gebhart/patrepeval huggingface dataset:
Structured sparse ternary weight coding of deep neural networks for efficient hardware implementations (2017)

Deep neural networks (DNNs) usually demand a large amount of operations for real-time inference. Especially, fully-connected layers contain a large number of weights, thus they usually need many off-chip memory accesses for inference. We propose a weight compression method for deep neural networks, which allows values of +1 or -1 only at predetermined positions of the weights so that decoding using a table can be conducted easily. For example, the structured sparse (8,2) coding allows at most two non-zero values among eight weights. This method not only enables multiplication-free DNN implementations but also compresses the weight storage by up to x32 compared to floating-point networks. Weight distribution normalization and gradual pruning techniques are applied to mitigate the performance degradation. The experiments are conducted with fully-connected deep neural networks and convolutional neural networks.
Performance of the 3-D PENCIL flash EPROM cell and memory array (1995)

A promising new 3-D Programmable Erasable Nonvolatile CylIndricaL (PENCIL) flash EPROM cell that offers significant area and performance advantages over conventional planar approaches has been implemented in a novel memory array. The 3-D PENCIL cell is a vertical device formed on the sidewalls of an etched silicon pillar. The cell is a single transistor stacked gate structure with the floating gate and control gate completely surrounding the pillar. Current flows vertically from the bit line contact at the top of the pillar to the source lying at the bottom of the pillar. When implemented in a novel self-aligned array, the cell size approaches the square of the minimum pitch and has an area less than half that of the conventional NOR type structure. The cell and array architecture also promise to be highly scalable. Experimental data reveals that the cells have up to 3/spl times/ larger read current than comparable planar cells, are suitable for 5 V only operation and have fast program and erase speeds at moderate voltage levels. Uniformity and endurance characteristics are also promising.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nilotinib exerts equipotent antiproliferative effects to imatinib and does not induce apoptosis in CD34+ CML cells (2007)

Chronic myeloid leukemia (CML) stem and progenitor cells overexpress BcrAbl and are insensitive to imatinib mesylate (IM). We therefore investigated whether these cells were efficiently targeted by nilotinib. In K562, the inhibitory concentration (IC50) of nilotinib was 30 nM versus 600 nM for IM, consistent with its reported 20-fold-higher potency. However, in primary CD34(+) CML cells, nilotinib and IM were equipotent for inhibition of BcrAbl activity, producing equivalent but incomplete reduction in CrkL phosphorylation at 5 microM. CML CD34(+) cells were still able to expand over 72 hours with 5 microM of either drug, although there was a concentration-dependent restriction of amplification. As for IM, the most primitive cells (CFSE(max)) persisted and accumulated over 72 hours with nilotinib and remained caspase-3 negative. Furthermore, nilotinib with IM led to further accumulation of this population, suggesting at least additive antiproliferative effects. These results confirmed that, like IM, the predominant effect of nilotinib is antiproliferative rather than proapoptotic.
Mitochondrial uncoupling, with low concentration FCCP, induces ROS-dependent cardioprotection independent of KATP channel activation (2006)

In the isolated rat heart, partial mitochondrial uncoupling with low-dose FCCP significantly improves post-ischaemic functional recovery via a ROS-dependent pathway. This cardioprotection is not mediated via the depletion of cellular ATP or mitochondrial K(ATP) channel activation.
Isolation and Bioactivity of 2-Aminoquinoline from Leucopaxillus albissimus (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsolation and Bioactivity of 2-Aminoquinoline from Leucopaxillus albissimusJürg R. PfisterCite this: J. Nat. Prod. 1988, 51, 5, 969–970Publication Date (Print):September 1, 1988Publication History Published online1 July 2004Published inissue 1 September 1988https://doi.org/10.1021/np50059a027RIGHTS & PERMISSIONSArticle Views214Altmetric-Citations28LEARN 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 InReddit PDF (158 KB) Get e-Alerts Get e-Alerts
Pre-oligodendrocytes from adult human CNS (1992)

CNS remyelination and functional recovery often occur after experimental demyelination in adult rodents. This has been attributed to the ability of mature oligodendrocytes and/or their precursor cells to divide and regenerate in response to signals in demyelinating lesions. To determine whether oligodendrocyte precursor cells exist in the adult human CNS, we have cultured white matter from patients undergoing partial temporal lobe resection for intractable epilepsy. These cultures contained a population of process-bearing cells that expressed antigens recognized by the O4 monoclonal antibody, but these cells did not express galactocerebroside (a marker for oligodendrocytes), glial fibrillary acidic protein (a marker for astrocytes), or vimentin. Selective elimination of O4-positive (O4+) cells by complement-mediated lysis resulted in inhibition of oligodendrocyte development in vitro. Since O4+ cells have an antigenic phenotype reminiscent of the rat adult oligodendrocyte-type 2 astrocyte progenitor and appear to develop into oligodendrocytes rather than type 2 astrocytes with time in culture, we call them "pre-oligodendrocytes." Neither pre-oligodendrocytes nor oligodendrocytes incorporated 3H-thymidine in response to rat astrocyte-conditioned medium, platelet-derived growth factor, insulin-like growth factor (IGF-1), or basic fibroblast growth factor (bFGF). However, IGF-1 increased the relative abundance of oligodendrocytes to pre-oligodendrocytes, while bFGF had the opposite effect. Cells with the antigenic phenotype of pre-oligodendrocytes were also identified in tissue prints of adult human white matter. We propose that, in human demyelinating diseases such as multiple sclerosis, pre-oligodendrocytes may divide and/or migrate in response to signals present in demyelinated lesions and thus facilitate remyelination.
A sham stimulation-controlled trial of rTMS of the unaffected hemisphere in stroke patients (2005)

The authors investigated the use of slow-frequency repetitive transcranial magnetic stimulation (rTMS) to the unaffected hemisphere to decrease interhemispheric inhibition of the lesioned hemisphere and improve motor function in patients within 12 months of a stroke. Patients showed a significant decrease in simple and choice reaction time and improved performance of the Purdue Pegboard test with their affected hand after rTMS of the motor cortex in the intact hemisphere as compared with sham rTMS.
Creutzfeldt-Jakob disease profile in patients homozygous for the PRNP E200K mutation (2000)

We identified 70 Creutzfeldt-Jakob disease patients with the previously described E200K mutation in the prion protein gene. The purpose of this study was to define the clinical features of E200K homozygous patients (n = 5), compared with heterozygotes. We found a statistically significant younger age at disease onset for the homozygous patients, although the average age at onset in this group was still in midlife. Disease features were not statistically different in the two groups. Possible explanations are discussed.
Synthesis and Structure−Activity Relationship of α-Sulfonylhydroxamic Acids as Novel, Orally Active Matrix Metalloproteinase Inhibitors for the Treatment of Osteoarthritis (2003)

The matrix metalloproteinases (MMPs) are a family of zinc-containing endopeptidases that play a key role in both physiological and pathological tissue degradation. These enzymes are strictly regulated by endogenous inhibitors such as tissue inhibitors of MMPs and alpha(2)-macroglobulins. Overexpression of these enzymes has been implicated in various pathological disorders such as arthritis, tumor metastasis, cardiovascular diseases, and multiple sclerosis. Developing effective small-molecule inhibitors to modulate MMP activity is one approach to treat these degenerative diseases. The present work focuses on the discovery and SAR of novel N-hydroxy-alpha-phenylsulfonylacetamide derivatives, which are potent, selective, and orally active MMP inhibitors.
GPS-free positioning in mobile ad-hoc networks (2005)

We consider the problem of node positioning in ad-hoc networks. We propose a distributed, infrastructure-free positioning algorithm that does not rely on Global Positioning System (GPS). The algorithm uses the distances between the nodes to build a relative coordinate system in which the node positions are computed in two dimensions. The main contribution of this work is to define and compute relative positions of the nodes in an ad-hoc network without using GPS. We further explain how the proposed approach can be applied to wide area ad-hoc networks.
Optically pumped ultraviolet AlGaInN quantum well laser at 340 nm wavelength (2004)

We have demonstrated and characterized an optically pumped room temperature pulsed laser at 340 nm, based on a separate confinement AlGaInN multiple quantum well heterostructure design. The lasing was achieved at threshold peak power of ∼800 kW/cm2. Gain spectroscopy showed modest peak modal gain on the order of 5 cm−1, suggesting that the combination of weak optical confinement and nonradiative recombination would lead to high threshold currents for comparably constructed diode lasers.
Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales (2020)

A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot, chameleon, and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms (the fastest reported to date), to interrogate particle behavior at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin-film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimize. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic "silver bullet" for improving the quality of every cryoEM sample preparation.
Functional importance of conserved domains in the flowering‐time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants (2001)

CONSTANS promotes flowering of Arabidopsis in response to long-day conditions. We show that CONSTANS is a member of an Arabidopsis gene family that comprises 16 other members. The CO-Like proteins encoded by these genes contain two segments of homology: a zinc finger containing region near their amino terminus and a CCT (CO, CO-Like, TOC1) domain near their carboxy terminus. Analysis of seven classical co mutant alleles demonstrated that the mutations all occur within either the zinc finger region or the CCT domain, confirming that the two regions of homology are important for CO function. The zinc fingers are most similar to those of B-boxes, which act as protein-protein interaction domains in several transcription factors described in animals. Segments of CO protein containing the CCT domain localize GFP to the nucleus, but one mutation that affects the CCT domain delays flowering without affecting the nuclear localization function, suggesting that this domain has additional functions. All eight co alleles, including one recovered by pollen irradiation in which DNA encoding both B-boxes is deleted, are shown to be semidominant. This dominance appears to be largely due to a reduction in CO dosage in the heterozygous plants. However, some alleles may also actively delay flowering, because overexpression from the CaMV 35S promoter of the co-3 allele, that has a mutation in the second B-box, delayed flowering of wild-type plants. The significance of these observations for the role of CO in the control of flowering time is discussed.
2-(Oxadiazolyl)- and 2-(thiazolyl)imidazo[1,2-a]pyrimidines as agonists and inverse agonists at benzodiazepine receptors (1991)

Oxadiazoles, like the benzoyl group in a series of imidazo[1,2-a]pyrimidines, have been found to be metabolically stable alternatives to ester groups in benzodiazepine-receptor ligands. This change has lead to a number of compounds which bind to the receptors and which exhibit potent agonist activity in a food-motivated conflict test thought to predict anxiolytic properties. Compounds 4, 5, and 13 were equipotent with chlordiazepoxide but showed little or no myorelaxant effects. Replacing the oxadiazole group by thiazole gave compounds such as 23 which binds to the benzodiazepine receptor but exhibits the intrinsic activity of a partial inverse agonist in vivo.
Epitopes recognized by the neutralizing antibodies of an HIV-1-infected individual. (1990)

Sera from individuals infected by HIV-1 usually neutralize multiple viral isolates. To determine the extent to which these neutralizing antibodies recognize a principal neutralizing determinant in the V3 region of the envelope protein gp120 (amino acids 308-332), one broadly neutralizing serum was fractionated by affinity chromatography on immobilized peptide columns. Antibodies that neutralize one isolate (HTLV-IIIMN) were substantially but not completely absorbed by the peptide corresponding to a portion of its V3 determinant, whereas the antibodies that neutralize two other isolates (HTLV-IIIB and HTLV-IIIRF) were not absorbed by homologous peptides corresponding to their neutralizing determinants. Neutralizing antibodies also failed to be absorbed by full length envelope protein gp160 and by two other envelope peptides previously reported to be broadly neutralizing epitopes (amino acids 254-274 and 735-752). We conclude that the infected individual had raised a type-restricted neutralizing response targeted at a linear epitope in the V3 region, and that broad neutralization resulted from recognition of epitopes not yet identified.
Hydroxylation of chlorzoxazone as a specific probe for human liver cytochrome P-450IIE1 (1990)

Human cytochrome P-450IIE1 has been implicated in the oxidation of a number of substrates, including protoxins and -carcinogens. To date, no drugs have been identified that are exclusive substrates for the protein and are applicable for use as noninvasive probes of the in vivo function of the enzyme in humans. Chlorzoxazone was found to be oxidized only to 6-hydroxychlorzoxazone in human liver microsomes. Results of steady-state kinetics are consistent with the view that only a single enzyme catalyzes the reaction. The microsomal reaction was strongly inhibited by rabbit anti-P-450IIE1 and, in a competitive manner, by known P-450IIE1 substrates. Rates of chlorzoxazone 6-hydroxylation in different human liver microsomal preparations were well correlated with levels of immunochemically measured P-450IIE1 and rates of (CH3)2NNO oxidation. Chlorzoxazone 6-hydroxylation was also found to be catalyzed by purified human liver P-450IIE1. These results provide strong evidence that P-450IIE1 is the primary catalyst of chlorzoxazone 6-hydroxylation in human liver. Rates of chlorzoxazone 6-hydroxylation vary considerably among human liver samples, and chlorzoxazone 6-hydroxylation may have potential use as a noninvasive probe in estimating the in vivo expression of human P-450IIE1 and its significance as a risk factor in the toxicity and carcinogenicity of a number of solvents, nitrosamines, and drugs.
[Current cooling methods for induction of mild hypothermia in cardiac arrest survivors]. (2009)

Induction of mild therapeutic hypothermia early after return of spontaneous circulation improves prognosis of cardiac arrest survivors. Rapid cooling of the patients and correct maintainance of the target therapeutic temperature followed by controlled slow rewarming can be achieved by several noninvasive and invasive methods of various efficacy. Elementary and the most frequently used methods are surface cooling via ice-packs and rapid intravenous administration of cold crystaloids. Mattress cooling systems and facilities for endovascular cathether-cooling are more sophisticated, manageable and ensure more precise titration of therapeutic temperature. Cooling caps and helmets leading to selective head cooling can be used as the complementary techniques. Several other methods are too instrumentation-intensive, too invasive or investigated in animal experiments only. Anyway, near future may bring a rapid development of new effective and safe cooling systems.
A CD36 Synthetic Peptide Inhibits Bleomycin-Induced Pulmonary Inflammation and Connective Tissue Synthesis in the Rat (2000)

Transforming growth factor (TGF)-beta1 is an important regulator of inflammation and fibrosis. TGF-beta1 is usually secreted as a biologically latent protein called latent TGF-beta1 (L-TGF-beta1). L-TGF-beta1 has no biologic effect unless L-TGF-beta1 is converted to its active form. Using a well-recognized model of lung injury induced by the antineoplastic antibiotic bleomycin (Blm), we demonstrated that 7 d after intratracheal Blm administration, total lung TGF-beta was maximally increased. This induction was due to TGF-beta1 production by alveolar macrophages that, when explanted, generated increased quantities of L-TGF-beta1 complexed with the glycoprotein thrombospondin (TSP)-1. The TSP-1/L-TGF-beta1 complex was associated with CD36, a receptor for TSP-1. The association of TSP-1/L-TGF-beta1 to CD36 was critical for plasmin-mediated release of mature TGF-beta1. In this paper we show that, compared with administration of Blm by itself, when a synthetic peptide of CD36 between amino acids 93 and 110 is given concomitantly with Blm to rats, alveolar macrophages generate markedly less active TGF-beta1, the rats gain weight more rapidly, and there is less inflammation, collagen I and III, and fibronectin synthesis. These findings demonstrate a novel in vivo mechanism of activation of L-TGF-beta1 in lung injury and the importance of alveolar macrophage- derived active TGF-beta1 in the pathogenesis of pulmonary inflammation and fibrosis.
Membrane protein secretases (1997)

A diverse range of membrane proteins of Type 1 or Type II topology also occur as a circulating, soluble form. These soluble forms are often derived from the membrane form by proteolysis by a group of enzymes referred to collectively as 'secretases' or 'sheddases'. The cleavage generally occurs close to the extracellular face of the membrane, releasing physiologically active protein. This secretion process also provides a mechanism for down-regulating the protein at the cell surface. Examples of such post-translational proteolysis are seen in the Alzheimer's amyloid precursor protein, the vasoregulatory enzyme angiotensin converting enzyme, transforming growth factor-alpha, the tumour necrosis factor ligand and receptor superfamilies, certain cytokine receptors, and others. Since the proteins concerned are involved in pathophysiological processes such as neurodegeneration, apoptosis, oncogenesis and inflammation, the secretases could provide novel therapeutic targets. Recent characterization of these individual secretases has revealed common features, particularly sensitivity to certain metalloprotease inhibitors and upregulation of activity by phorbol esters. It is therefore likely that a closely related family of metallosecretases controls the surface expression of multiple integral membrane proteins. Current knowledge of the various secretases are compared in this Review, and strategies for cell-free assays of such proteases are outlined as a prelude to their ultimate purification and cloning.
Structural characterization and corepressor binding of the Escherichia coli purine repressor (1992)

The Escherichia coli purine repressor, PurR, binds to a 16-bp operator sequence and coregulates the genes for de novo synthesis of purine and pyrimidine nucleotides, formation of a one-carbon unit for biosynthesis, and deamination of cytosine. We have characterized the purified repressor. Chemical cross-linking indicates that PurR is dimeric. Each subunit has an N-terminal domain of 52 amino acids for DNA binding and a C-terminal 289-residue domain for corepressor binding. Each domain was isolated after cleavage by trypsin. Sites for dimer formation are present within the corepressor binding domain. The corepressors hypoxanthine and guanine bind cooperatively to distinct sites in each subunit. Competition experiments indicate that binding of one purine abolishes cooperativity and decreases the affinity and the binding of the second corepressor. Binding of each corepressor results in a conformation change in the corepressor binding domain that was detected by intrinsic fluorescence of three tryptophan residues. These experiments characterize PurR as a complex allosteric regulatory protein.
Composition of Drosophila melanogaster Proteome Involved in Fucosylated Glycan Metabolism (2002)

The whole genome approach enables the characterization of all components of any given biological pathway. Moreover, it can help to uncover all the metabolic routes for any molecule. Here we have used the genome of Drosophila melanogaster to search for enzymes involved in the metabolism of fucosylated glycans. Our results suggest that in the fruit fly GDP-fucose, the donor for fucosyltransferase reactions, is formed exclusively via the de novo pathway from GDP-mannose through enzymatic reactions catalyzed by GDP-D-mannose 4,6-dehydratase (GMD) and GDP-4-keto-6-deoxy-D-mannose 3,5-epimerase/4-reductase (GMER, also known as FX in man). The Drosophila genome does not have orthologs for the salvage pathway enzymes, i.e. fucokinase and GDP-fucose pyrophosphorylase synthesizing GDP-fucose from fucose. In addition we identified two novel fucosyltransferases predicted to catalyze alpha1,3- and alpha1,6-specific linkages to the GlcNAc residues on glycans. No genes with the capacity to encode alpha1,2-specific fucosyltransferases were found. We also identified two novel genes coding for O-fucosyltransferases and a gene responsible for a fucosidase enzyme in the Drosophila genome. Finally, using the Drosophila CG4435 gene, we identified two novel human genes putatively coding for fucosyltransferases. This work can serve as a basis for further whole-genome approaches in mapping all possible glycosylation pathways and as a basic analysis leading to subsequent experimental studies to verify the predictions made in this work.