gebhart/patrepeval huggingface dataset:
Immobilization of polydiacetylene onto silica microbeads for colorimetric detection (2005)

Colorimetric polydiacetylene (PDA) undergoes a rapid blue-to-red color transition in response to a variety of environmental perturbations. It has been immobilized on planar substrates to serve as sensing devices for many biological applications. On the other hand, microbeads have been recognized to be a viable alternative to planar substrates for a variety of bioassays and have demonstrated a number of advantages over their planar counterpart. However, it remains a tremendous challenge to immobilize PDA on microbeads without changing its colorimetric properties because PDA is highly sensitive to the environment. In this work, PDA was immobilized onto silica microbeads using 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and CaCl2 as incorporation and pretreatment agents. It was found that the amount of PDA immobilized on silica microbeads increased with a decrease of the PDA/DMPC molar ratio and an increase of CaCl2 concentration. PDA retained its colorimetric properties after immobilization on the microbeads and underwent a blue-to-red color change upon exposure to phospholipase. These PDA/silica microbeads can be readily used for bead-based assay of biomolecules such as proteins, peptides, and many more.
Emended Description of Paenibacillus amylolyticus and Description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov. (1997)

The taxonomic position of unidentified group 6 of Bacillus circulans as described by Nakamura and Swezey (L.K. Nakamura and J. Swezey, Int. J. Syst. Bacteriol. 33:46-52, 1983) was determined, and the taxonomy of Paenibacillus amylolyticus was reexamined. The results of PCR amplification of a 16S rRNA gene fragment with a specific primer and comparative analysis of 16S rRNA gene sequences warranted placing the two taxa in the genus Paenibacillus. The levels of DNA reassociation among the strains revealed four groups (designated groups I, II, III, and 6), each with a high level of intragroup relatedness (> 72%). Clustering based on phenotypic characteristics correlated well with DNA relatedness grouping. P. amylolyticus strains were scattered in groups I, II, and III. Strains labeled the type strain of P. amylolyticus from different culture collections appeared in groups I and III. Strains found in group I were identified as P. amylolyticus sensu stricto, and the one strain found in group III was identified as Paenibacillus lautus. Group 6 encompassed strains formerly assigned to B. circulans group 6, and group II contained other strains identified as P. amylolyticus. Groups 6 and II were phenotypically and genetically distinct taxa that were distinguishable from the previously described species. These findings showed that groups 6 and II were new species, for which we propose the names Paenibacillus illinoisensis and Paenibacillus chibensis, respectively.
Ensembl 2014 (2013)

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
Vaccines for control of fertility and hormone‐dependent cancers (1997)

This article traces and reviews the development of vaccines against two reproductive hormones, luteinizing hormone release hormone (LHRH) and human chorionic gonadotrophin (hCG). The heterospecies dimer (HSD)-dehydrogenase hCG vaccine is the first to have completed phase II clinical trials providing evidence for the prevention of pregnancy in humans by immunization with this vaccine. The vaccine acts without blocking ovulation or disturbance of menstrual bleeding. Its effect is fully reversible and fertility is regained with decline of the antibodies. The antibody response in humans is directed against immunodominant epitopes located in the core part of beta hCG, distinct from the C-terminal region. However, problems arising from carrier-conjugated vaccines against 'self' hormones such as carrier-induced immuno-suppression on repeated immunization are evoked and solutions discussed. The LHRH vaccine, a model semi-synthetic vaccine, can be used in both sexes and has applications in regulation of fertility of animals. It has therapeutic applications as a cost-effective approach in clinical conditions where LHRH agonists and antagonists have therapeutic action. The vaccine has undergone phase I and II clinical trials in advanced-stage carcinoma of prostate patients with encouraging results.
Immunohistochemical study of N-epsilon-carboxymethyl lysine (CML) in human brain: relation to vascular dementia (2007)

CML staining in cortical neurons and cerebral vessels is related to the severity of cognitive impairment in people with cerebrovascular disease and only minimal Alzheimer pathology. These findings support the possibility that cerebral accumulation of AGEs may contribute to dementia in people with cerebrovascular disease.
Recycling immobilized antibodies. (1981)

Journal Article Recycling immobilized antibodies. Get access C R van den Akker, C R van den Akker Search for other works by this author on: Oxford Academic Google Scholar A P Schellekens A P Schellekens Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 27, Issue 11, 1 November 1981, Pages 1954–1955, https://doi.org/10.1093/clinchem/27.11.1954a Published: 01 November 1981
Genetic and epigenetic silencing of SCARA5 may contribute to human hepatocellular carcinoma by activating FAK signaling (2009)

The epigenetic silencing of tumor suppressor genes is a crucial event during carcinogenesis and metastasis. Here, in a human genome-wide survey, we identified scavenger receptor class A, member 5 (SCARA5) as a candidate tumor suppressor gene located on chromosome 8p. We found that SCARA5 expression was frequently downregulated as a result of promoter hypermethylation and allelic imbalance and was associated with vascular invasion in human hepatocellular carcinoma (HCC). Furthermore, SCARA5 knockdown via RNAi markedly enhanced HCC cell growth in vitro, colony formation in soft agar, and invasiveness, tumorigenicity, and lung metastasis in vivo. By contrast, SCARA5 overexpression suppressed these malignant behaviors. Interestingly, SCARA5 was found to physically associate with focal adhesion kinase (FAK) and inhibit the tyrosine phosphorylation cascade of the FAK-Src-Cas signaling pathway. Conversely, silencing SCARA5 stimulated the signaling pathway via increased phosphorylation of certain tyrosine residues of FAK, Src, and p130Cas; it was also associated with activation of MMP9, a tumor metastasis-associated enzyme. Taken together, these data suggest that the plasma membrane protein SCARA5 can contribute to HCC tumorigenesis and metastasis via activation of the FAK signaling pathway.
A tandem duplication causes the Kn1-O allele of Knotted, a dominant morphological mutant of maize. (1990)

Molecular and genetic techniques are used to define Kn1-O, a mutation which interferes with the normal differentiation of vascular tissue in leaves. Sequences associated with a previously cloned allele, Kn1-2F11, were used as hybridization probes in a Southern analysis of Kn1-O. By this analysis, Kn1-O lacks the Ds2 transposable element that causes Kn1-2F11 but instead is associated with a sequence duplication. Sequence and restriction analysis of genomic clones show that the duplication consists of a tandem array of two 17-kb repeats. Analysis of Kn1-O derivatives indicates that the duplication itself conditions the mutant phenotype; a severely knotted line, Kn1-Ox, has gained a repeat unit to form a triplication, whereas normal derivatives have either lost a repeat unit or sustained insertions that disrupt the tandem duplication. These insertions map near the central junction of the tandem duplication, suggesting that the mutant phenotype results from the novel juxtaposition of sequences. We discuss models that relate the tandem duplication of sequences to altered gene expression.
Inhibition of human scleral fibroblast proliferation with heparin. (1988)

Proliferation of fibroblasts is a serious problem in ocular trauma and surgical wound healing. Depending on the location of the injury, the growth of fibroblasts can lead to different problems. In glaucoma filtering surgery, fibroblast proliferation may contribute to scar tissue formation and premature wound closure. Fibroblastic growth in proliferative vitreoretinopathy may lead to the formation of preretinal membranes, which can contract, causing retinal detachment. In an effort to find a more effective method of inhibiting ocular fibroblast proliferation, we have investigated the effect of heparin, a sulfated polysaccharide, on the proliferation of fibroblasts obtained from the sclera of donor eyes. Heparin inhibits the incorporation of 3H-thymidine in a dose-dependent manner in the presence of fetal bovine serum (FBS). This inhibition is partially reversed by endothelial cell growth factor (ECGF). The heparin antagonist protamine sulfate causes a reversal of heparin inhibition and, in some instances, a significant increase in 3H-thymidine incorporation compared to serum controls. Heparin was equally effective in inhibiting cell proliferation in control and heparin-protamine sulfate-pretreated medium. These results were apparently unrelated to a direct toxic effect on cells, as a Trypan Blue exclusion assay showed no significant difference in viability when heparin treated cells were compared to control cells. Direct cell counts showed that heparin was effective in inhibiting cell proliferation over a long time period, but only if it was reinstilled every 2 days. Heparin treatment shows promise as a method for controlling fibroblast proliferation in the eye.
Behavior Monitoring in Self-Healing Service-Oriented Systems (2010)

Web services and service-oriented architecture (SOA) have become the de facto standard for designing distributed and loosely coupled applications. Many service-based applications demand for a mix of interactions between humans and Software-Based Services (SBS). An example is a process model comprising SBS and services provided by human actors. Such applications are difficult to manage due to changing interaction patterns, behavior, and faults resulting from varying conditions in the environment. To address these complexities, we introduce a self-healing approach enabling recovery mechanisms to avoid degraded or stalled systems. The presented work extends the notion of self-healing by considering a mixture of human and service interactions observing their behavior patterns. We present the design and architecture of the VieCure framework supporting fundamental principles for autonomic self-healing strategies. We validate our self-healing approach through simulations.
Production of Amyloid β Protein from Normal Amyloid β‐Protein Precursor (βAPP) and the Mutated βAPPS Linked to Familial Alzheimer's Diseasea (1993)

The approximately 4 kD (39-43 amino acid) polypeptide (amyloid beta protein, A beta) deposited as amyloid in Alzheimer's disease (AD) is derived from a set of 695-770 residue precursor proteins collectively referred to as the amyloid beta-protein precursor (beta APP). Using immunoblotting techniques, metabolic labeling, and sequencing we have analyzed beta APP derivatives in medium conditioned by: (1) human mononuclear leukemic (K562) cells expressing a model beta AP-bearing carboxyl-terminal beta APP derivative (2) human neuroblastoma (M17) cells transfected with constructs expressing full length beta APP and (3) M17 cells expressing only endogenous beta APP. In each case, we observed the release of a approximately 4 kD beta APP derivative essentially identical to the A beta found in AD amyloid. A similar, if not identical, beta APP fragment was readily detected in CSF from both Alzheimer's disease patients and controls. These observations indicate that the A beta is produced and released by normal processing of the beta APP. To determine if the production of A beta or A beta-tearing COOH-terminal beta APP derivatives is altered in cells expressing the mutant beta APPs linked to familial AD, we have compared M17 cells expressing wild type beta APP with those expressing mutant beta APPs (beta APP delta I or beta APP delta NL). After continuous metabolic labeling for 8 hours, cells expressing the beta APP delta NL mutant showed a 5-fold increase in the relative amount of an approximately 11.4 kD A beta-bearing carboxyl-terminal beta APP derivative, and they released 6-fold more 4 kD A beta into the medium. These observations provide strong evidence that: (1) the pathway producing A beta in cultured cells is highly relevant to AD and (2) the beta APP delta NL mutant causes AD because its processing is altered in a way that releases increased amounts of A beta.
Fondaparinux-related thrombocytopenia in a previous low-molecular-weight heparin (LMWH)-induced heparin-induced thrombocytopenia (HIT) (2008)

Fondaparinux-related thrombocytopenia in a previous low-molecular-weight heparin (LMWH)- induced heparin-induced thrombocytopenia (HIT) -
Detecting ventricular fibrillation (1995)

The short time Fourier transform (STFT), smoothed pseudo Wigner Ville distribution (SPWVD), and cone-shaped kernel distribution (CKD) have been used to compare the time-frequency distribution of normal sinus rhythm, ventricular tachycardia, ventricular flutter, and ventricular fibrillation signals. This work is a pilot study to illustrate that the CKD and SPWVD have better time and frequency resolution than the STFT. It demonstrates that accurate methods of computing the time-frequency domain should be found for ECG signals. Only then should future work be done to design discriminatory features and classifiers for arrhythmias.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid assay for mycobacterial growth and antibiotic susceptibility using gel microdrop encapsulation (1995)

Effective control of tuberculosis transmission in vulnerable population groups is dependent on rapid identification of the infectious agent and its drug susceptibility. However, the slow growth rate of mycobacteria has undermined the ability to quickly identify antimicrobial resistance. These studies describe a mycobacterial growth assay based on microencapsulation technology used in conjunction with flow cytometric analysis. Mycobacteria were encapsulated in agarose gel microdrops approximately 25 microns in diameter, and colony growth was monitored by using flow cytometry to evaluate the intensity of auramine staining after culture for various times at 37 degrees C. By this method, colony growth of Mycobacterium bovis and M. smegmatis could be quantified within 1 to 3 days after encapsulation. Inhibition of growth by rifampin and isoniazid was also evaluated in this time period, and the presence of an isoniazid-resistant subpopulation representing 3% of the total microorganisms could be detected. This use of encapsulation and flow cytometry has the potential to facilitate rapid and automated evaluation of inhibition of growth by antimicrobial agents and shorten the time frame for analysis of clinical specimens.
Hormonal regulation of caveolae internalization. (1995)

Caveolae undergo a cyclic transition from a flat segment of membrane to a vesicle that then returns to the cell surface. Here we present evidence that this cycle depends on a population of protein kinase C-alpha (PKC-alpha) molecules that reside in the caveolae membrane where they phosphorylate a 90-kD protein. This cycle can be interrupted by treatment of the cells with phorbol-12,13-dibutyrate or agents that raise the concentration of diacylglycerol in the cell. Each of these conditions displaces PKC-alpha from caveolae, inhibits the phosphorylation of the 90-kD protein, and prevents internalization. Caveolae also contain a protein phosphatase that dephosphorylates the 90-kD once PKC-alpha is gone. A similar dissociation of PKC-alpha from caveolae and inhibition of invagination was observed when cells were treated with histamine. This effect was blocked by pyrilamine but not cimetidine, indicating the involvement of histamine H1 receptors. These findings suggest that the caveolae internalization cycle is hormonally regulated.
Hypolipemic action of glucagon in experimental endogenous lipemia in the rat (1973)

The effect of glucagon on serum lipids and very low density lipoproteins (VLDL) has been examined in the eulipemic and the hyperlipemic rat. An inhibition of amino acid incorporation into hepatic lipoprotein apoprotein was observed, with an associated decrease in circulating VLDL apoprotein, decreased serum triglyceride concentration, and a loss of the pre-beta band as judged by serum lipoprotein electrophoresis. The data suggest that an important action of this hormone is to decrease the synthesis of the protein moiety of the VLDL; this may contribute to the hypolipemic action of glucagon by introducing a limitation in hepatic lipoprotein production.
Protein Phosphorylation in Amyloplasts Regulates Starch Branching Enzyme Activity and Protein–Protein Interactions (2004)

Protein phosphorylation in amyloplasts and chloroplasts of Triticum aestivum (wheat) was investigated after the incubation of intact plastids with gamma-(32)P-ATP. Among the soluble phosphoproteins detected in plastids, three forms of starch branching enzyme (SBE) were phosphorylated in amyloplasts (SBEI, SBEIIa, and SBEIIb), and both forms of SBE in chloroplasts (SBEI and SBEIIa) were shown to be phosphorylated after sequencing of the immunoprecipitated (32)P-labeled phosphoproteins using quadrupole-orthogonal acceleration time of flight mass spectrometry. Phosphoamino acid analysis of the phosphorylated SBE forms indicated that the proteins are all phosphorylated on Ser residues. Analysis of starch granule-associated phosphoproteins after incubation of intact amyloplasts with gamma-(32)P-ATP indicated that the granule-associated forms of SBEII and two granule-associated forms of starch synthase (SS) are phosphorylated, including SSIIa. Measurement of SBE activity in amyloplasts and chloroplasts showed that phosphorylation activated SBEIIa (and SBEIIb in amyloplasts), whereas dephosphorylation using alkaline phosphatase reduced the catalytic activity of both enzymes. Phosphorylation and dephosphorylation had no effect on the measurable activity of SBEI in amyloplasts and chloroplasts, and the activities of both granule-bound forms of SBEII in amyloplasts were unaffected by dephosphorylation. Immunoprecipitation experiments using peptide-specific anti-SBE antibodies showed that SBEIIb and starch phosphorylase each coimmunoprecipitated with SBEI in a phosphorylation-dependent manner, suggesting that these enzymes may form protein complexes within the amyloplast in vivo. Conversely, dephosphorylation of immunoprecipitated protein complex led to its disassembly. This article reports direct evidence that enzymes of starch metabolism (amylopectin synthesis) are regulated by protein phosphorylation and indicate a wider role for protein phosphorylation and protein-protein interactions in the control of starch anabolism and catabolism.
Development of a human interleukin-6 receptor antagonist. (1994)

Neutralizing monoclonal antibodies specific for human interleukin-6 (IL-6) bind two distinct sites on the IL-6 protein (sites I and II). Their interference with IL-6 receptor binding suggested that site I is a receptor-binding site of IL-6, whereas site II is important for signal transduction. Mutagenesis of site II could therefore result in the isolation of IL-6 receptor antagonists. To test this hypothesis, a panel of IL-6 mutant proteins was constructed that did not bind to a site II-specific monoclonal antibody. One such site II mutant protein (with double substitution of Gln-160 with Glu and Thr-163 with Pro) was found to be an antagonist of human IL-6. It was inactive on human CESS cells, weakly active on human HepG2 cells, but active on mouse B9 cells. It could specifically antagonize the activity of wild-type IL-6 on CESS and HepG2 cells. The binding affinity of this variant for the 80-kDa IL-6 receptor was similar to that of wild-type IL-6. High affinity binding to CESS cells, however, was abolished, suggesting that the mutant protein is inactive because the complex of the 80-kDa IL-6 receptor and the mutant protein cannot associate with the signal transducer gp130. The human IL-6 antagonist protein may be potentially useful as a therapeutic agent.
A Multilocus Genotyping Assay for Cardiovascular Disease (1998)

In our efforts to develop diagnostic tests for complex multifactorial disorders, and to assist the research community in evaluating genetic markers for predisposition to cardiovascular disease, we have developed a prototype assay to genotype up to 35 variable sites among 15 genes. The candidate markers in this panel were selected from biological pathways likely to contribute to the development and progression of cardiovascular disease. Each sample is amplified in two multiplex polymerase chain reactions that are then hybridized to an array of immobilized oligonucleotide probes. The assay has been applied to a population-based cohort representing 238 families; allele frequencies observed among 455 unrelated parents from this cohort agree with available literature values. Data from a cohort of 142 lipid-clinic patients were used to explore locus associations with arterial occlusion, as measured by quantitative angiography. This prototype assay provides a research tool for studies to assess the association of multiple markers with disease, and for clinical studies to evaluate marker association with patient responsiveness to experimental therapies.
Effects of ectopic overexpression of p21(WAF1/CIP1) on aneuploidy and the malignant phenotype of human brain tumor cells. (1996)

p21WAF1/CIP1 is a downstream effector of the p53 tumor suppressor gene and a universal cyclin-dependent kinase (CDK) inhibitor. To determine the ability of p21WAF1/CIP1 to function as a tumor suppressor, we constructed a replication-defective adenovirus vector containing p21WAF1/CIP1 (Adp21WAF1/CIP1) to effect ectopic overexpression in a p53-defective human astrocytoma cell line, U-373MG. We observed a marked decrease in CDC2 and CDK2 kinase activity associated with a corresponding decrease in the amount of CDC2 but not CDK2 protein; a decreased growth potential of Adp21WAF1/CIP1-infected cells demonstrated by diminished [3H]thymidine incorporation, increased cell doubling time and G1-arrested cell cycle; an association between Adp21WAF1/CIP1-infected cells and inhibition of aneuploid cell accumulation; and an alteration of the malignant phenotype of cells was evidenced by the loss of anchorage-independent growth in soft agar and the failure to induce tumorigenesis in both peripheral and intracerebral xenograft models, including the prevention of tumor formation Adp21WAF1/CIP1 infection 2 days post tumor cell implantation. Adp21WAF1/CIP1. Adp21WAF1/CIP1 appears to be a strong candidate for gene therapy studies based on these studies indicating that Adp21WAF1/CIP1 inhibits proliferation, tumorigenicity and aneuploidy in human brain tumor cells.
Smart Capsules (2002)

This chapter contains sections titled: Preparation and Structure General Aspects Physics and Chemistry of Core Removal Modification of Walls Properties and Utilization Permeability Control Stability and Mechanical Properties Chemistry and Physics in Nanovolumes