gebhart/patrepeval huggingface dataset:
Limitation of reperfusion injury by a monoclonal antibody to C5a during myocardial infarction in pigs (1995)

The complement system has been implicated in reperfusion injury during acute myocardial infarction. We therefore attempted to reduce reperfusion injury with a monoclonal antibody (MAb) to the complement component, C5a. In 13 control pigs and 9 pigs pretreated with this MAb, ischemia was induced by a 50-min occlusion of the left anterior descending coronary artery, followed by 3 h of reperfusion. Infarct area (as percent of risk area) was reduced from 58 +/- 5% in controls to 38 +/- 7% (P < 0.05) in MAb-treated animals. Heart rate-systolic blood pressure product, left ventricular (LV) first derivative of pressure, LV end-diastolic pressure, and coronary blood flow were similar (P > 0.05) in the two groups. At 15 min of reperfusion, immunoreactive factor Bb began to increase significantly (P < 0.05) in regional coronary venous plasma, consistent with activation of the alternative complement pathway. The anti-C5a MAb did not attenuate formation of the membrane attack complex (C5b-9) as assessed by a hemolytic complement assay. Myocardial myeloperoxidase activity, a marker of tissue neutrophil concentration, was similar in the risk regions of the two groups, suggesting that neutrophil infiltration was unaltered by the MAb. However, in vitro the MAb (15 and 30 micrograms/ml) reduced C5a-stimulated neutrophil aggregation (67.4 and 70.9%), chemotaxis (52.5 and 81.4%), degranulation (66.7 and 75.8%), and superoxide generation (26.7 and 100%). In conclusion, myocardial infarction-reperfusion is associated with activation of the alternative complement pathway. Furthermore, a MAb to C5a that inhibits neutrophil cytotoxic activity, but neither the membrane attack complex nor myocardial neutrophil accumulation, decreases infarct size in pigs. These data suggest an important role of the alternative complement pathway and C5a in the propagation of ischemia cardiac damage during reperfusion.
Type 1 Diabetic Mice Are Protected from Acetaminophen Hepatotoxicity (2003)

Streptozotocin (STZ)-induced diabetic (DB) mice challenged with single ordinarily lethal doses of acetaminophen (APAP), carbon tetrachloride (CCl4), or bromobenzene (BB) were resistant to all three hepatotoxicants. Mechanisms of protection against APAP hepatotoxicity were investigated. Plasma alanine aminotransferase, aspartate aminotransferase, and liver histopathology revealed significantly lower hepatic injury in DB mice after APAP administration. HPLC analysis of plasma and urine revealed lower plasma t1/2, increased volume of distribution (Vd), and increased plasma clearance (CLp) of APAP in the DB mice and no difference in APAP-glucuronide, a major metabolite in mice. Interestingly, covalent binding of 14C-labeled APAP to liver target proteins; arylation of APAP to 58, 56, and 44 kDa acetaminophen binding proteins (ABPs); and glutathione (GSH) depletion in the liver did not differ between nondiabetic (non-DB) and DB mice in spite of downregulated hepatic microsomal CYP2E1 and 1A2 proteins in the DB mice, known to be involved in bioactivation of APAP. Compensatory cell division measured via 3H-thymidine pulse labeling and immunohistochemical staining for proliferating cell nuclear antigen (PCNA) indicated earlier onset of S-phase in the DB mice after exposure to APAP. Antimitotic intervention of liver cell division by colchicine (CLC) after administration of APAP led to significantly higher mortality in the DB mice suggesting a pivotal role of liver cell division and tissue repair in the protection afforded by diabetes. In conclusion, the resistance of DB mice against hepatotoxic and lethal effects of APAP appears to be mediated by a combination of enhanced APAP clearance and robust compensatory tissue repair.
Software interconnection models (1987)

We present a formulation of interconnection models and present the unit and syntactic models — the primary models used for managing the evolution of large software systems. We discuss various tools that use these models and evaluate how well these models support the management of system evolution. We then introduce the semantic interconnection model. The semantic interconnection model incorporates the advantages of the unit and syntactic interconnection models and provides extremely useful extensions to them. By refining the grain of interconnections to level of semantics (that is, to the predicates that define aspects of behavior) we provide tools that are better suited to manage the details of evolution in software systems and that provide a better understanding of the implications of changes. We do this by using the semantic interconnection model to formalize the semantics of program construction, the semantics of changes, and the semantics of version equivalence and compatibility. Thus, with this formalization, we provide tools that are knowledgeable about the process of system construction and evolution and that work in symbiosis with the system builders to construct and evolve large software systems.
The M = 8,000 and 11,000 Outer Arm Dynein Light Chains from Chlamydomonas Flagella Have Cytoplasmic Homologues (1995)

We report here the molecular cloning of the M(r) = 8,000 and 11,000 dynein light chains (DLCs) from the outer arm of Chlamydomonas flagella. These two molecules, which are associated with the intermediate chains at the base of the soluble dynein particle, have predicted masses of 10.3 and 13.8 kDa, respectively, and are 40% identical. Southern blot analysis indicates that one gene exists for each DLC in the Chlamydomonas genome and only a single message was observed for each on Northern blots. Secondary structure predictions suggest that both molecules contain a highly amphiphilic alpha helix that is presumably involved in protein-protein interactions. Several DLC homologues were identified in the GenBank databases. One, predicted from the genomic sequence of Caenorhabditis elegans, is 88.8% identical with the M(r) = 8,000 Chlamydomonas DLC. A second, from rice callus cDNA, is 47% identical with the same DLC. As neither nematodes nor higher plants have motile cilia or flagella at any stage of their life cycles, these DLC homologues presumably must function within the cytoplasm where they may represent previously unrecognized components of cytoplasmic dynein.
Parallel replacement in finite state calculus (1996)

This paper extends the calculus of regular expressions with new types of replacement expressions that enhance the expressiveness of the simple replace operator defined in Karttunen (1995). Parallel replacement allows multiple replacements to apply simultaneously to the same input without interfering with each other. We also allow a replacement to be constrained by any number of alternative contexts. With these enhancements, the general replacement expressions are more versatile than two-level rules for the description of complex morphological alternations.
Identification of the two histidine residues responsible for the inhibition by malonyl‐CoA in peroxisomal carnitine octanoyltransferase from rat liver (2000)

Carnitine octanoyltransferase (COT), an enzyme that facilitates the transport of medium chain fatty acids through peroxisomal membranes, is inhibited by malonyl-CoA. cDNAs encoding full-length wild-type COT and one double mutant variant from rat peroxisomal COT were expressed in Saccharomyces cerevisiae. Both expressed forms were expressed similarly in quantitative terms and exhibited full enzyme activity. The wild-type-expressed COT was inhibited by malonyl-CoA like the liver enzyme. The activity of the enzyme encoded by the double mutant H131A/H340A was completely insensitive to malonyl-CoA in the range assayed (2-200 microM). These results indicate that the two histidine residues, H131 and H340, are the sites responsible for inhibition by malonyl-CoA. Another mutant variant, H327A, abolishes the enzyme activity, from which it is concluded that it plays an important role in catalysis.
Improved predictive models for plasma glucose estimation from multi-linear regression analysis of exhaled volatile organic compounds (2009)

Exhaled volatile organic compounds (VOCs) represent ideal biomarkers of endogenous metabolism and could be used to noninvasively measure circulating variables, including plasma glucose. We previously demonstrated that hyperglycemia in different metabolic settings (glucose ingestion in pediatric Type 1 diabetes) is paralleled by changes in exhaled ethanol, acetone, and methyl nitrate. In this study we integrated these gas changes along with three additional VOCs (2 forms of xylene and ethylbenzene) into multi-linear regression models to predict plasma glucose profiles in 10 healthy young adults, during the 2 h following an intravenous glucose bolus (matched samples of blood, exhaled and room air were collected at 12 separate time points). The four-gas model with highest predictive accuracy estimated plasma glucose in each subject with a mean R value of 0.91 (range 0.70-0.98); increasing the number of VOCs in the model only marginally improved predictions (average R with best 5-gas model = 0.93; with 6-gas model = 0.95). While practical development of this methodology into clinically usable devices will require optimization of predictive algorithms on large-scale populations, our data prove the feasibility and potential accuracy of breath-based glucose testing.
Exposure to Fine Particulate Air Pollution Is Associated With Endothelial Injury and Systemic Inflammation (2016)

Episodic PM<sub>2.5</sub> exposures are associated with increased endothelial cell apoptosis, an antiangiogenic plasma profile, and elevated levels of circulating monocytes and T, but not B, lymphocytes. These changes could contribute to the pathogenic sequelae of atherogenesis and acute coronary events.
Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.) (2015)

A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection. Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80%. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1(GS, UC) for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75% of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.
BMP4 regulates vascular progenitor development in human embryonic stem cells through a smad‐dependent pathway (2009)

The signals that direct pluripotent stem cell differentiation into lineage-specific cells remain largely unknown. Here, we investigated the roles of BMP on vascular progenitor development from human embryonic stem cells (hESCs). In a serum-free condition, hESCs sequentially differentiated into CD34+CD31-, CD34+CD31+, and then CD34-CD31+ cells during vascular cell development. CD34+CD31+ cells contained vascular progenitor population that gives rise to endothelial cells and smooth muscle cells. BMP4 promoted hESC differentiation into CD34+CD31+ cells at an early stage. In contrast, TGFbeta suppressed BMP4-induced CD34+CD31+ cell development, and promoted CD34+CD31- cells that failed to give rise to either endothelial or smooth muscle cells. The BMP-Smad inhibitor, dorsomorphin, inhibited phosphorylation of Smad1/5/8, and blocked hESC differentiation to CD34+CD31+ progenitor cells, suggesting that BMP Smad-dependent signaling is critical for CD34+CD31+ vascular progenitor development. Our findings provide new insight into how pluripotent hESCs differentiate into vascular cells.
Discriminative training of Markov logic networks (2005)

Many machine learning applications require a combination of probability and first-order logic. Markov logic networks (MLNs) accomplish this by attaching weights to first-order clauses, and viewing these as templates for features of Markov networks. Model parameters (i.e., clause weights) can be learned by maximizing the likelihood of a relational database, but this can be quite costly and lead to suboptimal results for any given prediction task. In this paper we propose a discriminative approach to training MLNs, one which optimizes the conditional likelihood of the query predicates given the evidence ones, rather than the joint likelihood of all predicates. We extend Collins’s (2002) voted perceptron algorithm for HMMs to MLNs by replacing the Viterbi algorithm with a weighted satisfiability solver. Experiments on entity resolution and link prediction tasks show the advantages of this approach compared to generative MLN training, as well as compared to purely probabilistic and purely logical approaches.
Inhibition of Endothelial Cell Migration, Intercellular Communication, and Vascular Tube Formation by Thromboxane A2 (1999)

The eicosanoid thromboxane A(2) (TXA(2)) is released by activated platelets, monocytes, and the vessel wall and interacts with high affinity receptors expressed in several tissues including endothelium. Whether TXA(2) might alter endothelial migration and tube formation, two determinants of angiogenesis, is unknown. Thus, we investigated the effect of the TXA(2) mimetic [1S-(1alpha, 2beta(5Z),3alpha(1E,3R), 4alpha]-7-[3-(3-hydroxy-4-(4'-iodophenoxy)-1-butenyl)-7-o xab icyclo- [2.2.1]heptan-2-yl]-5'-heptenoic acid (IBOP) on human endothelial cell (HEC) migration and angiogenesis in vitro. IBOP stimulation inhibited HEC migration by 50% and in vitro capillary formation by 75%. These effects of IBOP were time- and concentration-dependent with an IC(50) of 25 nM. IBOP did not affect integrin expression or cytoskeletal morphology of HEC. Since gap junction-mediated intercellular communication increases in migrating HEC, we determined whether IBOP might inhibit coupling or connexin expression in HEC. IBOP reduced the passage of microinjected dyes between HEC by 50%, and the effects of IBOP on migration and tube formation were mimicked by the gap junction inhibitor 18beta-glycyrrhetinic acid (1 microM) with a similar time course and efficacy. IBOP (24 h) did not affect the expression or phosphorylation of connexin 43 in whole HEC lysates. Immunohistologic examination of HEC suggested that IBOP may impair functional coupling by altering the cellular distribution of gap junctions, leading to increased connexin 43 internalization. Thus, this finding that TXA(2) mimetics can prevent HEC migration and tube formation, possibly by impairing intercellular communication, suggests that antagonizing TXA(2) signaling might enhance vascularization of ischemic tissue.
Adaptive Resonance Theory: Self-Organizing Networks for Stable Learning, Recognition, and Prediction (1995)

Adaptive Resonance Theory (ART) is a neural theory of human and primate information processing and of adaptive pattern recognition and prediction for technology. Biological applications to attentive learning of visual recognition categories by inferotemporal cortex and hippocampal system, medial temporal amnesia, corticogeniculate synchronization, auditory streaming, speech recognition, and eye movement control are noted. ARTMAP systems for technology integrate neural networks, fuzzy logic, and expert production systems to carry out both unsupervised and supervised learning. Fast and slow learning are both stable response to large non stationary databases. Match tracking search conjointly maximizes learned compression while minimizing predictive error. Spatial and temporal evidence accumulation improve accuracy in 3-D object recognition. Other applications are noted.
Imiquimod in clinical practice. (1998)

Applied topically, imiquimod induces the production of interferon-alpha plus other cytokines. Because intralesional interferon is effective in the treatment of condylomata acuminata (genital warts), topical imiquimod has also been investigated as a potential therapy for this condition. The dosing regimen found to best balance efficacy, side-effects and practicality is 5% imiquimod cream applied overnight by the patient three times weekly until warts clear, for up to 16 weeks. The largest double-blind trial to examine this protocol involved 311 patients with external anogenital warts who were randomized to use imiquimod 5% cream, imiquimod 1% cream or vehicle cream. Evaluation of all patients given medication at any time showed that 50% of those who received 5% imiquimod experienced clearing of all baseline warts, as compared to 21% of those who used 1% imiquimod and 11% of those treated with vehicle. Overall, 5% imiquimod treatment was significantly more effective than vehicle (P < 0.0001). Excluding patients who discontinued medication for reasons unrelated to therapy (such as moving out of town or poor compliance), 56% of those who received 5% imiquimod experienced complete clearing of baseline warts. Clearing also occurred in 27% of those who received imiquimod 1%. Recurrence of baseline warts occurred in 13% of patients whose warts cleared with 5% imiquimod. When applied overnight at home three times each week, topical imiquimod 5% cream is an effective therapy with acceptable side-effects. The recurrence rate is low and further studies to specifically compare recurrence rates are warranted.
Sensitivity to salts and organic compounds of soil bacteria isolated on diluted media. (1980)

Bacteria were isolated from soil on a 100-fold dilution of nutrient broth agar, a 10-fold dilution of alubumin yeast extract agar, or agar without additional nutrient. Their growth was severely suppressed by full strength nutrient broth but well supported by a 100-fold dilution of nutrient broth and these organisms were proposed to be called dilute nutrient broth (DNB) organisms.One percent each of peptone and meat extract, and 1% or 2% casamino acids severely suppressed growth of most of them. Glycine, arginine, serine, or lysine (10mM), yeast extract (0.1%), nicotinic acid or thiamine (20μg/ml), and sodium succinate (20-50mM) inhibited growth of many organisms though sensitivity of each organism to organic compounds was of a great variety. They were also highly sensitive to NaCl and KCl. Growth inhibition of some isolates by serine was recovered by coexisting threonine, alanine, or leucine and valine. Inhibitive effect of serine was also influenced by NaCl, KCl, CaCl2, or MgCl2.
Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. (2001)

The enrichment of nitrogen-fixing bacteria from the C4-fibre plants, Spartina pectinata, Miscanthus sinensis, Miscanthus sacchariflorus and Pennisetum purpureum, with nitrogen-free semi-solid media led to the isolation of Herbaspirillum-like strains among other diazotrophic bacteria. On the basis of physiological properties, phylogenetic analysis comparing 16S rDNA sequences and DNA-DNA hybridization experiments of chromosomal DNA the new isolates could be grouped together in a new species with the proposed name Herbaspirillum frisingense sp. nov. Morphological characteristics, such as cell size and shape, colony appearance, motility and flagellation are largely identical to the known species Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. On the basis of utilization of adipate (-), N-acetyl-D-glucosamine (+), meso-erythritol (-), L-rhamnose (-) and meso-inositol (-) Herbaspirillum frisingense sp. nov. can be distinguished from other known Herbaspirillum spp. Nitrogen-fixing capability was examined by PCR amplification of the nifD gene and an acetylene reduction assay, and was found with all isolates tested. 16S rDNA sequence similarity to the other Herbaspirillum spp. is 98.5-99.1%. In genomic DNA-DNA hybridization experiments Herbaspirillum frisingense sp. nov. forms a homogeneous group with 70-100+/-10% similarity, clearly distinct from Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans with 1-34% similarity. 16S rRNA-targeted oligonucleotide probes, specific for the whole genus Herbaspirillum and for three Herbaspirillum species were designed and are suitable for fluorescence in situ hybridization. The DNA G+C content of Herbaspirillum frisingense sp. nov. is 63+/-2 mol%, in agreement with the values of 61-65% for the genus. PCR fingerprinting exhibits a consistent pattern for groups of strains isolated from the same plant, suggesting a low genomic diversity among bacteria inhabiting C4-gramineous plant tissues. Low genetic DNA diversity seems to be common between probable endophytic bacterial isolates of the same taxon. The type strain of Herbaspirillum frisingense sp. nov. is GSF30T (= DSM 13128T).
High tissue content of soluble beta 1-40 is linked to cerebral amyloid angiopathy. (1994)

We developed two highly sensitive enzyme immunoassays for beta-protein with different specificities. One is specific for beta 1-40, while the other is equally sensitive to beta 1-38, beta 1-39, beta 1-40, and beta 1-42. With the enzyme immunoassays we investigated whether the soluble fraction from brain tissue contains beta 1-40 or other species of beta-protein. Aged control and Alzheimer's diseased brains showed highly variable values of beta 1-40, which was found to be the major beta species in their extracts. High tissue content of soluble beta 1-40 was not correlated to the abundance of senile plaques but was invariably associated with cerebral amyloid angiopathy. Thus, the tissue level of soluble beta 1-40 should be useful for the quantification of cerebral amyloid angiopathy.
Towards a Service-oriented Participatory Design Studio Supported by UCLP (2006)

The Participatory Design Studio (PDS) provides users across multiple sites the ability to effectively participate in a common design session. Users are provided a variety of shared resources, including the underlying high-speed network, cameras, displays, sound equipment, large data files, and software applications for communicating and for visualizing the artifact being designed. This paper explores the design and implementation of PDS, and describes how it leverages the benefits of a service-oriented architecture (SoA) to provide a highly adaptable, modular, and loosely coupled solution. PDS integrates systems that are hosted on a wide variety of platforms with different management and network domains. This integration goes beyond piping application data from one system to another. Web services provide a cost-effective solution for integrating these systems into a comprehensive SoA