current output is disclosed. The device includes low bandgap absorber regions that increase the range of wavelengths at which photogeneration of charge carriers takes place, and for which useful current can be collected. The low bandgap absorber regions may be strain balanced by strain-compensation regions, and the low bandgap absorber regions and strain-compensation regions may be formed from the same ternary semiconductor family. The device may be a solar cell, subcell, or other optoelectronic device with a metamorphic or lattice-mismatched base layer, for which the low bandgap absorber region improves the effective bandgap combination of subcells and current balance within the multijunction cell, for higher efficiency conversion of the solar spectrum.
Determination of total mercury in fillets of sport fishes collected from Folsom Reservoir, California, 2006 (2007)

This report presents the results of a study by the U.S. Geological Survey, done in cooperation with the U.S. Bureau of Reclamation, to determine mercury concentrations in selected sport fishes from Folsom Reservoir in California. Fillets were collected from each fish sample, and after homogenization and lyophilization of fish fillets, mercury concentrations were determined with a direct mercury analyzer utilizing the process of thermal combustion-gold amalgamation atomic absorption spectroscopy. Mercury concentrations in fillets ranged from 0.031 to 0.20 micrograms per gram wet weight in rainbow trout (Oncorhynchus mykiss) samples and 0.071 to 0.16 micrograms per gram wet weight in bluegill (Lepomis macrochirus) samples. Mercury concentration was 0.98 microgram per gram wet weight in a single spotted bass (Micropterus punctulatus) sample, which was the only one in the sample set which exceeded the U.S. Environmental Protection Agency's fish consumption advisory of 0.30 microgram per gram wet weight.
Modelling the Influence of Fuel Injection Parameters on Diesel Engine Emissions (1998)

&lt;div class="htmlview paragraph"&gt;Rate shaping of the fuel injection process is known to significantly impact emissions production in diesel engines. To demonstrate the ability of multidimensional engine modeling to quantify and explain the effect of rate shaping and injection duration, three injection profiles typical of common diesel fuel injection systems were investigated for three injection durations and injection timings. The present study uses an improved version of the KIVA-II engine simulation code employing the characteristic time combustion model, the Kelvin-Helmholtz and the Rayleigh-Taylor spray atomization mechanisms, the extended Zeldovich thermal NO&lt;sub&gt;&lt;i&gt;x&lt;/i&gt;&lt;/sub&gt; production model, and a single species soot model. Together, these models satisfactorily reproduce the known trends in engine behavior with respect to injection rate shaping and injection duration for a representative high-load high-speed operating condition at a fixed fueling rate; namely, increased NO&lt;sub&gt;&lt;i&gt;x&lt;/i&gt;&lt;/sub&gt; with decreased injection duration; decreased soot production with decreased injection duration. At high injection pressures, the falling injection profile produces more NO&lt;sub&gt;&lt;i&gt;x&lt;/i&gt;&lt;/sub&gt; and less soot than either the square or rising injection profile. The rising injection profile produces more soot and less NO&lt;sub&gt;&lt;i&gt;x&lt;/i&gt;&lt;/sub&gt; than the square profile. The computational results are also used to explain the origin of anomalous soot-NO&lt;sub&gt;&lt;i&gt;x&lt;/i&gt;&lt;/sub&gt; tradeoff trends where soot minima are seen as the injection timing is varied.&lt;/div&gt;
The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study (2020)

In a relatively younger national cohort with a low co-morbidity burden, COVID-19 was associated with low all-cause mortality. Independent risk factors for ICU admission included older age, male sex, higher BMI, and co-existing diabetes or chronic kidney disease.
Chemoselective Transfer Hydrogenation Reactions over Calcined-Layered Double Hydroxides (2000)

Abstract The transfer hydrogenation of aromatics containing various reducible groups has been carried out employing isopropanol as a hydrogen donor in the presence of different calcined LDHs. It was found that the NiII-AlIII (mol ratio 3) catalyst is highly active in bringing about chemoselective reduction compared to other calcined LDHs.
Resilient Distributed Estimation: Sensor Attacks (2018)

This paper studies multiagent distributed estimation under sensor attacks. Individual agents make sensor measurements of an unknown parameter belonging to a compact set, and, at every time step, a fraction of the agents' sensor measurements may fall under attack and take arbitrary values. We present the saturated innovation update (SRI) algorithm for distributed estimation resilient to sensor attacks. Under the iterative SRI algorithm, if less than one half of the agent sensors fall under attack, then, all of the agents' estimates converge at a polynomial rate (with respect to the number of iterations) to the true parameter. The resilience of SRI to sensor attacks does not depend on the topology of the interagent communication network, as long as it remains connected. We demonstrate the performance of SRI with numerical examples.
Synthesis of Perfluoroalkylated Bulky Triarylamines (2007)

The synthesis of two new triarylamine compounds bearing perfluoroalkylated side chains is described. Good thermal stabilities combined with a blue emission make these compounds promising candidates for materials applications.
Labeling by landscaping (2012)

State-of-the-art approaches to token labeling within text documents typically cast the problem either as a classification task, without using complex structural characteristics of the input, or as a sequential labeling task, carried out by a Conditional Random Field (CRF) classifier. Here we explore principled ways for structure to be brought to bear on the task. In line with recent trends in statistical learning of structured natural language input, we use a Support Vector Machine (SVM) classification framework deploying tree kernels. We then propose tree transformations and decorations, as a methodology for modeling complex linguistic phenomena in highly multi-dimensional feature spaces. We develop a general purpose tree engineering framework, which enables us to transcend the typically complex and laborious process of feature engineering. We build kernel based classifiers for two token labeling tasks: fine-grained event recognition, and lexical answer type detection in questions. For both, we show that in comparison with a corresponding linear kernel SVM, our method of using tree kernels improves recognition, thanks to appropriately engineering tree structures for use by the tree kernel. We also observe significant improvements when comparing with a CRF-based realization of structured prediction, itself performing at levels comparable to state-of-the-art.
The Evil Friend in Your Browser (2017)

On the one hand, browser extensions, e.g., for Chrome, are very useful, as they extend web browsers with additional functionality (e.g., blocking ads). On the other hand, they are the most dangerous code that runs in your browsers: extension can read and modify both the content displayed in the browser. As they also can communicate with any web-site or web-service, they can report both data and metadata to external parties. The current security model for browser extensions seems to be inadequate for expressing the security or privacy needs of browser users. Consequently, browser extensions are a juice target for attackers targeting web users.We present results of analysing over 2500 browser extensions on how they use the current security model and discuss examples of extensions that are potentially of high risk. Based on the results of our analysis of real world browser extensions as well as our own threat model, we discuss the limitations of the current security model form a user perspective. need of browser users.
Dynamically Self‐Assembling Metalloenzyme Models Based on Calixarenes (2006)

Giving it a tri: Ternary complexes formed from a macrocyclic host (p-sulfonatocalix[4]arene), an organic guest (2,3-diazabicyclo[2.2.2]oct-2-ene), and transition-metal ions (see picture) result in a host-assisted formation of a metal–ligand bond. The system displays a very high selectivity as a result of triple supramolecular recognition involving Coulombic interactions, hydrophobic guest binding, and weak metal–ligand interactions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z602999_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.
Al-2.82 Near-Field Scanning Optical Microcopy (Nsom) (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.