gebhart/patrepeval huggingface dataset:
Synchronization of HeLa Cells (2011)

HeLa is one of the oldest and most commonly used cell lines in biomedical research. Owing to the ease of which they can be effectively synchronized by various methods, HeLa cells have been used extensively for studies of the cell cycle. Here we describe several protocols for synchronization of HeLa cells from different phases of the cell cycle. Synchronization in G(1) phase can be achieved with the HMG-CoA reductase inhibitor lovastatin, S phase with a double thymidine block procedure, and G(2) phase with the CDK inhibitor RO3306. Cells can also be enriched in mitosis by treating with nocodazole and mechanical shake-off. Release of the cells from these blocks enables researchers to follow gene expression and other events through the cell cycle. We also describe several protocols, including flow cytometry, BrdU labeling, immunoblotting, and time-lapse microscopy, for validating the synchrony of the cells and monitoring the progression of the cell cycle after release.
Relation of Alleles of the Collagen Type Iα1 Gene to Bone Density and the Risk of Osteoporotic Fractures in Postmenopausal Women (1998)

The COLIA1 polymorphism is associated with reduced bone density and predisposes women to osteoporotic fractures.
Advantages of Using Same Species Enzyme for Replacement Therapy in a Feline Model of Mucopolysaccharidosis Type VI (1999)

In a feline model of mucopolysaccharidosis type VI (MPS VI), recombinant feline N-acetylgalactosamine-4-sulfatase (rf4S) administered at a dose of 1 mg/kg of body weight, altered the clinical course of the disease in two affected cats treated from birth. After 170 days of therapy, both cats were physically indistinguishable from normal cats with the exception of mild corneal clouding. Feline N-acetylgalactosamine-4-sulfatase was effective in reducing urinary glycosaminoglycan levels and lysosomal storage in all cell types examined except for corneal keratocytes and cartilage chondrocytes. In addition, skeletal pathology was nearly normalized as assessed by radiographic evidence and bone morphometric analysis. Comparison of results with a previous study in which recombinant human 4S (rh4S) was used at an equivalent dose and one 5 times higher indicated that rf4S had a more pronounced effect on reducing pathology than the same dose of rh4S, and in some instances such as bone pathology and lysosomal storage in aorta smooth muscle cells, it was as good as, or better than, the higher dose of rh4S. We conclude that in the feline MPS VI model the use of native or same species enzyme for enzyme replacement therapy has significant benefits.
Modification of Thiol Functionalized Aptamers by Conjugation of Synthetic Polymers (2009)

Aptamers are known for their short in vivo circulating half-life and rapid renal clearance. Their conjugation to poly(ethylene glycol) (PEG) is a way to improve their residence in the body. Two aptamers (AptD and AptF), having a disulfide protected thiol modification on the 3' end, have been conjugated to maleimide activated PEGs of various molecular weights and structures (linear PEG20; branched PEG20 and 40; PolyPEG17, 40, and 60 kDa). The high yield coupling (70-80% in most of the cases) could be achieved using immobilized tris[2-carboxyethyl]phosphine hydrochloride (TCEP) as reducing agent at pH 4. The affinity of PEGylated AptD for its target was reduced by conjugation to linear PEG20 and branched PEG40, but not to branched PEG20 and PolyPEGs. This work demonstrates an alternative approach to PEGylation of aptamers, and that the effect of PEG on the affinity for the target varies according to the structure and conformation of the synthetic polymer.
Növekedés, csőd és ciklusok. (A végtelen modell csonkítása és spektruma) [Growth, failure and cycles. (Truncation and spectrum of the infinite model)] (1995)

W. Leontief megalkotta a gazdasagi novekedes vegtelen linearis modelljet. A szamitasokat azonban a modell veges szeletevel vegezzuk. Ezt a veges reszt tobbfelekeppen is ki lehet valasztani. Az eredetileg publikalt forma a gazdasag felszamolasanak nyomvonalat adja meg. Ezert elterő megoldast javasolok. Ez maskeppen csonkitja veges meretűve a modell elmeletileg ketszeresen is vegtelen matrixat. A ketfajta csonkitas a gazdasagi csőd es a gazdasagi novekedes ket, egymastol jellegzetesen elterő palyajat adja. A novekedes teljes egyensulya mindig csak a csonkitatlan, azaz vegtelen matrix megoldasa lehet. Itt is felbukkan egy masodik, egyensulyi, amde csokkenő palya lehetősege. Mindezert megkiserlem a modellt - R. Godwin elmelete alapjan - a gazdasagi ingadozas modellezesere is felhasznalni. Ezzel mod nyilik a ciklusok időtartamanak es eloszlasanak kiszamitasara es a rendszer lehetseges mozgasformainak egyseges abrazolasara.
Efficient Gene Transfer Using Reversibly Cross-Linked Low Molecular Weight Polyethylenimine (2001)

Polyethylenimine (PEI) is a polycation with potential application as a nonviral vector for gene delivery. Here we show that after conjugation with homobifunctional amine reactive reducible cross-linking reagents, low molecular weight polyethylenimine efficiently mediates in vitro gene delivery to Chinese hamster ovary (CHO) cells. Two cross-linking reagents, dithiobis(succinimidylpropionate) (DSP) and dimethyl.3,3'-dithiobispropionimidate*2HCl (DTBP), were utilized based on their reactivity and chemical properties. Both reagents react with primary amines to form reducible cross-links; however, unlike DSP, the DTBP cross-linker maintains net polymer charge through amidine bond formation. PEI with a reported weight-average molecular weight (M(w)) of 800 Da was reacted with either DSP or DTBP at PEI primary amine:cross-link reactive group ratios of 1:1 and 2:1. The transfection efficiencies of the resulting cross-linked products were evaluated in CHO cells using a luciferase reporter gene under a cytomegalovirus (CMV) promoter. Our results show that cross-linked polymers mediate variable levels of transfection depending on the cross-linking reagent, the extent of conjugation, and the N/P ratio. In general, we found conjugate size to be proportional to gene transfer efficiency. Using gel retardation analysis, we also evaluate the capacity of the cross-linked polymers to condense plasmid DNA before and after reduction with 45 mM dithiothreitol (DTT). DTT mediated reduction of intra-cross-link disulfide bonds and inhibited condensation of DNA by conjugates cross-linked with DSP at a ratio of 1:1, but had little effect on the remaining polymers. Analogous intracellular reduction of transfection complexes by reduced glutathione could facilitate uncoupling of PEI from DNA to enhance gene expression.
TCR Gene Rearrangements and Expression of the Pre-T Cell Receptor Complex During Human T-Cell Differentiation (1999)

Recent studies have identified several populations of progenitor cells in the human thymus. The hematopoietic precursor activity of these populations has been determined. The most primitive human thymocytes express high levels of CD34 and lack CD1a. These cells acquire CD1a and differentiate into CD4+CD8+ through CD3−CD4+CD8− and CD3−CD4+CD8+β− intermediate populations. The status of gene rearrangements in the various TCR loci, in particular of TCRδ and TCRγ, has not been analyzed in detail. In the present study we have determined the status of TCR gene rearrangements of early human postnatal thymocyte subpopulations by Southern blot analysis. Our results indicate that TCRδ rearrangements initiate in CD34+CD1a− cells preceding those in the TCRγ and TCRβ loci that commence in CD34+CD1a+ cells. Furthermore, we have examined at which cellular stage TCRβ selection occurs in humans. We analyzed expression of cytoplasmic TCRβ and cell-surface CD3 on thymocytes that lack a mature TCRβ. In addition, we overexpressed a constitutive-active mutant of p56lckF505 by retrovirus-mediated gene transfer in sequential stages of T-cell development and analyzed the effect in a fetal thymic organ culture system. Evidence is presented that TCRβ selection in humans is initiated at the transition of the CD3−CD4+CD8− into the CD4+CD8+β− stage.
Identification of Splicing Silencers and Enhancers in Sense Alus: a Role for Pseudoacceptors in Splice Site Repression (2005)

Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3′ splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.
Two antigenically distinct species of human interferon. (1975)

Rabbit antisera prepared against interferon produced in human fibroblast cell cultures stimulated with poly(1).poly(C) neutralized the activity of interferon preparations produced in various human fibroblast cultures timulated either with poly(1)poly)C) or with viruses. However, these antisera showed no detectable neutralizing activity against interferon produced in cultures of human leukocytes. On the other hand, most rabbit antisera against the human leukocyte interferon were active in neutralizing both homologous interferon and fibroblast interferons. A preparation of antiserum against leukocyte interferon, active against both leukocyte and fibroblast interferons, was shown by affinity chromatography to have two distinct antibody populations, one of which was specific for the fibroblast interferon. We conclude that the heterologous neutralizing activity of sera from rabbits immunized with leukocyte interferon is liekly to be due to the presence of two antigenic species of interferon. The major antigenic species of leukocyte interferon preparations (designated "Le") is distinct from huamn fibroblast interferon. The minor species of leukocyte interferon ("F") is either identical with, or closely related to, interferon produced in human fibroblast cultures.
PCR primers to amplify 16S rRNA genes from cyanobacteria (1997)

We developed and tested a set of oligonucleotide primers for the specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR. PCR products were recovered from all cultures of cyanobacteria and diatoms that were checked but not from other bacteria and archaea. Gene segments selectively retrieved from cyanobacteria and diatoms in unialgal but nonaxenic cultures and from cyanobionts in lichens could be directly sequenced. In the context of growing sequence databases, this procedure allows rapid and phylogenetically meaningful identification without pure cultures or molecular cloning. We demonstrate the use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities.
Molecular cloning and functional characterization of two CYP619 cytochrome P450s involved in biosynthesis of patulin in Aspergillus clavatus (2009)

Patulin is an acetate-derived tetraketide mycotoxin produced by several fungal species, especially Aspergillus, Penicillium and Byssochlamys species. The health risks due to patulin consumption by humans have led many countries to regulate it in human food. Previous studies have shown the involvement of cytochrome P450 monooxygenases in the hydroxylation of two precursors of patulin, m-cresol and m-hydroxybenzylalcohol. In the present study, two cytochrome P450 genes were identified in the genome sequence of Aspergillus clavatus, a patulin-producing species. Both mRNAs were strongly co-expressed during patulin production. CYP619C2, encoded by the first gene, consists of 529 aa, while the second cytochrome, CYP619C3, consists of 524 aa. The coding sequences were used to perform the heterologous expression of functional enzymes in Saccharomyces cerevisiae. The bioconversion assays showed that CYP619C3 catalysed the hydroxylation of m-cresol to yield m-hydroxybenzyl alcohol. CYP619C2 catalysed the hydroxylation of m-hydroxybenzyl alcohol and m-cresol to gentisyl alcohol and 2,5-dihydroxytoluene (toluquinol), respectively. Except for the last compound, all enzyme products are known precursors of patulin. Taken together, these data strongly suggest the involvement of CYP619C2 and CYP619C3 in the biosynthesis of patulin. CYP619C2 and CYP619C3 are located near to two other genes involved in patulin biosynthesis, namely the 6-methylsalicylic acid synthase (6msas) and isoepoxydon dehydrogenase (idh) genes. The current data associated with an analysis of the sequence of A. clavatus suggest the presence of a cluster of 15 genes involved in patulin biosynthesis.
1,3-Dimethylimidazolin-2-ylidene Carbene Donor Ligation in Lanthanide Silylamide Complexes (1997)

The synthesis and X-ray crystal structures of Y[N(SiHMe2)2]3(carbene)x (carbene = 1,3-dimethylimidazolin-2-ylidene, x = 1, 2) are described. The donor capability of the strongly nucleophilic carbene ligand is expressed in both the displacement of two THF ligands by one carbene ligand in precursor compound Y[N(SiHMe2)2]3(THF)2 and by the addition of a second carbene ligand to yield the preferred (3 + 2) trigonal bipyramidal coordination geometry. In particular, the structural data reveal that the carbene ligands affect the coordination mode of the bis(dimethylsilyl)amide counterligands by forcing them to form close β-Si−H(silylamide)−yttrium agostic contacts. According to Pearson's terminology such carbene ligands have to be classified as hard donor ligands.
A single framework for vehicle roll, pitch, yaw estimation and obstacles detection by stereovision (2004)

This paper presents original framework and method for robust estimation of vehicle roll, pitch, yaw and obstacles detection using stereovision. The "v-disparity" algorithm for generic road obstacles detection, described and evaluated by Labayrade et al. (2002, 2003), is here extended to provide accurate and reliable values of the Euler angles of the vehicle. The algorithm can be divided in three main stages. The first one is designed for roll and pitch estimation. The second one is about obstacles detection and free road estimation. The third one concerns yaw estimation. Each stage is presented and experimental results are shown. In particular, the roll angle is estimated with a precision better than 0.2/spl deg/.
Infectious and Oncogenic Effect of DNA Extracted from Cells Infected with Polyoma Virus (1964)

SummaryThirty-five newborn hamsters were injected subcutaneously (approx. 70 μg) or intracerebrally (15 μg) with DNA from polyoma-infected cultures of embryonal mouse cells. All animals showed circulating antibodies and 26 of them presented tumors, mostly of subcutaneous localization, after intervals of 2 to 3 months. Fully grown hamsters appeared to be less sensitive; of 17 animals, 11 developed antibodies and 5 developed tumors. The same DNA preparations were shown to be capable of infecting primary cultures of mouse kidney cells. All the control series, in which use was made of DNA treated with DNase or of DNA originating from non-infected cells, have given negative results both in vivo and in vitro.
Mechanical tissue optical clearing devices: Enhancement of light penetration in ex vivo porcine skin and adipose tissue (2008)

Results of our study suggest that mechanical optical clearing may provide a means to deliver increased light fluence to dermal and adipose tissues.
Challenges for Research on Polyphenols from Foods in Alzheimer’s Disease: Bioavailability, Metabolism, and Cellular and Molecular Mechanisms (2008)

Polyphenols are the most abundant antioxidants in diet. Indeed, fruits, vegetables, beverages (tea, wine, juices), plants, and some herbs are loaded with powerful antioxidant polyphenols. Despite their wide distribution, research on human health benefits truly began in the mid-1990s (Scalbert, A.; Johnson, I. T.; Saltmarsh, M. Am. J. Clin. Nutr. 2005, 81, S15S-217S). Phenolic compounds have been receiving increasing interest from consumers and manufacturers because numerous epidemiological studies have suggested associations between consumption of polyphenol-rich foods or beverages and the prevention of certain chronic diseases such as cancers and cardiovascular diseases (Manach, C.; Mazur, A.; Scalbert, A. Curr. Opin. Lipidol. 2005, 16, 77-84; Duthie, S. J. Mol. Nutr. Food Res. 2007, 51, 665-674). Furthermore, in the past 10 years, research on the neuroprotective effects of dietary polyphenols has developed considerably. These compounds are able to protect neuronal cells in various in vivo and in vitro models through different intracellular targets (Ramassamy, C. Eur. J. Pharmacol. 2006, 545, 51-64). However, it is not at all clear whether these compounds reach the brain in sufficient concentrations and in a biologically active form to exert beneficial effects. On the other hand, it has become clear that the mechanisms of action of these polyphenols go beyond their antioxidant activity and the attenuation of oxidative stress. Therefore, there is a need for more research on their intracellular and molecular targets as special pathways underlying distinct polyphenol-induced neuroprotection. The focus of this review is aimed at presenting the role of some polyphenols from fruits, vegetables, and beverages in neuroprotection and particularly in Alzheimer's disease and the research challenges in this area.
A Combinatorial Approach for Polymer Design (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Combinatorial Approach for Polymer DesignStephen Brocchini, Kenneth James, Varawut Tangpasuthadol, and Joachim KohnView Author Information Department of Chemistry Rutgers, The State University of New Jersey New Brunswick, New Jersey 09803 Cite this: J. Am. Chem. Soc. 1997, 119, 19, 4553–4554Publication Date (Web):May 14, 1997Publication History Received5 February 1997Published online14 May 1997Published inissue 1 May 1997https://pubs.acs.org/doi/10.1021/ja970389zhttps://doi.org/10.1021/ja970389zrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1686Altmetric-Citations230LEARN 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:Cell physiology,Chemical structure,Contact angle,Monomers,Polymers Get e-Alerts
Bone Marrow–Derived Cardiomyocytes Are Present in Adult Human Heart (2003)

These data establish for the first time human bone marrow as a source of extracardiac progenitor cells capable of de novo cardiomyocyte formation.
Integrative Genomic Analysis Identifies NDRG2 as a Candidate Tumor Suppressor Gene Frequently Inactivated in Clinically Aggressive Meningioma (2005)

Although meningiomas are common central nervous system tumors, little is known about the genetic events responsible for malignant progression. In this study, we employed gene expression profiling to identify transcripts whose expression was lost in anaplastic (WHO grade III) versus benign (WHO grade I) meningioma. Approximately 40% of genes down-regulated in anaplastic meningioma were localized to chromosomes 1p and 14q. One specific gene located at 14q11.2, NDRG2, was consistently down-regulated in grade III meningioma, a finding which we validated at both the transcript and protein levels in independent sets of clinically and pathologically diverse meningiomas. Loss of NDRG2 expression was also seen in a subset of lower-grade meningiomas, including atypical meningiomas (WHO grade II) with clinically aggressive behavior. Furthermore, we found that the loss of NDRG2 expression was significantly associated with hypermethylation of the NDRG2 promoter. Collectively, these data identify NDRG2 as the first specific candidate tumor suppressor gene on chromosome 14q that is inactivated during meningioma progression. In addition, these findings highlight the utility of combining genomic, epigenetic, and expression data to identify clinically significant tumor biomarkers, and suggest that NDRG2 expression will be a useful and functionally relevant biomarker to predict aggressive behavior in patients with meningioma.
A Bidirectional Promoter Connects the Poly(ADP-ribose) Polymerase 2 (PARP-2) Gene to the Gene for RNase P RNA (2001)

Poly(ADP-ribose) polymerase 2 (PARP-2) is a DNA damage-dependent enzyme that belongs to a growing family of enzymes seemingly involved in genome protection. To gain insight into the physiological role of PARP-2 and to investigate mechanisms of PARP-2 gene regulation, we cloned and characterized the murine PARP-2 gene. The PARP-2 gene consists of 16 exons and 15 introns spanning about 13 kilobase pairs. Interestingly, the PARP-2 gene lies head to head with the gene encoding the mouse RNase P RNA subunit. The distance between the transcription start sites of the PARP-2 and RNase P RNA genes is 114 base pairs. This suggested that regulation of the expression of both genes may be coordinated through a bi-directional promoter. The PARP-2/RNase P RNA gene organization is conserved in the human. To our knowledge, this is the first report of a RNA polymerase II gene and an RNA polymerase III gene sharing the same promoter region and potentially the same transcriptional control elements. Reporter gene constructs showed that the 113-base pair intergenic region was indeed sufficient for the expression of both genes and revealed the importance of both the TATA and the DSE/Oct-1 expression control elements for the PARP-2 gene transcription. The expression of both genes is clearly independently regulated. PARP-2 is expressed only in certain tissues, and RNase P RNA is expressed in all tissues. This suggests that both genes may be subjected to multiple levels of control and may be regulated by different factors in different cellular contexts.