gebhart/patrepeval huggingface dataset:
Random circulant orthogonal matrix based Analog Compressed Sensing (2012)

Analog Compressed Sensing (CS) has attracted considerable research interest in sampling area. One of the promising analog CS technique is the recently proposed Modulated Wideband Converter (MWC). However, MWC has a very high hardware complexity due to its parallel structure. To reduce the hardware complexity of MWC, this paper proposes a novel Random Circulant Orthogonal Matrix based Analog Compressed Sensing (RCOM-ACS) scheme. By circularly shifting the periodic mixing function, the RCOM-ACS scheme reduces the number of physical parallel channels from m to 1 at the cost of longer processing time, where m is in the order of several dozen to several hundred in MWC. It is proved that the m×M measurement matrix of RCOM-ACS scheme satisfies the Restricted Isometry Property (RIP) condition with probability 1-M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-O(1)</sup> when m = O(rlog <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Mlog <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> r), where M is the length of the periodic mixing function, r denotes the sparsity of the input signal. Furthermore, to make a good tradeoff between processing time and hardware complexity, a short processing time RCOM-ACS scheme is proposed in this paper. Simulation results show that, the proposed schemes outperform MWC in terms of recovery performance.
Stereospecific synthesis of the 6.beta.-hydroxy metabolites of naltrexone and naloxone (1975)

The narcotic antagonists naltrexone (1a) and naloxone (2a) were stereospecifically reduced to the corresponding 6beta-hydroxy epimers 1b and 2b, respectively, with formamidinesulfinic acid in an aqueous alkaline medium. The reaction products were obtained with no detectable quantity of the 6alpha epimers 1c and 2c. The products 1b and 2b were formed in yields of 88.5 and 40%, respectively, and characterized by spectral methods. Compared to 1a and 2a, the stereospecific reduction products 1b and 2b and their 6alpha epimers 1c and 2c are all significantly less potent as narcotic antagonists in mice. Only 1c and 2c also possess antinociceptive activity.
Effects of stenting on adjacent vascular distensibility and neointima formation: role of nitric oxide (2001)

Intravascular stents increase long-term patency but their effects on the vascular mechanics of adjacent segments have not been studied. In this study, stents were deployed in the rabbit abdominal aorta after 1 week of normal diet, 1% cholesterol diet or 1% cholesterol diet with L-nitro arginine (L-NA 60 mg/l water). Intravascular ultrasound showed a small distal decrease in vessel distensibility (area/pressure * 100) before stenting. Distensibility was almost abolished by stenting (0.12 +/- 0.01, p < 0.001), but was increased proximal to the stent and decreased distal to the stent both acutely (proximal: 1.18 +/- 0.10 vs distal: 0.65 +/- 0.06, p < 0.001), and at 4 weeks (proximal: 1.05 +/- 0.08 vs distal: 0.37 +/- 0.07, p < 0.001). Nitric oxide (NO) activity was enhanced proximal to and within the stent, and remained constant distal to the stent, (versus control, proximal: 57 +/- 23%, stent: 136 +/- 35%, distal: 2 +/- 12%, p < 0.01). The I/M ratio was significantly higher proximal to and within the stent than in the distal segment (proximal: 0.40 +/- 0.10, stent: 0.37 +/- 0.12, distal: 0.12 +/- 0.11, p < 0.01). NO blockade with L-NA prevented hyperdistensibility proximally, and significantly increased the I/M ratio within the stent and distally (stent: 0.81 +/- 0.19, distal: 0.30 +/- 0.10, p < 0.05) but not proximally (0.38 +/- 0.09). In conclusion, aortic stenting increases proximal vascular distensibility and intimal lesion formation. Nitric oxide blockade augments intimal growth within but not proximal to the stent.
Induced change of critical current density profile in Nb/Al-AlOx/Nb Josephson junctions (2014)

A technique to induce spatial modulation of critical current density in niobium based Josephson devices by using a selective thermal annealing is reported. By depositing a carbon film onto selected region of the Josephson element it is possible to induce a localized heating, with a spatial resolution less than 1 μm, exploiting the much higher absorbance coefficient of carbon than the niobium one. The effectiveness of such technique is demonstrated by experimental measurement of the critical current vs. magnetic field, measured at T = 4.2 K, showing that the change of critical current density occurs only in the region corresponding to the absorber film area. Furthermore, the theoretical behaviour, by modelling a suitable step-like junction barrier shape, has been carried out to fit the experimental data in order to verify the selective modulation of critical current. This technique can be very useful in view of quantum computing experiments, Majorana fermions detection and superconducting magnetic sensors.
Interpolating Subdivision for Meshes of Arbitary Topology (1996)

Subdivision is a powerful paradigm for the generation of surfaces of arbitrary topology. Given an initial triangular mesh the goal is to produce a smooth and visually pleasing surface whose shape is controlled by the initial mesh. Of particular interest are interpolating schemes since they match the original data exactly, and are crucial for fast mutliresolution and wavelet techniques. Dyn, Gregory, and Levin introduced the Butterfly scheme [17], which yields C1 surfaces in the topologically regular setting. Unfortunately it exhibits undesirable artifacts in the case of an irregular topology. We examine these failures and derive an improved scheme, which retains the simplicity of the Butterfly scheme, is interpolating, and results in smoother surfaces.
Role of Staphylococcus aureus Global Regulators sae and σ B in Virulence Gene Expression during Device-Related Infection (2005)

The ability of Staphylococcus aureus to adapt to different environments is due to a regulatory network comprising several loci. Here we present a detailed study of the interaction between the two global regulators sae and sigmaB of S. aureus and their influence on virulence gene expression in vitro, as well as during device-related infection. The expression of sae, asp23, hla, clfA, coa, and fnbA was determined in strain Newman and its isogenic saeS/R and sigB mutants by Northern analysis and LightCycler reverse transcription-PCR. There was no indication of direct cross talk between the two regulators. sae had a dominant effect on target gene expression during device-related infection. SigmaB seemed to be less active throughout the infection than under induced conditions in vitro.
Orally administered -lactamase enzymes represent a novel strategy to prevent colonization by Clostridium difficile (2008)

Administration of oral recombinant beta-lactamase preserved the colonic microbiota of mice during parenteral beta-lactam antibiotic treatment and prevented the overgrowth of and toxin production by C. difficile in caecal contents. Oral beta-lactamase therapy may represent a novel approach towards preventing C. difficile infections in healthcare settings.
Immobilization of His-Tagged Proteins on Nickel-Chelating Nanolipoprotein Particles (2009)

Nanolipoprotein particles (NLPs) are nanometer-sized, discoidal particles that self-assemble from purified apolipoprotein and phospholipid. Their size and facile functionalization suggest potential application of NLPs as platforms for the presentation and delivery of recombinant proteins. To this end, we investigated incorporation of nickel-chelating lipids into NLPs (NiNLPs) and subsequent sequestration of polyhistidine (His)-tagged proteins. From initial lipid screens for NLP formation, the two phospholipids DMPC and DOPC were identified as suitable bulk lipids for incorporation of the nickel-chelating lipid DOGS-NTA-Ni into NLPs, and NiNLPs were successfully formed with varying amounts of DOGS-NTA-Ni. NiNLPs consisting of 10% DOGS-NTA-Ni with 90% bulk lipid (either DMPC or DOPC) were thoroughly characterized by size exclusion chromatography (SEC), non-denaturing gradient gel electrophoresis (NDGGE), and atomic force microscopy (AFM). Three different His-tagged proteins were sequestered on NiNLPs in a nickel-dependent manner, and the amount of immobilized protein was contingent on the size and composition of the NiNLP.
Protein Kinases as Small Molecule Inhibitor Targets in Inflammation (2007)

The human kinome describes a major group of intracellular signalling molecules. In the last few years, many molecules in the group have become targets for therapeutic interventions. Due to the conserved reaction mechanism of catalysis, protein kinases seem well "drugable" by small molecular weight inhibitors, thus opening the chance to novel oral bioavailable drug development. A large number of small molecule weight inhibitors for protein kinases have already been introduced into research and these molecules are extensively analysed in regard to their efficiency, potency and selectivity. Here we summarise the use of small molecule protein kinase inhibitors relevant for acute and chronic inflammation based on their essential role in cellular signaling mechanisms in immune cells such as macrophages, lymphoytes and granulocytes. We describe the progress made to develop inhibitors against Toll-like receptor associated kinases (IRAKs), against the MAPK kinase kinases Cot/Tpl-2 and TAK1, against Inhibitor-kappaB kinases (IKKs), against MAPK kinases (MEKs, MKKs), against MAPKs (ERK2, p38, JNKs) and against their downstream kinases MNK1 and MK2/3. This overview should help to keep up with the fast developing field and the continuously growing number of protein kinase inhibitors.
Phenanthrene-4,5-quinones: a synthesis of morphenol (1988)

Oxidation of 1,3,6,8-tetra-t-butyl-9,10-dihydrophenanthrene-4,5-diol (8), gave the corresponding 4,5-quinone (9), isolated as its oxepine valence isomer (19). Oxidation of 1,3,6,8-tetra-t-butylphenanthrene-4,5-diol (3) gave an even less stable quinone (4) which rearranged via its arene oxide valence isomer (26) to an enone (22). Acid-catalysed debutylation of this produced morphenol (24). The annelated analogue (27) of the phenanthrenequinone (4) showed no tendency to rearrange.
A simple convergence comparison of gallager codes under two message-passing schedules (2005)

The convergence rate of iterative decoding of Gallager codes on the additive white Gaussian noise (AWGN) channel using the sum-product algorithm (SPA) under the flooding schedule (FS) is compared with that under the turbo-decoding schedule (TDS). Analyses using extrinsic information transfer (EXIT) charts show that TDS exhibits a much faster convergence behavior than FS.
Nuclear analogs of .beta.-lactam antibiotics. 2. The total synthesis of 8-oxo-4-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acids (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNuclear analogs of .beta.-lactam antibiotics. 2. The total synthesis of 8-oxo-4-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acidsD. Boles Bryan, Ralph F. Hall, Kenneth G. Holden, William F. Huffman, and John G. GleasonCite this: J. Am. Chem. Soc. 1977, 99, 7, 2353–2355Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://pubs.acs.org/doi/10.1021/ja00449a063https://doi.org/10.1021/ja00449a063research-articleACS PublicationsRequest reuse permissionsArticle Views3104Altmetric-Citations81LEARN 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
Is antigen processing guided by major histocompatibility complex molecules? (1994)

Major histocompatibility complex class I (MHC-1) molecules bind peptide fragments derived from cytosolic antigens, and class II (MHC-2) molecules bind fragments of proteins that enter the endocytic pathway. How peptides of the right affinity and size are generated in vivo is still the focus of intense research. Current data are consistent with the view that precursor peptides of varying length are produced in the cytosol and transported into the endoplasmic reticulum lumen where nascent MHC-1 could sample the peptides for their affinity. High-affinity peptides would form stable complexes with MHC-1, which are resistant to proteolysis by luminal enzymes; peptides unable to bind to MHC-1 presumably undergo proteolysis in the lumen. On the other hand, multiple mechanisms are probably used to load MHC-2. Some proteins denatured in the acidic and reducing environment of the endosomes most likely bind to MHC-2 through the antigen's immunodominant region, and the exposed portions of the antigen are degraded by endosomal proteases. Other antigens must first be proteolysed into peptide fragments, which compete among themselves for binding to MHC-2, whereas heat shock proteins could also contribute peptides for MHC-2 loading. Because of their respective loading modes, there is a partial correlation between the MHC-2 binding affinity of the protein fragments and their in vivo immunodominance, which may not necessarily be the case for MHC-1.
A Link between Tear Instability and Hyperosmolarity in Dry Eye (2009)

These experiments provide a link between hyperosmolarity and tear instability, suggesting that hyperosmolar levels in the tear film may transiently spike during tear instability, resulting in corneal inflammation and triggering sensory neurons.
Elastic rod simulation by chain shape matching with twisting effect (2010)

One-dimensional deformable objects or elastic rods are widely used to represent threads, hair strands and elastic ropes in computer graphics. Such an object has the bending, stretching and twisting behaviors which are difficult to handle. To simulate deformable objects, a simple method called Lattice Shape Matching (LSM) [Rivers and James 2007] was recently proposed. LSM can handle the deformable objects ranging from soft bodies to stiff objects with an unconditional stability. For one-dimensional deformable objects, [Rungjiratananon et al. 2010] introduced a simplified model of LSM called Chain Shape Matching (CSM), which represents the one-dimensional deformable object by a chain of particles connected by segments. However, LSM and CSM can capture only the bending and stretching behaviors, but cannot handle twisting.
High-efficiency laser-diodes-pumped microthickness Yb:Y3Al5O12 slab laser (2005)

A high-efficiency and high-power Yb:Y3Al5O12 oscillator was developed based on the microthickness slab structure with high aspect ratio to obtain one-dimensional temperature gradient and to reduce the temperature increase in the crystal. Laser output power of 257W was obtained in cw oscillation with 42% optical conversion efficiency at a pump power of 608W.
Complete Amino Acid Sequence of a Lolium perenne (Perennial Rye Grass) Pollen Allergen, Lol p II (1989)

The complete amino acid sequence of a Lolium perenne (rye grass) pollen allergen, Lol p II was determined by automated Edman degradation of the protein and selected fragments. Cleavage of the protein by enzymatic and chemical techniques established an unambiguous sequence for the protein. Lol p II contains 97 amino acid residues, with a calculated molecular weight of 10,882. The protein lacks cysteine and glutamine and shows no evidence of glycosylation. Theoretical predictions by Fraga's (Fraga, S. (1982) Can. J. Chem. 60, 2606-2610) and Hopp and Woods' (Hopp, T. P., and Woods, K. R. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 3824-3828) methods indicate the presence of four hydrophilic regions, which may contribute to sequential or parts of conformational B-cell epitopes. Analysis of amphipathic regions by Berzofsky's method indicates the presence of a highly amphipathic region, which may contain, or contribute to, an Ia/T-cell epitope. This latter segment of Lol p II was found to be highly homologous with an antibody-binding segment of the major rye allergen Lol p I and may explain why immune responsiveness to both the allergens is associated with HLA-DR3.
Efficient sparse coding algorithms (2007)

Sparse coding provides a class of algorithms for finding succinct representations of stimuli; given only unlabeled input data, it discovers basis functions that capture higher-level features in the data. However, finding sparse codes remains a very difficult computational problem. In this paper, we present efficient sparse coding algorithms that are based on iteratively solving two convex optimization problems: an L
 1 
-regularized least squares problem and an L
 2 
-constrained least squares problem. We propose novel algorithms to solve both of these optimization problems. Our algorithms result in a significant speedup for sparse coding, allowing us to learn larger sparse codes than possible with previously described algorithms. We apply these algorithms to natural images and demonstrate that the inferred sparse codes exhibit end-stopping and non-classical receptive field surround suppression and, therefore, may provide a partial explanation for these two phenomena in V1 neurons.
Correlation of defense gene induction defects with powdery mildew susceptibility inArabidopsisenhanced disease susceptibility mutants (1998)

We investigated the relative importance of specific Arabidopsis thaliana genes in conferring resistance to bacterial versus fungal pathogens. We first developed a pathosystem involving the infection of Arabidopsis accession Columbia with a virulent isolate of the obligate biotrophic fungal pathogen Erysiphe orontii. E. orontii elicited the accumulation of mRNAs corresponding to the defense-related genes PR1, BGL2 (PR2), PR5 and GST1, but did not elicit production of the phytoalexin camalexin or the accumulation of defensin (PDF1.2) or thionin (THI2.1) mRNAs. We tested a set of 15 previously isolated Arabidopsis phytoalexin deficient (pad), non-expresser of PR (npr) and enhanced disease susceptibility (eds) mutants that are more susceptible to Pseudomonas syringae for their susceptibility to E. orontii. Four of these mutants (pad4-1, npr1-1, eds5-1 and a double npr1-1 eds5-1 mutant) as well as Arabidopsis lines carrying a nahG transgene exhibited enhanced susceptibility to E. orontii and reduced levels of PR gene expression. Comparison of the PR gene induction patterns in response to E. orontii in the various mutants and in the nahG transgenics suggests the existence of NPR1-independent salicylate-dependent and NPR1-independent salicylate-independent defense gene activation pathways. Eleven other eds and pad mutants did not show measurable enhanced susceptibility to E. orontii, suggesting that these mutants are defective in factors that are not important for the limitation of E. orontii growth.
High-resolution serum proteomic features for ovarian cancer detection. (2004)

Serum proteomic pattern diagnostics is an emerging paradigm employing low-resolution mass spectrometry (MS) to generate a set of biomarker classifiers. In the present study, we utilized a well-controlled ovarian cancer serum study set to compare the sensitivity and specificity of serum proteomic diagnostic patterns acquired using a high-resolution versus a low-resolution MS platform. In blinded testing sets, the high-resolution mass spectral data contained multiple diagnostic signatures that were superior to the low-resolution spectra in terms of sensitivity and specificity (P<0.00001) throughout the range of modeling conditions. Four mass spectral feature set patterns acquired from data obtained exclusively with the high-resolution mass spectrometer were 100% specific and sensitive in their diagnosis of serum samples as being acquired from either unaffected patients or those suffering from ovarian cancer. Important to the future of proteomic pattern diagnostics is the ability to recognize inferior spectra statistically, so that those resulting from a specific process error are recognized prior to their potentially incorrect (and damaging) diagnosis. To meet this need, we have developed a series of quality-assurance and in-process control procedures to (a) globally evaluate sources of sample variability, (b) identify outlying mass spectra, and (c) develop quality-control release specifications. From these quality-assurance and control (QA/QC) specifications, we identified 32 mass spectra out of the total 248 that showed statistically significant differences from the norm. Hence, 216 of the initial 248 high-resolution mass spectra were determined to be of high quality and were remodeled by pattern-recognition analysis. Again, we obtained four mass spectral feature set patterns that also exhibited 100% sensitivity and specificity in blinded validation tests (68/68 cancer: including 18/18 stage I, and 43/43 healthy). We conclude that (a) the use of high-resolution MS yields superior classification patterns as compared with those obtained with lower resolution instrumentation; (b) although the process error that we discovered did not have a deleterious impact on the present results obtained from proteomic pattern analysis, the major source of spectral variability emanated from mass spectral acquisition, and not bias at the clinical collection site; (c) this variability can be reduced and monitored through the use of QA/QC statistical procedures; (d) multiple and distinct proteomic patterns, comprising low molecular weight biomarkers, detected by high-resolution MS achieve accuracies surpassing individual biomarkers, warranting validation in a large clinical study.
Effects of Cisapride on Symptoms and Postcibal Small-Bowel Motor Function in Patients with Irritable Bowel Syndrome (1998)

Cisapride affects jejunal contraction characteristics and some symptoms in IBS.
Antigen co‐encapsulated with adjuvants efficiently drive protective T cell immunity (2007)

Compared to "live" vaccines, the immunogenicity of "subunit" vaccines based on recombinant antigen (Ag) is poor, presumably because exogenous Ag fails to effectively access the endosomal Ag-processing pathways of Ag-presenting cells (APC). To overcome this limitation, we exploited biodegradable poly(lactic-co-glycolic) microspheres (MP) co-entrapping Ag and Toll-like receptor (TLR) 9 or 7 ligands as an endosomal delivery device. In vitro, microspheres were rapidly phagocytosed by APC and translocated into phago-endosomal compartments, followed by degradation of the Ag and concurrent activation of endosomal TLR. As a consequence, full maturation of and cytokine secretion by APC as well as Ag-cross-presentation ensued. In vivo, "loaded" microspheres triggered clonal expansion of primary and secondary Ag-specific CD4 and CD8 T cells. The efficacy of CD8 T cell cross-priming was comparable to that of live vectors. The potency of T cell vaccination was demonstrated by protective and therapeutic interventions using infection- and tumor-model systems. These preclinical "subunit" vaccination data thus recommend MP as a generally applicable and powerful endosomal delivery device of exogenous Ag plus TLR-based adjuvants to vaccinate for protective and therapeutic CD4 and CD8 T cell immunity.