gebhart/patrepeval huggingface dataset:
Molecular resemblance of an AIDS-associated lymphoma and endemic Burkitt lymphomas: implications for their pathogenesis. (1989)

Non-Hodgkin lymphoma is a common feature of AIDS. Approximately 30-40% of these tumors exhibit clinical features suggestive of endemic Burkitt lymphoma: they are aggressive malignancies that occur in association with Epstein-Barr virus infection, they arise in the setting of immunosuppression, and they carry t(8;14) translocations without detectable rearrangement of the MYC oncogene. To understand the molecular basis of these parallels, we analyzed a case of Epstein-Barr-positive AIDS-associated undifferentiated lymphoma. Southern blots show that the tumor exhibits immunoglobulin joining segment rearrangement but no rearrangement of the MYC oncogene. Cloning of the rearranged joining segment allowed the isolation of recombinant clones encompassing the translocation breakpoint, and sequencing of the translocation junction disclosed that the breakpoint is situated 7 base pairs from the chromosome 14 site involved in a previously described endemic Burkitt lymphoma translocation. Furthermore, the breakpoint is situated far from MYC on chromosome 8, a constant finding in endemic Burkitt lymphomas. That the molecular architecture of the translocation in this case is strikingly similar to previously analyzed translocations from endemic Burkitt lymphomas strongly suggests that common molecular mechanisms must be operative in the pathogenesis of these tumors.
Patellins 1-6 and Trunkamide A: Novel Cyclic Hexa-, Hepta- and Octa-peptides From Colonial Ascidians, Lissoclinum sp. (1996)

Patellins 1-5 have been isolated from the colonial ascidian Lissoclinum patella from Viti Levu , Fiji. Patellins 1 and 2 are cyclic hexapeptides, while patellins 3-5 are cyclic octapeptides. Two of these peptides ( patellins 3 and 5), a new cyclic octapeptide ( patellin G), a new cyclic heptapeptide ( trunkamide A), and the known metabolite lissoclinolide have also been isolated from a Lissoclinum sp. collected on the Great Barrier Reef, Australia. All structures were determined by high-field n.m.r. and mass spectroscopic methods, and by h.p.l.c . Analysis of the constituent amino acids after hydrolysis of the peptides and derivatization according to Marfey's procedure.
Biodegradable Polymers for the Environment (2002)

Biodegradable polymers are designed to degrade upon disposal by the action of living organisms. Extraordinary progress has been made in the development of practical processes and products from polymers such as starch, cellulose, and lactic acid. The need to create alternative biodegradable water-soluble polymers for down-the-drain products such as detergents and cosmetics has taken on increasing importance. Consumers have, however, thus far attached little or no added value to the property of biodegradability, forcing industry to compete head-to-head on a cost-performance basis with existing familiar products. In addition, no suitable infrastructure for the disposal of biodegradable materials exists as yet.
The autonomic nervous system in functional bowel disorders (2000)

Communications along the brain-gut axis involve neural pathways as well as immune and endocrine mechanisms. The two branches of the autonomic nervous system are integrated anatomically and functionally with visceral sensory pathways, and are responsible for the homeostatic regulation of gut function. The autonomic nervous system is also a major mediator of the visceral response to central influences such as psychological stress and other central factors.
Spatial Analyses Identify the Geographic Source of Patients at a National Cancer Institute Comprehensive Cancer Center (2010)

Today, 62 NCI cancer centers serve a quarter of the U.S. population in their immediate communities. From the Baltimore experience, we might project that the population served by these centers is actually more extensive and varies by patient characteristics, cancer site, and probably cancer center services offered.
Vascular endothelial growth factor induces proliferation of breast cancer cells and inhibits the anti-proliferative activity of anti-hormones (2006)

Increased levels of vascular endothelial growth factor (VEGF) are associated with a poor response of breast cancer to anti-hormone treatment. Although VEGF is regarded as an endothelial-specific growth factor, recent reports have shown that VEGF can promote proliferation of other cell types, including breast tumor cells. We have characterized the proliferative effects of VEGF in breast cancer cell lines that are commonly used for understanding the role of estrogens, progestins, and anti-hormones on tumor growth. Since steroid hormones can increase the level of VEGF in certain breast cancer cells, we evaluated the effects of exogenous VEGF on the growth-suppressive effects of anti-estrogen (ICI 182,780) and RU-486 (anti-progestin mifepristone) in human breast cancer cells. VEGF165 and VEGF121 increased the proliferation of tumor cell lines that expressed VEGFR-2 (VEGF receptor 2) (flk/kdr) via the extracellular signal-regulated kinase/mitogen activated protein kinase (ERK/MAPK) pathway. Furthermore, VEGF induced the expression of the anti-apoptotic protein Bcl-2 and blocked down-regulation of Bcl-2 by ICI 182,780 and induced Bcl-2 in BT-474 and T47-D cells even in the presence of RU-486. Increased Bcl-2 levels in response to VEGF were associated with increased proliferation and survival of tumor cells even in the presence of anti-hormones. These results suggest that VEGF stimulates proliferation of VEGFR2-positive tumor cells, promotes survival via the expression and activity of Bcl-2 and overrides the growth-suppressive effects of anti-hormones. This represents a potential explanation for anti-hormone resistance and tumor progression in clinical samples. Thus, it may be useful to use combined modality treatment involving anti-hormones and anti-angiogenic agents to treat breast cancers that express elevated levels of VEGF.
Intravenous Gene Therapy With PIM-1 Via a Cardiotropic Viral Vector Halts the Progression of Diabetic Cardiomyopathy Through Promotion of Prosurvival Signaling (2011)

Pim-1 downregulation contributes in the pathogenesis of diabetic cardiomyopathy. Systemic delivery of human PIM-1 via cardiotropic adeno-associated virus serotype-9 represents a novel and effective approach to treat diabetic cardiomyopathy.
Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony (1997)

We have investigated the genetic evolution of three functionally distinct regions of the equine infectious anemia virus (EIAV) genome (env, rev, and long terminal repeat) during recurring febrile episodes in a pony experimentally infected with a well-characterized reference biological clone designated EIAV(PV). Viral populations present in the plasma of an EIAV(PV)-infected pony during sequential febrile episodes (18, 34, 80, 106, and 337 days postinfection) were amplified from viral RNA, analyzed, and compared to the inoculated strain. The comparison of the viral quasispecies showed that the inoculated EIAV(PV) quasispecies were all represented during the first febrile episode, but entirely replaced at the time of the second febrile episode, and that new predominant quasispecies were associated with each subsequent cycle of disease. One of the more surprising results was the in vivo generation of large deletion (up to 15 amino acids) in the principal neutralizing domain (PND) of gp90 during the third febrile episode. This deletion did not alter the competence for in vitro replication as shown by the analysis of a env chimeric clone with a partially deleted PND and did not altered the fitness of the virus in vivo, since this partially deleted envelope became the major population during the fourth febrile episode. Finally, we showed that the amino acid mutations were not randomly distributed but delineated eight variables regions, V1 to V8, with V3 containing the PND region. These studies provide the first detailed description of the evolution of EIAV genomic quasispecies during persistent infection and reveal new insights into the genetics and potential mechanisms of lentivirus genomic variation.
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis (2004)

Abstract Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization. Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size. Availability: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. Contact: psort-mail@sfu.ca, brinkman@sfu.ca Supplementary information: http://www.psort.org/psortb/supplementaryinfo.html
RAGE Control of Diabetic Nephropathy in a Mouse Model (2006)

Diabetic nephropathy is a major microvascular complication in long-standing diabetic patients who eventually undergo renal dialysis or transplantation. To prevent development of this disease and to improve advanced kidney injury, effective therapies directed toward the key molecular target are required. In this study, we examined whether inhibition of the receptor for advanced glycation end products (RAGE) could attenuate changes in the diabetic kidney. Here, we show that inactivation of the RAGE gene in a mouse model of diabetic nephropathy results in significant suppression of kidney changes, including kidney enlargement, increased glomerular cell number, mesangial expansion, advanced glomerulosclerosis, increased albuminuria, and increased serum creatinine compared with wild-type diabetic mice. The degree of kidney injury was proportional to RAGE gene dosage. Furthermore, we show that low-molecular weight heparin (LMWH) can bind RAGE at a mean equilibrium dissociation constant (K(d)) value of approximately 17 nmol/l and act as an antagonist to RAGE. LMWH treatment of mice significantly prevented albuminuria and increased glomerular cell number, mesangial expansion, and glomerulosclerosis in a dose-dependent manner; it also significantly improved the indexes of advanced-stage diabetic nephropathy. This study provides insight into the pathological role of RAGE in both early- and advanced-phase diabetic nephropathy and suggests that RAGE antagonists will be a useful remedy in the treatment of diabetic nephropathy.
Regulation of the Apaf-1/Caspase-9 Apoptosome by Caspase-3 and XIAP (2003)

The apoptosome is a multiprotein complex comprising Apaf-1, cytochrome c, and caspase-9 that functions to activate caspase-3 downstream of mitochondria in response to apoptotic signals. Binding of cytochrome c and dATP to Apaf-1 in the cytosol leads to the assembly of a heptameric complex in which each Apaf-1 subunit is bound noncovalently to a procaspase-9 subunit via their respective CARD domains. Assembly of the apoptosome results in the proteolytic cleavage of procaspase-9 at the cleavage site PEPD(315) to yield the large (p35) and small (p12) caspase-9 subunits. In addition to the PEPD site, caspase-9 contains a caspase-3 cleavage site (DQLD(330)), which when cleaved, produces a smaller p10 subunit in which the NH(2)-terminal 15 amino acids of p12, including the XIAP BIR3 binding motif, are removed. Using purified proteins in a reconstituted reaction in vitro, we have assessed the relative impact of Asp(315) and Asp(330) cleavage on caspase-9 activity within the apoptosome. In addition, we characterized the effect of caspase-3 feedback cleavage of caspase-9 on the rate of caspase-3 activation, and the potential ramifications of Asp(330) cleavage on XIAP-mediated inhibition of the apoptosome. We have found that cleavage of procaspase-9 at Asp(330) to generate p35, p10 or p37, p10 forms resulted in a significant increase (up to 8-fold) in apoptosome activity compared with p35/p12. The significance of this increase was demonstrated by the near complete loss of apoptosome-mediated caspase-3 activity when a point mutant (D330A) of procaspase-9 was substituted for wild-type procaspase-9 in the apoptosome. In addition, cleavage at Asp(330) exposed a novel p10 NH(2)-terminal peptide motif (AISS) that retained the ability to mediate XIAP inhibition of caspase-9. Thus, whereas feedback cleavage of caspase-9 by caspase-3 significantly increases the activity of the apoptosome, it does little to attenuate its sensitivity to inhibition by XIAP.
Comparative rates of antibiotic action against Staphylococcus epidermidis biofilms. (1992)

The relative resistance of S. epidermidis implant-associated infections to antibiotic therapy has been ascribed to a protective function of the gluelike biofilm matrix produced by strains of S. epidermidis in contact with artificial surfaces. Using a standardized S. epidermidis biofilm assay we determined the periods of exposure required by various antibiotics to produce cessation of biofilm metabolic activity. Rifampin has the superior rate of action, producing substantial disruption of biofilm activity by 7 hr of exposure, but leading to replacement of the susceptible bacterial cells by rifampin-resistant mutant survivors. Other antibiotics required longer periods of exposure, in excess of 48 hr, but produced a bactericidal outcome. Combinations of antibiotics with rifampin produced strikingly divergent results. Cefazolin and vancomycin (cell wall active antibiotics) produced a bactericidal outcome at 16 hr of exposure, whereas gentamicin (aminoglycoside) neutralized the rapid action of rifampin with metabolic activity maintained at 48 hr. We confirmed the selectively protective function of the S. epidermidis biofilm with regard to antibiotic action. In vitro biofilm assays may be of value in guiding antibiotic therapy in S. epidermidis implant-associated infection.
Dissociation of Paramyxovirus Interferon Evasion Activities: Universal and Virus-Specific Requirements for Conserved V Protein Amino Acids in MDA5 Interference (2010)

The V protein of the paramyxovirus subfamily Paramyxovirinae is an important virulence factor that can interfere with host innate immunity by inactivating the cytosolic pathogen recognition receptor MDA5. This interference is a result of a protein-protein interaction between the highly conserved carboxyl-terminal domain of the V protein and the helicase domain of MDA5. The V protein C-terminal domain (CTD) is an evolutionarily conserved 49- to 68-amino-acid region that coordinates two zinc atoms per protein chain. Site-directed mutagenesis of conserved residues in the V protein CTD has revealed both universal and virus-specific requirements for zinc coordination in MDA5 engagement and has also identified other conserved residues as critical for MDA5 interaction and interference. Mutation of these residues produces V proteins that are specifically defective for MDA5 interference and not impaired in targeting STAT1 for proteasomal degradation via the VDC ubiquitin ligase complex. Results demonstrate that mutation of conserved charged residues in the V proteins of Nipah virus, measles virus, and mumps virus also abolishes MDA5 interaction. These findings clearly define molecular determinants for MDA5 inhibition by the paramyxovirus V proteins.
Palladium/Acetic Acid Catalyzed Allylation of Some Pronucleophiles with Simple Alkynes (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPalladium/Acetic Acid Catalyzed Allylation of Some Pronucleophiles with Simple AlkynesIsao Kadota, Akinori Shibuya, Young Soo Gyoung, and Yoshinori YamamotoView Author Information Research Center for Organic Resources and Materials Chemistry Institute for Chemical Reaction Science Department of Chemistry, Graduate School of Science Tohoku University, Sendai 980-8578, Japan Cite this: J. Am. Chem. Soc. 1998, 120, 39, 10262–10263Publication Date (Web):September 17, 1998Publication History Received17 April 1998Published online17 September 1998Published inissue 1 October 1998https://pubs.acs.org/doi/10.1021/ja981299chttps://doi.org/10.1021/ja981299crapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2473Altmetric-Citations123LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Adducts,Allylation,Hydrocarbons,Organic acids,Substitution reactions Get e-Alerts
Survey of Synchronization Techniques for a TDMA Satellite-Switched System (1980)

On-board processing of signals in a communications satellite system is rapidly becoming a reality. To meet the needs in high capacity systems, new technologies are being developed, and one of the most recent is the system called time-division multiple-access, satellite-switched (TDMA/SS) which employs multiple spot beam zones. Since TDMA is employed, it is necessary for all earth stations to synchronize their time bases to a common reference which, in this case, is the sync window connection of the satellite. Synchronization for this system is a major problem which has been examined in detail in a number of different papers. This paper provides a survey of the various techniques which have been proposed in the past and gives a comparative analysis of the advantages and disadvantages of each. Factors taken into account include timing accuracy, bit energy to noise density ratio of difference signals, estimated delay for acquiring acquisition, tracking features, microcomputer implementation, and possible improvements for the future.
Analysis of sequence‐dependent curvature in matrix attachment regions (2001)

Sequence-dependent DNA conformations of matrix attachment regions (MARs) available in a database were calculated using the wedge model, and compared with randomly chosen genes, promoters, enhancers and transposons. The MARs had a longer bent part and higher angle/helical turn than the other regions. It is known that some MAR sequences have A-tracts that cause DNA bending, and we also found many A-tracts in examined MARs. Furthermore, non-random and clustered distribution of A-tracts shown here gave further evidence of the importance of A-tracts for MAR conformations. These results suggest that DNAs of MARs have a characteristic conformation instead of conserved sequence.
Local coronary supersensitivity to diverse vasoconstrictive stimuli in patients with variant angina. (1986)

It has been shown in different groups of patients with variant angina that coronary spasm can be reproduced by physiologic maneuvers and pharmacologic agents. It is not known, however, to what extent different stimuli can induce spasm in the same patient. To investigate whether coronary arterial spasm results from specific abnormal agonist-receptor interactions or from a local nonspecific coronary supersensitivity to different stimuli, 28 patients with vasospastic angina were submitted to a series of diverse vasoconstrictive stimuli known to provoke coronary spasm. Ergonovine, hyperventilation, handgrip, cold pressor, and exercise-tests, were carried out in all 28 patients. In the last 15 patients histamine was also administered. Spasm was provoked by ergonovine in 96% of patients, by hyperventilation in 54%, by histamine in 47%, by exercise in 46%, and by the cold pressor and handgrip tests in 11% and 7%, respectively. No significant differences were found in the responses to provocative tests of patients with normal coronary arteries or nonsignificant stenoses and those with significant lesions. In the same individual, spasm was induced by at least two vasoconstrictive stimuli, although with a different mechanism of action, in 82% of patients and spasm was induced by three or more stimuli in 39%. Tests were repeated in at least 23 patients and short-term reproducibility paralleled sensitivity. These results suggest that in patients with variant angina, a local nonspecific supersensitivity rather than an abnormal specific agonist-receptor interaction plays a major role in the genesis of coronary arterial spasm.
Roles of Buffer Layers in Epitaxial Growth of SrTiO3 Films on Silicon Substrates (1994)

Heteroepitaxial growth of SrTiO 3 (STO) films with and without buffer layers on Si(100) and (111) substrates has been conducted by a focused electron beam evaporation method. It has been found that thin metallic layers such as Ti and Sr are effective for improving the quality of overgrown STO films, which is probably due to the fact that the metallic layers deoxidize the surface SiO 2 layers on Si substrates. It has also been found that a Sr buffer layer is effective for obtaining fairly good epitaxial films on both Si(100) and (111) substrates, while a Ti buffer layer is effective for obtaining good electrical properties of the film and interface.