gebhart/patrepeval huggingface dataset:
Compressible dictionary learning for fast sparse approximations (2009)

By solving a linear inverse problem under a sparsity constraint, one can successfully recover the coefficients, if there exists such a sparse approximation for the proposed class of signals. In this framework the dictionary can be adapted to a given set of signals using dictionary learning methods. The learned dictionary often does not have useful structures for a fast implementation, i.e. fast matrix-vector multiplication. This prevents such a dictionary being used for the real applications or large scale problems. The structure can be induced on the dictionary throughout the learning progress. Examples of such structures are shift-invariance and being multi-scale. These dictionaries can be efficiently implemented using a filter bank. In this paper a well-known structure, called compressibility, is adapted to be used in the dictionary learning problem. As a result, the complexity of the implementation of a compressible dictionary can be reduced by wisely choosing a generative model. By some simulations, it has been shown that the learned dictionary provides sparser approximations, while it does not increase the computational complexity of the algorithms, with respect to the pre-designed fast structured dictionaries.
Hydrogen production by Cyanobacteria (2005)

The limited fossil fuel prompts the prospecting of various unconventional energy sources to take over the traditional fossil fuel energy source. In this respect the use of hydrogen gas is an attractive alternate source. Attributed by its numerous advantages including those of environmentally clean, efficiency and renew ability, hydrogen gas is considered to be one of the most desired alternate. Cyanobacteria are highly promising microorganism for hydrogen production. In comparison to the traditional ways of hydrogen production (chemical, photoelectrical), Cyanobacterial hydrogen production is commercially viable. This review highlights the basic biology of cynobacterial hydrogen production, strains involved, large-scale hydrogen production and its future prospects. While integrating the existing knowledge and technology, much future improvement and progress is to be done before hydrogen is accepted as a commercial primary energy source.
Euclidean supergravity in five dimensions (2016)

We construct a 5D, N=2 Euclidean theory of supergravity coupled to vector multiplets. Upon reducing this theory over a circle we recover the action of 4D, N=2 Euclidean supergravity coupled to vector multiplets.
Electrogenerated chemiluminescent determination of oxalate (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrogenerated chemiluminescent determination of oxalateIsrael. Rubinstein, Charles R. Martin, and Allen J. BardCite this: Anal. Chem. 1983, 55, 9, 1580–1582Publication Date (Print):August 1, 1983Publication History Published online1 May 2002Published inissue 1 August 1983https://pubs.acs.org/doi/10.1021/ac00260a030https://doi.org/10.1021/ac00260a030research-articleACS PublicationsRequest reuse permissionsArticle Views657Altmetric-Citations189LEARN 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
Optical resonators with ten million finesse (2007)

We report a significant improvement of the finesse and quality factor of a calcium fluoride whispering gallery mode optical resonator achieved with iterative thermal annealing. The initial and final values of the resonator finesse are F(i) approximately 5 x 10(5) and F(f) >/= 10(7) respectively. The measurements are conducted at room temperature in the laboratory atmosphere.
Simplified procedure for correcting both errors and erasures of Reed-Solomon code using Euclidean algorithm (1988)

It is well known that the Euclidean algorithm or its equivalent, continued fractions, can be used to find the error locator polynomial and the error evaluator polynomial in Berlekamp&apos;s key equation that is needed to decode a Reed-Solomon (RS) code. In the paper, a simplified procedure is developed and proved to correct erasures as well as errors by replacing the initial condition of the Euclidean algorithm by the erasure locator polynomial and the Forney syndrome polynomial. By this means, the errata locator polynomial and the errata evaluator polynomial can be obtained simultaneously and simply, by the Euclidean algorithm only. With this improved technique, the complexity of time-domain Reed-Solomon decoders for correcting both errors and erasures is reduced substantially from previous approaches. As a consequence, decoders for correcting both errors and erasures of RS codes can be made more modular, regular, simple, and naturally suitable for both VLSI and software implementation. An example illustrating this modified decoding procedure is given for a (15, 9) RS code.
Inflammation Dampened by Gelatinase A Cleavage of Monocyte Chemoattractant Protein-3 (2000)

Tissue degradation by the matrix metalloproteinase gelatinase A is pivotal to inflammation and metastases. Recognizing the catalytic importance of substrate-binding exosites outside the catalytic domain, we screened for extracellular substrates using the gelatinase A hemopexin domain as bait in the yeast two-hybrid system. Monocyte chemoattractant protein-3 (MCP-3) was identified as a physiological substrate of gelatinase A. Cleaved MCP-3 binds to CC-chemokine receptors-1, -2, and -3, but no longer induces calcium fluxes or promotes chemotaxis, and instead acts as a general chemokine antagonist that dampens inflammation. This suggests that matrix metalloproteinases are both effectors and regulators of the inflammatory response.
The Kondo Effect in C60 Single-Molecule Transistors (2003)

We have used an electromigration technique to fabricate C60-based single-molecule transistors. We detail the process statistics and the protocols used to infer the successful formation of a single-molecule transistor. At low temperatures each transistor acts as a single-electron device in the Coulomb blockade regime. Resonances in the differential conductance indicate vibrational excitations consistent with a known mode of C60. In several devices we observe conductance features characteristic of the Kondo effect, a coherent many-body state comprising an unpaired spin on the molecule coupled by exchange to the conduction electrons of the leads. The inferred Kondo temperature typically exceeds 50 K, and signatures of the vibrational modes persist into the Kondo regime.
Engineered Antibodies with Increased Activity to Recruit Complement (2001)

This manuscript describes two sites in a human IgG1 that, when mutated individually or in combination, result in a dramatic increase in C1q binding and complement-dependent cytotoxicity activity. These two residues, K326 and E333, are located at the extreme ends of the C1q binding epicenter in the C(H)2 domain of a human IgG. A mutation to tryptophan at K326 debilitates Ab-dependent cell-mediated cytotoxicity activity. In addition, substitutions of the residues E333 with serine and of K326 with tryptophan in a human IgG2 confer biological activity in the complement-dependent cytotoxicity assay in which the wild-type IgG2 is inactive. This study reveals that the residues K326 and E333 play a significant role in the control of the biological activity of an IgG molecule and can rescue the activity of an inactive IgG isotype.
MICROFACIES ANALYSIS OF SHIRANISH FORMATION AT HIJRAN SECTION- NE IRAQ (2012)

Shiranish Formation (Late Campanian- Maastrichtian) that cropping out north east Iraq, is studied by microfacies analysis of 52 thin section collected from Hijran Section, about 10 km west Shaqlawa Town, Governorate of Erbil. According to petrography, mineralogy and organic contents, rocks are subdivided to crystalline carbonate and microfacies units (biowackstone, packstone, and mudstone facies). Biowackstone facies have high ratio of the rock components, while the other facies have low ratio. Microfacies analysis led to relatively quiet deep marine environment.
Phenotypic Expression of Benign Familial Neonatal Convulsions Linked to Chromosome 20 (1994)

The phenotypic heterogeneity in this family, with an epilepsy syndrome determined by a single gene, was striking. This suggests that molecular genetic approaches to the common forms of idiopathic epilepsy, involving patients with clinically similar phenotypes from unrelated families, may be inappropriate.
Colloidal synthesis of metastable zinc-blende IV–VI SnS nanocrystals with tunable sizes (2011)

Here we report the colloidal synthesis of size-tunable SnS nanocrystals that have an unusual meta-stable cubic zinc-blende phase instead of the more stable layered orthorhombic phase. The single-crystalline zinc-blende SnS nanocrystals with sizes of 8 nm, 60 nm, and 700 nm were achieved by injecting the sulfur-oleylamine precursor into tin-oleylamine solution in the presence of hexamethyldisilazane (HMDS) at different temperatures. The morphology and structure of the SnS nanocrystals were studied by high-resolution electron microscopy techniques. The small SnS nanoparticles (∼8 nm and ∼60 nm) are nearly spherical and have the polyhedral shape. The large (∼700 nm) crystals display a unique crystal morphology that have T(d) symmetry with a truncated tetrahedron configuration, and the four truncated surfaces each outgrow to form a convex triangular pyramid corner. Careful structural analysis revealed that each of the crystal is enclosed by 4 low-index {111} hexangular facets and 12 high-index {220} triangular facets using a lift-out technique with a focused ion beam (FIB) and followed by high resolution electron microscope imaging. The direct band gaps of the different sized SnS nanocrystals range from 1.63 eV to 1.68 eV. These heavy-metal-free and low cost nanocrystals are highly efficient absorptive materials in the whole UV-visible range, suitable for applications in photovoltaic cells.
Zinc Inhibition of Mitochondrial Aconitase and Its Importance in Citrate Metabolism of Prostate Epithelial Cells (1997)

Prostate epithelial cells possess a uniquely limiting mitochondrial (m-) aconitase activity that minimizes their ability to oxidize citrate. These cells also possess uniquely high cellular and mitochondrial zinc levels. Correlations among zinc, citrate, and m-aconitase in prostate indicated that zinc might be an inhibitor of prostate m-aconitase activity and citrate oxidation. The present studies reveal that zinc at near physiological levels inhibited m-aconitase activity of mitochondrial sonicate preparations obtained from rat ventral prostate epithelial cells. Corresponding studies conducted with mitochondrial sonicates of rat kidney cells revealed that zinc also inhibited the kidney m-aconitase activity. However the inhibitory effect of zinc was more sensitive with the prostate m-aconitase activity. Zinc inhibition fit the competitive inhibitor model. The inhibitory effect of zinc occurred only with citrate as substrate and was specific for the citrate --> cis-aconitate reaction. Other cations (Ca2+, Mn2+, Cd2+) did not result in the inhibitory effects obtained with zinc. The presence of endogenous zinc inhibited the m-aconitase activity of the prostate mitochondrial preparations. Kidney preparations that contain lower endogenous zinc levels exhibited no endogenous inhibition of m-aconitase activity. Studies with pig prostate and seminal vesicle mitochondrial preparations also revealed that zinc was a competitive inhibitor against citrate of m-aconitase activity. The effects of zinc on purified beef heart m-aconitase verified the competitive inhibitor action of zinc. In contrast, zinc had no inhibitory effect on purified cytosolic aconitase. These studies reveal for the first time that zinc is a specific inhibitor of m-aconitase of mammalian cells. In prostate epithelial cells, in situ mitochondrial zinc levels inhibit m-aconitase activity, which provides a mechanism by which citrate oxidation is limited.
Flow of a Viscous Liquid on a Rotating Disk (1958)

Equations describing the flow of a Newtonian liquid on a rotating disk have been solved so that characteristic curves and surface contours at successive times for any assumed initial fluid distribution may be constructed. It is shown that centrifugation of a fluid layer that is initially uniform does not disturb the uniformity as the height of the layer is reduced. It is also shown that initially irregular fluid distributions tend toward uniformity under centrifugation, and means of computing times required to produce uniform layers of given thickness at given angular velocity and fluid viscosity are demonstrated. Contour surfaces for a number of exemplary initial distributions (Gaussian, slowly falling, Gaussian plus uniform, sinusoidal) have been constructed. Edge effects on rotating planes with rising rims, and fluid flow on rotating nonplanar surfaces, are considered.
Enantioselective Protonation of Silyl Enolates Catalyzed by a Binap⋅AgF Complex (2005)

Silver lining: A catalytic enantioselective protonation of trimethylsilyl enolates uses a binap/silver(I) fluoride complex as a chiral catalyst in a mixture of dichloromethane and methanol (see scheme). Various ketones with tertiary asymmetric carbon centers at the α position can be prepared with high enantioselectivities.
Structural Study of a DNA.cntdot.RNA Hybrid Duplex with a Chiral Phosphorothioate Moiety by NMR: Extraction of Distance and Torsion Angle Constraints and Imino Proton Exchange Rates (1994)

The solution structure of the thiophosphate-modified DNA.RNA hybrid duplex d(GCTATAApsTGG).r(CCAUUAUAGC) has been studied by NMR. Two samples with pure stereochemistry in the modified phosphate have been investigated. Two-dimensional NMR (2D NMR) methods have been applied to assign nearly all the resonances in both duplexes. Scalar coupling constants have been determined by comparing quantitative simulations with experimental double-quantum filtered COSY (DQF-COSY) cross-peaks. More than 300 distance constraints have been obtained from two-dimensional nuclear Overhauser spectroscopy (2D NOE) spectra recorded in D2O and H2O by using a complete relaxation matrix analysis as implemented in the program MARDIGRAS. This hybrid duplex presents a heteronomous structure. Riboses in the RNA strand are found in a N-type conformation typical of the A-form family as shown by the lack of H1'-H2' cross-peaks in DQF-COSY spectra and confirmed by the measured interproton distances. In contrast, the DNA strand adopts a different conformation with sugar puckers partially in the S-type domain, which is not in agreement with the A-family of structures. Coupling constants in deoxyriboses are not consistent with any single sugar conformation. Therefore, sugar pucker pseudorotation parameters are calculated according to a two-state dynamic equilibrium between N- and S-type conformers. In general, the population of major S conformer is lower than in double-stranded DNA duplexes, indicating that hybrid duplexes may be more flexible than pure DNA or RNA. The only differences observed in the spectra between the two stereoisomers studied originate from resonances of protons located near the modified phosphate. No significant differences in interproton distance have been detected, and only a slight difference of sugar pucker in the 5' neighbor has been found. The sulfur atom appears to be well-accommodated without further changes in the structure of the hybrid.
Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements (2012)

Nearly 30% of currently approved recombinant therapeutic proteins are produced in Escherichia coli. Due to its well-characterized genetics, rapid growth and high-yield production, E. coli has been a preferred choice and a workhorse for expression of non-glycosylated proteins in the biotech industry. There is a wealth of knowledge and comprehensive tools for E. coli systems, such as expression vectors, production strains, protein folding and fermentation technologies, that are well tailored for industrial applications. Advancement of the systems continues to meet the current industry needs, which are best illustrated by the recent drug approval of E. coli produced antibody fragments and Fc-fusion proteins by the FDA. Even more, recent progress in expression of complex proteins such as full-length aglycosylated antibodies, novel strain engineering, bacterial N-glycosylation and cell-free systems further suggests that complex proteins and humanized glycoproteins may be produced in E. coli in large quantities. This review summarizes the current technology used for commercial production of recombinant therapeutics in E. coli and recent advances that can potentially expand the use of this system toward more sophisticated protein therapeutics.
Plant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage (2005)

Circadian clocks are believed to confer an advantage to plants, but the nature of that advantage has been unknown. We show that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle. In wild type and in long- and short-circadian period mutants of Arabidopsis thaliana, plants with a clock period matched to the environment contain more chlorophyll, fix more carbon, grow faster, and survive better than plants with circadian periods differing from their environment. This explains why plants gain advantage from circadian control.
Counter-regulatory effect of sodium butyrate on tumour necrosis factor-alpha (TNF-α)-induced complement C3 and factor B biosynthesis in human intestinal epithelial cells (1999)

The various biological activities of butyrate have been well documented. In this study, we tested the effects of butyrate on TNF-alpha-induced complement C3 and factor B biosynthesis in human intestinal epithelial cells. The biosynthesis of C3, factor B and IL-8 was evaluated at the protein and mRNA levels. To evaluate transcriptional activation, the nuclear run-on assay was performed. The transcription factor-DNA binding activity was assessed by an electrophoretic gel mobility shift assay (EMSA). In the intestinal epithelial cell lines HT-29, T84 and Caco-2, sodium butyrate enhanced TNF-alpha-induced C3 secretion, but suppressed TNF-alpha-induced factor B and IL-8 secretion. Nuclear run-on assay revealed that transcriptional regulatory mechanisms are involved in the effects of sodium butyrate. The EMSAs indicated that sodium butyrate suppressed TNF-alpha-induced nuclear factor (NF)-kappaB- and activation protein (AP)-1-DNA binding activity, but enhanced TNF-alpha-induced activation of CCAAT/enhancer-binding protein (C/EBP)beta (NF-IL-6)-DNA binding activity. Sodium butyrate induced a counter-regulatory effect on TNF-alpha-induced C3 and factor B biosynthesis in human intestinal epithelial cells. Butyrate action has been discussed with its activity to induce histone hyperacetylation, but its counter-regulatory effect on complement biosynthesis may be closely associated with the modulation of transcription factor activation.
The response of GS‐NS0 myeloma cells to single and multiple pH perturbations (2002)

Animal cells are cultured in several types of vessels at laboratory and industrial scale the most common being the stirred tank and the air-lift. Economically, it is preferable to culture animal cells at the largest possible scale but the perceived sensitivity of animal cells to hydrodynamic shear has, until now, limited the aeration and agitation rates used. This has been reported to cause inhomogeneities in operational parameters such as dissolved oxygen concentration, temperature and pH. pH is of special interest during the latter stages of many animal cell fermentation because alkali additions, used for pH control, can cause large local pH perturbations of varying size and duration. The effect of single and multiple pH perturbations on the cell growth of a widely used GS-NS0 mouse myeloma cell line grown in batch culture was investigated. The effect of perturbation amplitude and duration was investigated using a single stirred tank reactor (STR). In the single STR system cells were subjected to one pH 8.0 or 9.0 perturbation ranging in duration from 0-90 minutes. No measurable decrease in viable cell number was seen for pH 8.0 perturbations of any duration whereas pH 9.0 perturbations lasting for 10 minutes caused a 15% decrease in viable cell number. The proportion of viable cells decreased with increasing perturbation time and a 90-minute exposure killed all of the cells. The effect of multiple pH perturbations on GS-NS0 cells was investigated using two connected STR's. More specifically the number of perturbations and the perturbation frequency were investigated. Cells were subjected to between 0 and 100 perturbations at pH 8.0; the time between each perturbation (frequency) was 6 minutes and each perturbation lasted for 200 seconds. Viable cell number decreased with increasing perturbation number, with 100 perturbations causing death of 27.5% of cells. Cells were also exposed to 10 perturbations at pH 9.0, each of 200 second duration at frequencies of either 6, 18 or 60 minutes. Approximately 8 times more cells were killed with perturbations at a 6-minute frequency (28.3% cell death) than at a 60-minute frequency (3.4% cell death).
High Cell-Free DNA Predicts Fatal Outcome among Staphylococcus aureus Bacteraemia Patients with Intensive Care Unit Treatment (2014)

High cf-DNA concentrations were observed among patients with high Pitt bacteraemia scores and ICU treatment. Pitt bacteraemia scores (≥ 4 points) and cf-DNA at day 3 from positive blood culture predicted death among SAB patients in ICU and were found to be independent prognostic markers. cf-DNA had no prognostic value among non-ICU patients.