gebhart/patrepeval huggingface dataset:
Molecular Cloning and Expression of a Novel β-1,6-N-Acetylglucosaminyltransferase That Forms Core 2, Core 4, and I Branches (1999)

Mucin-type O-glycans are classified according to their core structures. Among them, cores 2 and 4 are important for having N-acetyllactosamine side chains, which can be further modified to express various functional oligosaccharides. Previously, we discovered by cloning cDNAs that the core 2 branching enzyme, termed core 2 beta-1,6-N-acetylglucosaminyltransferase-leukocyte type (C2GnT-L), is highly homologous to the I branching beta-1, 6-N-acetylglucosaminyltransferase (IGnT) (Bierhuizen, M. F. A., Mattei, M.-G., and Fukuda, M. (1993) Genes Dev. 7, 468-478). Using these homologous sequences as probes, we identified an expressed sequence tag in dbEST, which has significant homology to C2GnT-L and IGnT. This approach, together with 5'and 3' rapid amplification of cDNA ends, yielded a human cDNA that encompasses a whole coding region of an enzyme, termed C2GnT-mucin type (C2GnT-M). C2GnT-M has 48.2 and 33.8% identity with C2GnT-L and IGnT at the amino acid levels. The expression of C2GnT-M cDNA directed the expression of core 2 branched oligosaccharides and I antigen on the cell surface. Moreover, a soluble chimeric C2GnT-M had core 4 branching activity in addition to core 2 and I branching activities. A soluble chimeric C2GnT-L, in contrast, almost exclusively contains core 2 branching activity. Northern blot analysis demonstrated that the C2GnT-M transcripts are heavily expressed in colon, small intestine, trachea, and stomach, where mucin is produced. In contrast, the transcripts of C2GnT-L were more widely detected, including the lymph node and bone marrow. These results indicate that the newly cloned C2GnT-M plays a critical role in O-glycan synthesis in mucins and might have distinctly different roles in oligosaccharide ligand formation compared with C2GnT-L.
Influence of topology on bacterial social interaction (2003)

The environmental topology of complex structures is used by Escherichia coli to create traveling waves of high cell density, a prelude to quorum sensing. When cells are grown to a moderate density within a confining microenvironment, these traveling waves of cell density allow the cells to find and collapse into confining topologies, which are unstable to population fluctuations above a critical threshold. This was first observed in mazes designed to mimic complex environments, then more clearly in a simpler geometry consisting of a large open area surrounding a square (250 x 250 microm) with a narrow opening of 10-30 microm. Our results thus show that under nutrient-deprived conditions bacteria search out each other in a collective manner and that the bacteria can dynamically confine themselves to highly enclosed spaces.
Treatment of phenylketonuria using minicircle-based naked-DNA gene transfer to murine liver (2014)

This study demonstrates that MC technology offers an improved safety profile and has the potential for the genetic treatment of liver diseases.
Increased susceptibility to light damage in an arrestin knockout mouse model of Oguchi disease (stationary night blindness) (1999)

The results indicate that constitutive signal flow due to arrestin knockout leads to photoreceptor degeneration. Excessive light accelerates the cell death process in pigmented arrestin knockout mice. Human patients with naturally occurring mutations that lead to nonfunctional arrestin and rhodopsin kinase have Oguchi disease, a form of stationary night blindness. The present findings suggest that such patients may be at greater risk of the damaging effects of light than those with other forms of retinal degeneration, and they provide an impetus to restrict excessive light exposure as a protective measure in patients with constitutive signal flow in phototransduction.
THE EXPRESSION OF MSX GENES DURING EARLY CRANIAL SUTURE EMBRYOGENESIS (2003)

The development of calvarial bones is tighly co-ordinated with the growth of the brain and needs of harmonious interactions between different tissues within the calvarial sutures. Premature fusion of cranial sutures, known as craniosynostosis, presumably involves disturbance of these interactions. Mutations in the homeobox-containg gene Msx2 cause human craniosynostosis syndrome. Msx genes, which are consist of Msx1, Msx2 and Msx3, are homeobox-containg transcripton factors, and were originally identified as homologue of Drosophila msh(muscle segment homeobox) gene. Msx1 and Msx2 genes, expressed mostly in overlapping patterns at multiple site of tissue interactions during vertebrate development, are associated with epithelial-mesenchymal interactions during organogenesis, targets of BMP and FGF signaling. To elucidate the function of Msx genes in the early morphogenesis of mouse cranial suture, we analyzed the expression of them by in situ hybridization during embryonic(E15-E18) stage, and did vivo experiments in E15.5 mouse using rhBMP-2, rhFGF-2 protein soaked bead. In the sagittal suture, Msx1 was expressed in the mesenchyme of suture and the dura mater, Msx2 was intensely expressed in the sutural mesenchyme and the dura mater. In the coronal suture both of Msx genes were expressed intensely in the sutural mesenchyme and expressed in the periosteum also. Msx1 had a broader expression pattern than Msx2. BMP2 beads induced expression of both Msx1 and Msx2, FGF2 beads induced expression of Msx1, but not Msx2. Taken together, these data suggest that Msx1 and Msx2 genes have important role in regulating the morphogenesis and maintenance of embryonic cranial suture. Both of Msx genes are expressed similarly but because of their upstream signaling, they function dependently or cooperatively according to change of signaling molecule.
Tin(II) amides: new reagents for the conversion of esters to amides (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTin(II) amides: new reagents for the conversion of esters to amidesWei Bo Wang and Eric J. RoskampCite this: J. Org. Chem. 1992, 57, 23, 6101–6103Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/jo00049a009https://doi.org/10.1021/jo00049a009research-articleACS PublicationsRequest reuse permissionsArticle Views1018Altmetric-Citations49LEARN 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 Get e-Alerts
Efficiency of Two Different Nine-Loci Short Tandem Repeat Systems for DNA Typing Purposes (1999)

The System-2 STR allows rapid testing with higher probabilities of attribution and a higher power of exclusion than with the comparison method with slab-gel electrophoresis.
ChemInform Abstract: Macrocyclic Inclusion Complexes. Synthesis, X‐Ray Structural Analysis, and Formation of Mono‐ and Dinuclear Transition‐Metal Complexes of Dipyridino Crown Ethers. (1990)

ChemInformVolume 21, Issue 13 Heterocyclic Compounds ChemInform Abstract: Macrocyclic Inclusion Complexes. Synthesis, X-Ray Structural Analysis, and Formation of Mono- and Dinuclear Transition-Metal Complexes of Dipyridino Crown Ethers. G. R. NEWKOME, G. R. NEWKOME Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorG. E. KIEFER, G. E. KIEFER Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorD. K. KOHLI, D. K. KOHLI Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorY.-J. XIA, Y.-J. XIA Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorF. R. FRONCZEK, F. R. FRONCZEK Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorG. R. BAKER, G. R. BAKER Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this author G. R. NEWKOME, G. R. NEWKOME Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorG. E. KIEFER, G. E. KIEFER Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorD. K. KOHLI, D. K. KOHLI Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorY.-J. XIA, Y.-J. XIA Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorF. R. FRONCZEK, F. R. FRONCZEK Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this authorG. R. BAKER, G. R. BAKER Dep. Chem., La. State Univ., Baton Rouge, LA 70803, USASearch for more papers by this author First published: March 27, 1990 https://doi.org/10.1002/chin.199013225Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume21, Issue13March 27, 1990 RelatedInformation
Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model (2011)

Conjugation is the main mode of horizontal gene transfer that spreads antibiotic resistance among bacteria. Strategies for inhibiting conjugation may be useful for preserving the effectiveness of antibiotics and preventing the emergence of bacterial strains with multiple resistances. Filamentous bacteriophages were first observed to inhibit conjugation several decades ago. Here we investigate the mechanism of inhibition and find that the primary effect on conjugation is occlusion of the conjugative pilus by phage particles. This interaction is mediated primarily by phage coat protein g3p, and exogenous addition of the soluble fragment of g3p inhibited conjugation at low nanomolar concentrations. Our data are quantitatively consistent with a simple model in which association between the pili and phage particles or g3p prevents transmission of an F plasmid encoding tetracycline resistance. We also observe a decrease in the donor ability of infected cells, which is quantitatively consistent with a reduction in pili elaboration. Since many antibiotic-resistance factors confer susceptibility to phage infection through expression of conjugative pili (the receptor for filamentous phage), these results suggest that phage may be a source of soluble proteins that slow the spread of antibiotic resistance genes.
Isolation and Characterization of Endothelial Progenitor Cells from Human Blood (2008)

Circulating endothelial progenitor cells (EPCs) in adult human peripheral blood were originally identified in 1997 by Asahara et al., which challenged the paradigm that vasculogenesis is a process restricted to embryonic development. Since their original identification, EPCs have been extensively studied as biomarkers to assess the risk of cardiovascular disease in human subjects and as a potential cell therapeutic for vascular regeneration. Endothelial colony-forming cells (ECFCs), which are a subtype of EPCs, were recently identified from circulating adult and human umbilical cord blood. In contrast to other types of EPCs, which display various monocyte/macrophage phenotypes and functions, ECFCs are characterized by robust proliferative potential, secondary and tertiary colony formation upon replating, and de novo blood vessel formation in vivo when transplanted into immunodeficient mice. In this unit, we describe detailed methodologies for isolation and characterization of ECFCs from both human peripheral and umbilical cord blood.
Separate sites for binding and nicking of bacteriophage lambda DNA by terminase. (1983)

The cohesive end site (cos) is the site of action of bacteriophage lambda terminase, the enzyme that introduces staggered nicks to generate the 12-base cohesive ends of mature lambda DNA. Deletion mutations that remove the lambda cohesive end sequence have been isolated after in vitro mutagenesis. The deletions were obtained by digesting the DNA of a cos duplication phage with S1 nuclease to remove the cohesive ends and adjacent base pairs, followed by blunt end ligation and DNA packaging into phage particles. cos2 is the result of a 22-base-pair deletion that exactly removes the segment of rotational symmetry that includes the cohesive end sequence. The cos2 mutation abolishes nicking by terminase but does not affect terminase binding. We conclude that cos contains two sites that interact with terminase: cosN, the nicking site; and cosB, a binding site for terminase.
A differential proteome in tumors suppressed by an adenovirus‐based skin patch vaccine encoding human carcinoembryonic antigen (2005)

We created an anti-tumor vaccine by using adenovirus as a vector which contains a cytomegalovirus early promoter-directed human carcinoembryonic antigen gene (AdCMV-hCEA). In an attempt to develop the skin patch vaccine, we epicutaneously vaccinated Balb/c mice with AdCMV-hCEA. After nine weeks post-immunization, vaccinated mice evoked a robust antibody titer to CEA and demonstrated the capability of suppressing in vivo growth of implanted murine mammay adenocarioma cell line (JC-hCEA) tumor cells derived from a female Balb/c mouse. Proteomic analysis of the tumor masses in the non-vaccinated naive and vaccinated mice reveal that six proteins change their abundance in the tumor mass. The levels of adenylate kinase 1, beta-enolase, creatine kinase M chain, hemoglobin beta chain and prohibitin were statistically increased whereas the level of a creatine kinase fragment, which is undocumented, was decreased in the tumor of vaccinated mice. These proteins may provide a vital link between early-stage tumor suppression and immune response of skin patch vaccination.
Short-Term Benefit From Oral Vancomycin Treatment of Regressive-Onset Autism (2000)

In most cases symptoms of autism begin in early infancy. However, a subset of children appears to develop normally until a clear deterioration is observed. Many parents of children with "regressive"-onset autism have noted antecedent antibiotic exposure followed by chronic diarrhea. We speculated that, in a subgroup of children, disruption of indigenous gut flora might promote colonization by one or more neurotoxin-producing bacteria, contributing, at least in part, to their autistic symptomatology. To help test this hypothesis, 11 children with regressive-onset autism were recruited for an intervention trial using a minimally absorbed oral antibiotic. Entry criteria included antecedent broad-spectrum antimicrobial exposure followed by chronic persistent diarrhea, deterioration of previously acquired skills, and then autistic features. Short-term improvement was noted using multiple pre- and post-therapy evaluations. These included coded, paired videotapes scored by a clinical psychologist blinded to treatment status; these noted improvement in 8 of 10 children studied. Unfortunately, these gains had largely waned at follow-up. Although the protocol used is not suggested as useful therapy, these results indicate that a possible gut flora-brain connection warrants further investigation, as it might lead to greater pathophysiologic insight and meaningful prevention or treatment in a subset of children with autism.
Fully Differentiated HIV-1 Specific CD8+ T Effector Cells Are More Frequently Detectable in Controlled than in Progressive HIV-1 Infection (2007)

These data indicate that although full maturation of epitope-specific CD8+ T cell responses is associated with viral control, the maturation status of HIV-1 specific CD8+ T cell responses within a given individual are quite heterogeneous, suggesting epitope-specific influences on CD8+ T cell function.
Fine Needle Aspiration Biopsy of Intraparotid Schwannoma (2003)

The diagnosis of intraparotid schwannoma can be made by examining cytologic material containing the characteristic Verocay bodies. The correct cytologic diagnosis of this entity helps to rule out morphologically similar primary salivary gland neoplasms and thereby permits the appropriate surgical procedure to ensue.
The human and simian immunodeficiency viruses HIV-1, HIV-2 and SIV interact with similar epitopes on their cellular receptor, the CD4 molecule (1988)

The cellular receptor for HIV-1 is the leucocyte differentiation antigen, CD4. Blocking of HIV-1 infectivity can be achieved with monoclonal antibodies (MAbs) to some, but not all epitopes of this antigen. We demonstrate here, by inhibition of virus infection, blocking of syncytium formation and inhibition of pseudotype infection with a panel of CD4 MAbs, that HIV-1, HIV-2 and simian immunodeficiency virus (SIV) isolates share the same cellular receptor, the CD4 glycoprotein. It is also shown that very similar epitopes of this molecule are involved in virus binding. We infer from these data that the binding sites on these viruses are highly conserved regions, and may therefore make good targets for potential vaccines. In addition, we show that cell surface expression of CD4 is similarly modulated after infection of cell lines by all the viruses.
Biologically Active Molecules with a “Light Switch” (2006)

Abstract Biologically active compounds which are light‐responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with “small molecules”, proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as “caged compounds”) or reversibly switched between an active and an inactive state.
Selective Gene Transfer into the Liver of Non-Human Primates with E1-Deleted, E2A-Defective, or E1-E4 Deleted Recombinant Adenoviruses (1998)

Preclinical studies were designed to investigate the feasibility and safety of recombinant adenoviruses transduced into the hepatic artery of nonhuman primates. The vectors used are recombinant adenoviruses deleted in E1 and contain either a temperature-sensitive mutation in the E2a gene, which encodes a defective DNA-binding protein at nonpermissive temperatures, or a deletion of the E4 region, including open reading frame (ORF) 6. Six 8- to 10-kg baboons underwent femoral artery cannulation, and angiographic techniques were used to introduce vector selectively into either a portion of the right lobe of the liver via a branch of the right hepatic artery or the common hepatic artery. Necropsies were performed at 4, 29, or 61 days. Serial sequential liver biopsies were performed in the baboons that survived 29 or 61 days. In the 2 baboons with vector transduction into the right hepatic artery, X-Gal histochemical analysis of the liver showed evidence of quantitatively increased gene transfer in the targeted lobe; however, gene transfer was present throughout the liver. Quantitative analysis of histopathology showed that portal inflammation was present throughout both livers transduced with the highest dose of vector. No differences were seen in the level of portal inflammation in targeted and untargeted lobes despite the observed qualitative and quantitative differences in gene expression. Southern blot analysis of total cellular DNA isolated from targeted and nontargeted lobes showed similar levels of viral DNA throughout the liver. Polymerase chain reaction (PCR) analysis was able to detect viral DNA sequence in gonads and brain as well as many other tissues in baboons treated with high-dose vector. In baboons treated with lower doses of an E1-E4 deleted vector expressing the human ornithine transcarbamylase (OTC) gene, DNA was detectable by nested PCR in liver but not gonads at days 29 and 61. The data suggest that intraarterial administration of recombinant adenoviral E1-E4 deleted vector is feasible and safe. At high doses of vector, widespread dissemination of vector DNA is seen. At low doses, hepatic gene transfer is not associated with vector DNA dissemination to gonads.
Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments (1984)

Deletion of an essential gene in Escherichia coli was accomplished by transformation of linear DNA fragments that have a Kanr gene segment flanked by sequences homologous to closely spaced regions on the E. coli chromosome. Selection for a double crossover within homologous sequences can effectively delete an entire gene. Cell viability is maintained by provision of the essential gene on a plasmid with a temperature-sensitive replicon, resulting in cells which have a temperature-sensitive phenotype.
The tolerability of venlafaxine (1998)

The need to reduce unwanted effects and improve the safety profile of a drug, particularly in overdose, must be an important consideration when assessing the overall value of a new treatment. Although accurately assessing the relative burden of the adverse effects of different drugs can be difficult, the current evidence suggests that the pharmacological properties of venlafaxine may underpin its favourable safety and tolerability profile. When compared to many of the first and second generation antidepressants, it appears to be relatively well tolerated, and preliminary data indicate that it is safe in overdose. Comparison with the SSRI fluoxetine revealed no significant differences in the safety profiles of the two drugs. With its extensive frist pass metabolism to the active metabolite O-desmethylvenlafaxine, the main focus for potential drug-drug interactions with venlafaxine is the effect it may have on the cytochrome P450 system. In vitro studies suggested that, when compared to SSRIs, venlafaxine had only a modest inhibitory effect on the metabolic capacity of the P450 system, and clinical studies have shown that it has minimal drug-drug interactions. Venlafaxine is consequently well tolerated in the elderly and in those requiring concomitant medication for physical illness. New data suggest that, whilst contraindicated during pregnancy, accidental exposure to venlafaxine does not appear to be associated with an increased risk of foetal abnormalities.