gebhart/patrepeval huggingface dataset:
Non-ionic Antisense Oligonucleotides (1989)

Organic chemists have long exercised their synthetic ingenuity to create novel nucleic acid analogues. In addition to the challenge offered by such syntheses, these efforts have focused on creating molecules whose properties would make them of use in a variety of biological applications, including use as antisense molecules.
Cloning of bcl-6, the locus involved in chromosome translocations affecting band 3q27 in B-cell lymphoma. (1993)

Chromosomal translocations involving band 3q27 and various chromosomal sites, including the sites of the immunoglobulin (Ig) loci (14q32, 2p12, 22q11), represent recurrent aberrations in non-Hodgkin's lymphoma (NHL). In order to identify the putative protooncogene involved in these translocations, we have cloned the breakpoints from two B-cell NHL cases carrying t(3;14)(q27;q32) translocations by screening genomic DNA libraries constructed from NHL biopsy samples with immunoglobulin probes. Several recombinant phages have been obtained from each case and shown to contain sequences from both 14q32 and 3q27 by fluorescence in situ hybridization mapping on metaphase chromosomes. In both cases, the translocation breakpoints were found within the switch region of the Ig heavy-chain locus on 14q32 and within the same 3-kilobase region on 3q27. When used in Southern blot hybridization, a probe from the 3q27 region detected rearrangements in an additional five NHL cases carrying 3q27 translocations with 14q32 or other genomic sites. The same probe detected a predominant 2.4-kilobase mRNA species in several lymphoid cell lines analyzed by Northern blot hybridization. These data suggest that chromosomal breakpoints in 3q27 cluster in the proximity of a transcribed gene which represents a candidate protooncogene (bcl-6) involved in B-cell NHL pathogenesis.
Different activation domains of Sp1 govern formation of multimers and mediate transcriptional synergism. (1991)

The process of transcriptional activation in eukaryotes by site-specific DNA-binding proteins is a key step in gene regulation. Here we have examined the properties of four distinct activator domains of the human transcription factor Sp1. In vivo transient cotransfection assays with Sp1 show that templates bearing multiple Sp1 sites activate transcription with a high degree of synergism. However, there is no evidence of cooperative binding of Sp1 to adjacent sites. Using deletion mutants of Sp1 we have determined that the glutamine-rich activation domains A and B and the previously uncharacterized carboxy-terminal domain D are all required for Sp1 to activate transcription synergistically. Gel-shift, DNase footprinting, and chemical cross-linking experiments reveal a strong correlation between the ability of Sp1 mutants to form homomultimeric complexes and their ability to activate transcription synergistically when bound to multiple sites. We have also examined the process of superactivation, in which a molecule of Sp1 tethered to DNA via its zinc fingers can be transcriptionally enhanced by interacting directly with fingerless Sp1 molecules. The domains involved in superactivation appear to be a subset of those necessary to achieve synergistic activation. These findings suggest that different domains of Sp1 carry out distinct functions and that the formation of multimeric complexes may direct synergism and superactivation.
Plk1 Phosphorylation of Orc2 and Hbo1 Contributes to Gemcitabine Resistance in Pancreatic Cancer (2012)

Although gemcitabine is the standard chemotherapeutic drug for treatment of pancreatic cancer, almost all patients eventually develop resistance to this agent. Previous studies identified Polo-like kinase 1 (Plk1) as the mediator of gemcitabine resistance, but the molecular mechanism remains unknown. In this study, we show that Plk1 phosphorylation of Orc2 and Hbo1 mediates the resistance to gemcitabine. We show that the level of Plk1 expression positively correlates with gemcitabine resistance, both in pancreatic cancer cells and xenograft tumors. Overexpression of Plk1 increases gemcitabine resistance, while inhibition of Plk1 sensitizes pancreatic cancer cells to gemcitabine treatment. To validate our findings, we show that inhibition of Plk1 sensitizes tumors to gemcitabine treatment in a mouse xenograft study. Mechanistically, we find that Plk1 phosphorylation of Orc2 maintains DNA replication on gemcitabine treatment. Furthermore, Plk1 phosphorylation of Hbo1 transcriptionally increases cFos expression and consequently elevates its target multidrug resistance 1 (MDR1), which was previously reported to confer chemotherapeutic drug resistance. Knockdown of cFos or MDR1 sensitizes gemcitabine-resistant cells to gemcitabine treatment. Finally, pancreatic cancer cells expressing Plk1-unphosphorylatable mutants of Orc2 or Hbo1 are more sensitive to gemcitabine than cells expressing wild-type Orc2 or Hbo1. In short, our study provides a mechanism for Plk1-mediated gemcitabine resistance, suggesting that Plk1 is a promising target for treatment of gemcitabine-resistant pancreatic cancer.
Oncogenic AKAP9-BRAF fusion is a novel mechanism of MAPK pathway activation in thyroid cancer (2005)

Genes crucial for cancer development can be mutated via various mechanisms, which may reflect the nature of the mutagen. In thyroid papillary carcinomas, mutations of genes coding for effectors along the MAPK pathway are central for transformation. BRAF point mutation is most common in sporadic tumors. By contrast, radiation-induced tumors are associated with paracentric inversions activating the receptor tyrosine kinases RET and NTRK1. We report here a rearrangement of BRAF via paracentric inversion of chromosome 7q resulting in an in-frame fusion between exons 1-8 of the AKAP9 gene and exons 9-18 of BRAF. The fusion protein contains the protein kinase domain and lacks the autoinhibitory N-terminal portion of BRAF. It has elevated kinase activity and transforms NIH3T3 cells, which provides evidence, for the first time to our knowledge, of in vivo activation of an intracellular effector along the MAPK pathway by recombination. The AKAP9-BRAF fusion was preferentially found in radiation-induced papillary carcinomas developing after a short latency, whereas BRAF point mutations were absent in this group. These data indicate that in thyroid cancer, radiation activates components of the MAPK pathway primarily through chromosomal paracentric inversions, whereas in sporadic forms of the disease, effectors along the same pathway are activated predominantly by point mutations.
Large Thermal Deflection Analysis of Composite Plates Using Finite Strip Method (1999)

In the present study, the large deflection behavior of antisymmetric angle ply laminates under combined transverse loading and temperature rise is simulated using the finite strip method based on the higher order shear deformation theory. The modified Newton-Raphson iteration is implemented for the nonlinear solution process, and a relaxation coefficient is introduced to eliminate possible divergence. The effects of transverse loading, temperature gradient, fiber orientation, number of plies, length to thickness ratio and matrix compressive strength are investigated through numerical examples.
Adequate vascular training opportunities can be provided without compromising patient care (2002)

OBJECTIVES: to review the results of index operations in vascular surgery and to evaluate the impact of a specialist vascular training programme on patient outcome. METHODS: we undertook a 5-year (January 1995-December 1999) review of the weekly-collected mortality and morbidity data. The total number, 30-day mortality and stroke rate of all index operations i.e. AAA repairs (ruptured and elective), carotid operations and infra-inguinal bypasses (above and below knee, elective and emergency) was recorded. The number of operations performed by trainees under supervision was recorded. RESULTS: in the 5-year period 991 index operation were done of which 738 (74%) were done by trainees. Operations done by trainees were supervised by a consultant in 82% of cases with no significant effect on death or stroke rates. Overall vascular trainees performed 75% of the index operations of which 82% were supervised. CONCLUSIONS: trainees under supervision performed three out of four index operations. The mortality and morbidity of index operations in our unit compared well with accepted best mortality and morbidity figures. Our unit provides good training opportunities for vascular trainees whilst maintaining satisfactory standards of patient care.
Aspartic acid residues at positions 190 and 192 of rat DNA polymerase .beta. are involved in primer binding (1991)

The sequence Gly-Asp-Met-Asp, spanning positions 189-192 of rat DNA polymerase beta, is similar to the sequence motif Gly-Asp-Thr-Asp that is highly conserved in a number of replicative DNA polymerases from eukaryotic cells, viruses, and phages. The role of this sequence in the catalytic function of rat DNA polymerase beta was investigated by individually changing each amino acid in this region by site-directed mutagenesis. The mutant enzymes DE190 and DE192, in which aspartic acid residues at positions 190 and 192, respectively, were replaced by glutamic acid, showed about 0.1% activity of the wild-type enzyme. On the other hand, the replacement of Gly-189 by alanine or Met-191 by isoleucine or threonine only slightly affected the enzyme activity. A gel mobility shift assay showed that DNA complexes with enzyme DE190 and especially with DE192 were less stable than the corresponding complex with the wild-type enzyme. Kinetic analysis with these mutant enzymes indicate that their Km's for primer DNA were about 10-fold higher than that of the wild type, while Km's for deoxyribonucleoside triphosphate were not changed. Since neither DE190 nor DE192 had any significant alteration in secondary structure, our results suggest that both Asp-190 and Asp-192 are located in the active site and are involved in the interaction of DNA polymerase beta with primer.
Chronic hyperalgesic priming in the rat involves a novel interaction between cAMP and PKCε second messenger pathways (2004)

Toward the goal of defining new pharmacological targets for the treatment of chronic pain conditions, in previous studies we established a model, termed 'hyperalgesic priming,' in which an acute inflammatory stimulus causes a long-lasting latent susceptibility to hyperalgesia induced by subsequent exposures to the inflammatory mediator, prostaglandin E2 (PGE2). Those investigations suggested the hypothesis that priming induces a novel linkage between the PGE2-activated second messenger cascade and the epsilon isoform of protein kinase C (PKCepsilon). In the present study, comparison of dose-response relations for hyperalgesia produced by PGE2, forskolin, 8-Br-cAMP, or the protein kinase A (PKA) catalytic subunit, in primed versus normal animals, demonstrated that priming-induced enhancement of the PGE2-activated second messenger cascade occurs downstream to adenylate cyclase and upstream to PKA. Therefore, PGE2-induced hyperalgesia in the primed animal is enhanced by the recruitment of a novel cAMP/PKCepsilon signaling pathway in addition to the usual cAMP/PKA pathway. These observations suggest that pharmacological disruption of the novel interaction between cAMP and PKCepsilon might provide a route toward the development of highly specific methods to reverse cellular processes that underlie chronic pain states.
Long-Range Order and Orientation of Cylinder-Forming Block Copolymers on Chemically Nanopatterned Striped Surfaces (2006)

Cylinder-forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) thin films were directed to assemble on chemically nanopatterned surfaces consisting of alternating stripes that were preferentially wet by the two blocks of the copolymer. The cylindrical domains oriented in the plane of the film and formed defect-free periodic arrays over large areas in registration with the underlying chemical surface pattern if three constraints were satisfied: the substrate pattern period (LS) was commensurate with the bulk intercylinder period of the block copolymer (LO), the initial film thickness was quantized with respect to the thickness of a half layer (L/2) or single layer of cylinders (L), and the widths of adjacent stripes of the chemical surface pattern were nearly equal.
Calcium Signalling and Gene Expression (1999)

A wide variety of compounds acting as extracellular signals cause changes in the free cytosolic Ca2+ concentration. These factors include hormones, growth factors, neurotransmitters, but also nutrient and metabolic activators. Ca2+ signalling is caused by mobilization of Ca2+ from internal stores and by well controlled and timed Ca2+ influx from the extracellular space. Ca2+ signals address Ca2+ dependent enzymes, most importantly Ca2+ sensitive protein kinases and phosphatases. The profound influence of Ca2+ signalling on gene expression has been recognized a long time ago. As Ca2+ signals are short-lived when compared to alterations in differentiated gene expression, it is generally considered that genes coding for short-lived transcription factors (i.e. fos, jun) are the immediate target of Ca2+ signalling. Transcription of these immediate early genes (IEG) can be activated without the need for protein synthesis. Ca2+ signalling affects differentiated gene expression via changes in the absolute and relative abundance of IEG products, which in turn control the expression of differentiated genes. Ca2+ signals can stimulate both transcriptional initiation as well as transcriptional elongation. Initiation of transcription is stimulated by the Ca2+ dependent phosphorylation of binding proteins addressing two response elements in the promoter of IEGs: the cAMP response element, CRE, and the serum response element, SRE. Distinct protein kinases are involved in either case. We study the elongation of transcripts of the IEG c-fos beyond the first intron which is favoured by Ca2+ signals, involving mechanisms which still are poorly understood. We can show that intron sequences contribute to the control of elongation by Ca2+, and that there is a strong interrelation between the transcription control by the promoter and by the intron.
BRCA1 expression in leukoplakia and carcinoma of the tongue (2003)

Subcellular localization of the BRCA1 gene product provided evidence of its involvement in the pathogenesis of tongue tumors.
Immunological Quantitation and Localization of ACAT-1 and ACAT-2 in Human Liver and Small Intestine (2000)

By using specific anti-ACAT-1 antibodies in immunodepletion studies, we previously found that ACAT-1, a 50-kDa protein, plays a major catalytic role in the adult human liver, adrenal glands, macrophages, and kidneys but not in the intestine. Acyl-coenzyme A:cholesterol acyltransferase (ACAT) activity in the intestine may be largely derived from a different ACAT protein. To test this hypothesis, we produced specific polyclonal anti-ACAT-2 antibodies that quantitatively immunodepleted human ACAT-2, a 46-kDa protein expressed in Chinese hamster ovary cells. In hepatocyte-like HepG2 cells, ACAT-1 comprises 85-90% of the total ACAT activity, with the remainder attributed to ACAT-2. In adult intestines, most of the ACAT activity can be immunodepleted by anti-ACAT-2. ACAT-1 and ACAT-2 do not form hetero-oligomeric complexes. In differentiating intestinal enterocyte-like Caco-2 cells, ACAT-2 protein content increases by 5-10-fold in 6 days, whereas ACAT-1 protein content remains relatively constant. In the small intestine, ACAT-2 is concentrated at the apices of the villi, whereas ACAT-1 is uniformly distributed along the villus-crypt axis. In the human liver, ACAT-1 is present in both fetal and adult hepatocytes. In contrast, ACAT-2 is evident in fetal but not adult hepatocytes. Our results collectively suggest that in humans, ACAT-2 performs significant catalytic roles in the fetal liver and in intestinal enterocytes.
Segmentation of partially occluded objects by local classification (2000)

An algorithm for supervised learning the segmentation of partially occluded objects is presented. It is based on the classification of object windows which are small compared to the object size but large enough to evaluate structural object features as well as colour. From the input windows, features are extracted by local principal component analysis and subsequently classified by a neural network of the local linear map type. The performance is checked on images of objects with partial occlusion which were artificially generated from the Columbia Object Image Library.
Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. (1993)

Random mutagenesis has been used to engineer the protease subtilisin E to function in a highly nonnatural environment--high concentrations of a polar organic solvent. Sequential rounds of mutagenesis and screening have yielded a variant (PC3) that hydrolyzes a peptide substrate 256 times more efficiently than wild-type subtilisin in 60% dimethylformamide. PC3 subtilisin E and other variants containing different combinations of amino acid substitutions are effective catalysts for transesterification and peptide synthesis in dimethylformamide and other organic media. Starting with a variant containing four effective amino acid substitutions (D60N, D97G, Q103R, and N218S; where, for example, D60N represents Asp-60-->Asn), six additional mutations (G131D, E156G, N181S, S182G, S188P, and T255A) were generated during three sequential rounds of mutagenesis and screening. The 10 substitutions are clustered on one face of the enzyme, near the active site and substrate binding pocket, and all are located in loops that connect core secondary structure elements and exhibit considerable sequence variability in subtilisins from different sources. These variable surface loops are effective handles for "tuning" the activity of subtilisin. Seven of the 10 amino acid substitutions in PC3 are found in other natural subtilisins. Great variability is exhibited among naturally occurring sequences that code for similar three-dimensional structures--it is possible to make use of this sequence flexibility to engineer enzymes to exhibit features not previously developed (or required) for function in vivo.
Pseudomonas aeruginosa AlgG is a polymer level alginate C5-mannuronan epimerase (1994)

Alginate is a viscous extracellular polymer produced by mucoid strains of Pseudomonas aeruginosa that cause chronic pulmonary infections in patients with cystic fibrosis. Alginate is polymerized from GDP-mannuronate to a linear polymer of beta-1-4-linked residues of D-mannuronate and its C5-epimer, L-guluronate. We previously identified a gene called algG in the alginate biosynthetic operon that is required for incorporation of L-guluronate residues into alginate. In this study, we tested the hypothesis that the product of algG is a C5-epimerase that directly converts D-mannuronate to L-guluronate. The DNA sequence of algG was determined, and an open reading frame encoding a protein (AlgG) of approximately 60 kDa was identified. The inferred amino terminus of AlgG protein contained a putative signal sequence of 35 amino acids. Expression of algG in Escherichia coli demonstrated both 60-kDa pre-AlgG and 55-kDa mature AlgG proteins, the latter of which was localized to the periplasm. An N-terminal analysis of AlgG showed that the signal sequence was removed in the mature form. Pulse-chase experiments in both E. coli and P. aeruginosa provided evidence for conversion of the 60- to the 55-kDa size in vivo. Expression of algG from a plasmid inan algG (i.e., polymannuronate-producing) mutant of P. aeruginosa restored production of an alginate containing L-guluronate residues. The observation that AlgG is apparently processed and exported from the cytoplasm suggested that it may act as a polymer-level mannuronan C5-epimerase. An in vitro assay for mannuronan C5 epimerization was developed wherein extracts of E. coli expressing high levels of AlgG were incubated with polymannuronate. Epimerization of D-mannuronate to L-guluronate residues in the polymer was detected enzymatically, using a L-guluronate-specific alginate lyase of Klebsiella aerogenes. Epimerization was also detected in the in vitro reaction between recombinant AlgG and poly-D-mannuronate, using high-performance anion-exchange chromatography. The epimerization reaction was detected only when acetyl groups were removed from the poly-D-mannuronate substrate, suggesting that AlgG epimerization activity in vivo may be sensitive to acetylation of the D-mannuronan residues. These results demonstrate that AlgG has polymer-level mannuronan C5-epimerase activity.
Morphological spectrum of cyclin D1‐positive mantle cell lymphoma: Study of 168 cases (2001)

Immunostaining for cyclin D1 is essential for reliable diagnosis of mantle cell lymphoma (MCL). However, a small number of cyclin D1-positive lymphomas other than MCL have been encountered. Our goal was to investigate the morphological spectrum of MCL as a disease entity, based on cyclin D1 overexpression. We reviewed 181 biopsy specimens obtained from 168 cases of cyclin D1-positive MCL. Typical findings were the presence of nodular (53.9% of cases) or diffuse (46.1%) histological patterns, containing mantle zone patterns (16.8%), naked germinal centers (33.5%) and perivascular hyaline deposition (83.2%). Unusual findings of residual germinal centers with a mantle cuff (four cases) and follicular colonization (two cases) were seen. High magnification showed a monotonous proliferation of tumor cells with cytological diversity including small (3.0%), intermediate (43.1%), medium (34.1%), medium-large (13.2%) and large (6.6%) cells. Pleomorphic and blastic/blastoid variants were encountered in 9.6 and 7.2% of cases, respectively. Three cases had foci of cells of considerable size, with a moderately abundant pale cytoplasm resembling marginal zone B cells. Two cases showed an admixture of cells which appeared transformed and mimicked the histology of chronic lymphocytic leukemia/small lymphocytic leukemia. In one, neoplastic mantle zones were surrounded by sheets of mature plasma cells, resembling the plasma cell type of Castleman's disease. An admixture of areas characteristic of MCL and of other larger cells, indicating histological progression or a composite lymphoma, were observed in seven cases. In high-grade lesions of five cases, nuclear staining of cyclin D1 was rarely detected. In our experience, cyclin D1 expression was also found in nine lymphomas other than MCL (five plasma cell myelomas, three Hodgkin's disease and one anaplastic large cell lymphoma). The application of cyclin D1 staining prompted us to recognize the broad morphological spectrum of MCL. MCL can be diagnosed with the application of cyclin D1 immunostaining, if careful attention is given to architectural and cytological features.