gebhart/patrepeval huggingface dataset:
Functional Analysis of Conserved Residues in the Putative “Finger” Domain of Telomerase Reverse Transcriptase (2001)

Telomerase is a ribonucleoprotein reverse transcriptase (RT) responsible for the maintenance of one strand of telomere terminal repeats. The catalytic protein subunit of telomerase, known generically as telomerase reverse transcriptase (TERT), exhibits significant homology to RTs encoded by retroviruses and retroelements. The polymerization mechanisms of telomerase may therefore be similar to those of the "conventional" RTs. In this study, we explored the extent of mechanistic conservation by analyzing mutations of conserved residues within the putative "finger" domain of TERT. Previous analysis has implicated this domain of retroviral RTs in nucleotide and RNA binding and in processivity control. Our results demonstrate that residues conserved between TERT and human immunodeficiency virus-1 RT are more likely than TERT-specific residues to be required for enzyme activity. In addition, residues presumed to make direct contact with either the RNA or nucleotide substrate appear to be functionally more important. Furthermore, distinct biochemical defects can be observed for alterations in the putative RNA- and nucleotide-binding TERT residues in a manner that can be rationalized by their postulated mechanisms of action. This study thus supports a high degree of mechanistic conservation between telomerase and retroviral RTs and underscores the roles of distinct aspects of telomerase biochemistry in telomere length maintenance.
Preparation and some properties of water-insoluble, whey protein-based microcapsules (2000)

A method, consisting of double emulsification and chemical cross-linking with glutaraldehyde was used to prepare whey protein-based microcapsules containing anhydrous milk fat as a model core. Effects of emulsion composition and pH on core retention, microstructure, and water-solubility of microcapsules were investigated. In all cases, core retention higher than 88% was accomplished and, in most cases, was not significantly affected by emulsion composition. In all cases, spherical microcapsules, 10-80 microm in diameter, were obtained. Outer topography and the inner structure of microcapsules were significantly affected by the pH of the emulsion. In all cases, microcapsules were practically water-insoluble. Microcapsules similar to the developed prototype may be suitable for controlled core release in application fields where chemical cross-linking is acceptable.
Adhesion properties of mutants of Staphylococcus aureus defective in fibronectin‐binding proteins and studies on the expression of fnb genes (1995)

Staphylococcus aureus 8325-4 has the potential to express two distinct cell wall-associated fibronectin-binding proteins called FnBPA and FnBPB. In order to test if both proteins are expressed in S. aureus and if both are required for promoting bacterial adhesion to fibronectin-coated surfaces, insertion mutations were isolated in each gene. A DNA fragment encoding tetracycline resistance was inserted into fnbA and a fragment encoding erythromycin resistance was inserted into fnbB. A double fnbAfnbB mutant was also constructed. The fnbA and fnbB single mutants showed no significant reduction in their adhesion to polymethylmethacrylate coverslips that had been coated in vitro with fibronectin. However, the double mutant was completely defective in adhesion. Monospecific antibodies directed against the non-conserved N-terminal regions of both proteins confirmed the lack of expression of FnBPs in the mutant strains. Wild-type fnbA and fnbB genes cloned seperately on a multicopy plasmid were each able to restore fully the adhesion-defective phenotype of the 8325-4 fnbAfnbB mutant. This demonstrates that both fnb genes are expressed in S. aureus and that both contribute to the ability of strain 8325-4 to adhere to fibronectin-coated surfaces. The double mutant was also defective in adhesion to coverslips that had been removed from tissue cages implanted subcutaneously in guinea-pigs, which suggests that fibronectin is important in promoting attachment of S. aureus to biomaterial in vivo.
Pseudomonas Aeruginosa Biofilms in Cystic fibrosis (2010)

The persistence of chronic Pseudomonas aeruginosa lung infections in cystic fibrosis (CF) patients is due to biofilm-growing mucoid (alginate-producing) strains. A biofilm is a structured consortium of bacteria, embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA. In CF lungs, the polysaccharide alginate is the major part of the P. aeruginosa biofilm matrix. Bacterial biofilms cause chronic infections because they show increased tolerance to antibiotics and resist phagocytosis, as well as other components of the innate and the adaptive immune system. As a consequence, a pronounced antibody response develops, leading to immune complex-mediated chronic inflammation, dominated by polymorphonuclear leukocytes. The chronic inflammation is the major cause of the lung tissue damage in CF. Biofilm growth in CF lungs is associated with an increased frequency of mutations, slow growth and adaptation of the bacteria to the conditions in the lungs, and to antibiotic therapy. Low bacterial metabolic activity and increase of doubling times of the bacterial cells in CF lungs are responsible for some of the tolerance to antibiotics. Conventional resistance mechanisms, such as chromosomal β-lactamase, upregulated efflux pumps, and mutations of antibiotic target molecules in the bacteria, also contribute to the survival of P. aeruginosa biofilms. Biofilms can be prevented by early aggressive antibiotic prophylaxis or therapy, and they can be treated by chronic suppressive therapy.
Severe 5-Fluorouracil Toxicity in a Patient with Decreased Dihydropyrimidine Dehydrogenase Activity (1993)

(1993). Severe 5-Fluorouracil Toxicity in a Patient with Decreased Dihydropyrimidine Dehydrogenase Activity. Cancer Investigation: Vol. 11, No. 2, pp. 239-240.
An identification approach to nonlinear state space model for industrial multivariable model predictive control (1998)

Extending application of model predictive control (MPC) technology has encountered new challenges from the chemical and polymer industries where the processes show strong nonlinear dynamic behaviour and necessitate nonlinear dynamic models for MPC. This paper presents an approach to identify nonlinear state space models from plant data. This approach uses a direct identification scheme and integrates several technologies including a hybrid linear-neural network model, principal component analysis and partial least squares modeling algorithms and online adaptation to address the robustness of the identification and the resultant model. Two examples are presented to demonstrate the features of the approach.
Histopathologic Alterations in the Decidua in Human Spontaneous Abortion: Loss of Cells With Large Cytoplasmic Granules (1987)

The histopathology of decidua obtained from the placental bed was evaluated by phloxine-tartrazine staining, which allows clear definition of cells with cytoplasmic granules. Mononuclear cells with large granules were seen in biopsy specimens taken from women at 8-31 weeks of normal pregnancy. In contrast, cells with large granules were missing in sections taken from the decidua of five women who were aborting or were destined to abort. Since the presence of suppressor cell activity in murine decidua correlates with the success of pregnancy and since this suppression is associated with small lymphocytes with cytoplasmic granules, the observations made using human placental bed biopsy material suggest that a possible suppressor cell deficiency might occur in the early stages of spontaneous abortion in human females.
Schlieren visualization of ultrasonic standing waves in mm-sized chambers for ultrasonic particle manipulation (2013)

The results show the great potential of schlieren visualization to investigate ultrasonic particle manipulation devices. Visualized are pressure fields, acoustic streaming, temperature effects and effects caused by fluid volumes of different density.
Cell Adhesion Mediated Drug Resistance (CAM-DR): Role of Integrins and Resistance to Apoptosis in Human Myeloma Cell Lines (1999)

Integrin-mediated adhesion influences cell survival and may prevent programmed cell death. Little is known about how drug-sensitive tumor cell lines survive initial exposures to cytotoxic drugs and eventually select for drug-resistant populations. Factors that allow for cell survival following acute cytotoxic drug exposure may differ from drug resistance mechanisms selected for by chronic drug exposure. We show here that drug-sensitive 8226 human myeloma cells, demonstrated to express both VLA-4 (alpha4beta1) and VLA-5 (alpha5beta1) integrin fibronectin (FN) receptors, are relatively resistant to the apoptotic effects of doxorubicin and melphalan when pre-adhered to FN and compared with cells grown in suspension. This cell adhesion mediated drug resistance, or CAM-DR, was not due to reduced drug accumulation or upregulation of anti-apoptotic Bcl-2 family members. As determined by flow cytometry, myeloma cell lines selected for drug resistance, with either doxorubicin or melphalan, overexpress VLA-4. Functional assays revealed a significant increase in alpha4-mediated cell adhesion in both drug-resistant variants compared with the drug-sensitive parent line. When removed from selection pressure, drug-resistant cell lines reverted to a drug sensitive and alpha4-low phenotype. Whether VLA-4-mediated FN adhesion offers a survival advantage over VLA-5-mediated adhesion remains to be determined. In conclusion, we have demonstrated that FN-mediated adhesion confers a survival advantage for myeloma cells acutely exposed to cytotoxic drugs by inhibiting drug-induced apoptosis. This finding may explain how some cells survive initial drug exposure and eventually express classical mechanisms of drug resistance such as MDR1 overexpression.
Capturing the World (2010)

Four articles provide different approaches for creating a digital representation of the world. Leading experts from TU Graz, Google, the University of Washington, TU Darmstadt, and Fraunhofer IGD explain what is possible today.
[Expression of telomerase activity in human lung cancer.]. (2000)

Telomerase activity may be useful both as a diagnostic marker to detect the existence of lung cancer and as a potential of high risk for lymph node metastasis.
Autophosphorylation promotes complex formation of recombinant hepatocyte growth factor receptor with cytoplasmic effectors containing SH2 domains. (1992)

Hepatocyte growth factor (HGF), also known as scatter factor (SF), is a polypeptide which induces motility and/or mitogenesis in epithelial cells. The receptor for HGF/SF, p190MET, is a two-chain transmembrane tyrosine kinase encoded by the MET proto-oncogene. To identify the cytoplasmic effectors involved in signal transduction we have produced the human HGF/SF receptor in insect cells (Sf9) by means of a recombinant baculovirus. Two 170-kDa forms of the receptor were synthesized in Sf9 cells: the uncleaved single-chain precursor (which is by far the more abundant) and the proteolytically processed two-chain molecule. Both receptor species are phosphorylated on tyrosine in vivo and are active kinases in vitro. The recombinant receptor binds and phosphorylates in vitro four known cytoplasmic transducers containing src homology region 2 (SH2) domains: the 85-kDa subunit of phosphatidylinositol 3-kinase (Pl 3-kinase), rasGAP, phospholipase-C gamma (PLC-gamma), and p59Fyn, a tyrosine kinase of the src family. In all cases the association is strictly dependent on tyrosine phosphorylation of the receptor, indicating that it occurs via specific interaction with the SH2 domains. These results show that the HGF/SF receptor has the sequence requirements for binding a spectrum of cytoplasmic transducers whose different combinations in target cells may result in the observed pleiotropic biological response.
DNA microsatellite instability in hyperplastic polyps, serrated adenomas, and mixed polyps: a mild mutator pathway for colorectal cancer? (1999)

The findings support the view that hyperplastic polyps may be fundamentally neoplastic rather than hyperplastic. A proportion of hyperplastic polyps may serve as a precursor of a subset (10%) of colorectal cancers showing the MSI-L phenotype, albeit through the intermediate step of serrated dysplasia. This represents a novel and distinct morphogenetic pathway for colorectal cancer.
Pretreatment with Interferon-a2a Modulates Perioperative Immunodysfunction in Patients with Renal Cell Carcinoma (2008)

Perioperative immunodysfunction can be modulated by preoperative administration of IFN- alpha2a. IFN-alpha2a decreased the level of VEGF and CD4+CD25+ regulatory T-cells implicating a potential combination with tyrosine kinase inhibitors and vaccines.
Extensive deposits of complement C3d and C5b-9 in the choriocapillaris of eyes of patients with diabetic retinopathy. (2002)

The presence of C3d, C5b-9, and vitronectin indicates that complement activation occurs to completion, possibly through the alternative pathway in the choriocapillaris in eyes affected by diabetic retinopathy. Complement activation at this site may evoke a spectrum of pathologic sequelae that could contribute to ocular tissue disease and visual impairment.
An Open-Label Study of Levetiracetam for the Treatment of Social Anxiety Disorder (2004)

This pilot study supports the safety and potential efficacy of a novel agent, levetiracetam, for the treatment of social anxiety disorder. Larger controlled trials are warranted to confirm these results.
Galvanic Replacement Reactions in Metal Oxide Nanocrystals (2013)

Galvanic replacement reactions provide a simple and versatile route for producing hollow nanostructures with controllable pore structures and compositions. However, these reactions have previously been limited to the chemical transformation of metallic nanostructures. We demonstrated galvanic replacement reactions in metal oxide nanocrystals as well. When manganese oxide (Mn3O4) nanocrystals were reacted with iron(II) perchlorate, hollow box-shaped nanocrystals of Mn3O4/γ-Fe2O3 ("nanoboxes") were produced. These nanoboxes ultimately transformed into hollow cagelike nanocrystals of γ-Fe2O3 ("nanocages"). Because of their nonequilibrium compositions and hollow structures, these nanoboxes and nanocages exhibited good performance as anode materials for lithium ion batteries. The generality of this approach was demonstrated with other metal pairs, including Co3O4/SnO2 and Mn3O4/SnO2.
Differential regulation of E2F transactivation by cyclin/cdk2 complexes. (1994)

The mammalian transcription factor E2F plays a critical role in the expression of genes required for cellular proliferation. To understand how E2F is regulated, we have developed a reconstituted in vitro transcription assay. Using this E2F-responsive assay, we can demonstrate that E2F-mediated transcription can be directly repressed by the tumor suppressor protein pRB. This inhibition is abolished by phosphorylation of pRB with either cyclin A/cdk2 or cyclin E/cdk2. However, these cyclin/kinase complexes exhibit differences in the ability to phosphorylate E2F. Only cyclin A/cdk2 can phosphorylate E2F effectively, and this phosphorylation abolishes its ability to bind DNA and mediate trans-activation. Thus, this in vitro transcriptional assay allows activation and inactivation of E2F transcription, and our findings demonstrate how transcriptional regulation of E2F can be linked to cell cycle-dependent activation of kinases.
Nonparametric Bayes Pachinko Allocation (2012)

Recent advances in topic models have explored complicated structured distributions to represent topic correlation. For example, the pachinko allocation model (PAM) captures arbitrary, nested, and possibly sparse correlations between topics using a directed acyclic graph (DAG). While PAM provides more flexibility and greater expressive power than previous models like latent Dirichlet allocation (LDA), it is also more difficult to determine the appropriate topic structure for a specific dataset. In this paper, we propose a nonparametric Bayesian prior for PAM based on a variant of the hierarchical Dirichlet process (HDP). Although the HDP can capture topic correlations defined by nested data structure, it does not automatically discover such correlations from unstructured data. By assuming an HDP-based prior for PAM, we are able to learn both the number of topics and how the topics are correlated. We evaluate our model on synthetic and real-world text datasets, and show that nonparametric PAM achieves performance matching the best of PAM without manually tuning the number of topics.
INTERFERONS AND THEIR ACTIONS (1987)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Transgene expression in dendritic cells to induce antigen-specific cytotoxic T cells in healthy donors. (1998)

Immunization with specific tumor-associated antigen (Ag) (TAA)-pulsed dendritic cells (DC) has proven to be efficacious in a variety of animal models and is being investigated for the treatment of cancer patients. Use of DC pulsed with specific peptides or transfected with TAA genes has been a focused area of investigation for the induction of potent tumor and viral immune responses. In this study we demonstrate transgene expression, including expression of the MART-1 gene, in DC transfected with plasmid DNA and cationic liposome complexes. These transiently transfected DC, derived from healthy donor monocytes cultured with granulocyte macrophage colony-stimulating factor and interleukin-4, express the transgene and can stimulate naive CD8+ T cells to elicit an antitumor immune response. These cytotoxic T lymphocytes (CTL) were capable of recognizing both known and unknown TAA epitopes and were able to exhibit cytolytic activity against human histocompatibility leukocyte Ag-matched tumor cells expressing the Ag. In addition to their cytolytic function, the CTL displayed an oligoclonal T-cell receptor repertoire, indicating that the presented Ag induced alterations in the T-cell population. The ability to induce tumor-specific CTL in vitro using gene-modified DC transiently expressing TAAs demonstrates the potential use of these Ag-presenting cells to generate future in vivo cancer vaccine strategies.
Prostate Apoptosis Response-4 Enhances Secretion of Amyloid β Peptide 1–42 in Human Neuroblastoma IMR-32 Cells by a Caspase-dependent Pathway (2001)

Prostate apoptosis response-4 (Par-4) is a leucine zipper protein that promotes neuronal cell death in Alzheimer's disease (AD). Neuronal degeneration in AD may result from extracellular accumulation of amyloid beta peptide (Abeta) 1-42. To examine the effect of Par-4 on Abeta secretion and to reconcile amyloid/apoptosis hypotheses of AD, we generated IMR-32 cell lines that overexpress Par-4 and/or its leucine zipper domain. Overexpression of Par-4 did not significantly affect levels of the endogenously expressed beta amyloid precursor protein but drastically increased the Abeta(1-42)/Abeta(total) ratio in the conditioned media about 6-8 h after trophic factor withdrawal. Time course analysis of caspase activation reveals that Par-4 overexpression exacerbated caspase activation, which is detectable within 2 h after trophic factor withdrawal. Furthermore, inhibition of caspase activity by the broad spectrum caspase inhibitor BD-fmk significantly attenuated the Par-4-induced increase in Abeta 1-42 production. In addition, the effects of Par-4 on secretion of Abeta 1-42 were consistently blocked by co-expression of the leucine zipper domain, indicating that the effect of Par-4 on Abeta secretion may require its interaction with other protein(s). These results suggest that Par-4 increases secretion of Abeta 1-42 largely through a caspase-dependent pathway after apoptotic cascades are initiated.
Refolding and crystallographic studies of eukaryotic proteins produced in Escherichia coli (1988)

Conference Article| April 01 1988 Refolding and crystallographic studies of eukaryotic proteins produced in Escherichia coli KIYOSHI NAGAI; KIYOSHI NAGAI *Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Search for other works by this author on: This Site PubMed Google Scholar HANS-CHRISTIAN THØGERSEN; HANS-CHRISTIAN THØGERSEN † Search for other works by this author on: This Site PubMed Google Scholar BONAVENTURA F. LUISI BONAVENTURA F. LUISI ‡ Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1988) 16 (2): 108–110. https://doi.org/10.1042/bst0160108 Article history Received: October 10 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation KIYOSHI NAGAI, HANS-CHRISTIAN THØGERSEN, BONAVENTURA F. LUISI; Refolding and crystallographic studies of eukaryotic proteins produced in Escherichia coli. Biochem Soc Trans 1 April 1988; 16 (2): 108–110. doi: https://doi.org/10.1042/bst0160108 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: Hb, haemoglobin, TMV, tobacco mosaic virus © 1988 Biochemical Society1988 Article PDF first page preview Close Modal You do not currently have access to this content.
Design, Synthesis, and Antifolate Activity of New Analogues of Piritrexim and Other Diaminopyrimidine Dihydrofolate Reductase Inhibitors with ω-Carboxyalkoxy or ω-Carboxy-1-alkynyl Substitution in the Side Chain (2005)

As part of a search for dihydrofolate reductase (DHFR) inhibitors combining the high potency of piritrexim (PTX) with the high antiparasitic vs mammalian selectivity of trimethoprim (TMP), the heretofore undescribed 2,4-diamino-6-(2',5'-disubstituted benzyl)pyrido[2,3-d]pyrimidines 6-14 with O-(omega-carboxyalkyl) or omega-carboxy-1-alkynyl groups on the benzyl moiety were synthesized and tested against Pneumocystis carinii, Toxoplasma gondii, and Mycobacterium avium DHFR vs rat DHFR. Three N-(2,4-diaminopteridin-6-yl)methyl)-2'-(omega-carboxy-1-alkynyl)dibenz[b,f]azepines (19-21) were also synthesized and tested. The pyridopyrimidine with the best combination of potency and selectivity was 2,4-diamino-5-methyl-6-[2'-(5-carboxy-1-butynyl)-5'-methoxy]benzyl]pyrimidine (13), with an IC(50) value of 0.65 nM against P. carinii DHFR, 0.57 nM against M. avium DHFR, and 55 nM against rat DHFR. The potency of 13 against P. carinii DHFR was 20-fold greater than that of PTX (IC(50) = 13 nM), and its selectivity index (SI) relative to rat DHFR was 85, whereas PTX was nonselective. The activity of 13 against P. carinii DHFR was 20 000 times greater than that of TMP, with an SI of 96, whereas that of TMP was only 14. However 13 was no more potent than PTX against M. avium DHFR, and its SI was no better than that of TMP. Molecular modeling dynamics studies using compounds 10 and 13 indicated a slight binding preference for the latter, in qualitative agreement with the IC(50) data. Among the pteridines, the most potent against P. carinii DHFR and M. avium DHFR was the 2'-(5-carboxy-1-butynyl)dibenz[b,f]azepinyl derivative 20 (IC(50) = 2.9 nM), whereas the most selective was the 2'-(5-carboxy-1-pentynyl) analogue 21, with SI values of >100 against both P. carinii and M. avium DHFR relative to rat DHFR. The final compound, 2,4-diamino-5-[3'-(4-carboxy-1-butynyl)-4'-bromo-5'-methoxybenzyl]pyrimidine (22), was both potent and selective against M. avium DHFR (IC(50) = 0.47 nM, SI = 1300) but was not potent or selective against either P. carinii or T. gondii DHFR.