gebhart/patrepeval huggingface dataset:
Alloimmunity and nonimmunologic risk factors in cardiac allograft vasculopathy (2003)

Graft vasculopathy is an accelerated form of coronary artery disease that occurs in transplanted hearts. Despite major advances in immunosuppression, the prevalence of the disease has remained substantially unchanged during the last two decades. According to the 'response to injury' paradigm, graft vasculopathy is the result of a continuous inflammatory response to tissue injury initiated by both alloantigen-dependent and independent stress responses. Experimental evidence suggests that these responses may become self-sustaining, as allograft re-transplantation into the donor strain at a later stage fails to prevent disease progression. Histological evidence of endothelitis and arteritis, in association with intima fibrosis and atherosclerosis, reflects the central role of alloimmunity and inflammation in the development of arterial lesions. Experimental results in gene-targeted mouse models indicate that cellular and humoral immune responses are both involved in the pathogenesis of graft vasculopathy. Circulating antibodies against donor endothelium are found in a significant number of patients, but their pathogenic role is still controversial. Alloantigen-independent factors include donor-transmitted coronary artery disease, surgical trauma, ischaemia-reperfusion injury, viral infections, hyperlipidaemia, hypertension, and glucose intolerance. Recent therapeutic advances include the use of novel immunosuppressive agents such as sirolimus (rapamycin), HMG-CoA reductase inhibitors, calcium channel blockers, and angiotensin converting enzyme inhibitors. Optimal treatment of cardiovascular risk factors remains of paramount importance.
Structure of acetylcholinesterase complexed with (−)‐galanthamine at 2.3 Å resolution (1999)

(-)-Galanthamine (GAL), an alkaloid from the flower, the common snowdrop (Galanthus nivalis), shows anticholinesterase activity. This property has made GAL the target of research as to its effectiveness in the treatment of Alzheimer's disease. We have solved the X-ray crystal structure of GAL bound in the active site of Torpedo californica acetylcholinesterase (TcAChE) to 2.3 A resolution. The inhibitor binds at the base of the active site gorge of TcAChE, interacting with both the choline-binding site (Trp-84) and the acyl-binding pocket (Phe-288, Phe-290). The tertiary amine group of GAL does not interact closely with Trp-84; rather, the double bond of its cyclohexene ring stacks against the indole ring. The tertiary amine appears to make a non-conventional hydrogen bond, via its N-methyl group, to Asp-72, near the top of the gorge. The hydroxyl group of the inhibitor makes a strong hydrogen bond (2.7 A) with Glu-199. The relatively tight binding of GAL to TcAChE appears to arise from a number of moderate to weak interactions with the protein, coupled to a low entropy cost for binding due to the rigid nature of the inhibitor.
A three-tier architecture for ubiquitous data access (2002)

We present a three-tier architecture of middleware that addresses challenges facing accessibility, availability, and consistency of data in mobile environments. The architecture supports the automatic hoarding of data from multiple, heterogeneous sources into possibly a variety of different mobile devices. The middle tier enables the automation of synchronization tasks in both connected mode (following disconnection) and weakly connected mode, where only intelligent and effective synchronization can be used in the presence of a low-bandwidth network. We present the three-tier architecture based on the Coda file system.
The Effect of Milk and Skim Milk Intake on Serum Lipids and Apoproteins in Postmenopausal Females. (1992)

The effects of milk and skim milk intake on serum lipids, apoprotein levels and fatty acid composition were investigated in postmenopausal females. After a 25-day intake of 200 ml/day of whole milk, the milk group had increased HDL and LDL cholesterol levels, with a slight decrease in the proportion of 18:0 fatty acids in the phospholipid fraction. The skim milk group, which had consumed 20 g/day of skim milk for 25 days, showed no changes. After intake of 400 ml/day of whole milk for 29 days, LDL, HDL and total cholesterol concentrations were even more increased and the VLDL-phospholipid concentration was decreased, with significant increases in apoA-I, apoA-II and apoB concentrations. In the skim milk group, consuming 40 g of skim milk per day for 29 days, total cholesterol, atherogenic index, HDL-triglyceride concentrations were decreased and HDL-phospholipid, apoA-I and apoA-II concentrations were increased. Daily skim milk consumption, which is effective in preventing osteoporosis, and careful selection of foods should be recommended for Japanese postmenopausal women who consume more than 200 ml/day of whole milk.
Synthesis, Structure and Characterization of New Olivacine Derivatives and Their Platinum(II) Complexes (2003)

Abstract Three unknown olivacine derivatives ( L ‐OCH 3 , L ‐OH, L ‐OAc) were synthesized according to a procedure that involves only a few steps, and used as ligands in the synthesis of neutral chelate platinum( II ) complexes. The ligands, as well as their platinum complexes were spectroscopically characterized with IR, 1 H/ 13 C NMR and UV/Vis spectroscopic techniques. The solid state structures of two ligands ( L ‐OCH 3 , L ‐OAc) and one complex {[( L ‐OCH 3 )PtCl 2 ]} were determined by X‐ray diffraction. Molecular structure analysis of the ligands and the complex indicated that complexation resulted in a change in the conformation of the bipyridine fragment of the compounds studied and caused other interesting effects. Two crystallographically independent molecules of the complex were revealed in the measured crystal, with short intramolecular H ··· H distances. The structural and energetic aspects of the conformational behavior of the ligand L ‐OCH 3 and the complex [( L ‐OCH 3 )PtCl 2 ] have been analyzed using semiempirical PM3 methods. In vitro antiproliferative activity was preliminarily estimated. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Adeno-Associated Virus Site-Specific Integration and AAVS1 Disruption (2004)

Adeno-associated virus (AAV) is a single-stranded DNA virus with a unique biphasic lifestyle consisting of both a productive and a latent phase. Typically, the productive phase requires coinfection with a helper virus, for instance adenovirus, while the latent phase dominates in healthy cells. In the latent state, AAV is found integrated site specifically into the host genome at chromosome 19q13.4 qtr (AAVS1), the only animal virus known to integrate in a defined location. In this study we investigated the latent phase of serotype 2 AAV, focusing on three areas: AAV infection, rescue, and integration efficiency as a function of viral multiplicity of infection (MOI); efficiency of site-specific integration; and disruption of the AAVS1 locus. As expected, increasing the AAV MOI resulted in an increase in the percentage of cells infected, with 80% of cells infected at an MOI of 10. Additional MOI only marginally effected a further increase in percentage of infected cells. In contrast to infection, we found very low levels of integration at MOIs of less than 10. At an MOI of 10, at which 80% of cells are infected, less than 5% of clonal cell lines contained integrated AAV DNA. At an MOI of 100 or greater, however, 35 to 40% of clonal cell lines contained integrated AAV DNA. Integration and the ability to rescue viral genomes were highly correlated. Analysis of integrated AAV indicated that essentially all integrants were AAVS1 site specific. Although maximal integration efficiency approached 40% of clonal cell lines (essentially 50% of infected cells), over 80% of cell lines contained a genomic disruption at the AAVS1 integration locus on chromosome 19 ( approximately 100% of infected cells). Rep expression by itself and in the presence of a plasmid integration substrate was able to mediate this disruption of the AAVS1 site. We further characterized the disruption event and demonstrated that it resulted in amplification of the AAVS1 locus. The data are consistent with a revised model of AAV integration that includes preliminary expansion of a defined region in AAVS1.
Clinical trial: the efficacy and safety of oral PF‐03491390, a pancaspase inhibitor – a randomized placebo‐controlled study in patients with chronic hepatitis C (2010)

PF-03491390 significantly reduced serum AST and ALT levels in patients with chronic HCV, and was well tolerated over 12 weeks.
Analysis of the Protein Composition of the Mouse Sperm Perinuclear Theca and Characterization of its Major Protein Constituent1 (1997)

The perinuclear theca (PT) is a cytoskeletal structure that covers the nucleus of mammalian spermatozoa and is believed to have a membrane-binding role. The objectives of this study were to analyze the protein composition of the mouse PT, to identify and sequence its major protein component, and to characterize this protein's transcriptional and translational origins during spermatogenesis. The PT was extracted from demembranated and acrosome-depleted mouse sperm heads by alkaline treatment. The protein profile of the PT extract was composed of several polypeptides, of which a 15-kDa subacrosomal protein predominated and was found to be immunocross-reactive with a previously cloned 15-kDa PT protein of the rat (PERF 15) that belongs to a family of lipid-binding proteins. A primer pair designed from rat PERF 15 cDNA was then used to screen a mouse testicular cDNA library by polymerase chain reaction (PCR). The deduced amino acid sequence obtained from the PCR product was almost identical to the testicular-specific rat PERF 15. Developmental Northern blots and in situ hybridization studies performed with riboprobes encoding the mouse PERF 15 cDNA revealed that mRNA levels were highest in round and early elongating mouse spermatids. Immunohistochemistry indicated that PERF 15 began to be expressed in the cytoplasm of mid-pachytene spermatocytes and appeared to reach maximum expression in the distal cytoplasm of late elongating mouse spermatids, long after transcriptional arrest. During the development of round and early elongated spermatids, the immunolabel became progressively concentrated over the anterior half of the spermatid nucleus, suggesting a subacrosomal deposition of PERF 15 during this phase of mouse spermiogenesis.
Lysophosphatidic acid and sphingosine 1-phosphate stimulate endothelial cell wound healing (2000)

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) are potent lipid growth factors with similar abilities to stimulate cytoskeleton-based cellular functions. Their effects are mediated by a subfamily of G protein-coupled receptors (GPCRs) encoded by endothelial differentiation genes (edgs). We hypothesize that large quantities of LPA and S1P generated by activated platelets may influence endothelial cell functions. Using an in vitro wound healing assay, we observed that LPA and S1P stimulated closure of wounded monolayers of human umbilical vein endothelial cells and adult bovine aortic endothelial cells, which express LPA receptor Edg2, and S1P receptors Edg1 and Edg3. The two major components of wound healing, cell migration and proliferation, were stimulated individually by both lipids. LPA and S1P also stimulated intracellular Ca(2+) mobilization and mitogen-activated protein kinase (MAPK) phosphorylation. Pertussis toxin partially blocked the effects of both lipids on endothelial cell migration, MAPK phosphorylation, and Ca(2+) mobilization, implicating G(i)/(o)-coupled Edg receptor signaling in endothelial cells. LPA and S1P did not cross-desensitize each other in Ca(2+) responses, suggesting involvement of distinct receptors. Thus LPA and S1P affect endothelial cell functions through signaling pathways activated by distinct GPCRs and may contribute to the healing of wounded vasculatures.
One- and Two-Photon Absorption Spectra of Short Conjugated Polyenes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOne- and Two-Photon Absorption Spectra of Short Conjugated PolyenesYi Luo, Hans Aagren, and Sven StafstroemCite this: J. Phys. Chem. 1994, 98, 32, 7782–7789Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/j100083a007https://doi.org/10.1021/j100083a007research-articleACS PublicationsRequest reuse permissionsArticle Views237Altmetric-Citations48LEARN 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 options Get e-Alerts
Human HtrA1 in the archived eyes with age-related macular degeneration. (2007)

This study successfully analyzes HtrA1 SNP and transcript expression in microdissected cells from archived paraffin fixed slides. Up-regulation of HtrA1 is detected in the macular lesions of AMD eyes. The data further suggest that rs11200638 in HtrA1 promoter is associated with AMD development.
Systematic Association of Genes to Phenotypes by Genome and Literature Mining (2005)

One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. Here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. We first mine the MEDLINE literature database for terms that reflect phenotypic similarities of species. Subsequently we predict the likely genomic determinants: genes specifically present in the respective genomes. In a global analysis involving 92 prokaryotic genomes we retrieve 323 clusters containing a total of 2,700 significant gene-phenotype associations. Some clusters contain mostly known relationships, such as genes involved in motility or plant degradation, often with additional hypothetical proteins associated with those phenotypes. Other clusters comprise unexpected associations; for example, a group of terms related to food and spoilage is linked to genes predicted to be involved in bacterial food poisoning. Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases.
Cloning of cDNA Encoding for a Novel Isozyme of Fructose 6-Phosphate,2-Kinase/Fructose 2,6-Bisphosphatase from Human Placenta (1996)

Two independent cDNA clones encoding fructose 6-phosphate, 2-kinase/fructose 2,6-bisphosphatase were isolated from a human placental cDNA library. The deduced amino acid sequences showed that one of the clones, 2K-1, was almost identical to the rat testis isozyme and the other, 2K-3, was different from any known isozymes expressed in mammalian tissues. The results of Southern blot analysis suggested that clones 2K-1 and 2K-3 were encoded as single copy genes and located in different parts of the genome. Since open reading frames of the cDNA clones were not complete, we obtained the 5'-end of the clone 2K-3 cDNA using the 5'-rapid amplification of cDNA end method. The entire cDNA (HP; 1,756 bp) had a coding capacity of 519 amino acids (M(r) = 59,410), and putative phosphorylation sites for protein kinases A and C on the C terminus. Northern blot analysis using a fragment of the HP as a probe showed that a major band of 5.4 kb, significantly different in size from known isozyme mRNAs such as liver (2.1 kb), muscle (1.9 kb), heart (4.0 kb), and testis (2.0 kb), was present in poly(A)+RNA preparations of human first trimester and term placentae. These results strongly suggested that this 5.4 kb mRNA codes a novel isozyme of fructose 6-phosphate,2-kinase/fructose 2,6-bisphosphatase.
Mussel-Inspired Histidine-Based Transient Network Metal Coordination Hydrogels (2013)

Transient network hydrogels cross-linked through histidine-divalent cation coordination bonds were studied by conventional rheologic methods using histidine-modified star poly(ethylene glycol) (PEG) polymers. These materials were inspired by the mussel, which is thought to use histidine-metal coordination bonds to impart self-healing properties in the mussel byssal thread. Hydrogel viscoelastic mechanical properties were studied as a function of metal, pH, concentration, and ionic strength. The equilibrium metal-binding constants were determined by dilute solution potentiometric titration of monofunctional histidine-modified methoxy-PEG and were found to be consistent with binding constants of small molecule analogs previously studied. pH-dependent speciation curves were then calculated using the equilibrium constants determined by potentiometric titration, providing insight into the pH dependence of histidine-metal ion coordination and guiding the design of metal coordination hydrogels. Gel relaxation dynamics were found to be uncorrelated with the equilibrium constants measured, but were correlated to the expected coordination bond dissociation rate constants.
trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis (1989)

We have used site-directed mutagenesis to delineate sequence specific domains within the human immunodeficiency virus type 1 (HIV-1) trans-acting-responsive (TAR) RNA element that are required for trans activation by the viral Tat protein. Our data in part corroborate a recent report [S. Feng and E. C. Holland, Nature (London) 334:165-167, 1988] that five nucleotides within the loop (+29 to +33) of the TAR hairpin are important for trans activation. We, however, found no absolute requirement for the CUGGG loop sequence. Mutants with substitutions within the loop retained between 9 and 50% activity compared with the wild type. A second sequence, important for trans activation, was found in the 3-base bulge loop (+22 to +24) of the TAR hairpin. Cross-trans-activation studies of mutant HIV-1 TAR elements with the HIV-2 Tat protein suggest that a similar recognition event(s) forms the basis for trans activation of HIV-1 and HIV-2.
Cell Cycle and Hormonal Control of Nuclear-Cytoplasmic Localization of the Serum- and Glucocorticoid-inducible Protein Kinase, Sgk, in Mammary Tumor Cells (1999)

The serum- and glucocorticoid-inducible kinase (sgk) is a novel serine/threonine protein kinase that is transcriptionally regulated in rat mammary tumor cells by serum under proliferative conditions or by glucocorticoids that induce a G1 cell cycle arrest. Our results establish that the subcellular distribution of Sgk is under stringent cell cycle and hormonal control. Sgk is localized to the perinuclear or cytoplasmic compartment as a 50-kDa hypophosphorylated protein in cells arrested in G1 by treatment with the synthetic glucocorticoid dexamethasone. In serum-stimulated cells, Sgk was transiently hyperphosphorylated and resided in the nucleus. Laser scanning cytometry, which monitors Sgk localization and DNA content in individual mammary tumor cells of an asynchronously growing population, revealed that Sgk actively shuttles between the nucleus (in S and G2/M) and the cytoplasm (in G1) in synchrony with the cell cycle. In cells synchronously released from the G1/S boundary, Sgk localized to the nucleus during progression through S phase. The forced retention of exogenous Sgk in either the cytoplasmic compartment, using a wild type sgk gene, or the nucleus, using a nuclear localization signal-containing sgk gene (NLS-Sgk), suppressed the growth and DNA synthesis of serum-stimulated cells. Thus, our study implicates the nuclear-cytoplasmic shuttling of sgk as a requirement for cell cycle progression and represents a novel convergence point of anti-proliferative and proliferative signaling in mammary tumor cells.
Latent Fluorophore Based on the Trimethyl Lock (2005)

Fluorescent molecules are essential for basic research in the biological sciences and have numerous practical applications. Herein is described the synthesis and use of a new class of latent fluorophores based on a novel design element, the trimethyl lock, that confers distinct advantages over extant fluorophores and pro-fluorophores. A diacetyl version of the latent fluorophore is stable in a biological environment, but rapidly yields rhodamine 110 upon acetyl-group hydrolysis by pig liver esterase or endogenous esterases in the cytosol and lysosomes of human cells. This design element is general and, hence, provides access to an ensemble of useful latent fluorophores.
Regulation of c-jun gene expression in HL-60 leukemia cells by 1-.beta.-D-arabinofuranosylcytosine. Potential involvement of a protein kinase C dependent mechanism (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegulation of c-jun gene expression in HL-60 leukemia cells by 1-.beta.-D-arabinofuranosylcytosine. Potential involvement of a protein kinase C dependent mechanismSurender Kharbanda, Rakesh Datta, and Donald KufeCite this: Biochemistry 1991, 30, 32, 7947–7952Publication Date (Print):August 13, 1991Publication History Published online1 May 2002Published inissue 13 August 1991https://pubs.acs.org/doi/10.1021/bi00246a011https://doi.org/10.1021/bi00246a011research-articleACS PublicationsRequest reuse permissionsArticle Views40Altmetric-Citations40LEARN 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
Induction of model trees for predicting continuous classes (1996)

Many problems encountered when applying machine learning in practice involve predicting a "class" that takes on a continuous numeric value, yet few machine learning schemes are able to do this. This paper describes a "rational reconstruction" of M5, a method developed by Quinlan (1992) for inducing trees of regression models. In order to accommodate data typically encountered in practice it is necessary to deal effectively with enumerated attributes and with missing values, and techniques devised by Breiman et al. (1984) are adapted for this purpose. The resulting system seems to outperform M5, based on the scanty published data that is available.