gebhart/patrepeval huggingface dataset:
The binDCT: fast multiplierless approximation of the DCT (2000)

This paper presents a family of fast biorthogonal block transforms called binDCT that can be implemented using only shift and add operations. The transform is based on a VLSI-friendly lattice structure that robustly enforces both linear phase and perfect reconstruction properties. The lattice coefficients are parameterized as a series of dyadic lifting steps providing fast, efficient, in place computation of the transform coefficients as well as the ability to map integers to integers. The new 8/spl times/8 transforms all approximate the popular 8/spl times/8 DCT closely, attaining a coding gain range of 8.77-8.82 dB, despite requiring as low as 14 shifts and 31 additions per eight input samples. Application of the binDCT in both lossy and lossless image coding yields very competitive results compared to the performance of the original floating-point DCT.
The protein kinase C-activated MAP kinase pathway of Saccharomyces cerevisiae mediates a novel aspect of the heat shock response. (1995)

The PKC1 gene of budding yeast encodes a homolog of the alpha, beta, and gamma isoforms of mammalian PKC that is proposed to regulate a MAPK-activation pathway. Mutants in this pathway undergo cell lysis resulting from a deficiency in cell wall construction when they attempt to grow at elevated temperatures. We show that the PKC1-regulated pathway is important for induced thermotolerance and that the MPK1 protein kinase (the MAPK of this pathway) is strongly activated by mild heat shock. This activation is sustained during growth at high temperature and is dependent on the function of pathway components proposed to function upstream of MPK1, including PKC1. Expression of genes under the control of known heat shock-inducible promoter elements (HSEs and STREs) was not compromised in PKC1 pathway mutants, indicating that this pathway mediates a novel aspect of the yeast heat shock response. We propose that the heat-induced signal for pathway activation is generated in response to weakness in the cell wall created during growth under thermal stress, perhaps as a result of increased membrane fluidity. Evidence is presented that the mechanism by which the cell detects this weakness is by measuring stretch of the plasma membrane.
Substrate specificity of acetyl coenzyme A synthetase. (1987)

Acetyl coenzyme A synthetase (EC 6.2.1.1) has been examined for its ability to accept various carboxylic acids as substrates in place of acetic acid. The activity of the enzyme with these substrates was monitored using a coupled enzyme assay and high pressure liquid chromatography (HPLC) analysis. Short chain carboxylic acids were found to be active including: propionic, acrylic, fluoroacetic, methacrylic, 3-chloropropionic, 3-bromopropionic, and propiolic. The kinetic parameters, Km and % Vmax of the carboxylic acid substrates, are reported and show that these acids are poorer substrates than acetic acid. Several of the acyl CoAs were synthesized on a preparative scale using enzyme catalysis, purified using preparative HPLC, and characterized using proton NMR spectroscopy. In the course of the NMR identification, a complete and fully resolved spectral assignment for all the protons of coenzyme A was made and is reported. The acyl-CoA analogs should be useful as substrate analogs and as potential affinity labels for enzymes that bind acetyl-CoA.
The international reference preparation of erythropoietin. (1966)

The WHO Expert Committee on Biological Standardization authorized the National Institute for Medical Research to establish an International Reference Preparation of Erythropoietin on the basis of the results of an international collaborative assay and to define an international unit with the agreement of the participants.The material investigated was a research standard (Erythropoietin Standard B) that had been in widespread use for some time. The preparation of this material and the estimation of its potency in terms of an earlier research standard (Erythropoietin Standard A) are described. By comparisons with other preparations of erythropoietin, it was found that Erythropoietin Standard B is a suitable standard for the bioassay of many preparations of erythropoietin in current use.On the basis of the information obtained, Erythropoietin Standard B has been established as the International Reference Preparation of Erythropoietin and the International Unit for Erythropoietin has been defined as the activity contained in 1.48 mg of the International Reference Preparation. This amount has equivalent biological activity to the unit of Erythropoietin Standard A and Standard B and thus ensures the continuity of the units already in widespread use.
A Consensus Sequence for Long-chain Fatty-acid Alcohol Oxidases from Candida Identifies a Family of Genes Involved in Lipid ω-Oxidation in Yeast with Homologues in Plants and Bacteria (2000)

The yeast Candida cloacae is capable of growing on alkanes and fatty acids as sole carbon sources. Transfer of cultures from a glucose medium to one containing oleic acid induced seven proteins of M(r) 102,000, 73,000, 61,000, 54,000, and 46,000 and two in the region of M(r) 45,000 and repressed a protein of M(r) 64,000. The induction of the M(r) 73,000 protein reached a 7-fold maximum 24 h after induction. The protein was confirmed by its enzyme activity to be a long-chain fatty-acid alcohol oxidase (LC-FAO) and purified to homogeneity from microsomes by a rapid procedure involving hydrophobic chromatography. An internal peptide of 30 amino acids was sequenced. A 1100-base pair cDNA fragment containing the LC-FAO peptide coding sequence was used to isolate a single exon genomic clone containing the full-length coding sequence of an LC-FAO (fao1). The fao1 gene product was expressed in Escherichia coli and was translated as a functional long-chain alcohol oxidase, which was present in the membrane fraction. In addition, full-length coding sequences for a Candida tropicalis LC-FAO (faoT) and a second C. cloacae LC-FAO (fao2) were isolated. The DNA sequences obtained had open reading frames of 2094 (fao1), 2091 (fao2), and 2112 (faoT) base pairs. The derived amino acid sequences of fao2 and faoT showed 89.4 and 76.2% similarities to fao1. The fao1 gene is much more highly induced on alkane than is fao2. Although this study describes the first known DNA sequences encoding LC-FAOs from any source, there are unassigned Arabidopsis sequences and an unassigned Mycobacterium sequence in the GenBank(TM) Data Bank that show strong homology to the described LC-FAO sequences. The conservation of sequence between yeast, plants, and bacteria suggests that an as yet undescribed family of long-chain fatty-acid oxidases exists in both eukaryotes and prokaryotes.
Effects of chemotherapeutic agents on expression of somatostatin receptors in pancreatic tumor cells. (2001)

Our results clearly show that the pancreatic tumor lines reduce the expression of high-affinity DOTA-LAN binding sites during application of chemotherapeutic drugs, which is accompanied by variable overexpression of low-affinity binding sites. In the case of gemcitabine, SSTRs are overexpressed during recovery from drug exposure within 4 d. These findings may have implications on the interpretation of scintigraphic results obtained by receptor ligands.
A Ten- to 15-year Follow-Up Observation of High Tibial Osteotomy in Medial Compartment Osteoarthrosis (1992)

High tibial osteotomy (HTO) was performed on 86 medially osteoarthritic knees in 78 patients. Twelve patients died during the follow-up period. Fifty-six knees of 51 patients were evaluated twice postoperatively: once at six years after surgery and again after ten to 15 years. Results were satisfactory in 88% of the knees at the six-year follow-up evaluation and in 63% at the post-ten-year follow-up evaluation. Ten-year follow-up results significantly deteriorated. The femorotibial angle (FTA) at the time of bone union after HTO was a significant factor that contributed to the ten-year results. In patients maintaining excellent improvement of knee function at the post-ten-year follow-up evaluation, the mean FTA at one year after surgery was 165 degrees; this value was constant through ten years after HTO. An FTA of 164 degrees-168 degrees should be attained to ensure favorable long-term results in HTO.
De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007)

A novel methodology for the automated de novo identification of peptides via integer linear optimization (also referred to as integer linear programming or ILP) and tandem mass spectrometry is presented in this article. The various features of the mathematical model are presented and examples are used to illustrate the key concepts of the proposed approach. A variety of challenging peptide identification problems, accompanied by a comparative study with five state-of-the-art methods, are examined to illustrate the proposed method's ability to address (a) residue-dependent fragmentation properties that result in missing ion peaks and (b) the variability of resolution in different mass analyzers. A preprocessing algorithm is utilized to identify important m/z values in the tandem mass spectrum. Missing peaks, due to residue-dependent fragmentation characteristics, are dealt with using a two-stage algorithmic framework. A cross-correlation approach is used to resolve missing amino acid assignments and to select the most probable peptide by comparing the theoretical spectra of the candidate sequences that were generated from the ILP sequencing stages with the experimental tandem mass spectrum. The novel, proposed de novo method, denoted as PILOT, is compared to existing popular methods such as Lutefisk, PEAKS, PepNovo, EigenMS, and NovoHMM for a set of spectra resulting from QTOF and ion trap instruments.
Remarkable destabilization of recombinant alpha-lactalbumin by an extraneous N-terminal methionyl residue (1998)

A recombinant bovine alpha-lactalbumin, possessing an additional N-terminal methionyl residue, was expressed in Escherichia coli. In order to address the effects of the N-terminal methionyl residue on conformational stability, the thermal stability of the recombinant alpha-lactalbumin was investigated by measuring temperature-dependence of circular dichroism spectra, and it was compared with that of authentic alpha-lactalbumin from bovine milk. The thermal stability of the recombinant alpha-lactalbumin was significantly lower than that of authentic alpha-lactalbumin. The enthalpy change of unfolding of the recombinant protein was found to be the same as that of the authentic one when compared at the same temperature. Therefore, the N-terminal methionyl residue seems to destabilize the conformation of recombinant alpha-lactalbumin through some entropic effects.
Synthèse et désamination enzymatique des C‐hydroxyméthyl‐3′‐ et C‐méthyl‐3′‐β‐D‐xylofurannosyl‐9‐adénines (1979)

Synthesis and enzymatic deamination of 3′‐ C ‐hydroxymethyl‐ and 3′‐ C ‐methyl‐β‐ D ‐xylofuranosyl‐9‐adenines The title compounds have been prepared by classical synthetic steps after having optimized the nature of the blocking groups. Both nucleosides were found to be substrates of adenosine aminohydrolase which proved that C(3′)‐branched‐chain sugar nucleosides can be deaminated when the branched‐chain is exo ( trans relative to the base) if a suitably disposed hydroxy group is available on the endo side of the furanose ring.
Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila (2005)

In Drosophila melanogaster, Dicer-2/R2D2 and Dicer-1 generate small interfering RNA (siRNA) and microRNA (miRNA), respectively. Here we identify a novel dsRNA-binding protein, which we named R3D1-L, that forms a stable complex with Dicer-1 in vitro and in vivo. While depletion of R3D1-L by RNAi causes accumulation of precursor miRNA (pre-miRNA) in S2 cells, recombinant R3D1-L enhances miRNA production by Dicer-1 in vitro. Furthermore, R3D1 deficiency causes miRNA-generating defect and severe sterility in male and female flies. Therefore, R3D1-L functions in concert with Dicer-1 in miRNA biogenesis and is required for reproductive development in Drosophila.
Electrogram analysis at the His bundle region and the proximal coronary sinus as a tool to predict left atrial origin of focal atrial tachycardias (2011)

Near-field and F components from RA and LA activation can be identified in the HB atrial EGM. Earliest atrial EGM analysis at the HB or CS can predict the need for LA access during FAT ablation.
An alternative technique for the computation of the designator in the retinex theory of color vision. (1986)

Accepting the first postulate of the retinex theory of color vision that there are three independent lightness-determining mechanisms (one for long waves, one for middle waves, and one for short waves), each operative with less than a millisecond exposure and each served by its own retinal pigment, a basic task of retinex theory becomes the determination of the nature of these mechanisms. Earlier references proposed several workable algorithms. [Land, E. H. (1959) Proc. Natl. Acad. Sci. USA 45, 115-129; Land, E. H. (1959) Proc. Natl. Acad. Sci. USA 45, 636-644; Land, E. H. (1983) Proc. Natl. Acad. Sci. USA 80, 5163-5169; Land, E. H. & McCann, J. J. (1971) J. Opt. Soc. Am. 61, 1-11; Land, E. H. (1986) Vision Res. 26, 7-21.] The present paper describes a relatively simple alternative technique for the computation of the designator in retinex theory and reports the general operational effectiveness of the new technique, including the competence, not possessed by earlier algorithms, for generating Mach bands.
Intestinal electrical stimulation improves delayed gastric emptying and vomiting induced by duodenal distension in dogs (2007)

The aim of this study was to investigate the effects of short-pulse intestinal electrical stimulation (IES) on duodenal distention-induced delayed gastric emptying and vomiting in dogs and its possible mechanisms. The study was performed in 12 dogs with jejunal electrodes and a duodenal cannula in three separate experiments to investigate the effects of IES on duodenal distension (DD)-induced delayed gastric emptying and discomfort signs, vagal efferent activity, and jejunal tone. We found that: (i) IES significantly accelerated gastric emptying of liquid delayed by distension (18.05 +/- 4.06%vs. 7.18 +/- 1.99%, P = 0.036 at 60 min). (ii) IES significantly reduced vomiting and discomfort/pain induced by distension. The average signs score was 15.33 +/- 1.37 during distension which decreased to 6.50 +/- 0.91 (P = 0.0002) with IES. (iii) IES did not change vagal afferent activity, which was assessed by the spectral analysis of the heart rate variability. (iv) IES decreased jejunal tone. In conclusion, IES with parameters commonly used in gastric electrical stimulation for nausea and vomiting associated with gastroparesis improves DD-induced delayed gastric emptying and prevents DD-induced vomiting and discomfort signs. Further studies are warranted to investigate the therapeutic potential of IES for gastrointestinal symptoms associated with disturbances in motility and sensory function in small intestine.
FAK Is Required for TGFβ-induced JNK Phosphorylation in Fibroblasts: Implications for Acquisition of a Matrix-remodeling Phenotype (2007)

Transforming growth factor beta (TGFbeta) plays a critical role in connective tissue remodeling by fibroblasts during development, tissue repair, and fibrosis. We investigated the molecular pathways in the transmission of TGFbeta signals that lead to features of connective tissue remodeling, namely formation of an alpha-smooth muscle actin (alpha-SMA) cytoskeleton, matrix contraction, and expression of profibrotic genes. TGFbeta causes the activation of focal adhesion kinase (FAK), leading to JNK phosphorylation. TGFbeta induces JNK-dependent actin stress fiber formation, matrix contraction, and expression of profibrotic genes in fak+/+, but not fak-/-, fibroblasts. Overexpression of MEKK1, a kinase acting upstream of JNK, rescues TGFbeta responsiveness of JNK-dependent transcripts and actin stress fiber formation in FAK-deficient fibroblasts. Thus we propose a FAK-MEKK1-JNK pathway in the transmission of TGFbeta signals leading to the control of alpha-SMA cytoskeleton reorganization, matrix contraction, and profibrotic gene expression and hence to the physiological and pathological effects of TGFbeta on connective tissue remodeling by fibroblasts.
Total synthesis of the marine natural product .DELTA.9(12)-capnellene. Reversal of regiochemistry in the intramolecular 1,3-diyl trapping reaction (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of the marine natural product .DELTA.9(12)-capnellene. Reversal of regiochemistry in the intramolecular 1,3-diyl trapping reactionR. Daniel Little, Gary L. Carroll, and Jeffrey L. PetersenCite this: J. Am. Chem. Soc. 1983, 105, 4, 928–932Publication Date (Print):February 1, 1983Publication History Published online1 May 2002Published inissue 1 February 1983https://pubs.acs.org/doi/10.1021/ja00342a048https://doi.org/10.1021/ja00342a048research-articleACS PublicationsRequest reuse permissionsArticle Views572Altmetric-Citations41LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Characterization of PDK2 Activity Against Protein Kinase B γ (2002)

Protein kinase B (PKB), also known as Akt, is a serine/threonine protein kinase controlled by insulin, various growth factors, and phosphatidylinositol 3-kinase. Full activation of the PKB enzyme requires phosphorylation of a threonine in the activation loop and a serine in the C-terminal tail. PDK1 has clearly been shown to phosphorylate the threonine, but the mechanism leading to phosphorylation of the serine, the PDK2 site, is unclear. A yeast two-hybrid screen using full-length human PKBgamma identified protein kinase C (PKC) zeta, an atypical PKC, as an interactor with PKBgamma, an association requiring the pleckstrin homology domain of PKBgamma. Endogenous PKBgamma was shown to associate with endogenous PKCzeta both in cos-1 cells and in 3T3-L1 adipocytes, demonstrating a physiological interaction. Immunoprecipitates of PKCzeta, whether endogenous PKCzeta from insulin-stimulated 3T3-L1 adipocytes or overexpressed PKCzeta from cos-1 cells, phosphorylated S472 (the C-terminal serine phosphorylation site) of PKBgamma, in vitro. In vivo, overexpression of PKCzeta stimulated the phosphorylation of approximately 50% of the PKBgamma molecules, suggesting a physiologically meaningful effect. However, pure PKCzeta protein was incapable of phosphorylating S472 of PKBgamma. Antisense knockout studies and use of a PDK1 inhibitor showed that neither PKB autophosphorylation nor phosphorylation by PDK1 accounted for the S472 phosphorylation in PKCzeta immunoprecipitates. Staurosporine inhibited the PKCzeta activity but not the PDK2 activity in PKCzeta immunoprecipitates. Together these results indicate that an independent PDK2 activity exists that physically associates with PKCzeta and that PKCzeta, by binding PKBgamma, functions to deliver the PDK2 to a required location. PKCzeta thus functions as an adaptor, associating with a staurosporine-insensitive PDK2 enzyme that catalyzes the phosphorylation of S472 of PKBgamma. Because both PKCzeta and PKB have been proposed to be required for mediating a number of crucial insulin responses, formation of an active signaling complex containing PKCzeta, PKB, and PDK2 is an attractive mechanism for ensuring that all the critical sites on targets such as glycogen synthase kinase-3 are phosphorylated.
Cell Therapy of α-Sarcoglycan Null Dystrophic Mice Through Intra-Arterial Delivery of Mesoangioblasts (2003)

Preclinical or clinical trials for muscular dystrophies have met with modest success, mainly because of inefficient delivery of viral vectors or donor cells to dystrophic muscles. We report here that intra-arterial delivery of wild-type mesoangioblasts, a class of vessel-associated stem cells, corrects morphologically and functionally the dystrophic phenotype of virtually all downstream muscles in adult immunocompetent alpha-sarcoglycan (alpha-SG) null mice, a model organism for limb-girdle muscular dystrophy. When mesoangioblasts isolated from juvenile dystrophic mice and transduced with a lentiviral vector expressing alpha-SG were injected into the femoral artery of dystrophic mice, they reconstituted skeletal muscle in a manner similar to that seen in wild-type cells. The success of this protocol was mainly due to widespread distribution of donor stem cells through the capillary network, a distinct advantage of this strategy over previous approaches.
Electrically driven jets (1969)

Abstract Fine jets of slightly conducting viscous fluids and thicker jets or drops of less viscous ones can be drawn from conducting tubes by electric forces. As the potential of the tube relative to a neighbouring plate rises, viscous fluids become nearly conical and fine jets come from the vertices. The potentials at which these jets or drops first appear was measured and compared with calculations. The stability of viscous jets depends on the geometry of the electrodes. Jets as small as 20 μm in diameter and 5 cm long were produced which were quite steady up to a millimetre from their ends. Attempts to describe them mathematically failed. Their stability seems to be due to mechanical rather than electrical causes, like that of a stretched string, which is straight when pulled but bent when pushed. Experiments on the stability of water jets in a parallel electric field reveal two critical fields, one at which jets that are breaking into drops become steady and another at which these steady jets become unsteady again, without breaking into drops. Experiments are described in which a cylindrical soap film becomes unstable under a radial electric field. The results are compared with calculations by A. B. Basset and after a mistake in his analysis is corrected, agreement is found over the range where experiments are possible. Basset’s calculations for axisymmetrical disturbances are extended to those in which the jet moves laterally. Though this is the form in which the instability appears, calculations about uniform jets do not seem to be relevant. In an appendix M. D. Van Dyke calculates the attraction between a long cylinder and a perpendicular plate at a different potential.
The ubiquitin-proteasome pathway: The complexity and myriad functions of proteins death (1998)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.