gebhart/patrepeval huggingface dataset:
Oxidation of lovastatin in the solid state and its stabilization with natural antioxidants. (2001)

Oxidative instability of the hydroxy methylglutaryl Co-A reductase inhibitor lovastatin in the solid state and stabilization with natural antioxidants (ascorbic acid, rutin, gallic acid, quercetin and caffeic acid) was investigated. Lovastatin in the solid state and binary mixtures with 10% (w/w), 25% (n/n), 12.5% (n/n) and 6.3% (n/n) of each of the antioxidants were prepared. Oxidation experiments were performed on the scanning calorimeter using dynamic oxygen atmosphere. The amount of non-oxidized lovastatin was determined using HPLC. The results of the experiments have shown that lovastatin is unstable to oxidation under higher temperatures and in the presence of oxygen, and that some antioxidants markedly stabilize the drug. The most significant antioxidative effect was seen with caffeic acid and rutin, followed by gallic acid and quercetin. Ascorbic acid was only moderately effective. The results prove that flavonoids do have significant antioxidative potential. This phenomenon can be used to improve oxidative stability of drugs such as lovastatin which are sensitive to the presence of oxygen.
Building XML statistics for the hidden web (2003)

There have been several techniques proposed for building statistics for static XML data. However, very little work has been done in the area of building XML statistics for data sources that export XML views of data that is stored in relational or other databases. For such data sources, we need statistics that are built in an on-line manner, by observing the XML queries to the data sources and their results. In this paper, we present a technique for building on-line XML statistics by observing the XPath queries issued to a data source and their result sizes. These XPath queries select parts of the virtual XML document representing the XML view of the data at the data source. We convert these XPath queries to a more abstract and generalized form that we call annotated path expressions. We present a technique for storing these annotated path expressions and information about their selectivity for use in estimating the selectivity of future XPath queries. We also present an experimental evaluation of our proposed approach.
A clinically relevant population of leukemic CD34+CD38− cells in acute myeloid leukemia (2012)

Relapse of acute myeloid leukemia (AML) is thought to reflect the failure of current therapies to adequately target leukemia stem cells (LSCs), the rare, resistant cells presumed responsible for maintenance of the leukemia and typically enriched in the CD34(+)CD38(-) cell population. Despite the considerable research on LSCs over the past 2 decades, the clinical significance of these cells remains uncertain. However, if clinically relevant, it is expected that LSCs would be enriched in minimal residual disease and predictive of relapse. CD34(+) subpopulations from AML patients were analyzed by flow cytometry throughout treatment. Sorted cell populations were analyzed by fluorescence in situ hybridization for leukemia-specific cytogenetic abnormalities (when present) and by transplantation into immunodeficient mice to determine self-renewal capacity. Intermediate (int) levels of aldehyde dehydrogenase (ALDH) activity reliably distinguished leukemic CD34(+)CD38(-) cells capable of engrafting immunodeficient mice from residual normal hematopoietic stem cells that exhibited relatively higher ALDH activity. Minimal residual disease detected during complete remission was enriched for the CD34(+)CD38(-)ALDH(int) leukemic cells, and the presence of these cells after therapy highly correlated with subsequent clinical relapse. ALDH activity appears to distinguish normal from leukemic CD34(+)CD38(-) cells and identifies those AML cells associated with relapse.
T-Lymphocyte Clones (1983)

To date, the most successful uses of T-cell clones have been in the demonstration that a single type of cell can perform multiple functions. However, their potential usefulness is enormous, and the study of cell interactions using clonal populations has just begun. The development and study of more cloned populations will surely lead to a clearer analysis of cellular interactions in the immune system. The use of T-cell clones and hybridomas to analyze T-cell receptors and/or factors is well under way, and will continue to be an area of intense investigation. Molecular biologists will undoubtedly make more extensive use of T-cell clones in the future, both as a source of cloning material and as transfection recipients. The most exciting area for development, from a medical point of view, is the potential for use of these cell lines or their products in immunotherapy and in providing a mechanism for specifically modulating the immune response.
Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria (2001)

Intrinsic transcription terminators are functionally defined as sites that bring about termination in vitro with purified RNA polymerase alone. Based on studies in Escherichia coli, intrinsic termination requires a palindromic stretch followed by a trail of T (or U) residues in the coding strand. We have developed a highly efficient algorithm to identify hairpin potential sequences in bacterial genomes in order to build a general model for intrinsic transcription termination. The algorithm was applied to analyze the Mycobacterium tuberculosis genome. We find that hairpin potential sequences are concentrated in the immediate downstream of stop codons. However, most of these structures either lack the U trail entirely or have a mixed A/U trail reflecting an evolutionarily relaxed requirement for the U trail in the mycobacterial genome. Predicted atypical structures were shown to work efficiently as terminators both inside the mycobacterial cell and in vitro with purified RNA polymerase. The results are discussed in light of the kinetic competition models for transcription termination. The algorithm identifies >90% of experimentally tested terminators in bacteria and is an invaluable tool in identifying transcription units in whole genomes.
Gestión integral de los aprovisionamientos (III) (2003)

La importancia que tiene una adecuada gestion de los aprovisionamientos viene dada porque, en primer lugar, es determinante para la cuenta de resultados de la empresa. Esta circunstancia explica el creciente interes que esta alcanzando en la actualidad en cualquier tentativa de reduccion de los costes de produccion en la empresa, bien porque tiene un efecto directo sobre los beneficios o bien porque a traves de una correcta gestion resulta sumamente facil alcanzar una mejora importante en los resultados economicos, sin requerir, por ello, una elevada inversion ni provocar problemas excesivamente complejos con respecto a la mano de obra y a las tecnologias necesarias.
Cloning and Characterization of Two Novel Thyroid Hormone Receptor β Isoforms (2000)

Thyroid hormone (T(3)) activates nuclear receptor transcription factors, encoded by the TRalpha (NR1A1) and TRbeta (NR1A2) genes, to regulate target gene expression. Several TR isoforms exist, and studies of null mice have identified some unique functions for individual TR variants, although considerable redundancy occurs, raising questions about the specificity of T(3) action. Thus, it is not known how diverse T(3) actions are regulated in target tissues that express multiple receptor variants. I have identified two novel TRbeta isoforms that are expressed widely and result from alternative mRNA splicing. TRbeta3 is a 44.6-kDa protein that contains an unique 23-amino-acid N terminus and acts as a functional receptor. TRDeltabeta3 is a 32.8-kDa protein that lacks a DNA binding domain but retains ligand binding activity and is a potent dominant-negative antagonist. The relative concentrations of beta3 and Deltabeta3 mRNAs vary between tissues and with changes in thyroid status, indicating that alternative splicing is tissue specific and T(3) regulated. These data provide novel insights into the mechanisms of T(3) action and define a new level of specificity that may regulate thyroid status in tissue.
Classical mutagenesis in higher plants (2002)

For a long time, mutagenesis research in plants focused on crop improvement and, especially for crop plants, opimised protocols were developed with barley being one of the favourite species. However, the interest in mutagenesis has shifted to basic plant research in the last 20 years, when the power of mutant approaches in combination with molecular techniques to investigate the molecular nature of the genes became fully appreciated
Interleukin 1 receptor antagonist is a member of the interleukin 1 gene family: evolution of a cytokine control mechanism. (1991)

Interleukin 1 receptor antagonist (IL-1ra) is a protein that binds to the IL-1 receptor and blocks the binding of both IL-1 alpha and -beta without inducing a signal of its own. Human IL-1ra has some sequence identity to human IL-1 beta, but the evolutionary relationship between these proteins has been unclear. We show that the genes for human, mouse, and rat IL-1ra are similar to the genes for IL-1 alpha and IL-1 beta in intron-exon organization, indicating that gene duplication events were important in the creation of this gene family. Furthermore, an analysis of sequence comparisons and mutation rates for IL-1 alpha, IL-1 beta, and IL-1ra suggests that the duplication giving rise to the IL-1ra gene was an early event in the evolution of the gene family. Comparisons between the mature sequences for IL-1ra, IL-1 alpha, and IL-1 beta suggest that IL-1ra has a beta-stranded structure like to IL-1 alpha and IL-1 beta, consistent with the three proteins being related. The N-terminal sequences of IL-1ra appear to be derived from a region of the genome different than those of IL-1 alpha and IL-1 beta, thus explaining their different modes of biosynthesis and suggesting an explanation for their different biological activities.
The development and assessment of DNA and oligonucleotide probes for the specific detection of Bacillus anthracis (1993)

Two DNA probes and a number of oligonucleotide probes were designed from the virulence factor genes of Bacillus anthracis. These probes were tested for specificity against 52 B. anthracis strains and 233 Bacillus strains encompassing 23 other species. A rapid slot blotting technique was used for screening the large numbers of isolates involved. All probes tested appeared to be specific for B. anthracis under high stringency conditions. These probes could differentiate between virulent and avirulent strains. The probes were also applied to the detection of B. anthracis in routine environmental and clinical samples. A non-radioactive hybridization and detection system based on digoxigenin-11-dUTP was developed.
A new DNA binding mode for CAP. (1990)

In the absence of cyclic AMP, the Escherichia coli cyclic AMP receptor protein (CAP) binds without detectable sequence specificity to restriction fragments containing lac and crp promoter sequences. Under standard conditions (10 mM Tris, 1 mM EDTA, pH 8.0), our estimates of the equilibrium constant and cooperativity parameter for complex formation are 114,000 +/- 1400 M-1 and 1.3 +/- 0.8, respectively. Thus, this interaction lacks the substantial cooperativity previously reported for CAP binding to genomic DNAs. Using the electrophoresis mobility shift assay, we find that complexes of increasing CAP content differ by a highly uniform mobility decrement. This result is most consistent with a binding mode in which little or no DNA bending occurs. The ability of CAP to distinguish between restriction fragments and genomic DNA, shown by the difference in binding cooperativity, suggests the existence of previously unsuspected DNA sequences or structures that modulate its binding cooperativity.
Disease-specific protein corona sensor arrays may have disease detection capacity (2019)

Protein corona sensor array technology identifies diseases through specific proteomics pattern recognition.
Superconformal Filling of High Aspect Ratio through Glass Vias (TGV) for Interposer Applications Using TNBT and NTBC Additives (2015)

Cu superconformal filling of through glass vias (TGV) of aspect ratios (AR) 6:1 and 10:1 for glass interposer applications is achieved by DC electroplating in the presence of the additives tetranitroblue tetrazolium Cl− (TNBT) and nitroblue tetrazolium Cl− (NTBC) in acidic CuSO4/ Cl− formulations. Filling takes place by the so-called 'butterfly' mechanism that nucleates hemispherical or X-shaped Cu plugs in the centers of TGV's while keeping the thickness on external surfaces low. Holes of AR 6:1 are filled in 3 h at 2.5 mA.cm−2, using a bath composed of 40 ppm TNBT, 80 ppm Cl−, 0.88 M CuSO4, and 0.3 M CH3COOH under stagnant conditions. Increasing [TNBT] to 80 ppm and [Cl−] to 120 ppm in the presence of 0.3 M CH3COOH allows filling of 10:1 AR holes in 12.5 h at 1.0 mA.cm−2 while maintaining thin surface plating. In the case of NTBC, 6:1 holes are filled in 4–5 h at 2.5–4.0 mA.cm−2, and 10:1 holes are filled in 12–13 h at 1.0 to 1.5 mA.cm−2 in a slowly stirred bath containing 0.88 M CuSO4, 80 ppm Cl−, 0.6 M H2SO4, and 45–50 ppm NTBC. Optimization of bath composition is necessary to avoid void-formation in the holes. Effects of composition on overvoltage and Cu surface topography are discussed.
Group transfer polymerization — A critical overview (1993)

Abstract Available evidence on the mechanism of group transfer polymerization is presented. The data are discussed in terms of the possibility that the chain carriers are enolate anions rather than the originally suggested pentacoordinate silicon complexes.
Single Molecule DNA Restriction Analysis in the Light Microscope (2000)

A combination of single molecule fluorescence intensity analysis and optical mapping is developed to identify individual fluorescently labeled DNA molecules on the basis of restriction patterns generated by different enzymes. Fluorescently labeled lambda-phage DNA molecules each bound to a polystyrene microsphere as a handle are held and moved by optical tweezers. The single DNA molecules are stretched by hydrodynamic flow. The restriction endonucleases Apa I, Sma I and EcoR I with one, three and five expected cutting sites on the lambda-phage DNA molecule are used for enzymatic digestion of the DNA molecules. The DNA restrictions are observed after microinjection of the enzyme into the flow towards the DNA molecule in real time (video frequency) on a microscope cover slide. The fluorescence intensity of the DNA fragments is measured and their length in terms of base pairs is calculated. Comparison with the length expected from sequence data reveals a single DNA fragment sensitivity.
Effect of polyoxyethylene sorbate compounds (Tweens) on colonial morphology, growth, and ultrastructure ofMycobacterium paratuberculosis (1990)

Polyoxyethylene sorbate (Tween) compounds were tested to compare their growth stimulation effects on Mycobacterium paratuberculosis. Three low passage and three high passage clinical isolates and ATCC strain 19698 were used. Tween 20, 40, 60, and 80 were tested at concentrations of 0, 0.001, 0.01, 1.0, and 3.0% (w/v) in radiometric broth culture media and in Middlebrook 7H9 agar plates. Scanning and transmission electron microscopy were used to examine cell wall appearance and ultrastructure, respectively. In broth culture, 0.1% (w/v) Tween 60 most dramatically enhanced growth of M. paratuberculosis ATCC strain 19698. The effects of Tween 40 and 80 on growth took a bimodal form, enhancing growth at concentration ranges of 0-0.01% and 0.1-1.0% (w/v) but suppressing growth at concentrations of 0.01-0.1% (w/v). Two of three high passage clinical isolates grew optimally in the presence of 1.0% (w/v) Tween 80, while the remaining high passage isolate and all three low passage isolates grew best in media containing 0.1% (w/v) Tween 80. Colonial morphology of all strains grown on Middlebrook 7H9 agar without Tween 80 was irregular and granular whereas colonies on plate media containing greater than 0.01% (w/v) Tween 80 were entire, smooth, and domed. Scanning electron microscopy also revealed a transition from rough to smooth cell walls with increasing Tween 80 concentration. Transmission electron microscopy showed the presence of low electron dense intracellular vacuoles in Tween 80 grown M. paratuberculosis cells. Thus, Tweens altered colonial morphology, the cell wall surface, and ultrastructure of M. paratuberculosis and stimulated its growth in vitro in a concentration-dependent, and often bimodal, fashion.(ABSTRACT TRUNCATED AT 250 WORDS)
3D Source Designature Using Source-receiver Symmetry in the Shot Tau-px-py Domain (2015)

While sufficient for many deep water datasets, vertical source designature in shallow water environments can lead to unsatisfactory levels of ringing and amplitude striping, particularly on outer streamers where the assumption of a vertical farfield signature is least accurate. In this paper we modify the tau-px-py Radon equations to introduce a 3D directional designature algorithm. Assuming source-receiver propagation symmetry, a 3D source re-signature operation is introduced and solved with an iteratively re-weighted least squares solver. The results of the strategy lead to improved spatial consistency and a reduction in the level of amplitude striping in the output data. Data examples from a real-world dual-level source project with variable-depth streamers from the North Sea are shown.
Three Novel MYB Proteins with One DNA Binding Repeat Mediate Sugar and Hormone Regulation of α-Amylase Gene Expression (2002)

The expression of alpha-amylase genes in cereals is induced by both gibberellin (GA) and sugar starvation. All alpha-amylase genes isolated from cereals contain a TATCCA element or its variants at positions approximately 90 to 150 bp upstream of the transcription start sites. The TATCCA element was shown previously to be an important component of the GA response complex and the sugar response complex of alpha-amylase gene promoters. In the present study, three cDNA clones encoding novel MYB proteins with single DNA binding domains were isolated from a rice suspension cell cDNA library and designated OsMYBS1, OsMYBS2, and OsMYBS3. Gel mobility shift experiments with OsMYBSs showed that they bind specifically to the TATCCA element in vitro. Yeast one-hybrid experiments demonstrated that OsMYBS1 and OsMYBS2 bind to the TATCCA element and transactivate a promoter containing the TATCCA element in vivo. Transient expression assays with barley half-seeds showed that OsMYBS1 and OsMYBS2 transactivate a promoter containing the TATCCA element when sugar is provided, whereas OsMYBS3 represses transcription of the same promoter under sugar starvation. Transient expression assays also showed that these three OsMYBSs cooperate with a GA-regulated transcription factor, HvMYBGa, in the transactivation of a low-pI barley alpha-amylase gene promoter in the absence of GA. Two-hybrid experiments with barley half-seeds showed that OsMYBS1 is able to form a homodimer. The present study demonstrates that differential DNA binding affinity, promoter transactivation ability, dimerization, and interactions with other protein factors determine the biological function of OsMYBSs. This study also suggests that common transcription factors are involved in the sugar and hormonal regulation of alpha-amylase gene expression in cereals.
The E2 molecule (CD99) specifically triggers homotypic aggregation of CD4+ CD8+ thymocytes. (1995)

We have previously described E2 as a 32-kDa transmembrane glycoprotein displaying an isomorphism, as two epitopes (defined by mAbs O662 and L129) are widely distributed on T cells whereas two epitopes are restricted to T cell subsets (defined by mAbs D44 and 12E7). E2, the MIC-2 gene product, is involved in T cell adhesion because anti-E2 mAbs against pan T epitopes block spontaneous T cell rosettes. Pan T E2 mAbs are also able to induce exposure of the phosphatidylserine at the thymocyte surface but not at the surface of mature T lymphocytes, an event most likely linked to adhesion phenomena. We now show here that the anti-E2 mAbs (0662 and L129) that block rosettes and induce phosphatidylserine exposure at the thymocyte surface, and not those reacting with epitopes not involved in adhesion, also trigger aggregation of certain immature T cell lines and no other cell lines tested. Among the normal cells tested, anti-E2 mAbs exclusively induce homotypic aggregation of CD4+ CD8+ human thymocytes. This phenomenon is temperature, energy, and Mg++ dependent, and requires an intact cytoskeleton. These adhesion properties are rather characteristic of integrins. Nevertheless, mAb against beta 1, beta 2, and beta 3 integrin chains, as well as those against alpha-chains known to be present on thymocytes, are unable to block corticothymocyte aggregation. We conclude that E2 triggers on corticothymocytes and no other T cells a homotypic adhesion pathway most likely mediated by an uncharacterized integrin.
cDNA Cloning and Functional Analysis of the p97 Subunit of the 26S Proteasome, a Polypeptide Identical to the Type‐1 Tumor‐Necrosis‐Factor‐Receptor‐Associated Protein‐2/55.11 (1996)

Molecular cloning of cDNA for a new regulatory subunit, designated p97, of the human 26S proteasome showed that the polypeptide consists of 908 amino acid residues with a calculated molecular mass of 100184 Da and an isoelectric point of 4.94. Computer analysis showed that p97 is very similar to type-1 tumor-necrosis-factor (TNF)-receptor-associated protein (TRAP)-2 and 55.11, both of which were identified recently as binding proteins of the cytoplasmic domain of type-1 TNF receptor by yeast two-hybrid screening. This finding suggests that the 26S proteasome might serve as a mediator molecule in the TNF signaling pathway in cells. Computer-assisted similarity analysis also revealed the high sequence similarity of p97 with a yeast protein whose function is yet unknown, the gene for which is here termed NAS1 (non-ATPase subunit 1). Disruption of NAS1 resulted in several phenotypes, including lethality and temperature-sensitive growth, depending on the genetic background of the cells used. The human p97 cDNA suppressed the growth defect of nas1 disruptant cells, when expressed from single-copy or multi-copy vectors, indicating that p97 is functionally equivalent to yeast Nas1p. Culturing of the temperature-sensitive nas1 cells at the restrictive temperature promoted the accumulation polyubiquitinated cellular proteins, implying that the 26S proteasome requires a functional Nas1p subunit for ubiquitin-dependent proteolysis. These results indicate that p97/Nas1p plays an important regulatory role in the function of the 26S proteasome.