gebhart/patrepeval huggingface dataset:
Functional analysis of structural genes for NAD+‐dependent formate dehydrogenase in Saccharomyces cerevisiae (2002)

Co-consumption of formate by aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae CEN.PK 113-7D led to an increased biomass yield relative to cultures grown on glucose as the sole carbon and energy substrate. In this respect, this strain differed from two previously investigated S. cerevisiae strains, in which formate oxidation did not lead to an increased biomass yield on glucose. Enzyme assays confirmed the presence of a formate-inducible, cytosolic and NAD(+)-dependent formate dehydrogenase. To investigate whether this enzyme activity was entirely encoded by the previously reported FDH1 gene, an fdh1Delta null mutant was constructed. This mutant strain still contained formate dehydrogenase activity and remained capable of co-consumption of formate. The formate dehydrogenase activity in the mutant was demonstrated to be encoded by a second structural gene for formate dehydrogenase (FDH2) in S. cerevisiae CEN.PK 113-7D. FDH2 was highly homologous to FDH1 and consisted of a fusion of two open reading frames (ORFs) (YPL275w and YPL276w) reported in the S. cerevisiae genome databases. Sequence analysis confirmed that, in the database genetic background, the presence of two single-nucleotide differences led to two truncated ORFs rather than the full-length FDH2 gene present in strain CEN.PK 113-7D. In the latter strain background an fdh1Deltafdh2Delta double mutant lacked formate dehydrogenase activity and was unable to co-consume formate. Absence of formate dehydrogenase activity did not affect growth on glucose as sole carbon source, but led to a reduced biomass yield on glucose-formate mixtures. These findings are consistent with a role of formate dehydrogenase in the detoxification of exogenous formate.
Expression of mage genes in transitional‐cell carcinomas of the urinary bladder (1995)

Human genes MAGE-1 and MAGE-3 code for distinct antigens, which are recognized on melanoma cells by autologous cytolytic T lymphocytes (CTL). These antigens may constitute useful targets for anti-cancer immunotherapy, since no expression of MAGE genes has been observed in normal tissues other than testis. Out of 57 samples of primary transitional-cell carcinomas of the bladder, 12 (21%) expressed MAGE-1 and 20 (35%) expressed MAGE-3. All but one of the tumors expressing MAGE-1 also expressed MAGE-3. Genes MAGE-2 and MAGE-4, which are closely related to MAGE-1 and MAGE-3, were expressed by 30% and 33% of the tumors respectively. MAGE expression was more frequent in advanced tumor stages: 61% of the invasive tumors (stage > or = T2) were positive for expression of at least one of the four genes, whereas only 28% of the superficial tumors (stages Ta and T1) expressed these genes.
Activation of pro-(matrix metalloproteinase-2) (pro-MMP-2) by thrombin is membrane-type-MMP-dependent in human umbilical vein endothelial cells and generates a distinct 63 kDa active species (2001)

Thrombin, a critical enzyme in the coagulation cascade, has also been associated with angiogenesis and activation of the zymogen form of matrix metalloproteinase-2 (MMP-2 or gelatinase-A). We show that thrombin activated pro-MMP-2 in a dose- and time-dependent manner in cultured human umbilical-vein endothelial cells (HUVECs) to generate a catalytically active 63kDa protein that accumulated as the predominant form in the conditioned medium. This 63kDa thrombin-activated MMP-2 is distinct from the 62kDa species found following concanavalin A or PMA stimulated pro-MMP-2 activation. Hirudin and leupeptin blocked thrombin-induced pro-MMP-2 activation, demonstrating that the proteolytic activity of thrombin is essential. However, activation was also dependent upon membrane-type-MMP (MT-MMP) action, since it was blocked by EDTA, o-phenanthroline, hydroxamate metalloproteinase inhibitors, tissue inhibitor of metalloproteinase-2 (TIMP-2) and TIMP-4, but not TIMP-1. Thrombin inefficiently cleaved recombinant 72kDa pro-MMP-2, but efficiently cleaved the 64kDa MT-MMP-processed intermediate form in the presence of cells. Thrombin also rapidly (within 1h) increased cellular MT-MMP activity, and at longer time points (&amp;gt;6h) it increased expression of MT1-MMP mRNA and protein. Thus signalling via proteinase-activated receptors (PARs) may play a role in thrombin-induced MMP-2 activation, though this does not appear to involve PAR1, PAR2, or PAR4 in HUVECs. These results indicate that in HUVECs the activation of pro-MMP-2 by thrombin involves increased MT-MMP activity and preferential cleavage of the MT-MMP-processed 64kDa MMP-2 form in the presence of cells. The integration of these proteinase systems in the vascular endothelium may be important during thrombogenesis and tissue remodelling associated with neovascularization.
Efficient Gene Targeting Mediated by Adeno-Associated Virus and DNA Double-Strand Breaks (2003)

Gene targeting is the in situ manipulation of the sequence of an endogenous gene by the introduction of homologous exogenous DNA. Presently, the rate of gene targeting is too low for it to be broadly used in mammalian somatic cell genetics or to cure genetic diseases. Recently, it has been demonstrated that infection with recombinant adeno-associated virus (rAAV) vectors can mediate gene targeting in somatic cells, but the mechanism is unclear. This paper explores the balance between random integration and gene targeting with rAAV. Both random integration and spontaneous gene targeting are dependent on the multiplicity of infection (MOI) of rAAV. It has previously been shown that the introduction of a DNA double-stranded break (DSB) in a target gene can stimulate gene targeting by several-thousand-fold in somatic cells. Creation of a DSB stimulates the frequency of rAAV-mediated gene targeting by over 100-fold, suggesting that the mechanism of rAAV-mediated gene targeting involves, at least in part, the repair of DSBs by homologous recombination. Absolute gene targeting frequencies reach 0.8% with a dual vector system in which one rAAV vector provides a gene targeting substrate and a second vector expresses the nuclease that creates a DSB in the target gene. The frequencies of gene targeting that we achieved with relatively low MOIs suggest that combining rAAV vectors with DSBs is a promising strategy to broaden the application of gene targeting.
Use of rpsL for dominance selection and gene replacement in Streptomyces roseosporus (1997)

We developed a gene replacement system using the rpsL gene of Streptomyces roseosporus and demonstrated its utility by constructing a deletion in the S. roseosporus glnA gene. A 1.3-kb BamHI fragment that hybridized to the Mycobacterium smegmatis rpsL gene was subcloned from an S. roseosporus cosmid library and sequenced. Plasmid pRHB514 containing the rpsL gene conferred streptomycin sensitivity (Sm(S)) to the Sm(r) S. roseosporus TH149. The temperature-sensitive plasmid pRHB543 containing rpsL and the S. roseosporus glnA gene disrupted with a hygromycin resistance (Hm(r)) gene was introduced into S. roseosporus TH149, and recombinants containing single and double crossovers were obtained after a temperature increase. Southern hybridization analysis revealed that single crossovers occurred in the glnA or rpsL genes and that double crossovers resulted in replacement of the chromosomal glnA gene with the disrupted glnA. Glutamine synthetase activity was undetectable in the recombinant containing the disrupted glnA gene.
CK20 gene expression: technical limits for the detection of circulating tumor cells. (1999)

The suitability of CK20 mRNA expression as a marker for the detection of minimum residual disease in patients with cancer of epithelial origin was evaluated. A sensitive nested RT-PCR assay with multiple replicates was optimised to detect a minimum number of circulating tumor cells expressing cytokeratin 20 (CK20) mRNA. Using this optimal procedure, we examined CK20 mRNA expression in ten epithelial and seven leukemic cell lines, in eight bladder tumors, in peripheral blood samples from 18 tumor patients and from 29 healthy controls and in 8 bone marrow samples from healthy donors. CK20 mRNA was found in 13 of 18 (72%) blood samples from patients with cancer of epithelial origin and in all the epithelial tumor cells tested. However, CK20 mRNA was also detected in 21 of 29 (72%) bloods, in 8 of 8 bone marrow samples from healthy donors and in 4 of 7 leukemic cell lines. These results highlight a requirement for either determination of threshold levels of CK20 normal expression or the development of quantitative techniques to distinguish between a tumor-specific CK20 gene expression and a low level background transcription of this marker. These results would also advise caution in using CK20 as a tumor specific marker in clinical investigations.
Construction of Bacterial Artificial Chromosome (BAC/PAC) Libraries (1999)

This unit describes the construction of BAC and PAC libraries. Two vectors, pCYPAC2 and pPAC4 have been used for preparing PAC libraries, and a new BAC vector pBACe3.6 has been developed for construction of BAC libraries. A support protocol describes preparation of PAC or BAC vector DNA for cloning by digestion with BamHI or EcoRI, simultaneous dephosphorylation with alkaline phosphatase, and subsequent purification through pulsed-field gel electrophoresis (PFGE). For the preparation of high-molecular weight DNA for cloning, support protocols provide procedures for embedding total genomic DNA from lymphocytes or animal tissue cells, respectively, in InCert agarose. Another support protocol details the next steps for the genomic DNA: partial digestion with MboI or with a combination of EcoRI endonuclease and EcoRI methylase, and subsequent size fractionation by preparative PFGE. The final support protocol covers the isolation of BAC and PAC plasmid DNA for analyzing clones.
Platelet-rich plasma effects on degenerative disc disease: analysis of histology and imaging in an animal model (2011)

This percutaneous needle puncture technique is an effective method for creating a degenerative disc model without posterior destabilization of the spine. The administration of PRP has a protective effect on damaged discs in the acute and delayed injection settings representing clinical treatment with PRP in the early versus late stages of the degenerative process. It appears that earlier intervention in the disease process would be more beneficial than PRP treatment of already severely degenerated discs.
Obstacle avoidance and navigation in the real world by a seeing robot rover (2018)

Robotics Institute
Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation (1999)

The recA gene of Escherichia coli is the prototype of the recA/RAD51/DMC1/uvsX gene family of strand transferases involved in genetic recombination. In order to find mutations in the recA gene important in catalytic turnover, a genetic screen was conducted for dominant lethal mutants. Eight single amino acid substitution mutants were found to prevent proper chromosome segregation and to kill cells in the presence or absence of an inducible SOS system. All mutants catalyzed some level of recombination and constitutively stimulated LexA cleavage. The mutations occur at the monomer-monomer interface of the RecA polymer or at residues important in ATP hydrolysis, implicating these residues in catalytic turnover. Based on an analysis of the E96D mutant, a model is presented in which slow RecA-DNA dissociation prevents chromosome segregation, engendering lexA-independent, lethal filamentation of cells.
Ifenprodil, a Novel NMDA Receptor Antagonist : Site and Mechanism of Action (2001)

Ifenprodil is a novel N-methyl-D-aspartate (NMDA) receptor antagonist that selectively inhibits receptors containing the NR2B subunit. As such, it has become widely used as a tool to study subtypes of NMDA receptors both in vitro and in vivo, and as a tool for molecular studies of the properties and regulation of NMDA receptors. Ifenprodil has an unusual form of activity-dependence and its mechanism of action may involve an increase in proton inhibition of NMDA receptors. These properties are shared by analogs or derivatives of ifenprodil, some of which may be lead compounds for therapeutically useful NMDA antagonists. Such antagonists have potential as neuroprotectants, anticonvulsants, analgesics, and for the treatment of Parkinson's disease and other disorders of the nervous system. The location of the ifenprodil binding site on NMDA receptors and the structural and mechanistic basis of its effects are still unknown. Recent work suggests that at least part of the ifenprodil binding site is located in the R1/R2 domain of the NR1 subunit. This region, like the S1/S2 agonist binding domain, shares homology with bacterial periplasmic binding proteins.
BAT-26, an indicator of the replication error phenotype in colorectal cancers and cell lines. (1997)

Instability of microsatellites is a hallmark of the DNA replication error phenotype (RER+) due to the inactivation of mismatch repair genes. In humans, microsatellite instability has first been described in colorectal tumors developing in either hereditary nonpolyposis colorectal cancer or sporadic patients. Colorectal tumorigenesis in RER+ and RER- tumors is probably due to distinct mechanisms, and RER+ tumors have a better prognosis than RER- tumors. The study of the RER status of a tumor may thus be important in the future to determine biological prognosis factors and investigate therapeutical strategies. The RER status of 134 primary tumors and 26 cell lines derived from colorectal cancers was established by PCR amplification and analysis of a minimum of 32 microsatellite loci. This characterization allowed us to unambiguously classify 35 primary tumors and 7 cell lines as RER+. Typing of a single poly(A) tract, BAT-26, was sufficient to confirm the RER status of 159 of these 160 tumors and cell lines. Moreover, in DNA from unaffected individuals, normal tissues of a subset of the RER+ patients, and all RER- tumors or cell lines, BAT-26 was quasi-monomorphic, showing only minor size variations. BAT-26 alleles showing shortening from 4 to 15 bp were observed in all but 1 of the RER+ tumors and cell lines. The size difference between the range of normal large alleles and unstable small alleles was sufficient to be detected by electrophoresis on conventional polyacrylamide gels stained with ethidium bromide. We thus propose a simple, low-cost, and rapid method to screen for the RER status of colorectal cancer primary tumors and cell lines, even in the absence of matching normal DNA and, in most cases, without the need for radioactivity. This method could easily be set up in routine laboratories.
X-Ray Diffraction in Liquids: Primary Normal Alcohols (1927)

Evidence for a molecular space array in liquid primary normal alcohols, methyl to lauryl.---The x-ray diffraction in liquids has long been known. The suggestion has been repeatedly made that the effect is caused by fragmentary crystals. The viewpoint here taken is that there is a molecular space array, not crystalline, which is named cybotaxis. Evidence of the cybotactic state in liquid primary normal alcohols, methyl to lauryl, is adduced. By Mo $K\ensuremath{\alpha}$ x-ray diffraction ionization curves, two significant distances are measured, the first linearly dependent upon the content of carbon atoms and the second practically independent of this change in molecular length. The latter is thus the distance of separation perpendicular to the chain, and is 4.6A with lauryl, decreasing slowly to 4.4A with butyl and then rapidly to 3.8A with methyl. The value 4.6A is in striking agreement with the work of Adam on surface films of saturated fatty acids. The increase of the first distance, linearly with carbon content, is in harmony with the work of M\"uller and Saville and others, in that the increase is about 1.3A per carbon atom, and leads to the conclusion that the diffraction is produced by planes containing the polar groups, which are not perpendicular to the direction of the parallel chain molecules. Comparison of peaks in the liquid and solid states show that the spacings are not the same and the phenomena is not caused by crystal fragments. The cybotactic state permits mobility, but not random motion and is peculiar to the substance. The distances computed are the most probable spacings. The molecules may be regarded as having the same orientation in a small group, too small to give optical anisotropy. The discussion does not, therefore, extend to liquid crystals but adheres to the more general condition. The conception of the cybotactic state is helpful in an understanding of solutions and other liquid phenomena. The theories of Raman and Ramanathan, Debye and Zernike and Prins are suggestive in that they indicate that a definite molecular space array is not necessary for the production of a single diffraction halo. But they in no sense negate the evidence here adduced for a cybotactic state.
Respiratory Virus-Induced TLR7 Activation Controls IL-17–Associated Increased Mucus via IL-23 Regulation (2010)

The response to respiratory syncytial virus (RSV), negative strand ssRNA virus, depends upon the ability to recognize specific pathogen-associated targets. In the current study, the role of TLR7 that recognizes ssRNA was examined. Using TLR7(-/-) mice, we found that the response to RSV infection in the lung was more pathogenic as assessed by significant increases in inflammation and mucus production. Although there appeared to be no effect of TLR7 deficiency on type I IFN, the pathology was associated with an alteration in T cell responses with increases in mucogenic cytokines IL-4, IL-13, and IL-17. Examination of dendritic cells from TLR7(-/-) animals indicated a preferential activation of IL-23 (a Th17-promoting cytokine) and a decrease in IL-12 production. Neutralization of IL-17 in the TLR7(-/-) mice resulted in a significant decrease in the mucogenic response in the lungs of the RSV-infected mice. Thus, without TLR7-mediated responses, an altered immune environment ensued with a significant effect on airway epithelial cell remodeling and goblet cell hyper/metaplasia, leading to increased mucus production.
Portable cost-effective EEG data acquisition system (2011)

Neuro-cognitive dysfunctions are common clinical abnormalities found in society. They require objective analysis by various instruments; an important technique involves monitoring electroencephalogram (EEG) signals. To date, EEG machines have been robust, costly and require patients to come to a hospital for test. Therefore, we have constructed a simple, cheap and portable EEG instrument for wider patient use. It consists of two active digital EEG probes with two channels each, making it a four-channel portable acquisition system. It is further connected through a two-wire serial bus to the acquisition unit, which comprises an analogue to digital converter (ADC) and an ARM board processor with 2 GB memory and USB interface. The whole system is placed in a small box making it highly portable for wider use in clinical settings.
Third Keystone Symposium on Cellular Immunology and the Immunotherapy of Cancer Introduction (1998)

Departments of Molecular Genetics and Biochemistry and Surgery, University of Pittsburgh School of Medicine. Pittsburgh, Pennsylvania. U.S.A.
Biologically Active CD40 Ligand Is Elevated in Sickle Cell Anemia (2006)

Platelet-derived sCD40L is elevated in SCA, further elevated in crises, and biologically active. The participation of sCD40L in SCA plasma-induced production of B cells, tissue factor, and ICAM-1 suggests that CD40L may contribute to the chronic inflammation and increased thrombotic activity known to occur in SCA.
End-to-end adaptive rate based congestion control scheme for ABR service in wide area ATM networks (2002)

The ATM Forum is currently in the process of adopting an end-to-end adaptive rate based control scheme to support a class of best effort service known as available bit rate service (ABR). This is a reactive control method where the source rate adapts to the state of the network based on the feedback it receives from the network. The performance of such reactive feedback control schemes are sensitive to the latency in the feedback loop. In wide area networks the virtual channels traversing large hops can have very poor performance because of large propagation delays. We show that the performance of virtual channels (VCs) traversing a large number of hops in WANs can be substantially improved by giving priority to network transit traffic over traffic entering the network. We investigate the performance of the control in the presence of high priority variable bit rate traffic. The study shows that the priority scheme exhibits a robust behavior and ensures a fair share of the bandwidth for all VCs, regardless of the number of hops they traverse even under extreme loading conditions.
Effect of Food and a Monoglyceride Emulsion Formulation on Danazol Bioavailability (1993)

The bioavailability of a single 100-mg dose of danazol delivered from the commercial formulation (hard gelatin capsule) and from an experimental lipid emulsion formulation of danazol was studied in 11 healthy female volunteers in both fed and fasted states. The emulsion formulation (fasted) increased bioavailability fourfold compared with the capsule (P = .0001); the difference, however, was not significant in the fed state. Food increased the bioavailability of the capsule formulation more than threefold over fasted administration (P = .0001). In a separate study of 12 female volunteers, single doses of the emulsion formulation of danazol administered with food demonstrated essentially dose-proportional pharmacokinetics over the dose range studied (50-200 mg). The authors conclude that factors that increase the extent of solubilization lead to significant enhancement in the bioavailability of danazol.
Preparation and Estrogenic Activity of Stilbestrol Analogs (1962)

スチルベストロ-ルの2個のエチル基をメトキシ基で置換した化合物も,スチルベストロ-ルと同様に発情作用を現わすであろうと考えて,1,2-ジメトキシ-L2-ビス-(ρ-メトキシフェニル)-エチレン(III)および1,2-ジメトキシ-1,2-ピス-(ρ-メトキシメトキシフェニル)-エチレン(IV)をあらたに合成した。これらの化合物は1回皮下注射法で去勢マウスに対する発情作用を膣垢法で検したところ,いずれも50γで試験動物100%に発情を起した。
Crystal and molecular structure of cephalotaxine (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal and molecular structure of cephalotaxineSatish K. Arora, Robert B. Bates, Raymond A. Grady, Gabriel Germain, Jean P. Declercq, and Richard G. PowellCite this: J. Org. Chem. 1976, 41, 3, 551–554Publication Date (Print):February 1, 1976Publication History Published online1 May 2002Published inissue 1 February 1976https://pubs.acs.org/doi/10.1021/jo00865a030https://doi.org/10.1021/jo00865a030research-articleACS PublicationsRequest reuse permissionsArticle Views90Altmetric-Citations18LEARN 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