gebhart/patrepeval huggingface dataset:
Stereoselective Synthesis of Unnatural Spiroisoxazolinoproline-Based Amino Acids and Derivatives (2002)

A route to spiroisoxazolinoproline-based amino acid derivatives is reported in which exo-methyleneprolinate 4 (tert-butyl ester) reacts as a dipolarophile with nitrile oxides to generate spiroisoxazolinoprolinates 7/10/11 in good yields (70-75%) and with ca. 1:4 cis:trans diastereoselectivity. tert-Butyl spiroisoxazolinoprolinates were separable by column chromatography and amenable to scale-up leading to single diastereoisomers of N-Boc and N-Fmoc protected spiroisoxazolinoproline amino acids.
The 1.62 Å structure of Thermoascus aurantiacus endoglucanase: completing the structural picture of subfamilies in glycoside hydrolase family 5 (2002)

The crystal structure of Thermoascus aurantiacus endoglucanase (Cel5A), a family 5 glycoside hydrolase, has been determined to 1.62 A resolution by multiple isomorphous replacement with anomalous scattering. It is the first report of a structure in the subfamily to which Cel5A belongs. Cel5A consists solely of a catalytic module with compact eight-fold beta/alpha barrel architecture. The length of the tryptophan-rich substrate binding groove suggests the presence of substrate binding subsites -4 to +3. Structural comparison shows that two glycines are completely conserved in the family, in addition to the two catalytic glutamates and six other conserved residues previously identified. Gly 44 in particular is part of a type IV C-terminal helix capping motif, whose disruption is likely to affect the position of an essential conserved arginine. One aromatic residue (Trp 170 in Cel5A), not conserved in term of sequence, is nonetheless spatially conserved in the substrate binding groove. Its role might be to force the bend that occurs in the polysaccharide chain on binding, thus favoring substrate distortion at subsite -1.
Immunohistochemical and in situ hybridization analysis of p53 in human endometrial carcinoma of the uterus. (1993)

We examined the immunohistochemical localization of p53, a tumor suppressor gene, in thirty-three specimens of uterine endometrial carcinoma which included one case of carcinosarcoma, eleven specimens of endometrial hyperplasia and ten specimens of normal endometrium. We also analyzed the association between the immunolocalization of p53 protein and the clinical and pathological parameters of endometrial concern. We also determined whether p53 mRNA is overexpressed in these specimens by in situ hybridization and simultaneous immunohistochemistry and in situ hybridization. Immunohistochemistry was performed using the monoclonal antibodies pAbDO-7 and pAb1801, and polyclonal antibody pAbCM-1. Immunoreactive p53 was observed in the nuclei of the cancer cells in 15/33 (45%) by pAbDO-7, 11/26 (42%) by pAb1801, and 16/33 (48%) by pAbCM-1. No p53 immunoactivity could be detected in either hyperplasia or normal endometrium except for a case in which the endometrium was in the secretory phase. There was no significant relationship between p53 immunostaining as determined by pAbDO-7, and age, clinical stage, histological grade or depth of myometrial invasion. We employed the 35S-labeled antisense single stranded synthetic oligonucleotide probe, ON102, to perform in situ hybridization and simultaneous immunohistochemistry and in situ hybridization. In every case of endometrial carcinoma studied, no significant accumulation of the p53 hybridization signal was observed in carcinoma cells. This indicated that overexpression of p53, as observed by immunohistochemical staining, is not due to an increase in the steady-state level of p53 mRNA in carcinoma cells. These results suggest that immunostaining of p53 is associated with the malignant phenotype, but does not correlate with the biological behavior of human endometrial carcinoma.
Use of GFP as a Reporter for the Analysis of Sequence‐Specific Proteases (2001)

This unit describes a rapid fluorescent assay for sequence-specific proteases. A recombinant His-tagged substrate-GFP fusion protein containing the sequence-specific protease-recognition sequence is used as substrate. Batch metal-chelate chromatography separates uncleaved substrate-GFP fusion protein from GFP released by proteolysis and proteolytic activity is determined by measuring the fluorescence of GFP remaining in solution.
Image Signature Robust to Caption Superimposition for Video Sequence Identification (2006)

This paper proposes an image signature robust to caption superimposition for video sequence identification. A new image signature which is a set of local features is developed for a high-speed frame-by-frame matching of video sequences. The signature of a frame is obtained by partitioning the image into blocks and extracting the local feature representing the dominant type of edge direction from each block. The similarity between the signatures is calculated by comparing the edge types of the corresponding blocks, and counting the number of the blocks having the same edge type. A weighting scheme based on the probability of caption superimposition for each block can be applied to the similarity calculation to improve the matching performance. The experimental results of the video sequence identification show that the proposed signature achieves precision of 99.65% and recall of 99.45%, improving both the precision and the recall by more than 30% compared with the conventional signature.
Active Support Vector Machine Classification (2000)

An active set strategy is applied to the dual of a simple reformulation of the standard quadratic program of a linear support vector machine. This application generates a fast new dual algorithm that consists of solving a finite number of linear equations,with a typically large dimensionality equal to the number of points to be classified. However,by making novel use of the Sherman-Morrison-Woodbury formula,a much smaller matrix of the order of the original input space is inverted at each step. Thus,a problem with a 32-dimensional input space and 7 million points required inverting positive definite symmetric matrices of size 33×33 with a total running time of 96 minutes on a 400 MHz Pentium II. The algorithm requires no specialized quadratic or linear programming code,but merely a linear equation solver which is publicly available. 1
Effect of Ventilation Equipment on Imposed Work of Breathing (2001)

Up to 7 cmH2O of PSV may be required to reduce WOB(i) related to the ventilator, circuit and humdification devices. This pressure support does not address the additional resistive effect of the endotracheal or tracheotomy tube. Higher levels of PSV may therefore be required to offset WOB(i).
Spike-timing dependent plasticity (2010)

Spike Timing Dependent Plasticity (STDP) is a temporally asymmetric form of Hebbian learning induced by tight temporal correlations between the spikes of pre- and postsynaptic neurons. As with other forms of synaptic plasticity, it is widely believed that it underlies learning and information storage in the brain, as well as the development and refinement of neuronal circuits during brain development (e.g. Bi and Poo, 2001; SjÃ¶strÃ¶m et al., 2008). With STDP, repeated presynaptic spike arrival a few milliseconds before postsynaptic action potentials leads in many synapse types to long-term potentiation (LTP) of the synapses, whereas repeated spike arrival after postsynaptic spikes leads to long-term depression (LTD) of the same synapse. The change of the synapse plotted as a function of the relative timing of pre- and postsynaptic action potentials is called the STDP function or learning window and varies between synapse types. The rapid change of the STDP function with the relative timing of spikes suggests the possibility of temporal coding schemes on a millisecond time scale.
Regulatory elements of the erythropoietin gene (1991)

Because the human hepatoma cell line Hep3B produces erythropoietin (Epo) in a regulated fashion, it can be used to investigate the cis- acting regulatory elements of the Epo gene. Comparison of primate and mouse sequences shows strong homology not only in the coding sequence but also within the 5′ flanking region, the first intron, and the 3′ flanking region. These portions of the Epo gene were inserted 5′ and 3′ to a reporter gene, human growth hormone (GH). 5A is a 1,192-base pair (bp) HindIII-Xbal fragment that extends from 378 bp 5′ to the cap site through the first intron. To obviate the problem of false initiation of translation from the Epo ATG start codon, this site was changed to TAG by site-directed mutagenesis. 3A is a 255-bp Accl-BglII fragment that extends 67 bp upstream from the Epo termination codon and covers most of the 3′ noncoding region of homology. The plasmid DNAs were transfected by electroporation into Hep3B cells with RSVCAT as an internal standard to correct for transfection efficiency. One aliquot of cells was exposed to 50 mumol/L CoCl2 or to 1% O2. At the end of the incubations, GH and Epo were measured in the cell media and the cell pellet was assayed for CAT. Production of GH was stimulated 1.7-fold by cobalt or hypoxia. Furthermore, addition of 3A to the GH gene, irrespective of orientation, stimulated GH production 2.6-fold with CoCl2 and 2.3-fold with hypoxia. Stable cell lines were produced by cotransfection of the above constructions, along with the selectable marker pSV-Neo. In two clones, exposure to hypoxia resulted in much more marked (16-fold) induction of GH. Stimulus of both GH and Epo production by hypoxia was partially abrogated by carbon monoxide. These results demonstrate the presence of promoter and enhancer elements within the human Epo gene that are appropriately responsive to hypoxia and cobalt.
P-Selectin and Platelet Clearance (1998)

P-selectin is an adhesion receptor for leukocytes expressed by activated platelets and endothelial cells. To assess a possible role of P-selectin in platelet clearance, we adapted an in vivo biotinylation technique in mice. Wild-type and P-selectin-deficient mice were infused with N-hydroxysuccinimido biotin. The survival of biotinylated platelets was followed by flow cytometry after labeling with fluorescent streptavidin. Both wild-type and P-selectin-deficient platelets presented identical life spans of about 4.7 days, suggesting that P-selectin does not play a role in platelet turnover. When biotinylated platelets were isolated, activated with thrombin, and reinjected into mice, the rate of platelet clearance was unchanged. In contrast, storage of platelets at 4 degreesC caused a significant reduction in their life span in vivo but again no significant differences were observed between the two genotypes. The infused thrombin-activated platelets rapidly lost their surface P-selectin in circulation, and this loss was accompanied by the simultaneous appearance of a 100-kD P-selectin fragment in the plasma. This observation suggests that the platelet membrane P-selectin was shed by cleavage. In conclusion, this study shows that P-selectin, despite its binding to leukocytes, does not mediate platelet clearance. However, the generation of a soluble form of P-selectin on platelet activation may have biological implications in modulating leukocyte recruitment or thrombus growth.
Inactivation of Aerosolized Viruses in Continuous Air Flow with Axial Heating (2010)

Thermal inactivation of viruses has been studied in relevance to food sterilization, water purification, and other “non-aerosol” applications, in which heat treatment is applied for a relatively long time. No data are available on the inactivation of airborne viruses exposed to dry heat for a short time, although this is relevant to bio-defense and indoor air quality control. In this study, we investigated inactivation of aerosolized MS2 viruses in a continuous air flow chamber with axial heating resulted from exposures during ∼ 0.1–1 s. For an airborne virion, the characteristic exposure temperature, T e , was defined utilizing the air temperature profiles in the chamber. The tests were conducted at two air flow rates, Q, which allowed for establishing different thermal flow regimes and exposure time intervals. The experimentally determined inactivation factor, IF, was subjected to correction to account for the temperature profiles. At T e up to ∼ 90°C (Q = 18 L/min) and up to ∼ 140°C (Q = 36 L/min), the loss of viral infectivity was relatively modest (≤ 10). However, IF increased exponentially as T e rose from ∼ 90°C to ∼ 160°C (for 18 L/min) or from ∼ 140°C to ∼ 230°C (for 36 L/min). Under specific thermal exposure conditions (∼ 170°C and ∼ 250°C, respectively), IF exceeded ∼ 2.4 × 104 (∼ 99.996% infectivity loss)—the maximum quantifiable in this study. The airborne MS2 virions exposed to hot air for < 1 s were found to have survived much higher temperatures than those subjected to thermal treatment in liquid for minutes or hours. The findings are significant for establishing limitations of the heat-based bioaerosol control methods.
Sensitivity to nikkomycin Z in Candida albicans: role of peptide permeases (1984)

The uptake of tritiated nikkomycin Z, a potent inhibitor of chitin synthetase, is mediated by a peptide transport system in Candida albicans. Kinetic transport assays with radioactive di- and tripeptides and competition studies suggest that two distinct systems operate in this yeast. Nikkomycin Z was transported through one of these systems, common to di- and tripeptides. A peptide transport-deficient mutant was isolated on the basis of its resistance to nikkomycin Z. The mutant lost most of its capacity to take up dipeptides but simultaneously increased its ability to transport tripeptides. These results indicate that C. albicans handles peptides through multiple transport systems and adjusts their expression to environmental conditions.
Kinase Domain Mutations in Cancer: Implications for Small Molecule Drug Design Strategies (2009)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTKinase Domain Mutations in Cancer: Implications for Small Molecule Drug Design StrategiesJack A. Bikker*, Natasja Brooijmans, Allan Wissner, and Tarek S. MansourView Author Information Chemical Sciences, Wyeth Research, 401 North Middletown Road, Pearl River, New York 10965* To whom correspondence should be addressed. Telephone: 845 602 8819. Facsimile: 845 602 5682. E-mail: [email protected]Cite this: J. Med. Chem. 2009, 52, 6, 1493–1509Publication Date (Web):February 24, 2009Publication History Received22 August 2008Published online24 February 2009Published inissue 26 March 2009https://pubs.acs.org/doi/10.1021/jm8010542https://doi.org/10.1021/jm8010542review-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views7894Altmetric-Citations144LEARN 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 SUBJECTS:Drug resistance,Genetics,Inhibitors,Monomers,Peptides and proteins Get e-Alerts
Adenosine A2A Receptor Is Involved in Cell Surface Expression of A2B Receptor (2010)

The A2A and A2B adenosine receptors (A2AR and A2BR) are implicated in many physiological processes. However, the mechanisms of their intracellular maturation and trafficking are poorly understood. In comparative studies of A2AR versus A2BR expression in transfected cells, we noticed that the levels of cell surface expression of A2BR were significantly lower than those of A2AR. A large portion of the A2BR was degraded by the proteasome. Studies of cell surface expression of A2BR chimeric molecules in transfectants suggested that A2BR does not have the dominant forward transport signal for export from the endoplasmic reticulum to the cell surface. A2BR surface expression was increased in A2BR chimeras where the A2BR carboxyl terminus (CT) was replaced or fused with the A2AR CT. Co-transfection of A2AR with A2BR enhanced surface expression of A2BR though the F(X)(6)LL motif in the A2AR CT. The requirements of A2AR expression for better A2BR cell surface expression was not only established in transfectants but also confirmed by observations of much lower levels of A2BR-induced intracellular cAMP accumulation in response to A2BR-activating ligand in splenocytes from A2AR(-/-) mice than in wild type mice. The results of mechanistic studies suggested that poor A2BR expression at the cell surface might be accounted for mainly by the lack of a dominant forward transport signal from the endoplasmic reticulum to the plasma membrane; it is likely that A2BR forms a hetero-oligomer complex for better function.
FACILE AND EFFICIENT SYNTHESIS OF ISOLONGIFOLENONE (2008)

(2008). FACILE AND EFFICIENT SYNTHESIS OF ISOLONGIFOLENONE. Organic Preparations and Procedures International: Vol. 40, No. 4, pp. 405-410.
Modified disease activity scores that include twenty-eight-joint counts development and validation in a prospective longitudinal study of patients with rheumatoid arthritis (1995)

The Modified DAS are as valid as disease activity scores that include more comprehensive joint counts.
Silhouette maps for improved texture magnification (2004)

Texture mapping is a simple way of increasing visual realism without adding geometrical complexity. Because it is a discrete process, it is important to properly filter samples when the sampling rate of the texture differs from that of the final image. This is particularly problematic when the texture is magnified or minified. While reasonable approaches exist to tackle the minified case, few options exist for improving the quality of magnified textures in real-time applications. Most simply bilinearly interpolate between samples, yielding exceedingly blurry textures. In this paper, we address the real-time magnification problem by extending the silhouette map algorithm to general texturing. In particular, we discuss the creation of these silmap textures as well as a simple filtering scheme that allows for viewing at all levels of magnification. The technique was implemented on current graphics hardware and our results show that we can achieve a level of visual quality comparable to that of a much larger texture.
The NMR Structure of the Pulmonary Surfactant-Associated Polypeptide SP-C in an Apolar Solvent Contains a Valyl-Rich .alpha.-Helix (1994)

The nuclear magnetic resonance (NMR) structure of the pulmonary surfactant-associated lipoplypeptide C (SP-C) was determined in a mixed solvent of C2H3Cl/C2H3OH/ 1 M HCl 32:64:5 (v/v). Sequence-specific 1H NMR assignments and the collection of conformational constraints were achieved with two-dimensional 1H NMR, and the structure was calculated with the distance geometry program DIANA. The root mean square deviations for the well-defined polypeptide segment of residues 9-34 calculated for the 20 best energy-minimized DIANA conformers relative to their mean are 0.5 and 1.3 A for the polypeptide backbone atoms N, C alpha, and C', and for all heavy atoms, respectively. The 35-residue polypeptide chain of SP-C forms an alpha-helix between positions 9 and 34, which includes two segments of seven and four consecutive valyls that are separated by a single leucyl residue. The N-terminal hexapeptide segment, which includes two palmitoylcysteinyls, is flexibly disordered. The length of the alpha-helix is about 37 A, and the helical segment of residues 13-28, which contains exclusively aliphatic residues with branched side chains, is 23-A long and about 10 A in diameter. The alpha-helix is outstandingly regular, with virtually identical chi 1 angles for all valyl residues. The observation of a helical structure of SP-C was rather unexpected, considering that Val is generally underrepresented in alpha-helices, and it provides intriguing novel insights into the structural basis of SP-C functions as well as into general structural aspects of protein-lipid interactions in biological membranes.
Structure–activity relationship of truncated and substituted analogues of the intracellular delivery vector Penetratin (2000)

Abstract: Peptides derived from the third α‐helix of the homeodomain (residues 43–58; Penetratin) of Antennapedia, a Drosophila homeoprotein, were prepared by simultaneous multiple synthesis. Sets of N‐ and C‐terminally truncated peptides, as well as a series of alanine substitution analogues, were studied. Cell penetration assays using human cell cultures with these peptides revealed that the C‐terminal segment 52 Arg‐Arg‐Met‐Lys‐Trp‐Lys‐Lys 58 of the parent sequence was necessary and sufficient for efficient cell membrane translocation. Individual Ala substitutions of the peptide’s basic residues led to markedly decreased cell internalization ability, whereas replacement of hydrophobic residues was tolerated surprisingly well. Subcellular localization was seen to be affected by substitutions, with analogues being addressed preferentially to the cytosol or to the nucleus. Conformational constriction of the Penetratin sequence through placement and oxidation of flanking cysteine residues afforded a cyclic disulfide peptide which had lost most of its membrane translocation capacity.
Brain and Blood microRNA Expression Profiling of Ischemic Stroke, Intracerebral Hemorrhage, and Kainate Seizures (2009)

MicroRNAs (miRNAs) regulate gene expression and have a critical role in many biologic and pathologic processes. We hypothesized that miRNA expression profiles in injured brain (hippocampus) would show common as well as unique profiles when compared with those of blood. Adult, untouched, control rats were compared with rats with sham surgeries, ischemic strokes, brain hemorrhage (lysed blood, fresh blood, or thrombin), and kainate-induced seizures. Brain and whole-blood miRNA expression profiles were assessed 24 h later using TaqMan rodent miRNA arrays. MicroRNA response profiles were different for each condition. Many miRNAs changed more than 1.5-fold in brain and blood after each experimental manipulation, and several miRNAs were upregulated or downregulated in both brain and blood after a given injury. A few miRNAs (e.g., miR-298, miR-155, and miR-362-3p) were upregulated or downregulated more than twofold in both brain and blood after several different injuries. The results show the possible use of blood miRNAs as biomarkers for brain injury; that selected blood miRNAs may correlate with miRNA changes in the brain; and that many of the mRNAs, previously shown to be regulated in brain and blood after brain injury, are likely accounted for by changes in miRNA expression.
Epidemiology of Carbapenem-Resistant Enterobacteriaceae in 7 US Communities, 2012-2013 (2015)

In this population- and laboratory-based active surveillance system in 7 states, the incidence of CRE was 2.93 per 100<000 population. Most CRE cases were isolated from a urine source, and were associated with high prevalence of prior hospitalizations or indwelling devices, and discharge to long-term care settings.
A new haplotype of PDCD1 is associated with rheumatoid arthritis in Hong Kong Chinese (2005)

Our results support the involvement of PDCD1 as a susceptibility gene for RA in the Chinese population.