gebhart/patrepeval huggingface dataset:
DNA sequences necessary for packaging of bacteriophage lambda DNA. (1983)

The extent of DNA flanking the "cohered cohesive end" site of bacteriophage lambda DNA, which is required for packaging, was determined by using defined DNA fragments and a cosmid in vivo packaging assay. From the right end of lambda DNA a 20- to 36-base-pair stretch extending from the center of the cohered cohesive ends is shown to be required, whereas the packaging efficiency of cosmids extending to 70 base pairs into the left lambda arm is reduced to 10% (compared to a fragment extending until about 80 base pairs). A 60-base-pair stretch of the left arm leaves an efficiency of only 1%. The segment thus delineated, by the nature of the assay, is both necessary and sufficient for the binding of packaging proteins to the DNA, the packaging of DNA itself, the DNA cleavage, and successful injection of the DNA into a bacterial host. By contrast, in vitro packaging of restriction fragments of mature lambda DNA directly demonstrated the selectivity of the packaging proteins for the fragment originating from the left end of the DNA. The results of the two complementary experiments are discussed in terms of the various steps before, during, and after packaging for which different sequences flanking and including the cohered cohesive ends might be required.
Regulation of a Ca2+-sensitive Adenylyl Cyclase in an Excitable Cell (2000)

In nonexcitable cells, we had previously established that Ca(2+)-sensitive adenylyl cyclases, whether expressed endogenously or heterologously, were regulated exclusively by capacitative Ca(2+) entry (Fagan, K. A., Mahey, R. and Cooper, D. M. F. (1996) J. Biol. Chem. 271, 12438-12444; Fagan, K. A., Mons, N., and Cooper, D. M. F. (1998) J. Biol. Chem. 273, 9297-9305). Relatively little is known about how these enzymes are regulated by Ca(2+) in excitable cells, where they predominate. Furthermore, no effort has been made to determine whether the prominent voltage-gated Ca(2+) entry, which typifies excitable cells, overwhelms the effect of any capacitative Ca(2+) entry that may occur. In the present study, we placed the Ca(2+)-stimulable, adenylyl cyclase type VIII in an adenovirus vector to optimize its expression in the pituitary-derived GH(4)C(1) cell line. In these cells, a modest degree of capacitative Ca(2+) entry could be discerned in the face of a dramatic voltage-gated Ca(2+) entry. Nevertheless, both modes of Ca(2+) entry were equally efficacious at stimulating adenylyl cyclase. A striking release of Ca(2+) from intracellular stores, triggered either by ionophore or thyrotrophin-releasing hormone, was incapable of stimulating the adenylyl cyclase. It thus appears as though the intimate colocalization of adenylyl cyclase with capacitative Ca(2+) entry channels is an intrinsic property of these molecules, regardless of whether they are expressed in excitable or nonexcitable cells.
Metal Ion-Dependent Modulation of the Dynamics of a Designed Protein (1993)

The peptide alpha 4 is a designed four-helix bundle that contains a highly simplified hydrophobic core composed exclusively of leucine residues; its tertiary structure is therefore largely dictated by hydrophobic forces. This small protein adopts a structure with properties intermediate between those of the native and molten globule states of proteins: it is compact, globular, and has very stable helices, but its apolar side chains are mobile and not as well packed as in many natural proteins. To induce a more native-like state, two Zn(2+)-binding sites were introduced into the protein, thereby replacing some of the non-specific hydrophobic interactions with more geometrically restrictive metal-ligand interactions. In the metal-bound state, this protein has properties that approach those of native proteins. Thus, hydrophobic interactions alone are sufficient to drive polypeptide chain folding nearly to completion, but specific interactions are required for a unique structure.
Percutaneous implantation of a valve in the descending aorta in lambs (2002)

Percutaneously implanted valves in the descending aorta of lambs with aortic insufficiency function well in the early follow-up. This technique might become an interesting alternative to the standard approach in patients in whom perioperative risk is high.
Tissue response to microfibers of different polymers: Polyester, polyethylene, polylactic acid, and polyurethane (2002)

Tissue response to single polymer microfibers of polyester (PET), polyethylene (PE), poly(L-lactic acid) (PLA), and polyurethane (PU) was assessed using a rat subcutaneous model. Fibers of diameters ranging from 1 to 15 microm were aligned parallel to each other on polycarbonate frames and implanted in the subcutaneous dorsum in the subscapular region. After 5 weeks of implantation, fibrous capsule thickness was significantly less for fibers of diameters 1-5 than for those of 11-15 microm for all polymers tested. For PET and PU, 75.0 and 71.4% respectively of the 1-5 microm fibers had no capsule, while for PE and PLA only 45.5 and 56.3% respectively had no capsule. For 1-5 microm fibers, PE had significantly thicker capsules than PET and PU. Reducing fiber diameters from 6-10 to 1-5 microm induced a greater reduction in capsule thickness than changing polymers among PET, PE, and PLA. PU showed the least encapsulation of all polymers, demonstrating significantly thinner capsules than PET, PE, and PLA for 6-10 and 11-15 microm fibers.
The Epidemiology of Chlamydial Infections in Childhood: A Serological Investigation (1984)

Blood samples from 382 children between the ages of one and 15 years were tested for anti-chlamydial antibody. A low prevalence of antibody against Chlamydia trachomatis was found among children under the age of seven years. Antibody against the Chlamydial agent C IOL-207 was rare before the age of five years, but was found with increasing prevalence in older children. It is suggested that the mode of transmission of the two agents is different and that C IOL-207 may be transmitted at school.
[Evaluation: a theoretical-practical approach]. (1990)

The study presents a theoretical review and analysis of the evaluation of the teaching-learning process, as it occurs in the work of 2 nd. and 3rd. degrees teachers. A bibliographical review of the tendencies Evaluation and Mastery, Evaluation and is Prognosis, Evaluation and Transfer is made. The theoretical lines are afterwards compared with the speeches of the teachers interviewed with this purpose. The authors conclude that the three studied tendencies were found in the interviews, but no one was exclusive.
Iterative Deterministic Equivalents for the Performance Analysis of Communication Systems (2011)

In this article, we introduce iterative deterministic equivalents as a novel technique for the performance analysis of communication systems whose channels are modeled by complex combinations of independent random matrices. This technique extends the deterministic equivalent approach for the study of functionals of large random matrices to a broader class of random matrix models which naturally arise as channel models in wireless communications. We present two specific applications: First, we consider a multi-hop amplify-and-forward (AF) MIMO relay channel with noise at each stage and derive deterministic approximations of the mutual information after the Kth hop. Second, we study a MIMO multiple access channel (MAC) where the channel between each transmitter and the receiver is represented by the double-scattering channel model. We provide deterministic approximations of the mutual information, the signal-to-interference-plus-noise ratio (SINR) and sum-rate with minimum-mean-square-error (MMSE) detection and derive the asymptotically optimal precoding matrices. In both scenarios, the approximations can be computed by simple and provably converging fixed-point algorithms and are shown to be almost surely tight in the limit when the number of antennas at each node grows infinitely large. Simulations suggest that the approximations are accurate for realistic system dimensions. The technique of iterative deterministic equivalents can be easily extended to other channel models of interest and is, therefore, also a new contribution to the field of random matrix theory.
Identification of regulatory elements in 16S rRNA gene of Acinetobacter species isolated from water sample (2008)

A bacterial strain, designated AcBz01, was isolated from a water sample collected from Gomti River, Lucknow, India, and identified using a molecular approach. On the basis of the bacterial 16S rRNA gene sequence phylogeny and comparison of this gene sequence with sequences in Ribosomal Database project II, evidence given in this study, it is proposed that isolate is closely related to members of the genus Acinetobacter. Identification and annotation of regulatory elements in the 16S rRNA gene and characterization of their interaction with the respective transcription factor can provide basis for better understanding of the mechanism of network of gene interaction of functionally related genes. The identification of such sites is relevant for locating promoter boundary of a gene and it also allows the prediction of specific gene expression pattern and response to disturbances in a known signaling pathway. Computational identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Acinetobacter sp. was performed using BPROM tool. We predicted the regulatory elements are TSS, -10 box, -35 box and three Transcription Factor (narP, ompR and fadR) with their binding sites in the upstream region of 16S rRNA gene of Acinetobacter sp. AcBz01. The GenBank accession number for 16S rRNA gene of Acinetobacter sp. AcBz01 is EU931637.
Biologic properties in vitro of a recombinant human granulocyte- macrophage colony-stimulating factor (1986)

Recombinant human granulocyte-macrophage colony-stimulating factor (rH GM-CSF) was purified to homogeneity from medium conditioned by COS cells transfected with a cloned human GM-CSF cDNA and shown to be an effective proliferative stimulus in human marrow cultures for GM and eosinophil colony formation. The specific activity of purified rH GM- CSF in human marrow cultures was calculated to be at least 4 X 10(7) U/mg protein. Clone transfer experiments showed that this proliferation was due to direct stimulation of responding clonogenic cells. Acting alone, rH GM-CSF did not stimulate erythroid colony formation, but in combination with erythropoietin, increased erythroid and multipotential colony formation in cultures of peripheral blood cells. rH GM-CSF had no proliferative effects on adult or fetal murine hematopoietic cells, did not induce differentiation in murine myelomonocytic WEHI-3B cells, and was unable to stimulate the survival or proliferation of murine hematopoietic cell lines dependent on murine multi-CSF (IL 3). rH GM- CSF stimulated antibody-dependent cytolysis of tumor cells by both mature human neutrophils and eosinophils and increased eosinophil autofluorescence and phagocytosis by neutrophils. From a comparison of these effects with those of semipurified preparations of human CSF alpha and -beta, it was concluded that rH GM-CSF exhibited all the biologic activities previously noted for CSF alpha.
Activation, proliferation, and differentiation of progenitor cells into hepatocytes in the D-galactosamine model of liver regeneration. (1993)

Rat liver regeneration was studied from 24 hours to 8 days after a single intraperitoneal injection of D-galactosamine (GalN). Morphological changes in the liver were analyzed in parallel with sequential changes in expression of histone-3 mRNA (a marker of cell proliferation), fetal alpha-fetoprotein (AFP) mRNA and gamma-glutamyl transpeptidase (GGT) (markers of fetal hepatocytes), and albumin mRNA and glucose-6-phosphatase (G6Pase) (markers of adult hepatocytes). Proliferation of nonparenchymal epithelial cells (NPC), detected in situ by [3H]thymidine labeling or histone-3 mRNA expression, began after 24 hours primarily in the portal area around the bile ducts. After 2 days, histone-3 labelling intensity increased in rows and clusters of NPC which expanded from the portal zone and invaded into the parenchyma. On days 3 and 5, NPC expressing his-3 mRNA expanded further, forming pseudo-ducts and islet-like structures (NPC structures). Proliferating NPC were positive for GGT. Some GGT positive cells were also positive for the fetal form of AFP mRNA, which lagged behind GGT by 24 hours and peaked on day 5. On day 3, some cells with the appearance of NPC expressed albumin mRNA. Double label in situ hybridization for fetal AFP and albumin mRNAs and dual histochemistry for GGT and G6Pase showed simultaneous expression of these markers in NPC on day 5. Other cells expressing fetal AFP mRNA or GGT on day 5 had a morphological appearance between NPC and hepatocytes (transitional cells). Proliferation of hepatocytes began on day 2, reached maximum on day 5 and then declined. Proliferating hepatocytes did not express fetal AFP mRNA or GGT. These findings indicate that after GalN injury, the liver responds by activation of progenitor cells that proliferate and then differentiate into mature hepatocytes. Adult hepatocytes can also proliferate after GAlN injury, but these hepatocytes do not undergo dedifferentiation/redifferentiation during regeneration of the hepatic lobule.
Increase of methicillin resistance in Staphylococcus aureus caused by deletion of a gene whose product is homologous to lytic enzymes (1997)

A spontaneous high-level methicillin-resistant mutant, SRM1648, for which the MIC of methicillin is 1,600 microg/ml, was isolated on a plate containing 400 microg of the antibiotic/ml on which had been cultured the low-level methicillin-resistant Staphylococcus aureus SR17238, for which the MIC is 6.3 microg/ml. Analysis of the chromosomal DNAs of the mutant and the parental strains by the restriction landmark genomic scanning method with two-dimensional electrophoresis of restriction fragments revealed a 1.6-kb deletion in the chromosome of the mutant. The HindIII fragment of 2.5 kb containing this deleted region was cloned into a plasmid vector and introduced into the parental strain. A deletion mutant reconstructed in the presence of a low concentration of methicillin by integration and excision of the recombinant plasmid exhibited a high level of resistance (methicillin MIC, 1,600 microg/ml), confirming that the deletion had caused the elevation of the resistance level. Sequence analysis indicated that the deletion occurred in three consecutive open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed high homology with both RelA and SpoT of Escherichia coli, which are involved in the synthesis and hydrolysis of guanosine 5',3'-polyphosphate, and that of the third ORF showed a relatively high homology to the lytic enzyme encoded by the lytC gene of Bacillus subtilis. We also isolated another high-level resistant mutant with a deletion within the third ORF, which suggested that inactivation of some lytic enzyme resulted in the increased resistance.
Heterochromatic Silencing and HP1 Localization in Drosophila Are Dependent on the RNAi Machinery (2004)

Genes normally resident in euchromatic domains are silenced when packaged into heterochromatin, as exemplified in Drosophila melanogaster by position effect variegation (PEV). Loss-of-function mutations resulting in suppression of PEV have identified critical components of heterochromatin, including proteins HP1, HP2, and histone H3 lysine 9 methyltransferase. Here, we demonstrate that this silencing is dependent on the RNA interference machinery, using tandem mini-white arrays and white transgenes in heterochromatin to show loss of silencing as a result of mutations in piwi, aubergine, or spindle-E (homeless), which encode RNAi components. These mutations result in reduction of H3 Lys9 methylation and delocalization of HP1 and HP2, most dramatically in spindle-E mutants.
Isolation of tumor suppressor genes from MEN-1 related neoplasms (1994)

Multiple Endocrine Neoplasia type 1 (MEN 1) is a cancer predisposition syndrome marked by the development of tumors in specific endocrine tissues such as the pituitary, parathyroid and pancreatic islets. Genetic linkage studies have mapped the MEN 1 gene to 11q13, and allelic loss in related tumors suggests that the gene is a tumor suppressor. Because inactivation of tumor suppressors may be accompanied by underexpression, subtractive hybridization was used to isolate potential candidate genes underexpressed in MEN 1 tumors. cDNA was synthesized from tumor and normal parathyroid tissue by RT-PCR. Biotinylated tumor cDNA was used as a driver and normal cDNA as a tester in subtractive hybridization. Following annealing of the driver and tester amplicons, the biotinylated strands were removed with streptavidin. The subtracted material was then used as a probe to isolate clones from a normal pancreatic islet library. Screening 2 x 10{sup 5} plaques yielded 14 positive clones. Of 6 clones analyzed, 3 were confirmed to be underexpressed in parathyroid tumors. Sequence analysis identified 2 clones as human ribosomal protein S10 (RPS10, chromosome 6) and 1 as the islet amyloid polypeptide (1AP, chromosome 12). The precise function of human RPS10 is not known but the related RPS6 functionsmore » as a tumor suppressor in Drosophila. 1AP has been implicated in modulation of G protein activity. The remaining positive clones will be mapped to determine if any fall on chromosome 11q13, and additional subtractions with parathyroid and pancreatic islet neoplasms are underway.« less
Experimental study of ectopic-free tissue transfer of rabbit epigastric flap using small-caliber vascular grafts (1999)

Ectopic intraperitoneal free-tissue grafting using small-caliber artificial vascular grafts is reported. The vascular grafts were polyurethane tubes (inner diameter 1.4 mm; outer diameter 1.9 mm; length 15 mm) with a coating of the antithrombotic agents argatroban and 2-hydroxyethylmethacrylate-styrene block copolymer (HS)on the inner surface. The patency of the artificial vessels was investigated in an ectopic-free rabbit epigastric flap in which grafts were used for anastomosis between the femoral and renal vessels. The mean patent duration of uncoated controls (n = 10) was 128 +/- 37 min. Flap viability after one week (n = 17) and the patency of the coated grafts were investigated histologically. The flap take rate was 65%, the arterial graft patency rate 41%, and the venous graft patency rate 24%. The HS-treated surface combined with the argatroban slow-release system exhibited improvement of flap survival in an intraperitoneal ectopic -free grafting model.
In vitro cytotoxicity of salvicine, a novel diterpenoid quinone. (1999)

Salvicine exhibited potent cytotoxic activities against various human tumor cell lines, and blocked K562 leukemia cells in G1 phase of cell cycle.
Human Growth Hormone Enhances Chondrogenesis and Osteogenesis in a Tissue Culture System of Chondroprogenitor Cells* (1989)

GH is a systemic promoter of skeletal growth which increases the synthesis of insulin-like growth factor I in parenchymal tissues as well as in peripheral tissues such as the liver and growing cartilage. The present study was designed to examine whether GH possesses a direct effect on cellular proliferation and differentiation in mouse condylar cartilage. Cartilage progenitor cells were cultured in the form of a tissue culture on top of collagen sponges in medium containing 10% fetal calf serum and were treated with 50 ng/ml GH for 6 days. Three-day incubation with GH caused a marked increase in DNA synthesis and in the size of the culture, which developed into a nodule of differentiated chondrocytes and a well developed perichondrial layer around it. The effect of GH was even more pronounced after 6 days in culture; at which time a distinct network of trabeculae was noted throughout the extracellular matrix. The trabeculae contained osteocyte-like cells and were in close contact with both osteoblast-like and osteoclast-like cells. Using antibodies against bone-specific antigens, i.e. osteocalcin and osteopontin, provided further support for the notion that the newly formed trabecular formation was comprised of bone matrical components. Untreated control cultures lacked such structures, but contained hyaline-like cartilage. It, therefore, seems reasonable to suggest that GH induces a strong stimulatory effect on progenitor cell proliferation, cartilage differentiation, and extracellular mineralization, which supports de novo bone formation in vitro.
Adhesion to Fibronectin Maintains Regenerative Capacity During Ex Vivo Culture and Transduction of Human Hematopoietic Stem and Progenitor Cells (1998)

Recent reports have indicated that there is poor engraftment from hematopoietic stem cells (HSC) that have traversed cell cycle ex vivo. However, inducing cells to cycle in culture is critical to the fields of ex vivo stem cell expansion and retroviral-mediated gene therapy. Through the use of a xenograft model, the current data shows that human hematopoietic stem and progenitor cells can traverse M phase ex vivo, integrate retroviral vectors, engraft, and sustain long-term hematopoiesis only if they have had the opportunity to engage their integrin receptors to fibronectin during the culture period. If cultured in suspension under the same conditions, transduction is undetectable and the long-term multilineage regenerative capacity of the primitive cells is severely diminished.
Nitrogen Metabolism in the Stalk Tissue of Maize (1991)

During ear development in maize (Zea mays L.), nitrogenous compounds are translocated from vegetative organs to the kernels. At anthesis, the stalk contains approximately 40% of the total plant N, and contributes 45% of the N remobilized to the ear. Therefore, the stalk has an important function as a temporary reservoir for N. Little is known of the metabolism of maize stalks, and this paper describes initial studies of enzymes of N metabolism. High in vitro activity of glutamine synthetase (GS) in maize stalk samples throughout ear development contrasted with a peak in activity of glutamate synthase soon after anthesis and negligible nitrate reductase. With fresh sections of stalk tissue collected at anthesis, (15)N-feeding experiments confirmed high GS and low nitrate reductase activities. Two isoforms of GS were separated from extracts from stalk tissue: GS1, the cytoplasmic form, increased to maximum levels at 2 weeks postanthesis and remained fairly high thereafter; whereas the plastidic form, GS2, declined progressively during kernel development. Western blot analysis confirmed the presence of constantly high levels of GS protein after anthesis. The levels of GS proteins decreased after transfer of N-starved, hydroponically grown plants to N-rich conditions in order to restrict remobilization of N. In contrast, transfer of plants grown under abundant N conditions to N-free medium, which encourages N remobilization, resulted in a relative increase in GS protein. Because glutamine is the major form of N transported in maize, the results indicate that GS, specifically the GS1 isoform, has a central role in the remobilization on nitrogenous compounds from the stalk to the ear.