gebhart/patrepeval huggingface dataset:
Matrix Factorization on GPUs with Memory Optimization and Approximate Computing (2018)

Matrix factorization (MF) discovers latent features from observations, which has shown great promises in the fields of collaborative filtering, data compression, feature extraction, word embedding, etc. While many problem-specific optimization techniques have been proposed, alternating least square (ALS) remains popular due to its general applicability e.g. easy to handle positive-unlabeled inputs, fast convergence and parallelization capability. Current MF implementations are either optimized for a single machine or with a need of a large computer cluster but still are insufficient. This is because a single machine provides limited compute power for large-scale data while multiple machines suffer from the network communication bottleneck. To address the aforementioned challenge, accelerating ALS on graphics processing units (GPUs) is a promising direction. We propose the novel approach in enhancing the MF efficiency via both memory optimization and approximate computing. The former exploits GPU memory hierarchy to increase data reuse, while the later reduces unnecessary computing without hurting the convergence of learning algorithms. Extensive experiments on large-scale datasets show that our solution not only outperforms the competing CPU solutions by a large margin but also has a 2x-4x performance gain compared to the state-of-the-art GPU solutions. Our implementations are open-sourced and publicly available.
Fundamentals and technology for monolithically integrated RF MEMS switches with ultra-nanocrystalline diamond dielectric/CMOS devices (2010)

Most current capacitive RF-MEMS switch technology is based on conventional dielectric materials such as SiO<sub>2</sub> and Si<sub>3</sub>N<sub>4</sub>. However, they suffer not only from charging problems but also stiction problems leading to premature failure of an RF-MEMS switch. Ultrananocrystalline diamond (UNCD<sup>(R)</sup> (2-5 nm grains) and nanocrystalline diamond (NCD) (10- 100 nm grains) films exhibit one of the highest Young's modulus (~ 980-1100 GPa) and demonstrated MEMS resonators with the highest quality factor (Q ≥10,000 in air for NCD) today, they also exhibit the lowest force of adhesion among MEMS/NEMS materials (~10 mJ/m<sup>2</sup>-close to van der Waals' attractive force for UNCD) demonstrated today. Finally, UNCD exhibits dielectric properties (fast discharge) superior to those of Si and SiO<sub>2</sub>, as shown in this paper. Thus, UNCD and NCD films provide promising platform materials beyond Si for a new generation of important classes of high-performance MEMS/NEMS devices.
DICON: Interactive Visual Analysis of Multidimensional Clusters (2011)

Clustering as a fundamental data analysis technique has been widely used in many analytic applications. However, it is often difficult for users to understand and evaluate multidimensional clustering results, especially the quality of clusters and their semantics. For large and complex data, high-level statistical information about the clusters is often needed for users to evaluate cluster quality while a detailed display of multidimensional attributes of the data is necessary to understand the meaning of clusters. In this paper, we introduce DICON, an icon-based cluster visualization that embeds statistical information into a multi-attribute display to facilitate cluster interpretation, evaluation, and comparison. We design a treemap-like icon to represent a multidimensional cluster, and the quality of the cluster can be conveniently evaluated with the embedded statistical information. We further develop a novel layout algorithm which can generate similar icons for similar clusters, making comparisons of clusters easier. User interaction and clutter reduction are integrated into the system to help users more effectively analyze and refine clustering results for large datasets. We demonstrate the power of DICON through a user study and a case study in the healthcare domain. Our evaluation shows the benefits of the technique, especially in support of complex multidimensional cluster analysis.
Antibodies to Malaria Vaccine Candidates Pvs25 and Pvs28 Completely Block the Ability of<i>Plasmodium vivax</i>To Infect Mosquitoes (2000)

Transmission-blocking vaccines are one strategy for controlling malaria, whereby sexual-stage parasites are inhibited from infecting mosquitoes by human antibodies. To evaluate whether the recently cloned Plasmodium vivax proteins Pvs25 and Pvs28 are candidates for a transmission-blocking vaccine, the molecules were expressed in yeast as secreted recombinant proteins. Mice vaccinated with these proteins adsorbed to aluminum hydroxide developed strong antibody responses against the immunogens, although for Pvs28, this response was genetically restricted. Antisera against both recombinant Pvs25 and Pvs28 recognized the corresponding molecules expressed by cultured sexual-stage parasites isolated from patients with P. vivax malaria. The development of malaria parasites in mosquitoes was completely inhibited when these antisera were ingested with the infected blood meal. Pvs25 and Pvs28, expressed in Saccharomyces cerevisiae, are as yet the only fully characterized transmission-blocking vaccine candidates against P. vivax that induce such a potent antiparasite response.
Wavelength Calibration of a Dispersive Near-Infrared Spectrometer Using Trichloromethane as a Calibration Standard (2000)

Since differences in wavelength calibration between instruments are arguably a primary source of error encountered in the transfer of calibration models from one instrument to another in near-infrared (NIR) spectroscopy, a readily available, convenient, inexpensive secondary wavelength calibration standard for the NIR spectral region is needed. This paper describes the advantages of trichloromethane as a wavelength standard for the calibration of dispersive NIR spectrometers used in the transmission mode. The spectrum of trichloromethane, taken with a Fourier transform NIR spectrometer whose wavenumber scale was calibrated with the ro-vibrational lines of ethyne as determined by the National Institute of Standards and Technology (NIST), is presented. The wavelengths of four strong, sharp, well-resolved bands of trichloromethane were determined with the calibrated Fourier transform NIR spectrometer and were found to be 1152.13 ± 0.01 nm (3 v 1 ), 1410.21 ± 0.01 nm (2 v 1 + v 4 ), 1691.9 ± 0.7 nm (2 v 1 ), and 1861.22 ± 0.01 nm ( v 1 + 2 v 4 ). These bands were then used to calibrate the wavelength scale of a commercial 0.25 m monochromator equipped with a 300 line mm −1 grating. The calibration revealed that, while the wavelength scale of the monochromator was linear, there was a systematic error of about + 12 nm in the NIR region.
Extracting subnanometer single shells from ultralong multiwalled carbon nanotubes (2005)

We report a simple but powerful method for engineering multi-walled carbon nanotubes (MWNTs) by using manipulation by an atomic-force microscope. The successive shell-by-shell extraction process of ultralong MWNTs allows the exposure of the innermost single-walled carbon nanotubes (SWNTs), which have diameters as small as approximately 0.4 nm. The inner-shell extraction process changes the electrical characteristics of the MWNTs. Whereas the outer hollowed-out nanotubes show either metallic or semiconducting character, the innermost SWNTs of small diameter exhibit predominantly metallic transport properties.
Synthesis and antiviral activity of 1,2,4-triazole-3-thiocarboxamide and 1,2,4-triazole-3-carboxamidine ribonucleosides (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and antiviral activity of 1,2,4-triazole-3-thiocarboxamide and 1,2,4-triazole-3-carboxamidine ribonucleosidesJoseph T. Witkowski, Roland K. Robins, Gyaneshwar P. Khare, and Robert W. SidwellCite this: J. Med. Chem. 1973, 16, 8, 935–937Publication Date (Print):August 1, 1973Publication History Published online1 May 2002Published inissue 1 August 1973https://pubs.acs.org/doi/10.1021/jm00266a014https://doi.org/10.1021/jm00266a014research-articleACS PublicationsRequest reuse permissionsArticle Views590Altmetric-Citations72LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An asymmetric SRAM cell to lower gate leakage (2004)

We introduce a new Static Random Access Memory (SRAM) cell that offers high stability and reduces gate leakage power in caches while maintaining low access latency. Our design exploits the strong bias towards zero at the bit level exhibited by the memory value stream of ordinary programs. Compared to conventional symmetric high-performance cell, our new cell reduces total leakage by more than 24% in the zero state at high temperature. With one cell design, total cache leakage is reduced by 24% at high temperature with no performance or stability loss. At low temperatures, where gate leakage is dominant, our cell reduces total cache leakage by 43%. We show that the new cell can be combined in an orthogonal fashion with asymmetric dual-V/sub t/ cells to lower both gate and subthreshold leakage, reducing total leakage by 45% to 60% with comparable performance and stability.
Microbial production of uridine. Part II. Regulation of pyrimidine nucleotide biosynthesis in cytidine deaminase-negative mutants of Bacillus subtilis. (1989)

The role of uridine and cytidine compounds in regulating pyrimidine nucleotide biosynthesis de novo was studied with cytidine deaminase-negative mutants of Bacillus subtilis. In the wild type strain, the formation of six enzymes for uridine S'-monophosphate (UMP) biosynthesis was severely repressed by exogenous cytidine or uracil, whereas the formation of the enzymes in a cytidine deaminase-negative mutant was repressed only by uracil. On the other hand, the formation of cytidine 5'-triphosphate (CTP) synthetase was not affected by uracil. This enzynme was repressed only when a cytidine deaminase-negative mutant was grown in the presence of excess cytidine. Studies on feedback inhibition also showed that the activity of CTP synthetase was inhibited by cytidine nucleotides, but not by uridine nucleotides.
s-SHIP Associates with Receptor Complexes Essential for Pluripotent Stem Cell Growth and Survival (2006)

Embryonic stem (ES) cells are pluripotent cells that have the ability to either self-renew or differentiate into any cell type found in the mammalian body. The signaling pathways required for self-renewal of these cells are yet to be defined. Previously we identified a stem cell-specific isoform of the protein SH2 domain-containing 5'-inositol phosphatase (SHIP) that we call s-SHIP, which is expressed in both pluripotent ES cells and adult tissue-specific multipotent cells, such as hematopoietic stem cells (HSCs). s-SHIP lacks an SH2 domain but contains a 5'-inositol phosphatase domain and several protein-protein interaction domains that potentially enable its participation in many different signaling pathways. Here we show that s-SHIP associates with gp130, which forms a heterodimeric complex with the leukemia inhibitory factor receptor (LIFR). Signaling through LIFR and other receptors that heterodimerize with gp130 is critical for growth and survival of ES cells and HSCs. Our findings provide biochemical evidence that s-SHIP participates in signaling pathways important for the maintenance of pluripotent stem cell populations.
Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction (2012)

Evidence is accumulating in support of the functional importance of subcellular RNA localization in diverse biological contexts. In different cell types, distinct RNA localization patterns are frequently observed, and the available data indicate that this is achieved through a series of highly coordinated events. Classically, cis-elements within the RNA to be localized are recognized by RNA-binding proteins (RBPs), which then direct specific localization of a target RNA. Until now, the precise control of the spatiotemporal parameters inherent to regulating RNA localization has not been experimentally possible. Here, we demonstrate the development and use of a chemically-inducible RNA-protein interaction to regulate subcellular RNA localization. Our system is composed primarily of two parts: (i) the Tet Repressor protein (TetR) genetically fused to proteins natively involved in localizing endogenous transcripts; and (ii) a target transcript containing genetically encoded TetR-binding RNA aptamers. TetR-fusion protein binding to the target RNA and subsequent localization of the latter are directly regulated by doxycycline. Using this platform, we demonstrate that enhanced and controlled subcellular localization of engineered transcripts are achievable. We also analyze rules for forward engineering this RNA localization system in an effort to facilitate its straightforward application to studying RNA localization more generally.
A novel liquid organic hydrogen carrier system based on catalytic peptide formation and hydrogenation (2015)

Hydrogen is an efficient green fuel, but its low energy density when stored under high pressure or cryogenically, and safety issues, presents significant disadvantages; hence finding efficient and safe hydrogen carriers is a major challenge. Of special interest are liquid organic hydrogen carriers (LOHCs), which can be readily loaded and unloaded with considerable amounts of hydrogen. However, disadvantages include high hydrogen pressure requirements, high reaction temperatures for both hydrogenation and dehydrogenation steps, which require different catalysts, and high LOHC cost. Here we present a readily reversible LOHC system based on catalytic peptide formation and hydrogenation, using an inexpensive, safe and abundant organic compound with high potential capacity to store and release hydrogen, applying the same catalyst for loading and unloading hydrogen under relatively mild conditions. Mechanistic insight of the catalytic reaction is provided. We believe that these findings may lead to the development of an inexpensive, safe and clean liquid hydrogen carrier system.
Least squares superposition codes of moderate dictionary size, reliable at rates up to capacity (2010)

Sparse superposition codes are developed for the additive white Gaussian noise channel with average codeword power constraint. Codewords are linear combinations of subsets of vectors, with the possible messages indexed by the choice of subset. Decoding is by least squares, tailored to the assumed form of linear combination. Communication is shown to be reliable with error probability exponentially small for all rates up to the Shannon capacity.
Immunotherapy of Cancer with Dendritic Cells Loaded with Tumor Antigens and Activated Through mRNA Electroporation (2010)

Since decades, the main goal of tumor immunologists has been to increase the capacity of the immune system to mediate tumor regression. Considerable progress has been made in enhancing the efficacy of therapeutic anticancer vaccines. First, dendritic cells (DCs) have been identified as the key players in orchestrating primary immune responses. A better understanding of their biology and the development of procedures to generate vast amounts of DCs in vitro have accelerated the development of potent immunotherapeutic strategies for cancer. Second, tumor-associated antigens have been identified which are either selectively or preferentially expressed by tumor cells and can be recognized by the immune system. Finally, several studies have been performed on the genetic modification of DCs with tumor antigens. In this regard, loading the DCs with mRNA, which enables them to produce/process and present the tumor antigens themselves, has emerged as a promising strategy. Here, we will first overview the different aspects that must be taken into account when generating an mRNA-based DC vaccine and the published clinical studies exploiting mRNA-loaded DCs. Second, we will give a detailed description of a novel procedure to generate a vaccine consisting of tumor antigen-expressing dendritic cells with an in vitro superior capacity to induce anti-tumor immune responses. Here, immature DCs are electroporated with mRNAs encoding a tumor antigen, CD40 ligand (CD40L), CD70, and constitutively active (caTLR4) to generate mature antigen-presenting DCs.
Peripheral partitioning and tree decomposition for partial scan (2002)

We propose a new partial scan technique that incurs significantly less area overhead than the pipeline technique (all feedback cycles including self-loops are broken) and yet achieves very high test coverage in short CPU times. Our proposal selects scan flip-flops so that the circuit satisfies two key properties in the test mode. First, the circuit is partitioned into peripherally interacting finite state machines (peripheral partitions). Peripheral partitions do not have combinational paths between flip-flops belonging to different partitions. Second, the flip-flop dependency graph (S-graph) of each peripheral partition has a tree structure. Our technique does not require self-loops to be broken. We believe that peripheral partitions with tree structure S-graphs inherently require low sequential test generation resources. We develop an efficient algorithm for peripheral partitioning and tree decomposition of the S-graph. The scan flip-flop selection algorithm iteratively partitions the S-graph into disjoint sub-graphs with the tree structure. We report results on all the large circuits in the ISCAS 89 benchmark set. These results show that our technique produces scan circuits for which very high (near 100%) fault efficiency is achievable in extremely short CPU times. The high fault efficiencies achieved by our technique are comparable to that of pipeline circuits. However, the area overhead for our technique is significantly less than the pipeline case.
Substrates and Controls for the Quantitative Detection of Active Botulinum Neurotoxin in Protease-Containing Samples (2013)

Botulinum neurotoxins (BoNTs) are used in a wide variety of medical applications, but there is limited pharmacokinetic data on active BoNT. Monitoring BoNT activity in the circulation is challenging because BoNTs are highly toxic and are rapidly taken up by neurons and removed from the bloodstream. Previously we reported a sensitive BoNT "Assay with a Large Immunosorbent Surface Area" that uses conversion of fluorogenic peptide substrates to measure the intrinsic endopeptidase activity of bead-captured BoNT. However, in complex biological samples, protease contaminants can also cleave the substrates, reducing sensitivity and specificity of the assay. Here, we present a novel set of fluorogenic peptides that serve as BoNT-specific substrates and protease-sensitive controls. BoNT-cleavable substrates contain a C-terminal Nle, while BoNT-noncleavable controls contain its isomer ε-Ahx. The substrates are cleaved by BoNT subtypes A1-A3 and A5. Substrates and control peptides can be cleaved by non-BoNT proteases (e.g., trypsin, proteinase K, and thermolysin) while obeying Michaelis-Menten kinetics. Using this novel substrate/control set, we studied BoNT/A1 activity in two mouse models of botulism. We detected BoNT/A serum activities ranging from ~3600 to 10 amol/L in blood of mice that had been intravenously injected 1 h prior with BoNT/A1 complex (100 to 4 pg/mouse). We also detected the endopeptidase activity of orally administered BoNT/A1 complex (1 μg) in blood 5 h after administration; activity was greatest 7 h after administration. Redistribution and elevation rates for active toxin were measured and are comparable to those reported for inactive toxin.
Platycodon grandiflorus Root Extract Attenuates Body Fat Mass, Hepatic Steatosis and Insulin Resistance through the Interplay between the Liver and Adipose Tissue (2016)

The Platycodon grandiflorus root, a Korean medicinal food, is well known to have beneficial effects on obesity and diabetes. In this study, we demonstrated the metabolic effects of P. grandiflorus root ethanol extract (PGE), which is rich in platycodins, on diet-induced obesity. C57BL/6J mice (four-week-old males) were fed a normal diet (16.58% of kilocalories from fat), high-fat diet (HFD, 60% of kilocalories from fat), and HFD supplemented with 5% (w/w) PGE. In the HFD-fed mice, PGE markedly suppressed the body weight gain and white fat mass to normal control level, with simultaneous increase in the expression of thermogenic genes (such as SIRT1, PPARα, PGC1α, and UCP1), that accompanied changes in fatty acid oxidation (FAO) and energy expenditure. In addition, PGE improved insulin sensitivity through activation of the PPARγ expression, which upregulates adiponectin while decreasing leptin gene expression in adipocytes. Furthermore, PGE improved hepatic steatosis by suppressing hepatic lipogenesis while increasing expression of FAO-associated genes such as PGC1α. PGE normalized body fat and body weight, which is likely associated with the increased energy expenditure and thermogenic gene expression. PGE can protect from HFD-induced insulin resistance, and hepatic steatosis by controlling lipid and glucose metabolism.
Synthesis and antiviral activity of certain 5'-monophosphates of 9-D-arabinofuranosyladenine and 9-D-arabinofuranosylhypoxanthine (1975)

A number of 5'-phosphates of 9-D-arabinofuranosyladenine and 9-D-arabinofuranosylhypoxanthine were prepared and tested against a variety of DNA viruses in tissue culture. The syntheses of the antiviral agent 9-beta-D-arabinofuranosylhypoxanthine 5'-monophosphate (6) and a series of related nucleotides, 9-beta-D-arabinofuranosyladenine 5'-O-methylphosphate (3), 9-beta-D-arabinofuranosylhypoxanthine 5'-O-methylphosphate (7), 9-beta-D-arabinofuranosylhypaxanthine cyclic 3',5'-phosphate (13), and 9-alpha-D-arabinofuranosylhypoxanthine 5'-monophosphate (17), are described. The concepts underlying the development of these antiviral agents are discussed. Comparison of the anti-DNA viral activity is made with 9-beta-D-arabinofuranosyladenine (ara-A). Reproducible antiviral activity against three DNA viruses in vitro at nontoxic dosage levels is demonstrated by 3,6, and other related nucleotides.