gebhart/patrepeval huggingface dataset:
Long-term patency rates, complications and cost-effectiveness of polytetrafluoroethylene (PTFE) grafts for hemodialysis access: a prospective study that compares Impra versus Gore-tex grafts (1998)

Manufacturers of polytetraflouroethylene (PTFE) grafts used for chronic hemodialysis access describe specific advantages for their respective grafts, which presumably result in greater graft patency rates, reduced complications and decreased overall costs. There are few data available in the literature to support or contradict these alleged benefits. Therefore, this prospective study was undertaken to evaluate and compare patency rates, complications and costs between two of the leading brands of PTFE that are currently being marketed for use as hemodialysis access grafts. Totals of 190 primary PTFE grafts (100 Gore-tex (W. L. Gore and Associates, Flagstaff, AZ) and 90 Impra (C. R. Bard Inc., Tempe, AZ)) were implanted in 168 consecutive patients with end-stage renal disease. A policy of non-interventions was employed for patent grafts, as no attempt was made to assist primary patency. Grafts that occluded during follow-up underwent secondary revision to maintain patency. There was no difference in primary and secondary patency by life-table analysis between Gore-tex and Impra grafts at 2 years (P > 0.53 and P > 0.13, respectively). There was also no significant difference between Gore-tex and Impra in the number of days before the first thrombectomy or in the number of thrombectomies or revisions per graft (P > O.50). Likewise, the incidence of complications was similar between the two grafts. The cost of graft implantation and maintenance of patency was not significantly different between Gore-tex and Impra grafts. It is concluded that either graft can be used for hemodialysis access with similar expected outcomes for at least 2 years following implantation.
Current bursts in lipid bilayers initiated by colloidal quantum dots (2005)

Inorganic semiconductor nanocrystals, also called quantum dots, have recently attracted considerable interest as fluorescent labels. We report that CdSe QDs initiate current bursts in lipid bilayer membranes upon application of a bias voltage. The current bursts observed resemble those produced by the peptaibol class of antibiotics such as alamethicin and trichorzins. The current fluctuations are dependent on the bias voltage and on the concentration of the quantum dots applied to the membrane. Our data suggest that quantum dots with dipole moments similar to alamethicin are influenced by an external electric field, which creates a torque resulting in the insertion into the lipid membrane. We predict that at least three quantum dots are required to form a pore due to aggregation that leads to a macroscopic conductance.
Plexiform-like lesions and increased tissue factor expression in a rat model of severe pulmonary arterial hypertension (2007)

Severe pulmonary arterial hypertension (PAH) occurs in idiopathic form and in association with diverse diseases. The pathological hallmarks are distal smooth muscle hypertrophy, obliteration of small pulmonary arteriole lumens, and disorganized cellular proliferation in plexiform lesions. In situ thrombosis is also observed. A detailed understanding of the disease progression has been hampered by the absence of an animal model bearing all the pathological features of human disease. To create a model with these characteristics, we gave young (200-g) rats monocrotaline 1 wk following left pneumonectomy; controls with vehicle treatment or sham operation were also studied. In experimental rats, pulmonary arteries had distal smooth muscle hypertrophy and proliferative perivascular lesions. The lesions had a plexiform appearance, occurred early in disease development, and were composed of cells expressing endothelial antigens. Three-dimensional microangiography revealed severe vascular pruning and disorganized vascular networks. We found that expression of tissue factor (TF), the membrane glycoprotein that initiates coagulation, facilitates angiogenesis, and mediates arterial injury in the systemic circulation, was increased in the pulmonary arterioles and plexiform-like lesions of the rats. TF was also heavily expressed in the vessels and plexiform lesions of humans with pulmonary arterial hypertension. We conclude that plexiform-like lesions can be reproduced in rats, and this model will facilitate experiments to address controversies about the role of these lesions in PAH. Increased TF expression may contribute to the prothrombotic diathesis and vascular cell proliferation typical of human disease.
Radioiodinated Capsids Facilitate In Vivo Non-Invasive Tracking of Adeno-Associated Gene Transfer Vectors (2017)

Viral vector mediated gene therapy has become commonplace in clinical trials for a wide range of inherited disorders. Successful gene transfer depends on a number of factors, of which tissue tropism is among the most important. To date, definitive mapping of the spatial and temporal distribution of viral vectors in vivo has generally required postmortem examination of tissue. Here we present two methods for radiolabeling adeno-associated virus (AAV), one of the most commonly used viral vectors for gene therapy trials, and demonstrate their potential usefulness in the development of surrogate markers for vector delivery during the first week after administration. Specifically, we labeled adeno-associated virus serotype 10 expressing the coding sequences for the CLN2 gene implicated in late infantile neuronal ceroid lipofuscinosis with iodine-124. Using direct (Iodogen) and indirect (modified Bolton-Hunter) methods, we observed the vector in the murine brain for up to one week using positron emission tomography. Capsid radioiodination of viral vectors enables non-invasive, whole body, in vivo evaluation of spatial and temporal vector distribution that should inform methods for efficacious gene therapy over a broad range of applications.
A protective protein antigen of Rickettsia rickettsii has tandemly repeated, near-identical sequences (1990)

The nucleotide sequence of a Rickettsia rickettsii gene that encodes a high-molecular-mass surface antigen (190 kilodaltons), which elicits protective immunity, was determined. The 6,747-nucleotide gene coded for a 2,249-amino-acid protein with a calculated molecular weight of 224,321. A 3.8-kilobase PstI fragment proximal to the 5' end of the gene was found to consist of 13 highly related tandem repeats which constituted over 40% of the coding region. The repeated sequences could be divided into either a 225-nucleotide, 75-amino-acid unit (type I) or a 216-nucleotide, 72-amino-acid unit (type II), with extensive homology between the two types of repeating units. The deduced amino acid sequence for these repeat units, overall, was slightly hydrophobic with short hydrophilic domains. The carboxy-terminal (nonrepetitive) portion of the deduced protein sequence was hydrophilic, with potential surface-exposed epitopes. The full-length reading frame was reconstructed in Escherichia coli, and transient expression of the 190-kilodalton antigen was demonstrated; however, the protein appeared to be severely degraded by proteases and was apparently toxic to E. coli. The conservation of this unique repetitive gene structure, coupled with results from previous reports showing the protective properties of the 190-kilodalton antigen, suggests that this protein plays an important role in the pathogenesis of and immunity to Rocky Mountain spotted fever.
The Methylation Effect in Medicinal Chemistry (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTThe Methylation Effect in Medicinal ChemistryEliezer J. Barreiro*†‡§, Arthur E. Kümmerle†§, and Carlos A. M. Fraga†‡§View Author Information† Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, CP 68.006, 21941-902 Rio de Janeiro, RJ, Brazil‡ Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil§ Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, BrazilPhone: 55-21-25626644. E-mail: [email protected]. Website: http://www.farmacia.ufrj.br/lassbio.Cite this: Chem. Rev. 2011, 111, 9, 5215–5246Publication Date (Web):June 1, 2011Publication History Received18 February 2011Published online1 June 2011Published inissue 14 September 2011https://pubs.acs.org/doi/10.1021/cr200060ghttps://doi.org/10.1021/cr200060greview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views18979Altmetric-Citations659LEARN 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-Alertsclose SUBJECTS:Alkyls,Inhibitors,Pharmaceuticals,Reaction products,Receptors Get e-Alerts
A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047 (2009)

Abstract Background Polyamines regulate important cellular functions and polyamine dysregulation frequently occurs in cancer. The objective of this study was to use a systems approach to study the relative effects of PG-11047, a polyamine analogue, across breast cancer cells derived from different patients and to identify genetic markers associated with differential cytotoxicity. Methods A panel of 48 breast cell lines that mirror many transcriptional and genomic features present in primary human breast tumours were used to study the antiproliferative activity of PG-11047. Sensitive cell lines were further examined for cell cycle distribution and apoptotic response. Cell line responses, quantified by the GI<sub>50 </sub>(dose required for 50% relative growth inhibition) were correlated with the omic profiles of the cell lines to identify markers that predict response and cellular functions associated with drug sensitivity. Results The concentrations of PG-11047 needed to inhibit growth of members of the panel of breast cell lines varied over a wide range, with basal-like cell lines being inhibited at lower concentrations than the luminal cell lines. Sensitive cell lines showed a significant decrease in S phase fraction at doses that produced little apoptosis. Correlation of the GI<sub>50 </sub>values with the omic profiles of the cell lines identified genomic, transcriptional and proteomic variables associated with response. Conclusions A 13-gene transcriptional marker set was developed as a predictor of response to PG-11047 that warrants clinical evaluation. Analyses of the pathways, networks and genes associated with response to PG-11047 suggest that response may be influenced by interferon signalling and differential inhibition of aspects of motility and epithelial to mesenchymal transition. See the related commentary by Benes and Settleman: <url>http://www.biomedcentral.com/1741-7015/7/78</url>
Adsorption and Conformation of Polymeric Surfactants at the Solid–Liquid Interface (2012)

This chapter contains sections titled: Theories of Polymer Adsorption Experimental Techniques for Studying Polymeric Surfactant Adsorption Measurement of the Adsorption Isotherm Measurement of the Fraction of Segments p Determination of the Segment Density Distribution ρ(z) and Adsorbed Layer Thickness δh Examples of the Adsorption Isotherms of Nonionic Polymeric Surfactants Adsorbed Layer Thickness Results Kinetics of Polymer Adsorption References
Monoclonal antibodies to a glycolipid antigen on human neuroblastoma cells. (1985)

Using a somatic cell hybridization technique, four murine monoclonal antibodies (three immunoglobulin M and one immunoglobulin G3) were produced against a human neuroblastoma cell surface glycolipid antigen. They reacted strongly with all human neuroblastoma tumor-containing specimens and six of eight human neuroblastoma cell lines. More than 98% of each neuroblastoma cell population possessed this surface antigen, and in the presence of complement, 100% of them were killed. While melanoma and osteogenic sarcoma carried this antigen, leukemia and most Ewing's and Wilms' tumors did not. There was no cross-reaction with 30 normal or remission bone marrow samples and none with normal human tissues other than neurons in vitro. This antigen was neuraminidase sensitive, separable on thin-layer chromatogram, and did not modulate after combining with the monoclonal antibodies. These antibodies could detect less than 0.1% tumor cells deliberately seeded in the bone marrow samples. Because of their unique properties, these monoclonal antibodies may have diagnostic and therapeutic potentials.
Effects of Fluoxetine Treatment on Striatal Dopamine Transporter Binding and Cerebrospinal Fluid Insulin-Like Growth Factor-1 in Children with Autism (2011)

A positive effect of fluoxetine has been shown in some children with autism. The present study was undertaken to correlate striatal dopamine transporter (DAT) binding and cerebrospinal fluid insulin-like growth factor-1 (CSF-IGF-1) with clinical response in autistic children (n=13, age 5-16 years) after a 6-month fluoxetine treatment. Good clinical responders (n=6) had a decrease (p=0.031) in DAT binding as assessed using single-photon emission computed tomography with [123I]-nor-β-CIT, whereas poor responders had a trend to an increase. An increase in CSF-IGF-1 (p=0.003) was detected after the treatment period, but no correlation between the clinical response and CSF-IGF-1 was found. In conclusion, fluoxetine decreases DAT binding indicating alleviation of the hyperdopaminergic state and increases CSF-IGF-1 concentration, which may also have a neuroprotective effect against dopamine-induced neurotoxicity in autistic children.
Molecular genetics and nomenclature of proteases of Porphyromonas gingivalis (1999)

The strategies used by bacterial pathogens to establish and maintain themselves in the host represent one of the fundamental aspects of microbial pathogenesis. Characterization of these strategies and the underlying molecular machinery offers new opportunities both to our understanding of how organisms cause disease in susceptible individuals and to the development of novel therapeutic measures designed to undermine or interfere with these determinants of successful survival. With respect to the microbial aetiology of the periodontal diseases, a growing body of evidence suggests that the proteolytic enzymes of Porphyromonas gingivalis represent key survival and, by extrapolation, virulence determinants of this periodontal bacterium. This in turn has led to international efforts to characterize these enzymes at the gene and protein level. Approximately 20 protease genes of P. gingivalis with different names and accession numbers have been deposited in the gene databases and a correspondingly heterogeneous nomenclature system is employed for the products of these genes in the literature. However, it is evident, through comparison of these gene sequences and through gene inactivation studies, that the genetic structure of the proteases of this organism, particularly those with specificity for arginyl and lysyl peptide bonds, is less complicated than originally thought. The major extracellular and surface associated arginine specific protease activity is encoded by 2 genes which we recommend be designated rgpA and rgpB (arg-gingipains A & B). Similarly we recommend that the gene encoding the major lysine specific protease activity is designated kgp (lys-gingipain). These three genes, which account for all the extracellular/surface arginine and lysine protease activity in P. gingivalis, belong to a family of sequence-related proteases and haemagglutinins.
Uniformly modified 2'-deoxy-2'-fluoro-phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets (1993)

"Uniformly" modified phosphodiester or phosphorothioate oligonucleotides incorporating 2'-deoxy-2'-fluoroadenosine, -guanosine, -uridine, and -cytidine, reported herein for the first time, when hybridized with RNA afforded consistent additive enhancement of duplex stability without compromising base-pair specificity. CD spectra of the 2'-deoxy-2'-fluoro-modified oligonucleotides hybridized with RNA indicated that the duplex adopts a fully A-form conformation. The 2'-deoxy-2'-fluoro-modified oligonucleotides in phosphodiester form were not resistant to nucleases; however, the modified phosphorothioate oligonucleotides were highly nuclease resistant and retained exceptional binding affinity to the RNA targets. The stabilizing effects of the 2'-deoxy-2'-fluoro modifications on RNA-DNA duplexes were shown to be superior to those of the 2'-O-methylribo substitutions. RNA hybrid duplexes with uniformly 2'-deoxy-2'-fluoro-modified oligonucleotides did not support HeLa RNase H activity; however, incorporation of the modifications into "chimeric" oligonucleotides has been shown to activate mammalian RNase H. "Uniformly" modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides afforded antisense molecules with (1) high binding affinity and selectivity for the RNA target and (2) stability toward nucleases.
A Noninvasive Method for Determining Patterns of Milk Intake in the Breast-Fed Infant (1989)

A noninvasive adaptation of the test-weighing method has been devised for continuously monitoring milk intake in breast-fed infants. This procedure consists of counting the number of swallows from videotaped sessions of individual feeds and correlating them to the corresponding pre- and postnursing weights of the infants. The method has been tested on four nursing sessions in twins aged 1 1/2 to 2 1/2 months. A high correlation was found between swallow counts and weight gain of the babies. The patterns of milk intake as monitored by these two parameters were similar. This method has the advantage of not disrupting the natural nursing process because test-weighing during the feeding session is not necessary. In addition, it allows for longitudinal studies and uses relatively simple equipment, i.e., a balance and a video camera. It is further suggested that monitoring swallowing in the manner described herein may be a valuable addition to studies on sucking behavior in human infants. Finally, it is noted from the data presented that the pattern of milk transfer in a mother breast-feeding twins is different from that observed in mothers breast-feeding singletons who were monitored by means of a cross-sectional test-weighing procedure.
Spontaneous Hybridization Between Oilseed Rape (Brassica napus) and Weedy B. campestris (Brassicaceae): A Risk of Growing Genetically Modified Oilseed Rape (1994)

Frequencies of spontaneous hybridization between oilseed rape (Brassica napus L.) and weedy Brassica campesíris ssp. campestris L. were measured in agricultural fields. Hybrids were identified by enzyme electrophoresis, random amplified polymorphic DNA (RAPD) analysis, chromosome counting, morphology, and pollen fertility. When the two species were mixed 1:1, B. campestris produced 13% hybrid seeds and oilseed rape 9%. In two experiments with single plants of the self-incompatible B. campestris widely spaced within fields of oilseed rape, 56% and 93% hybrid seeds were produced. Analysis of a weedy population of B. campestris in oilseed rape revealed 60% hybrid seeds. Backcrossing of the hybrids to the weedy species seems to occur as supported by the finding in a natural population of two B. campestris-like plants with a marker specific to oilseed rape. The results suggest that transgenes could be dispersed from oilseed rape to B. campestris.
Body Image, Eating Disorders, and Obesity—An Emerging Synthesis (1996)

A new technique is introduced for doping gold nanoclusters by using a metal surface such as Ag, Cu and Cd as a source of heteroatoms. The importance of the thiol ligand in the doping process is examined by following the reactions with MALDI-TOF mass spectrometry in the presence and the absence of the thiols on the surface. The doping reactions depend greatly on the type of the cluster and the availability of the ligand which is a crucial element for alloying. The thiol acts as a messenger exchanging the metal atoms between the cluster and the metal surface as revealed by the XPS studies performed on the metal surfaces.
Benign prostatic hyperplasia (1994)

Department of Urology, Mayo Clinic and Mayo Foundation, Rochester, Minnesota *Department of Urology, New York University Medical Center, New York, USA Joseph E. Oesterling, Department of Urology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
AgoFISH: cost-effective in situ labelling of genomic loci based on DNA-guided dTtAgo protein (2019)

A cost-effective and simple method for <italic>in situ</italic> labelling of genomic loci utilizing the DNA-guided DNA binding activity of the nuclease-deficient Argonaute protein in <italic>Thermus thermophilus</italic> (dTtAgo).
The regulatory utilization of genetic redundancy through responsive backup circuits (2006)

Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such "responsive backup circuits" in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.