gebhart/patrepeval huggingface dataset:
Updating OWL2 ontologies using pruned rulesets (2015)

Evolution in Semantic Web content produces difference files (deltas) that track changes between ontology versions. These changes may represent ontology modifications or simply changes in application data. An ontology is typically expressed in a combination of OWL and RDF knowledge representation languages. A data repository that represents an ontology may be large and may be duplicated over the Internet, often in the form of a relational datastore. The deltas can be used to reduce the storage and bandwidth overhead involved in disseminating ontology updates. Minimising the delta size can be achieved by reasoning over the underlying knowledge base. OWL 2 is a development of the OWL 1 standard that incorporates new features to aid application construction. Among the sub languages of OWL 2, OWL 2 RL/RDF provides an enriched rule set that extends the semantic capability of the OWL environment. This additional semantic content can be exploited in change detection approaches that strive to minimise the alterations to be made when ontologies are updated. The presence of blank nodes (i.e. nodes that are neither a URI nor a literal) in RDF collections provides a further challenge to ontology change detection. This is a consequence of the practical problems they introduce when comparing data structures before and after update. In the light of OWL 2 RL/RDF, this paper examines the potential for reducing the delta size by pruning the application of unnecessary rules from the reasoning process and using an approach to delta generation that produces the smallest number of updates. It also assesses the impact of alternative approaches to handling blank nodes during the change detection process in ontology structures. The results indicate that pruning the rule set is a potentially expensive process but has the benefit of reducing the joins over relational data stores when carrying out the subsequent inferencing.
The Value of Feedback in an Early Field Experience: Peer, Teacher, and Supervisor Coaching (2001)

Abstract This study investigated the value of multiprong feedback to preservice teachers in an early field experience. The three sources of feedback were university supervisor, directing teacher, and peer coach. Thirty-four elementary education students beginning their final year were paired for placement with a classroom teacher. Qualitative data sources were peer coaching data forms, dialogue journals, and course evaluations. An anonymous survey yielded quantitative data. Students indicated they valued feedback from all three sources, though feedback from the two professionals (supervisor and teacher) was somewhat more valuable. The issues students asked their peers to give feedback on most often related to classroom management and pedagogy. It was concluded that paired placement of preservice teachers in an early field experience with a structured process of regular peer observation and feedback can be a valuable supplement to feedback from the directing teacher and university supervisor.
Morphometric changes in the heights and anteroposterior diameters of the lumbar intervertebral discs with age. (1991)

Changes in the heights and anteroposterior diameters of human lumbar intervertebral discs have been studied by means of measurements from radiographs. The results confirm previous reports that there is overall increase in the various dimensions of the disc with age. Growth of the discs apparently does not follow a linear pattern. There are alternating periods of overgrowth and thinning. After the 5th decade of life there is an appreciable decline of disc height. The significance of the findings is discussed.
Spread-spectrum communications (1993)

The characteristics of spread-spectrum systems that account for their growing use are examined. They offer low probability of intercept, signal hiding, and jammer rejection. Spread spectrum also provides a measure of immunity to multipath interference and multiple access capability, making it ideal for radar, telephone, local area networks, and many other applications. The two primary techniques commonly used frequency hopping and direct sequence, are described along with their advantages and disadvantages.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Formation of Physical Hydrogels via Host−Guest Interactions of β-Cyclodextrin Polymers and Copolymers Bearing Adamantyl Groups (2008)

In this paper, we would like to present a novel system of host−guest hydrogels. By polymerizing adamantyl containing acrylamide monomers (12−15) with water soluble comonomers, we synthesized various copolymers bearing guest components. As host system we applied easily accessible β-cyclodextrin polymers with Mn values of about 30K−100K g mol−1. The viscosity of the resulting hydrogel could be influenced by the concentration of both substances, by the length of the carbon spacer chain of the guest monomer, by the pH value or by the conformation of the β-cyclodextrin polymers. Moreover, the hydrogels stayed stable in solutions of starch hydrolyzing enzyme taka-diastase from Aspergillus oryzae.
REGULATORY SEQUENCES INVOLVED IN THE PROMOTION AND TERMINATION OF RNA TRANSCRIPTION (1979)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Concurrent mutations in six amino acids in β-glucuronidase improve its thermostability (2007)

To achieve a thermostable beta-glucuronidase (GUS) and identify key mutation sites, we applied in vitro directed evolution strategy through DNA shuffling and obtained a highly thermostable mutant GUS gene, gus-tr, after four rounds of DNA shuffling and screening. This variant had mutations in 15 nucleic acid sites, resulting in changes in 12 amino acids (AAs). Using gus-tr as the template, we further performed site-directed mutagenesis to reverse the individual mutation to the wild-type protein. We found that six sites (Q493R, T509A, M532T, N550S, G559S and N566S) present in GUS-TR3337, were the key AAs needed to confer its high thermostability. Of these, Q493R and T509A were not reported previously as important residues for thermostability of GUS. Furthermore, all of these six mutations must be present concurrently to confer the high thermostability. We expressed the gus-tr3337 gene and purified the GUS-TR3337 protein that contained the six AA mutations. Compared with the wild-type protein which lost its activity completely after 10 min at 70 degrees C, the mutant GUS-TR3337 protein retained 75% of its activity when heated at 80 degrees C for 10 min. The GUS-TR3337 exhibited high activity even heated at 100 degrees C for 30 min on nitrocellulose filter. The comparison of molecular models of the mutated and wild-type enzyme revealed the relation of protein function and these structural modifications.
Design of a pictorial knowledgebase (1987)

Intelligent Pictorial Databases increase the ease and the efficiency with which pictorial information can be utilized. In this paper, a frame-based pictorial knowledge representation is presented. Representation of geometric, color, and texture information is considered. Aggregation, generalization/ specialization, class/individualization, and inheritance of pictorial knowledge are exploited. The resulting knowledge representation is implemented in KPE, a knowledge programming tool developed in [6].
Dietary Fats and the Risk of Incident Alzheimer Disease (2003)

High intake of unsaturated, unhydrogenated fats may be protective against Alzheimer disease, whereas intake of saturated or trans-unsaturated (hydrogenated) fats may increase risk.
Species‐dependent binding of serum albumins to the streptococcal receptor protein G (1990)

The interaction of the serum albumin binding domain from streptococcal protein G to serum albumins isolated from different species was investigated. The highest affinity to protein G was found for serum albumins from rat, man and mouse. A medium binding was found for serum albumin from rabbit, cow, hen and horse, while little or no binding was found for ovalbumin and serum albumin from sheep. The interaction between human serum albumin and protein G showed rapid binding kinetics at the temperatures 7, 22 and 37 degrees C. Furthermore, the ability of different serum albumins to function as affinity ligands when covalently coupled to a solid support was tested. The results show that protein G derivatives could be eluted at different pH depending on the origin of the serum albumin. It was also possible to elute the streptococcal receptor efficiently from the mouse serum albumin matrix with human serum albumin. Based on these results, a gene fusion system for recovery of sensitive proteins by affinity purification is described, where high yields are obtained under mild elution conditions.
Cancer-Testis Antigen Lymphocyte Antigen 6 Complex Locus K Is a Serologic Biomarker and a Therapeutic Target for Lung and Esophageal Carcinomas (2007)

Gene expression profile analyses of non-small cell lung carcinomas (NSCLC) and esophageal squamous cell carcinomas (ESCC) revealed that lymphocyte antigen 6 complex locus K (LY6K) was specifically expressed in testis and transactivated in a majority of NSCLCs and ESCCs. Immunohistochemical staining using 406 NSCLC and 265 ESCC specimens confirmed that LY6K overexpression was associated with poor prognosis for patients with NSCLC (P = 0.0003), as well as ESCC (P = 0.0278), and multivariate analysis confirmed its independent prognostic value for NSCLC (P = 0.0035). We established an ELISA to measure serum LY6K and found that the proportion of the serum LY6K-positive cases was 38 of 112 (33.9%) NSCLC and 26 of 81 (32.1%) ESCC, whereas only 3 of 74 (4.1%) healthy volunteers were falsely diagnosed. In most cases, there was no correlation between serum LY6K and conventional tumor markers of carcinoembryonic antigen (CEA) and cytokeratin 19-fragment (CYFRA 21-1) values. A combined ELISA for both LY6K and CEA classified 64.7% of lung adenocarcinoma patients as positive, and the use of both LY6K and CYFRA 21-1 increased sensitivity in the detection of lung squamous cell carcinomas and ESCCs up to 70.4% and 52.5%, respectively, whereas the false positive rate was 6.8% to 9.5%. In addition, knocked down of LY6K expression with small interfering RNAs resulted in growth suppression of the lung and esophageal cancer cells. Our data imply that a cancer-testis antigen, LY6K, should be useful as a new type of tumor biomarker and probably as a target for the development of new molecular therapies for cancer treatment.
Molecular Genetic Studies of Gene Identification for Osteoporosis: The 2009 Update (2010)

Osteoporosis is a complex human disease that results in increased susceptibility to fragility fractures. It can be phenotypically characterized using several traits, including bone mineral density, bone size, bone strength, and bone turnover markers. The identification of gene variants that contribute to osteoporosis phenotypes, or responses to therapy, can eventually help individualize the prognosis, treatment, and prevention of fractures and their adverse outcomes. Our previously published reviews have comprehensively summarized the progress of molecular genetic studies of gene identification for osteoporosis and have covered the data available to the end of September 2007. This review represents our continuing efforts to summarize the important and representative findings published between October 2007 and November 2009. The topics covered include genetic association and linkage studies in humans, transgenic and knockout mouse models, as well as gene-expression microarray and proteomics studies. Major results are tabulated for comparison and ease of reference. Comments are made on the notable findings and representative studies for their potential influence and implications on our present understanding of the genetics of osteoporosis.
MHC Class II epitope predictive algorithms (2010)

Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide-MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles.
Kanamycin reveals the role played by glutamate receptors in shaping plant resource allocation (2005)

Ionotropic glutamate receptors (iGluRs) play important roles in neurotransmission in animals. There is growing evidence that iGluRs also play important roles in plants. Using a chemical genetics approach, which combined a pH-homeostasis mutant of Arabidopsis thaliana (de-etiolated3), several different iGluR agonists, molecular modelling, and reporter gene expression in transgenic plants, we provide evidence that iGluR agonism can induce dramatic changes in plant development and metabolism. Systematic hypothesis testing revealed a signalling circuit that integrates amino acid and sugar signals to affect elongation growth and the deposition of carbon into starch and lignins. The data show that aminoglycoside antibiotics, such as kanamycin, and polyamines impinge upon this circuit. These findings provide a mechanism for the conversion of amino acid and sugar signals into an appropriate response at the gene expression level, and underline the similarities in iGluR agonism between animals and plants.
<title>Telerobot control using enhanced stereo viewing</title> (1995)

A telerobot control system using stereoscopic viewing has been developed. The objective of the system is to implement a world-model mapping capability using live stereo video to provide an operator with three-dimensional image information of an unstructured environment and to use stereo computer graphics renderings of wire-frame models of sought-after features in the environment in order to relate robotic task information. The operator visually correlates or matches the stereo video image of the environment with the graphic image to register the world model space to the manipulator's environment. This allows operator control of the manipulator through teleoperation in unstructured environments with a change-over to autonomous operation when the operation can be restricted and a task becomes repetitive. Details of the robot control, stereo imaging, and system control components are provided.
Nonmyeloablative Allogeneic Immunotherapy for Solid Tumors (2004)

Over the past decade, considerable advances have been made in the field of allogeneic hematopoietic stem cell transplantation. Recognition that transplanted donor immune cells can cure patients with leukemia has led to the development of nonmyeloablative or “low-intensity” conditioning regimens, which have expanded the application of allogeneic transplantation to a growing number of hematological malignancies. The improved safety and preliminary success of this transplant approach have justified applying allogeneic immunotherapy to patients with treatment-refractory solid tumors.
2.5D full‐wavefield viscoacoustic invercion1 (1995)

Abstract Full‐wavefield inversion for distributions of acoustic velocity, density and Q on a vertical slice through a25D model is implemented for common‐source gathers in a cross‐hole geometry. The wavefield extrapolation used is 3D, so all geometrical spreading, scattering, reflection, and transmission effects are correctly and automatically compensated for. In order to keep the number of unknowns tractable, application was limited to 2.5D models of known geometry; the latter assurnes a prior step, such as tomography, to fix the layer geometries. With the model geometry fixed, reliable solutions are obtained using synthetic data from only two independent source locations. Solutions from data with noisy and missing traces are comparable to those from noise‐free data, but with higher residuals. When the source locations are spatially widely separated, conunon‐source gathers may be summed and treated as a single wavefield to yield the same model estimates as when the individual source wavefields are treated separately, at substantially reduced cost. Inversions for full 3D parameter distributions can be handled with the same software, requiring only solution for more unknowns.
A General Method for Saturation Mutagenesis of Cloned DNA Fragments (1985)

A new procedure for generating and isolating random single-base substitutions in cloned DNA fragments is presented. The mutations are generated by treatment of single-stranded DNA with various chemicals, followed by the synthesis of the complementary strand with reverse transcriptase. Misincorporation frequently occurs when the enzyme encounters a damaged base in the mutagenized template DNA. The resulting duplex DNA fragments containing random single-base substitutions are cloned, amplified as a population, and isolated from wild-type DNA by preparative denaturing gradient gel electrophoresis. The physical separation of mutant DNA fragments makes it possible to isolate and characterize large numbers of site-directed single-base substitutions in the absence of a phenotypic selection. This procedure should be generally applicable to the fine-structure genetic analysis of regulatory and protein-coding sequences.
Serological studies on the incidence of canine enteritis viruses. (1980)

The extended genealogy tree disclosed three groups of NDs according to the estimated time needed for a step to occur: the stem ND, HD, with 32.5 years/step, the trunk NDs ALS, FTD, PD and CJD, with 6.7-13.7 years/step; and the crown NDs PDM, PDD, AD and DLB, with 2.3-3.8 years/step. Thus, the NDs cluster into three groups according to both the number of steps and the number of years for a step to occur.
Sumatriptan Inhibits Neurogenic Vasodilation of Dural Blood Vessels in the Anaesthetized Rat—Intravital Microscope Studies (1997)

This study used intravital microscopy to measure the diameter of dural arteries in anaesthetized rats. Electrical stimulation of the surface of a closed cranial window produced increases in dural vessel diameter which were blocked by the CGRP receptor antagonist human-alpha CGRP(8-37) but unaffected by the NK1 receptor antagonist RP67580. Sumatriptan (3 and 10 mg kg-1, i.v.) significantly reduced the response to electrical stimulation. In contrast, sumatriptan (3 mg kg-1) had no effects on the response to exogenously administered CGRP. These results indicate that neurokinins play no role in neurogenic vasodilation in this preparation and that neurogenic vasodilation in rat dural vessels is mediated predominantly by CGRP. Furthermore, the data indicate that sumatriptan attenuates neurogenic vasodilation, probably by inhibiting the release of CGRP from perivascular trigeminal nerve endings innervating the dura. These experimental data parallel the clinical findings that CGRP levels are elevated in migraine and normalized, concomitantly with headache relief, by sumatriptan.
Using Embryonic Stem Cells to Introduce Mutations into the Mouse Germ Line1 (1991)

It is now possible, through the use of a number of experimental technologies, to transfer genetic information into mouse embryos to stably alter the genetic constitution of mice. This experimental approach, namely the generation of so-termed "transgenic" animals, is affording new insights into a wide variety of biological problems. This review focuses on one system for the generation of transgenic mice, which utilizes tissue culture cell lines of embryonic stem cells, termed ES cells. The remarkable property of ES cells is that they retain the potential to reform an embryo; when they are replaced inside a carrier embryo, they resume normal development and contribute to all the tissues of the live-born chimeric animal. Recent experiments, using a repertoire of gene transfer techniques, have shown that ES cells are amenable to a variety of experimental manipulations in tissue culture. Moreover, it has been demonstrated that these genetically altered cells can be transferred into the germ line of chimeric mice, thus allowing the production of unique strains of animals for study. The applications of the ES cell system are reviewed, with particular emphasis on their use for the generation of random insertional mutations using a retrovirally mediated mutagenesis approach. Finally, the use of ES cells in conjunction with the recently described technique of homologous recombination, or "gene targeting," is discussed. This technology allows the generation of animals carrying extremely precise genetic modifications of endogenous genes.
Heparin and Heparan Sulfate Block Angiotensin IIInduced Hypertrophy in Cultured Neonatal Rat Cardiomyocytes (1996)

Our findings in this study strongly suggest that heparin and heparan sulfate are potent inhibitors of cardiomyocyte hypertrophy and that endogenous heparin-like substances negatively regulate cardiomyocyte hypertrophy.
Electrospray ionization mass spectrometry for the quantitation of albumin in human serum (1997)

Capillary reversed-phase liquid chromatography was coupled to electrospray ionization mass spectrometry for determining the concentration of human serum albumin (HSA) in a fresh frozen serum reference material. A biotinylated HSA (bHSA) was prepared and used as an internal standard for the serum albumin determination. The average HSA concentration of the serum sample was determined by mass spectrometry to be 41.5 ± 2.8 g/L at the 95% confidence limit for the measured value. The HSA concentration of the fresh frozen serum was also assayed using the bromocresol green dye-binding method, producing a value of 42.3 ± 1.5 g/L. Calibration curves generated from HSA standards spiked with bHSA showed excellent linearity and the relative standard deviation for replicate analysis of a bHSA spiked serum sample was less than 3%.
Coproexamination for botulinal toxin and clostridium botulinum. A new procedure for laboratory diagnosis of botulism. (1977)

Stool or serum specimens or both from 318 persons pertaining to 165 botulism investigations over a three-year period were examined. Botulinal toxin was detected in stools of 19 of 56 patients and in sera of 20 of 60 patients with clinical botulism; it was not detected in specimens from 246 persons with an illness other than botulism or well contacts of patients. Clostridium botulinum was identified in stools of 36 of 60 clinical botulism patients and in four of 27 asymptomatic contacts of patients with botulism victims, but not in stools of 65 persons not associated with confirmed botulism. When stool and serum samples were examined, confirmatory evidence was obtained for 72.9% of the botulism cases. Detection of botulinal toxin or C botulinum in the stool of a persons should be considered evidence supporting the clinical diagnosis of botulism.