gebhart/patrepeval huggingface dataset:
DNA Typing of Human Leukocyte Antigen Sequence Polymorphisms by Peptide Nucleic Acid Probes and MALDI-TOF Mass Spectrometry (1997)

A novel analytical method using PNA probes detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) was applied to type sequence polymorphisms within the human leukocyte antigen (HLA), DQA locus. Streptavidin-coated magnetic beads were used to immobilize biotinylated DNA. PNA probes representing possible alleles were then prepared for the immobilized DNA hybridization. The nonspecific PNA probes were removed with stringent washes. The PNA/DNA/beads conjugate was analyzed by MALDI-TOFMS. The genotype of the DNA was determined by the detected molecular masses of the released PNA probes. Reproducible and accurate genotyping was achieved by this analytical method.
THE WHISKER WEAVING ALGORITHM: A CONNECTIVITY-BASED METHOD FOR CONSTRUCTING ALL-HEXAHEDRAL FINITE ELEMENT MESHES (1996)

This paper introduces a new algorithm called whisker weaving for constructing unstructured, all-hexahedral finite element meshes. Whisker weaving is based on the Spatial Twist Continuum (STC), a global interpretation of the geometric dual of an all-hexahedral mesh. Whisker weaving begins with a closed, all-quadrilateral surface mesh bounding a solid geometry, then constructs hexahedral element connectivity advancing into the solid. The result of the whisker weaving algorithm is a complete representation of hex mesh connectivity only: Actual mesh node locations are determined afterwards. The basic step of whisker weaving is to form a hexahedral element by crossing or intersecting dual entities. This operation, combined with seaming or joining operations in dual space, is sufficient to mesh simple block problems. When meshing more complex geometries, certain other dual entities appear such as blind chords, merged sheets, and self-intersecting chords. Occasionally specific types of invalid connectivity arise. These are detected by a general method based on repeated STC edges. This leads into a strategy for resolving some cases of invalidities immediately. The whisker weaving implementation has so far been successful at generating meshes for simple block-type geometries and for some non-block geometries. Mesh sizes are currently limited to a few hundred elements. While the size and complexity of meshes generated by whisker weaving are currently limited, the algorithm shows promise for extension to much more general problems.
Role of intonation patterns in conveying emotion in speech (1999)

In a production and perception study the relation was studied between the emotion or attitude expressed in an utterance, and the intonation pattern realized on that utterance. In the production study, the pitch curves of emotional utterances were labelled in terms of the IPO intonation grammar. One intonation pattern, the `1&amp;amp;A&amp;apos;, was produced in all emotions studied. Some other patterns were specifically used in expressing some of these emotions. In the perception study, in which the perceptual relevance of these findings was checked, the communicative role of the intonation patterns found in the database was tested. This listening test provided converging evidence on the contribution of specific intonation patterns to the perception of some of the emotions and attitudes studied. Some intonation patterns, such as final `3C&amp;apos; and `12&amp;apos;, which were specifically produced in some emotion, also introduced a perceptual bias towards that emotion. In that sense, the results from the perception study supported those from the production study. 1.
Alkene and carbon monoxide derivatives of copper(I) and silver(I) .beta.-diketonates (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkene and carbon monoxide derivatives of copper(I) and silver(I) .beta.-diketonatesG. Doyle, K. A. Eriksen, and D. VanEngenCite this: Organometallics 1985, 4, 5, 830–835Publication Date (Print):May 1, 1985Publication History Published online1 May 2002Published inissue 1 May 1985https://pubs.acs.org/doi/10.1021/om00124a005https://doi.org/10.1021/om00124a005research-articleACS PublicationsRequest reuse permissionsArticle Views549Altmetric-Citations70LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Gene recognition based on DAG shortest paths (2001)

We describe DAGGER, an ab initio gene recognition program which combines the output of high dimensional signal sensors in an intuitive gene model based on directed acyclic graphs. In the first stage, candidate start, donor, acceptor, and stop sites are scored using the SNoW learning architecture. These sites are then used to generate a directed acyclic graph in which each source-sink path represents a possible gene structure. Training sequences are used to optimize an edge weighting function so that the shortest source-sink path maximizes exon-level prediction accuracy. Experimental evaluation of prediction accuracy on two benchmark data sets demonstrates that DAGGERis competitive with ab initio gene finding programs based on Hidden Markov Models.
Evaluation of Mixtures of Wild-Type HIV-1 and HIV-1 with Resistance Point Mutations against Reverse Transcriptase Inhibitors (1998)

The presence of resistance-related mutations in 185 serial proviral DNA samples from 108 HIV-infected patients was monitored using the line probe assay (LiPA). The proportions of wild-type and mutant virus in each sample were determined. Subsequent samples from the same patient were analysed. Resistance mutations were detected in 58 of 108 patients studied (53.7%), 53 of 73 (72.6%) treated with antivirals and 5 of 35 (14.2%) untreated. The mutations were against zidovudine (51), lamivudine (1), zidovudine and lamivudine (4), zidovudine and zalcitabine (1) and zidovudine and didanosine (1). Among the 58 patients with resistant virus, 168 related mutations were observed: 161 to zidovudine (90 in codon 70, 25 in codon 41 and 46 in codon 215), 5 to lamivudine (codon 184), 1 to zalcitabine (codon 69) and 1 to didanosine (codon 74). Mixtures of wild-type and resistant mutants were detected in 76 of 90 (84.4%) mutated at codon 70, 28 of 46 (60.8%) mutated at codon 215 and in 21 of 25 (84%) mutated at codon 41. The mutations at codon 184 were mixtures of wild-type and resistant in 4 of 5 samples. The agreement between LiPA and sequencing was 96.5%. LiPA was more sensitive for the detection of mutants that were present at low frequency. The analysis of sequential samples from the same patient allowed evaluation of the dynamics of appearance of the resistant mutants.
THE UBIQUITIN-CONJUGATION SYSTEM (1992)

The ubiquitin/proteasome system is believed to be the major nonlysosomal proteolytic system of eukaryotic cells. It is present in the cytosol and the nucleus but apparently absent from the lumen of membrane-enclosed organelles, i. e., the endoplasmic reticulum, the Golgi and vesicular system, mitochondria, chloroplasts, and peroxisomes (for reviews see Finley and Chau, 1991; Jentsch, 1992a,b; Hershko and Ciechanover, 1992; Ciechanover, 1994; Hochstrasser, 1995; Smith et al., 1996). Substrates of this pathway include soluble proteins, subunits of oligomeric protein complexes, and integral membrane proteins. An important function of this pathway is the elimination of abnormal proteins (e. g., misfolded, misassembled) generated under normal and, in particular, stress conditions. Moreover, it is assumed that most naturally short-lived proteins of the cytosol and the nucleus are degraded by this pathway. Known substrates include proteins with important regulatory roles such as transcription factors, cell cycle regulators, and signal transducers.
Multidimensional High-Throughput Screening of Displacers (2005)

A multidimensional, batch high-throughput screening (MD-HTS) protocol was developed to investigate the effects of various parameters on the selectivity of ion-exchange protein displacement systems. A variety of molecules were screened, and the results were employed to provided insights into the influence of displacer chemistry and concentration, resin chemistry, and mobile-phase salt counterion on the efficacy and selectivity of these nonlinear chromatographic systems. These results open up the possibility of tailoring the selectivity of displacement separations by choosing appropriate combinations of operating conditions using the MD-HTS technique. The screens were also employed for the identification of displacers and conditions for the separation of a challenging protein mixture by selective displacement chromatography. Column displacements were carried out with potential lead compounds identified from the MD-HTS screens, and the results confirmed that selective displacement could indeed be achieved for this model mixture. Furthermore, the results indicated that this approach is particularly useful when the order of elution is not changed, but the inherent selectivity is increased in the presence of the displacer. The results presented in this paper demonstrate the utility of the MD-HTS technique for rapid method development in protein ion-exchange displacement chromatography.
MOGA Novartis oncology cancer achievement award 2012 (2013)

The Medical Oncology Group of Australia, together with Novartis Oncology, presents the Cancer Achievement Award to recognise an outstanding Australian contribution to cancer research and control. The award formally recognises the contributions made by scientists, clinicians and other health care professionals to the scientific study of cancer in Australia. Since 1999, this award has been presented to 13 leaders in the field of Australian oncology. The recipient of the 2012 Award was Professor Michael Barton OAM, Research Director of the Collaboration for Cancer Outcomes Research and Evaluation (CCORE) and the Ingham Institute for Applied Medical Research at Liverpool Hospital. The award was received by Professor Barton at the Medical Oncology Group of Australia Annual Scientific Meeting in Brisbane on 10th August 2012, at which he delivered the following address.
Multiferroic BaTiO 3 -CoFe 2 O 4 Nanostructures (2004)

We report on the coupling between ferroelectric and magnetic order parameters in a nanostructured BaTiO3-CoFe2O4 ferroelectromagnet. This facilitates the interconversion of energies stored in electric and magnetic fields and plays an important role in many devices, including transducers, field sensors, etc. Such nanostructures were deposited on single-crystal SrTiO3 (001) substrates by pulsed laser deposition from a single Ba-Ti-Co-Fe-oxide target. The films are epitaxial in-plane as well as out-of-plane with self-assembled hexagonal arrays of CoFe2O4 nanopillars embedded in a BaTiO3 matrix. The CoFe2O4 nanopillars have uniform size and average spacing of 20 to 30 nanometers. Temperature-dependent magnetic measurements illustrate the coupling between the two order parameters, which is manifested as a change in magnetization at the ferroelectric Curie temperature. Thermodynamic analyses show that the magnetoelectric coupling in such a nanostructure can be understood on the basis of the strong elastic interactions between the two phases.
A Micro Biuret Method for Protein Determination Determination of Total Protein in Cerebrospinal Fluid (1953)

AbstractA rapid and convenient colorimetric method for the determination of small amounts of protein, based on the biuret reaction and readings at 330 mμ, is described. The "micromethod" allows the determination of 10 to 200 mg per cent protein with an acurassy of ± 1.5 mg per cent. An "ultra micro" modification allows determinations of 10 to 400 micrograms protein.The method is applied for the determination of total protein in 1 ml of cerebrospinal fluid.
Inhibition of leukemia cell proliferation by receptor-mediated uptake of c-myb antisense oligodeoxynucleotides. (1992)

Exposure of human leukemia HL-60 cells to an oligodeoxynucleotide complementary to an 18-base sequence (codons 2-7) of c-myb-encoded mRNA has previously been shown to result in inhibition of cell proliferation. Because HL-60 cells express high levels of transferrin receptor we adapted a DNA delivery system based on receptor-mediated endocytosis to introduce myb oligomers complexed with a transferrin-polylysine conjugate into those cells. A DNA.RNA duplex resistant to S1 nuclease digestion was detected as early as 12 hr after culture of HL-60 cells in the presence of the myb antisense/transferrin-polylysine complex. Exposure of HL-60 cells to the myb antisense/transferrin-polylysine complex resulted in rapid and profound inhibition of proliferation and loss of cell viability much more pronounced than that occurring in cells exposed to free myb antisense oligodeoxynucleotides. The transferrin-polylysine/myb sense complex or the transferrin-polylysine conjugate alone had no effect on HL-60 cell proliferation and viability. These findings indicate that myb synthetic oligodeoxynucleotides enter efficiently into HL-60 by transferrin receptor-mediated endocytosis and exert a profound biological effect. Such a delivery system could exploit other ligand-receptor interactions for the selective delivery of oncogene-targeted antisense oligodeoxynucleotides.
Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV. (1990)

DNA damage generated by oxygen radicals includes base-free apurinic/apyrimidinic (AP) sites and strand breaks that bear deoxyribose fragments. The yeast Saccharomyces cerevisiae repairs such DNA lesions by using a single major enzyme. We have cloned the yeast structural gene (APN1) encoding this AP endonuclease/3'-repair diesterase by immunological screening of a yeast genomic DNA expression library in lambda gt11. Gene disruption experiments confirm that the Apn1 protein accounts for greater than or equal to 97% of both AP endonuclease and DNA 3'-repair diesterase activities in yeast cell-free extracts. The DNA and predicted amino acid sequences for the APN1 gene are homologous to those for the nfo gene encoding DNA endonuclease IV of Escherichia coli. This conservation of structure between a eukaryotic enzyme and its prokaryotic counterpart underscores the fundamental nature of their roles in DNA repair.
Inhibitory effect of K-76 monocarboxylic acid, an anticomplementary agent, on the C3b inactivator system. (1981)

K-76COOH caused dose-dependent inhibition of the degradation, by C3b inactivator (C3bINA) and beta 1H, of membrane-bound C3b on EAC1-3b and of free C3b in the fluid phase, i.e., cleavage of the C3b alpha' peptide chain. K-76COOH primarily attacked C3bINA but not beta 1H or C3b. K-76COOH inhibited the suppression of immune adherence reactivity and the manifestation of conglutination reactivity of EAC1-3b cells by C3bINA and beta 1H. The drug also inhibited the reaction between conglutinin and EAC1-3b' cells derived from EAC1-3b by treatment with C3bINA and beta 1H. EAC1-3b cells did not form rosettes with either Daudi or Raji lymphoblastoid cells. Treatment with C3bINA and beta 1H rendered EAC1-3b cells reactive with Daudi cells, and this change was inhibited by K-76COOH. EAC1-3b cells became able to form rosettes with Raji cells after addition of beta 1H. This rosette formation was enhanced by further addition of C3bINA, and this enhancement was also suppressed by K-76COOH.
Production of a discrete, heterogeneous population of β‐galactosidase polypeptides using baculovirus expression vectors (1992)

Gel electrophoresis analysis of immunoprecipitated beta-galactosidase and polyhedrin-beta-galactosidase expressed in Spodoptera frugiperda cells infected with recombinant Autograph californica nuclear polyhedrosis virus revealed the existence of a population of discrete beta-galactosidase polypeptides. Several of the polypeptides observed in the fusion protein expression experiments exhibit a consistent pattern of slightly greater molecular weight when compared to the nonfusion beta-galactosidase that is compatible with the hypothesis that these fusion protein fragments retain the N-terminal polyhedrin residues. Pulse-chase experiments showed that overall beta-galactosidase degradation occurred at a negligible rate compared to the synthesis rate at 96 h postinfection, yet the fragments are observed for short pulse times. Degradation of several different beta-galactosidase polypeptides was observed 24 h postinfection. Ribonucleic acid hybridization analysis of lacZ transcripts shows significant heterogeneity that may result from premature transcription termination. Although a proteolytic origin cannot be excluded, the data assembled suggest that premature termination of transcription or translation is the likely cause for the heterogeneous population of immunoreactive peptides observed. Many discrete forms of beta-galactosidase polypeptides were also observed in studies with Escherichia coli, indicating that production of these heterogeneous forms is not a consequence of heterologous expression of the enzyme.
Up-regulation of Delta-like 4 Ligand in Human Tumor Vasculature and the Role of Basal Expression in Endothelial Cell Function (2005)

The Notch signaling pathway and the delta-like 4 ligand (DLL4) play key roles in embryonic vascular development. Many of the pathways involved in embryonic vascular development also play important roles in tumor angiogenesis. In this study, we assessed the expression of DLL4 in primary renal cancer and investigated the biological function of DLL4 in primary endothelial cells. Using real-time quantitative PCR and in situ hybridization, we showed that the expression of DLL4 was up-regulated within the vasculature of clear cell-renal cell carcinoma almost 9-fold more than normal kidney and was correlated with the expression of vascular endothelial growth factor (VEGF). The expression of DLL4 in endothelial cells was up-regulated by VEGF and basic fibroblast growth factor synergistically, and by hypoxia through hypoxia-inducible factor 1alpha. Down-regulation of DLL4 expression with RNA interference led to decreased expression of HEY1 and EphrinB2, and the inhibition of endothelial cell proliferation, migration, and network formation, all of which are important processes in tumor angiogenesis. The inhibition of proliferation occurred via the induction of cell cycle arrest in G0-G1 by increased expression of p21 and decreased phosphorylation of retinoblastoma. We conclude that an optimal window of the DLL4 expression is essential for tumor angiogenesis and that selective modulation of the DLL4 expression within human tumors may represent a potential novel antiangiogenic therapy.
Theoretical study of the UV-induced desorption of molecular oxygen from the reduced TiO2 (110) surface (2003)

We investigate the UV-induced desorption of O2 from a reduced TiO2 rutile surface. The desorption mechanism considered is a direct, optical excitation of the adsorbate-substrate complex. The low-lying excited electronic states of the adsorbate-surface system and the transition dipole moments are calculated with a cluster model. We also estimate the effects of nonadiabatic coupling on the desorption yield. As a consequence of the localized nature of the adsorption process, ground state properties calculated with the cluster model agree well with previous results obtained with a slab model. To reduce the size of the calculation, we use optimal orbitals for each of the interacting electronic states, followed by transformation to biorthonormal orbital sets. Comparison with experimental photodesorption cross-section data shows excellent agreement for photon energies close to the vertical transition energy. At higher energies, we speculate that substrate-mediated electronic excitation mechanisms must be included in the model.
Reduced surface expression and binding of fibronectin by thrombin-stimulated thrombasthenic platelets. (1983)

Thrombin stimulation results in increased surface expression of endogeneous fibronectin and binding of plasma fibronectin to human platelets. Platelets of patients with Glanzmann's thrombasthenia, a bleeding disorder, exhibit reduced thrombin-induced platelet aggregation, little or no clot retraction, and abnormal platelet spreading on glass surfaces. Thrombin stimulation of patient platelets from four thrombasthenic kindreds resulted in little fibronectin binding. Nevertheless, thrombin did induce serotonin secretion from these cells, indicating that stimulation was occurring. Thrombasthenic platelets did not inhibit thrombin-stimulated fibronectin binding to coincubated normal cells, suggesting that their defect was not due to the presence of a soluble inhibitor of fibronectin binding. Thrombin-stimulated afibrinogenemic platelets bound similar quantities of fibronectin to normal cells, indicating that the thrombasthenic deficit is not secondary to reduced fibrinogen content or binding. The thrombasthenic cells had an endogenous fibronectin content of 2.9 +/- 0.7 micrograms/10(9) platelets, whereas cells simultaneously prepared from five normal individuals contained 1.8 +/- 0.7 micrograms/10(9) platelets, a statistically insignificant difference. Nevertheless, thrombin stimulation did not increase expression of endogeneous fibronectin antigen on the surface of the thrombasthenic platelets as judged by immunofluorescence. These defects in platelet fibronectin binding and surface expression may account for some of the manifestations of Glanzmann's thrombasthenia.
Specific serum IgE antibodies to bacterial antigens in allergic lung disease* (1982)

A radio-allergosorbent test (RAST) to measure specific IgE antibodies in man to whole bacterial cells of Streptococcus pneumoniae, Staphylococcus aureus and Haemophilus influenzae was developed to investigate different well-defined lung diseases (chronic bronchitis, allergic bronchopulmonary aspergillosis (ABPA), bronchial asthma allergic rhinitis, cystic fibrosis) and also in urticaria as compared with non-atopic blood donors. In addition, total IgE values and skin prick tests were assessed in these patients. The ABPA group gave the highest specific IgE RAST scores to all three bacteria, whilst the chronic bronchitis and cystic fibrosis groups also gave raised RAST scores with H. influenzae. There was a positive correlation between the patients' Sta. aureus and Str. pneumoniae immediate-type skin reactions and their RAST scores and total serum IgE concentrations, but there was only a low incidence of immediate-type skin test positivity to H. influenzae.