gebhart/patrepeval huggingface dataset:
Genomic evidence for two functionally distinct gene classes (1998)

Analyses of complete genomes indicate that a massive prokaryotic gene transfer (or transfers) preceded the formation of the eukaryotic cell. In comparisons of the entire set of Methanococcus jannaschii genes with their orthologs from Escherichia coli, Synechocystis 6803, and the yeast Saccharomyces cerevisiae, it is shown that prokaryotic genomes consist of two different groups of genes. The deeper, diverging informational lineage codes for genes which function in translation, transcription, and replication, and also includes GTPases, vacuolar ATPase homologs, and most tRNA synthetases. The more recently diverging operational lineage codes for amino acid synthesis, the biosynthesis of cofactors, the cell envelope, energy metabolism, intermediary metabolism, fatty acid and phospholipid biosynthesis, nucleotide biosynthesis, and regulatory functions. In eukaryotes, the informational genes are most closely related to those of Methanococcus, whereas the majority of operational genes are most closely related to those of Escherichia, but some are closest to Methanococcus or to Synechocystis.
Control of Influenza and Poliomyelitis with Killed Virus Vaccines (1977)

The requirements for inducing immunity against an infectious disease are outlined, and the application of these requirements to the development of effective vaccines (vaccinology) is discussed. Influenza and poliomyelitis are examined from this viewpoint, and data are presented that demonstrate the effectiveness of killed virus vaccines against these diseases. A comparison between live and killed poliovirus vaccines suggests the desirability of returning to the use of a killed virus vaccine for the eradication of polio. The natural history of influenza and experience with vaccination suggest that influenza might be brought under effective control by routine immunization in childhood with a polyvalent killed virus vaccine potentiated by an immunologic adjuvant.
Assessment of surface bonding strength in Al clad steel strip using electrical resistivity and peeling tests (2006)

Aluminium clad steel strip successfully combines the surface properties of an aluminium alloy coating with the satisfactory mechanical properties of the steel substrate. The production of Al clad steel strip by rolling, however, is a more efficient and economical approach compared with other processes. In this investigation, trilayer strips of aluminium/steel/aluminium were produced using the cold roll bonding technique. The bonding strength between the layers and the electrical resistivity of the samples were measured using a peeling test and four point probe test, respectively. The effects of reduction of thickness, the friction condition between the outer layer and rolls, and the rolling velocity on the bonding strength and electrical resistivity of the samples were assessed. Finally, it is shown that the resistivity test can be used as a non-destructive test for the evaluation of the quality of bonding between the layers of aluminium clad steel strip.
Role of Zinc in the Structure and Toxic Activity of Botulinum Neurotoxin (1998)

Zn2+-protease activity of botulinum neurotoxin causes the blockage of neurotransmitter release resulting in botulism disease. We have investigated the role of Zn2+ in the biological activity of type A botulinum neurotoxin by removing the bound Zn2+ by EDTA treatment, followed by monitoring its structure in terms of secondary and tertiary folding (second derivative UV, FT-IR, and circular dichroism spectroscopy) and function in terms of its effect on the release of norepinephrine from PC12 cells. The single Zn2+ bound to each neurotoxin molecule was reversibly removed by EDTA treatment, whereas the biological activity of the neurotoxin was irreversibly lost. Based on the Amide III IR spectral analysis, the alpha-helical content of neurotoxin increased from 29% to 42% upon removal of Zn2+, which reverted to 31% upon treatment with 1:5 molar excess of exogenous Zn2+. Second derivative UV spectroscopy revealed no change in surface topography of Tyr residues with removal of Zn2+. However, near-UV circular dichroism signals suggested significant alterations in the topography of Phe and Tyr residues that could be buried in the protein matrix. Thermal unfolding experiments suggested that removal of Zn2+ results in the formation of the molten globule-like structure of type A botulinum neurotoxin. Tertiary structural changes introduced by Zn2+ removal were irreversible, which correlated well with the irreversibility of the biological activity of the neurotoxin. On the basis of these results, we suggest that Zn2+ plays a significant structural role in addition to its catalytic role in Zn2+-protease activity of type A botulinum neurotoxin.
Directions and Recent Advances in Papr Reduction Methods (2006)

In this paper methods for peak-to-average power ratio reduction in multicarrier systems are overviewed. Major advantages and drawback of the existing methods are summarized. New directions of research in this field are indicated and some promising methods exhibiting good performance and low cost are presented
Endurance exercise performance: the physiology of champions (2007)

Efforts to understand human physiology through the study of champion athletes and record performances have been ongoing for about a century. For endurance sports three main factors--maximal oxygen consumption (.VO(2,max)), the so-called 'lactate threshold' and efficiency (i.e. the oxygen cost to generate a given running speed or cycling power output)--appear to play key roles in endurance performance. and lactate threshold interact to determine the 'performance .VO(2)' which is the oxygen consumption that can be sustained for a given period of time. Efficiency interacts with the performance .VO(2) to establish the speed or power that can be generated at this oxygen consumption. This review focuses on what is currently known about how these factors interact, their utility as predictors of elite performance, and areas where there is relatively less information to guide current thinking. In this context, definitive ideas about the physiological determinants of running and cycling efficiency is relatively lacking in comparison with .VO(2,max) and the lactate threshold, and there is surprisingly limited and clear information about the genetic factors that might pre-dispose for elite performance. It should also be cautioned that complex motivational and sociological factors also play important roles in who does or does not become a champion and these factors go far beyond simple physiological explanations. Therefore, the performance of elite athletes is likely to defy the types of easy explanations sought by scientific reductionism and remain an important puzzle for those interested in physiological integration well into the future.
High Aspect Ratio Trench Filling Using Two‐Step Subatmospheric Chemical Vapor Deposited Borophosphosilicate Glass for <0.18 μm Device Application (1999)

As a premetal dielectric, borophosphosilicate glass (BPSG) has been widely used for device planarization. In order to meet the stringent gap filling requirements as the device evolves toward smaller feature sizes, the current BPSG deposition process using ozone/tetraethoxysilane chemistry was fully characterized to explore its extendibility for achieving high aspect ratio gap filling. Based on the characterization results, a two‐layer film deposition process was developed to accommodate the gap filling capability as well as the system throughout. Without stretching the thermal budget, the current process is able to achieve void‐free gap filling at a >6:1 aspect ratio, 0.06 μm width, even with reentrant profile. Other film properties, including film stress, moisture absorption, dopant profile and flow, were also studied extensively. Postdeposition film reflow can be performed using either conventional furnace or rapid thermal annealing, the reflowed profile depends on annealing temperature as well as ambient gases. A low thermal budget can be maintained using a steam anneal. © 1999 The Electrochemical Society. All rights reserved.
Efficacy of aqueous extract of garlic & allicin in experimental shigellosis in rabbits. (1991)

The aqueous extract of garlic (Allium sativum) and allicin both showed significant in vitro antibacterial activity against isolates of multiple drug-resistant Shigella dysenteriae 1, Sh. flexneri Y, Sh. sonnei and enterotoxigenic Escherichia coli. The minimum inhibitory concentrations of the aqueous extract and allicin against Sh. flexneri Y were 5 and 0.4 microliters/ml, respectively. The two agents also showed promising in vivo antibacterial activity against Sh. flexneri Y when tested in the rabbit model of experimental shigellosis, fully curing the infected rabbits within 3 days. On the contrary, 4 of the 5 rabbits in the control group died within 48 h. The rectal swab of rabbits of the experimental groups became free of the challenge bacteria on the second day of treatment. The antibacterial activity against the challenge strain was observed in the sera of the treated rabbits with 30-60 min of administration of the agents. The LD50 values of the aqueous extract and allicin in mice were 173.78 ml/kg and 204.17 microliters/kg of body weight, respectively. At the therapeutic dose, the two agents did not show any adverse effects on the standard biochemical profile of blood.
Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein. (1996)

Type II restriction endonucleases are dimers of two identical subunits that together form one binding site for the double-stranded DNA substrate. Cleavage within the palindromic recognition site occurs in the two strands of the duplex in a concerted manner, due to the action of two catalytic centers, one per subunit. To investigate how the two identical subunits of the restriction endonuclease EcoRV cooperate in binding and cleaving their substrate, heterodimeric versions of EcoRV with different amino acid substitutions in the two subunits were constructed. For this purpose, the ecorV gene was fused to the coding region for the glutathione-binding domain of the glutathione S-transferase and a His6-tag, respectively. Upon cotransformation of Escherichia coli cells with both gene fusions stable homo- and heterodimers of the EcoRV variants are produced, which can be separated and purified to homogeneity by affinity chromatography over Ni-nitrilotriacetic acid and glutathione columns. A steady-state kinetic analysis shows that the activity of a heterodimeric variant with one inactive catalytic center is decreased by 2-fold, demonstrating that the two catalytic centers operate independently from each other. In contrast, heterodimeric variants with a defect in one DNA-binding site have a 30- to 50-fold lower activity, indicating that the two subunits of EcoRV cooperate in the recognition of the palindromic DNA sequence. By combining a subunit with an inactive catalytic center with a subunit with a defect in the DNA-binding site, EcoRV heterodimers were produced that only nick DNA specifically within the EcoRV recognition sequence.
Efficient generation of the 15S configuration in prostaglandin synthesis. Attractive interactions in stereochemical control of carbonyl reduction (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEfficient generation of the 15S configuration in prostaglandin synthesis. Attractive interactions in stereochemical control of carbonyl reductionE. J. Corey, Konrad B. Becker, and Ravi K. VarmaCite this: J. Am. Chem. Soc. 1972, 94, 24, 8616–8618Publication Date (Print):November 1, 1972Publication History Published online1 May 2002Published inissue 1 November 1972https://pubs.acs.org/doi/10.1021/ja00779a074https://doi.org/10.1021/ja00779a074research-articleACS PublicationsRequest reuse permissionsArticle Views668Altmetric-Citations112LEARN 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
Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor. (1992)

The murine Pax-2 gene contains a protein coding domain homologous to the Drosophila paired-box, first described in certain developmental control genes of the segmentation type. Polyclonal antibodies recognize two Pax-2 proteins that are encoded by differentially spliced mRNAs. The Pax-2 proteins can bind a DNA sequence known to interact with the paired domain of a Drosophila protein. By immunocytochemistry, expression of Pax-2 could be localized to the nuclei of condensing mesenchyme cells and their epithelial derivatives in the developing kidney. Expression is abruptly down-regulated as the tubular epithelium differentiates. High levels of Pax-2 expression could also be detected in the epithelial cells of human Wilms tumors. These data suggest that Pax-2 is a transcription factor active during the mesenchyme-to-epithelium transition in early kidney development and in Wilms tumor.
Internal anal sphincter atrophy in patients with systemic sclerosis (2011)

Patients with SSc (both Sx and ASx) have thin and atrophic IAS, suggesting that IAS atrophy develops even in ASx patients and this may be amenable to treatment with sacral neuromodulation.
Identification of a Hemin Utilization Protein of Moraxella catarrhalis (HumA) (2004)

Moraxella catarrhalis is a major cause of acute otitis media in young children and has also been implicated as an important cause of exacerbations in adults with underlying pulmonary disease. Due to the considerable level of antibiotic resistance and the high degree of carriage rates in young children, it is likely that the incidence of M. catarrhalis infections will continue to rise. M. catarrhalis is a strict human respiratory pathogen, and this bacterium uses both transferrin and lactoferrin receptors to fulfill the essential iron requirement for survival in vivo. However, these are the only described iron acquisition systems for this organism. In this report we have demonstrated that M. catarrhalis can also utilize hemin as a sole source of iron for growth. In addition, we have identified and characterized an outer membrane protein with homology (26 to 28% similarity) to other known hemin binding and uptake proteins in related gram-negative organisms (i.e., Bordetella and Yersinia spp.). This newly described M. catarrhalis protein, termed HumA, is capable of directly binding to hemin coupled to a solid-phase matrix. M. catarrhalis HumA expressed on the surface of an Escherichia coli hemA-deficient strain (K-12 EB53) is fully capable of complementing the defect and thus restoring the ability of this strain to grow in the presence of hemin. When M. catarrhalis is grown in the presence of hemin, HumA expression is clearly increased as shown by Western blotting with polyclonal antiserum developed against a HumA peptide. In addition, growth analyses revealed that a HumA-deficient mutant of M. catarrhalis (7169::humA) is restricted for growth in the presence of hemin as the sole iron source compared to the wild-type strain. We conclude that HumA is an essential component of a hemin uptake and utilization system previously undescribed for M. catarrhalis, thus providing another mechanism of iron acquisition that may facilitate persistent colonization of the mucosal surface.
Synthesis and properties of dithymidine phosphate analogues containing 3′-thiothymidine (1990)

Dithymidine-3'-S-phosphorothioate (d(TspT)) has been prepared from a 5'-O-monomethoxytritylthymidine-3'-S-phosphorothioamidite (7) by activation with 5-(p-nitrophenyl)tetrazole in the presence of 3'-O-acetylthymidine. The resulting dinucleoside phosphorothioite is readily oxidised to the corresponding 3'-S-phosphorothioate using either tetrabutylammonium (TBA) periodate or TBA oxone and has been deprotected under standard conditions to yield d(TspT). This dithymidine phosphate analogue is comparatively resistant to hydrolysis by nuclease P1, but the P-S bond is readily cleaved by aqueous solutions of either iodine or silver nitrate. Dithymidine-3'-S-phosphorodithioate (d[Tsp(s)T]) was prepared in an analogous fashion using sulphur to oxidise the intermediate dinucleoside phosphorothioite. Absolute stereochemistry has been assigned to the diastereoisomers of d[Tsp(s)T] by comparing their physical and chemical properties to those of the dinucleoside phosphorothioates.
Practical notes on two Volterra filter identification direct methods (2003)

A survey of direct methods for identification of discrete Volterra systems is given. The Lee-Schetzen method and Korenberg's fast orthogonal algorithm (FOA) are reviewed. These methods are still useful and can be used as reference for other methods. We give practical considerations and suggestions for optimal use of these two methods coming up from the study of statistical simulations up to the third order.
Cell-surface and mitotic-spindle RHAMM: moonlighting or dual oncogenic functions? (2008)

Tumor cells use a wide variety of post-translational mechanisms to modify the functional repertoire of their transcriptome. One emerging but still understudied mechanism involves the export of cytoplasmic proteins that then partner with cell-surface receptors and modify both the surface-display kinetics and signaling properties of these receptors. Recent investigations demonstrate moonlighting roles for the proteins epimorphin, FGF1, FGF2, PLK1 and Ku80, to name a few, during oncogenesis and inflammation. Here, we review the molecular mechanisms of unconventional cytoplasmic-protein export by focusing on the mitotic-spindle/hyaluronan-binding protein RHAMM, which is hyper-expressed in many human tumors. Intracellular RHAMM associates with BRCA1 and BARD1; this association attenuates the mitotic-spindle-promoting activity of RHAMM that might contribute to tumor progression by promoting genomic instability. Extracellular RHAMM-CD44 partnering sustains CD44 surface display and enhances CD44-mediated signaling through ERK1 and ERK2 (ERK1/2); it might also contribute to tumor progression by enhancing and/or activating the latent tumor-promoting properties of CD44. The unconventional export of proteins such as RHAMM is a novel process that modifies the roles of tumor suppressors and promoters, such as BRCA1 and CD44, and might provide new targets for therapeutic intervention.
Effect of titanium surface roughness on proliferation, differentiation, and protein synthesis of human osteoblast‐like cells (MG63) (1995)

The effect of surface roughness on osteoblast proliferation, differentiation, and protein synthesis was examined. Human osteoblast-like cells (MG63) were cultured on titanium (Ti) disks that had been prepared by one of five different treatment regimens. All disks were pretreated with hydrofluroic acid-nitric acid and washed (PT). PT disks were also: washed, and then electropolished (EP); fine sandblasted, etched with HCl and H2SO4, and washed (FA); coarse sandblasted, etched with HCl and H2SO4, and washed (CA); or Ti plasma-sprayed (TPS). Standard tissue culture plastic was used as a control. Surface topography and profile were evaluated by brightfield and darkfield microscopy, cold field emission scanning electron microscopy, and laser confocal microscopy, while chemical composition was mapped using energy dispersion X-ray analysis and elemental distribution determined using Auger electron spectroscopy. The effect of surface roughness on the cells was evaluated by measuring cell number, [3H]thymidine incorporation into DNA, alkaline phosphatase specific activity, [3H]uridine incorporation into RNA, [3H]proline incorporation into collagenase digestible protein (CDP) and noncollagenase-digestible protein (NCP), and [35S]sulfate incorporation into proteoglycan. Based on surface analysis, the five different Ti surfaces were ranked in order of smoothest to roughest: EP, PT, FA, CA, and TPS. A TiO2 layer was found on all surfaces that ranged in thickness from 100 A in the smoothest group to 300 A in the roughest. When compared to confluent cultures of cells on plastic, the number of cells was reduced on the TPS surfaces and increased on the EP surfaces, while the number of cells on the other surfaces was equivalent to plastic. [3H]Thymidine incorporation was inversely related to surface roughness. Alkaline phosphatase specific activity in isolated cells was found to decrease with increasing surface roughness, except for those cells cultured on CA. In contrast, enzyme activity in the cell layer was only decreased in cultures grown on FA- and TPS-treated surfaces. A direct correlation between surface roughness and RNA and CDP production was found. Surface roughness had no apparent effect on NCP production. Proteoglycan synthesis by the cells was inhibited on all the surfaces studied, with the largest inhibition observed in the CA and EP groups. These results demonstrate that surface roughness alters osteoblast proliferation, differentiation, and matrix production in vitro. The results also suggest that implant surface roughness may play a role in determining phenotypic expression of cells in vivo.