gebhart/patrepeval huggingface dataset:
Relationship between the Unicellular Red Alga Porphyridium sp. and Its Predator, the Dinoflagellate Gymnodinium sp (1989)

Contamination of algae cultivated outdoors by various microorganisms, such as bacteria, fungi, algae, and protozoa, can affect growth and product quality, sometimes causing fast collapse of the cultures. The main contaminant of Porphyridium cultures grown outdoors in Israel is a Gymnodinium sp., a dinoflagellate that feeds on the alga. Comparison of the effects of various environmental conditions, i.e., pH, salinity, and temperature, on Gymnodinium and Porphyridium species revealed that the Gymnodinium sp. has sharp optimum curves, whereas the Porphyridium sp. has a wider range of optimum conditions and is also more resistant to extreme environmental variables. The mode of preying on the alga was observed, and the specificity of the Gymnodinium sp. for the Porphyridium sp. was shown. In addition, Gymnodinium extract was shown to contain enzymatic degrading activity specific to the Porphyridium sp. cell wall polysaccharide.
The Thermal Rearrangement of 1,5-Hexadiyne and Related Compounds (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Thermal Rearrangement of 1,5-Hexadiyne and Related CompoundsWilliam D. Huntsman and Harry J. WristersCite this: J. Am. Chem. Soc. 1967, 89, 2, 342–347Publication Date (Print):January 1, 1967Publication History Published online1 May 2002Published inissue 1 January 1967https://pubs.acs.org/doi/10.1021/ja00978a030https://doi.org/10.1021/ja00978a030research-articleACS PublicationsRequest reuse permissionsArticle Views424Altmetric-Citations94LEARN 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 Get e-Alerts
Ocular and systemic safety of bevacizumab and ranibizumab in patients with neovascular age-related macular degeneration (2013)

Although rare, adverse events with off-label use of bevacizumab are more common than with ranibizumab. Continued study into long-term safety of the two agents is warranted.
Structural Insights and Biological Effects of Glycogen Synthase Kinase 3-specific Inhibitor AR-A014418 (2003)

Glycogen synthase kinase 3 (GSK3) is a serine/threonine kinase that has been implicated in pathological conditions such as diabetes and Alzheimer's disease. We report the characterization of a GSK3 inhibitor, AR-A014418, which inhibits GSK3 (IC50 = 104 +/- 27 nM), in an ATP-competitive manner (Ki = 38 nM). AR-A014418 does not significantly inhibit cdk2 or cdk5 (IC50 > 100 microM) or 26 other kinases demonstrating high specificity for GSK3. We report the co-crystallization of AR-A014418 with the GSK3beta protein and provide a description of the interactions within the ATP pocket, as well as an understanding of the structural basis for the selectivity of AR-A014418. AR-A014418 inhibits tau phosphorylation at a GSK3-specific site (Ser-396) in cells stably expressing human four-repeat tau protein. AR-A014418 protects N2A neuroblastoma cells against cell death mediated by inhibition of the phosphatidylinositol 3-kinase/protein kinase B survival pathway. Furthermore, AR-A014418 inhibits neurodegeneration mediated by beta-amyloid peptide in hippocampal slices. AR-A014418 may thus have important applications as a tool to elucidate the role of GSK3 in cellular signaling and possibly in Alzheimer's disease. AR-A014418 is the first compound of a family of specific inhibitors of GSK3 that does not significantly inhibit closely related kinases such as cdk2 or cdk5.
Roles of the disulfide bond and the carboxy-terminal region of the S1 subunit in the assembly and biosynthesis of pertussis toxin (1990)

A Bordetella pertussis expression system was developed to analyze the structure-function relationship, in vivo assembly, and biosynthesis of pertussis toxin. The toxin structural gene was first deleted from the B. pertussis chromosome; into the resulting B. pertussis strain the toxin gene was introduced on a low-copy-number, broad-host-range plasmid. The amount of pertussis toxin produced and secreted with this expression system was in the same order of magnitude as that produced by B. pertussis Tohama I, indicating that although the plasmid may be present in more than one copy per cell, overproduction of the toxin was not achieved in B. pertussis. Expression of mutant pertussis toxin genes in which the codon for Cys-41 was deleted or altered or in which the carboxy-terminal region was deleted showed that both the single intrachain disulfide bond and the carboxy-terminal region of S1 are essential for the stable expression, assembly, and secretion of S1. On the other hand, the B oligomer was efficiently secreted in the culture medium in the absence of the S1 subunit. The secreted B oligomer contained S2, S3, and S4 subunits as evidenced by enzyme-linked immunosorbent assay and was fully functional with respect to haptoglobin binding. Furthermore, the deletion of the hydrophobic carboxy-terminal region has a drastic effect on S1 subunit solubility; however, inclusion of the hydrophobic region was not sufficient for assembly and secretion, indicating that other interactions involving amino acids beyond residue 207 of the S1 subunit are also required.
Identification of a Novel Isopeptidase with Dual Specificity for Ubiquitin- and NEDD8-conjugated Proteins (2000)

Covalent conjugation of proteins by ubiquitin or ubiquitin-like molecules is an important form of post-translational modification and plays a critical role in many cellular processes. Similar to the concept of phosphorylation and dephosphorylation, these conjugates are regulated by a large number of deconjugating enzymes. Here, we report the cloning of a 2,141-base pair DNA fragment from human placenta cDNA library by a strategy that involves expressed sequence tag data base searching, polymerase chain reaction, and rapid amplification of cDNA ends. Nucleotide sequence analysis revealed that the cloned cDNA contains an open reading frame of 1,143 base pairs encoding a novel protease, USP21, which is composed of 381 residues with a calculated molecular mass of 43 kDa. The human USP21 gene is located on chromosome 1q21 and encodes a member of the ubiquitin-specific protease family with highly conserved Cys and His domains. The activity and specificity of USP21 were determined by using a COS cell expression system in vivo. We showed that USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. Furthermore, USP21 is capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates. As expected from its biochemical activity, overexpression of USP21 has a profound growth inhibitory effect on U2OS cells. Thus, USP21 is the first ubiquitin-specific protease shown to have dual specificity for both ubiquitin and NEDD8 and may play an important role in the regulation of cell growth.
H-Bonding Controls the Regio-selectivities on the Acid-catalyzed Reaction of Fluorenone with Phenol Derivatives (2010)

Electrophilic substitution reaction is the most widely used procedure for introducing functional groups to the aromatic ring. Activated electrophiles containing carbonyl functions such as aldehydes and acyl halides are added smoothly to phenol and its derivatives under catalytic condition. However, it is rare the reaction of carbonyl compounds like ketones with aromatic rings to form a carbon-carbon bond, and to be considered unusual due to the unfavorable equilibrium.
γδ T cells are secondary participants in acute graft‐versus‐host reactions initiated by CD4+ αβT cells (1996)

To examine the role of T cell subpopulations in an acute graft-versus-host (GVH) reaction, gamma delta T cells and alpha beta T cells expressing one of the two prototypic V beta families were negatively isolated from adult blood samples and injected into allogeneic chick embryos. CD4+ alpha beta T cells expressing either V beta 1 or V beta 2 receptors were equally capable of inducing acute GVH reactions, consistent with the idea that alpha beta T cell alloreactivity is determined by CDR3 variability. By themselves, the gamma delta T cells were incapable of inducing GVH reactions. However, host gamma delta T cells were recruited into the donor alpha beta T cell-initiated lesions, where they were activated and induced to proliferate. The data suggest that gamma delta T cells may play a secondary role in GVH reactions.
Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription (2000)

The activities of several mRNA processing factors are coupled to transcription through binding to RNA polymerase II (Pol II). The largest subunit of Pol II contains a repetitive carboxy-terminal domain (CTD) that becomes highly phosphorylated during transcription. mRNA-capping enzyme binds only to phosphorylated CTD, whereas other processing factors may bind to both phosphorylated and unphosphorylated forms. Capping occurs soon after transcription initiation and before other processing events, raising the question of whether capping components remain associated with the transcription complex after they have modified the 5' end of the mRNA. Chromatin immunoprecipitation in Saccharomyces cerevisiae shows that capping enzyme cross-links to promoters but not coding regions. In contrast, the mRNA cap methyltransferase and the Hrp1/CFIB polyadenylation factor cross-link to both promoter and coding regions. Remarkably, the phosphorylation pattern of the CTD changes during transcription. Ser 5 phosphorylation is detected primarily at promoter regions dependent on TFIIH. In contrast, Ser 2 phosphorylation is seen only in coding regions. These results suggest a dynamic association of mRNA processing factors with differently modified forms of the polymerase throughout the transcription cycle.
Interleukin 6 Enhances Glycolysis through Expression of the Glycolytic Enzymes Hexokinase 2 and 6-Phosphofructo-2-kinase/Fructose-2,6-bisphosphatase-3 (2010)

Enhanced glycolysis is important for oncogenesis and for the survival and proliferation of cancer cells in the tumor microenvironment. Recent studies have also shown that proinflammatory cytokine signaling, such as that mediated by nuclear factor kappaB and signal transducer and activator of transcription 3 (STAT3), is important for the generation of inflammation-associated tumors. However, the link between inflammation and enhanced glycolysis has not been identified. In the present study, we found that the proinflammatory cytokine interleukin (IL)-6 enhanced glycolysis in mouse embryonic fibroblasts and human cell lines. Moreover, STAT3 activated by IL-6 enhanced the expression of the glycolytic enzymes hexokinase 2 and 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3). Ectopic expression of PFKFB3 enhanced glycolysis, suggesting that the IL-6-STAT3 pathway enhances glycolysis through the induction of these enzymes. Our findings may provide a novel mechanism for inflammation-associated oncogenesis.
Detection of feline immunodeficiency virus (FIV) nucleic acids in FIV-seronegative cats (1992)

A study was undertaken to determine the rate of viral transmission among naive specific-pathogen-free (SPF) cats living in close contact with feline immunodeficiency virus (FIV)-infected cats. Twenty SPF cats were housed in the same rooms with experimentally FIV-infected seropositive and virus culture-positive cats for 2 to 4 years and were monitored for the presence of FIV nucleic acids and antibodies. Only 1 of the 20 cats became seropositive and virus culture positive and developed signs of disease. Genomic DNA from bone marrow and peripheral blood mononuclear cells (PBMC) of 10 of 19 healthy-appearing seronegative cats became positive for FIV DNA by the polymerase chain reaction. Twenty-eight SPF cats housed as groups in separate quarters and never exposed to FIV-infected cats were uniformly negative for FIV DNA. FIV RNA transcripts were detected in concanavalin A-stimulated PBMC cultures from 4 of 10 FIV DNA-positive, seronegative cats by in situ hybridization. PBMC from three of four naive SPF cats acquired FIV nucleic acids after the cats were transfused with blood and bone marrow from FIV genome-positive, seronegative donors. Three of five FIV-seronegative cats housed for years with naturally FIV-infected cats in a private household were also found to harbor FIV DNA, indicating that the same phenomenon occurred in the field. These findings demonstrate that cats living in close contact with FIV-infected seropositive cats can acquire FIV nucleic acids without developing detectable levels of serum antibodies or disease.
Prolonged ectopic calcification induced by BMP‐2–derived synthetic peptide (2004)

Bone morphogenetic protein-2 (BMP-2) promotes the formation and regeneration of bone and cartilage, and therefore constitutes the most promising candidate for a bone repair material. However, it also has a wide range of functions, such as in organogenesis and apoptosis. Therefore, we investigated a novel synthetic peptide corresponding to residues 73-92 of BMP-2. This peptide bound to a BMP-2-specific receptor and elevated both alkaline phosphatase activity and osteocalcin mRNA in the murine cell line, C3H10T1/2. The 73-92 peptide also induced ectopic calcification when conjugated to a covalently crosslinked alginate gel. Here we report that the 73-92 peptide-conjugated alginate gel showed prolonged ectopic calcification for up to 7 weeks in rat calf muscle. In contrast, rhBMP-2-impregnated collagen gel showed maximum ectopic calcification at 3 weeks, and the calcified products that had formed disappeared after 5 weeks. Histological examination showed that the 73-92 peptide-conjugated alginate gel induced many osteoblast-like cells and few osteoclasts. In contrast, rhBMP-2-impregnated collagen gel induced many osteoclasts. These results suggest that the 73-92 peptide on alginate gel remains active at the implanted site, continuously induces differentiation of osteoblast precursor cells into osteoblasts, and activates osteoblasts to promote ectopic calcification.
EspH, a new cytoskeleton‐modulating effector of enterohaemorrhagic and enteropathogenic Escherichia coli (2003)

Enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) are closely related pathogens. During infection, EPEC and EHEC use a type III secretion system (TTSS) to translocate effector proteins into the infected cells and thereby modify specific host functions. These include transient filopodium formation which is Cdc42-dependent. Filopodia formation is followed by assembly of actin pedestals, the process enhanced by inhibition of Cdc42. We discovered that orf 18 of the enterocyte effacement locus encodes a new effector, which we termed EspH. We show that EspH is translocated efficiently into the infected cells by the TTSS and localizes beneath the EPEC microcolonies. Inactivation of espH resulted in enhanced formation of filopodia and attenuated the pedestals formation. Furthermore, overexpression of EspH resulted in strong repression of filopodium formation and heightened pedestal formation. We also demonstrate that overexpression of EspH by EHEC induces marked elongation of the typically flat pedestals. Similar pedestal elongation was seen upon infection of COS cells overexpressing EspH. EspH transiently expressed by the COS cells was localized to the membrane and disrupted the actin cytoskeletal structure. Our findings indicate that EspH is a modulator of the host actin cytoskeleton structure.
Structural Variations on N‐acetylneuraminic acid, 20. Synthesis of some 2,3‐didehydro‐2‐deoxysialic Acids structurally varied at C‐4 and their behavior towards Sialidase from Vibrio cholerae (1991)

Abstract The peracetylated methyl ester 1 of N‐acetylneuraminic acid was transformed into the oxazoline derivative 2 , which was hydrogenated with Pd/C/H 2 to give the 4‐deoxy‐Neu5Ac2en derivative 3 . Acid cleavage of the oxazoline 2 by trifluoroacetic acid (THF) gave the 4‐epi‐Neu5Ac2en derivative 4a , which was saponified to the known 4‐epi‐Neu5Ac2en 4b . Treatment of 4a with triphenylphosphane/diethylazodicarboxylate (DEAD)/HN 3 in toluene gave the 4‐azido‐4‐deoxy‐Neu5Ac2en derivative 5a as well as the 4‐epi‐azido‐4‐deoxy‐Neu5Ac2en derivative 6a . Both epimers could be saponified yielding the free dehydrosialic acid derivatives 5b and 6b . Furthermore, 4‐formamido‐4‐deoxy‐Neu5Ac2en 7b was prepared via the derivative 7a , which was formed from 5a by reaction with triphenylphosphane/formyl acetate. In addition, the free dehydrosialic acid derivatives 5b and 6b were transformed into the stable PN ylides 8 and 10 , but only 8 could be hydrolyzed to the triethylammonium salt of 4‐amino‐4‐deoxy‐Neu5Ac2en 9a , which was converted into the zwitter ionic compound 9b . Finally 4‐acetamido‐4‐deoxy‐Neu5Ac2en 11e was prepared from 4‐acetamido‐4‐deoxy‐N‐acetylneuraminic acid 10 via the derivatives 11a and 11b by well‐known methods. The compounds 4b, 5b, 6b, 7b, 9b , and 11c were investigated as inhibitors of Vibrio cholerae sialidase, and their K i values were determined.
Polynucleotides. XL. Synthesis and properties of poly 2'-azido-2'-deoxyadenylic acid (1976)

Poly 2′-azido-2′-deoxyadenylic acid (Poly Az) was synthesized from 2′-azido-2′-deoxyadenosine diphosphate by polynucleotide phosphorylase. Poly (Az) has U.V. absorption properties similar to poly (A) and hypochromicity of 40% at 0.1 M Na + and neutrality. CD curve also resembled to that of poly (A), but has smaller ellipticity. Titration of poly (Az) with HCl gave a transition at pH 5.5, but exact structure of the acid-form complex was not elucidated. Upon mixing with poly (U), poly (Az) forms a 1:1 and 1:2 complexes having Tm's somewhat higher than that of poly (A)· poly (U) complex in the same condition. A number of polynucleotides containing analogs of pyrimidine and purine nucleosides have been reported. 2 Among these polynucleotides, ones which have 2′-substituted nucleosides are especially interesting because they have natural 3′-5′-phosphodiester linkages and are suitable for elucidating physical and biological properties of polynucleotides. However, up to the present they have been limited to only 2′-substituted pyrimidine nucleotides, i,e. 2′-halogeno-, 3 azido-, 4 methoxy-, 5 and ethoxy-, 6 compounds. We have found a new method for the synthesis of 2′-azido and 2′-amino-2′-deoxyadenosine and guanosine 7 by way of purine cyclonucleosides, 8 which are readily available from the naturally occurring nucleosides. In this communication we report the synthesis of poly 2′-azido-2′-deoxyadenosine (poly (Az)) and its physical properties, such as UV, C.D., Tm and hybridization with poly (U).
The 69-84 amino acid region of the parathyroid hormone molecule is essential for the interaction of the hormone with the binding sites with carboxyl-terminal specificity. (1996)

We evaluated the competitive inhibitory effect of intact PTH, the amino-terminal PTH(1-34) fragment, and a series of truncated carboxyl-terminal PTH fragments on the binding of internally 35S-labeled human PTH(1-84) ([35S]hPTH(1-84)) to osteoblastic cells (ROS 17/2.8), in order to identify the minimum and critical elements within the PTH molecule for the interaction with the binding sites specific for the carboxyl-terminal region of the hormone. When the amino-terminal region of the PTH molecule was truncated stepwise, hPTH(35-84), hPTH(53-84) and hPTH(69-84), but not hPTH(70-84), significantly inhibited the [35S]hPTH(1-84) binding. On the other hand, the simple deletion of the carboxyl-terminal glutamine at position 84 of hPTH(53-84) [hPTH(53-83)] resulted in blunting the inhibitory effect of the peptide on the [35S]hPTH(1-84) binding. Furthermore, hPTH(35-84), hPTH(53-84) and hPTH(69-84), but not hPTH(70-84) nor hPTH(53-83), augmented the inhibitory effect of the amino-terminal PTH fragment [hPTH(1-34)] on the [35S]hPTH(1-84) binding. Of special interest was that the combination of hPTH(1-34) and hPTH(35-84) reproduced the inhibitory effect of unlabeled hPTH(1-84) on the [35S]hPTH(1-84) binding, on an equimolar basis. The 69-84 region of the PTH molecule thus appears to be crucial for binding to the carboxyl-terminal specific binding sites for PTH in osteoblasts. The interaction of the amino-terminal and carboxyl-terminal regions of a PTH molecule with their own respective binding sites seemed to occur in a fairly independent manner.
NRG1 fusion in a French cohort of invasive mucinous lung adenocarcinoma (2016)

Invasive mucinous lung adenocarcinoma (IMA) is a rare subtype of lung adenocarcinoma with no effective treatment option in advanced disease. KRAS mutations occur in 28-87% of the cases. NRG1 fusions were recently discovered in KRAS-negative IMA cases and otherwise negative for known driver oncogenes and could represent an attractive therapeutic target. Published data suggest that NRG1 fusions occur essentially in nonsmoking Asian women. From an IMA cohort of 25 French patients of known ethnicity, driver oncogenes EGFR, KRAS, BRAF, ERBB2 mutations, and ALK and ROS1 rearrangements presence were analyzed. In the IMA samples remaining negative for these driver oncogenes, an NRG1 rearrangement detection was performed by FISH. A driver oncogene was identified in 14/25 IMA, namely 12 KRAS mutations (48%), one ROS1 rearrangement (4%), and one ALK rearrangement (4%). The detection of NRG1 rearrangement by FISH was conducted in the 11 pan-negative IMA. One sample was NRG1FISH-positive and 100% of the tumor nuclei analyzed were positive. This NRG1-positive patient was a 61-year-old nonsmoking woman of Vietnamese ethnicity and was the sole patient of Asian ethnicity of the cohort. She died 6 months after the diagnosis with a pulmonary multifocal disease. NRG1FISH detection should be considered in patients with IMA pan-negative for known driver oncogenes. These results might suggest that NRG1 fusion is more frequent in IMA from Asian patient. Larger studies are needed.
Liquid-crystal prisms for tip-tilt adaptive optics (1994)

Results from an electrically addressed liquid-crystal cell producing continuous phase profiles are presented. The adaptive deflection of a beam of light for use in a tip-tilt adaptive optics system is demonstrated. We compare the optical performance of liquid-crystal prisms with experimental data on atmospheric seeing at the William Herschel Telescope.