gebhart/patrepeval huggingface dataset:
Regulation of dorsal-ventral patterning: the ventralizing effects of the novel Xenopus homeobox gene Vox (1996)

The formation of the dorsal-ventral axis in Xenopus laevis is elicited by a signaling cascade on the dorsal side of the embryo initiated by cortical rotation. These early developmental events impart an initial axial polarity to the embryo. By the time gastrulation occurs, the embryo has established opposing dorsal and ventral regulatory regions. Through a dynamic process, the embryo acquires a definitive pattern that reflects the distribution of future cell fates. Here we present a novel homeobox gene, Vox, whose expression reflects this dynamic process. Vox is first expressed throughout the embryo and subsequently eliminated from the notochord and neural plate. Ectopic expression of Vox demonstrates that the normal function of this gene may be to suppress dorsal genes such as Xnot and chordin, and induce ventral and paraxial genes such as Bmp-4 and MyoD. Ectopic expression of BMP-4 ventralizes embryos and positively regulates the expression of Vox, suggesting that these genes are components of a reciprocal regulatory network.
Future Automotive Fuels (1972)

&lt;div class="htmlview paragraph"&gt;The national concern over air quality and the understanding of the role of the internal combustion engine powered passenger car as a contributor of atmospheric pollutants has imposed new design criteria upon both the automobile manufacturer and the petroleum refiner. For the passenger car engine builder these criteria have been specified by the emission standards required by the Clean Air Amendments of 1970. With certain exceptions, gasolines for these low-emitting passenger cars have not yet been specified nor have their required quality and performance characteristics been clearly spelled out. This paper attempts to judge the influence of emission control requirements on future gasoline quality. Lead anti-knocks, hydrocarbon compositions and gross physical properties are among the factors considered and an effort is made to quantify the effects of changes in these characteristics on emissions and to estimate their impact on the industry. It is concluded that future automotive fuels, i.e., fuels that will be produced for future emission controlled vehicles, will be a blend of liquid hydrocarbons, free of lead alkyl anti-knocks and other catalyst poisons, and with hydrocarbon composition and volatility modestly adjusted to provide optimum emissions control at lowest overall system cost.&lt;/div&gt;
Effects of Anti-ε on Total and Specific IgE Levels in Adult Mice (1985)

Adult (2- to 3-month-old) female CBA/J mice were injected intraperitoneally with heavy chain specific rabbit anti-IgE (anti-epsilon) to determine its effects on total and specific serum IgE. Animals receiving 10 X 250 micrograms injections over a 50-day period displayed significantly increased (10 X levels of serum IgE compared to rabbit gamma-globulin or untreated controls. If animals were immunized with castor allergen (CA) prior to anti-epsilon treatments their IgE anti-CA titers were significantly suppressed, although their total IgE levels were not significantly different compared to controls. In a second series of experiments, mice which received increased quantities (3 X more) of anti-epsilon had no detectable serum IgE (within 30 days post anti-epsilon treatment), significantly decreased titers of IgE antibody, and reduced numbers of IgE bearing spleen and mesenteric lymph node cells. These studies indicate that anti-epsilon injections in adult mice can significantly alter total and specific IgE levels.
Synthesis, surface functionalization, and properties of freestanding silicon nanocrystals (2006)

Freestanding silicon nanoparticles (FS-nc-Si) have intriguing chemical and optical properties. The present contribution outlines known synthetic methodologies and protocols for surface functionalization. Recent advancements in tailoring the photoluminescence properties of FS-nc-Si and future research directions will be briefly discussed.
SHARE: A METHODOLOGY AND ENVIRONMENT FOR COLLABORATIVE PRODUCT DEVELOPMENT (1994)

The SHARE project seeks to apply information technologies in helping design teams gather, organize, re-access, and communicate both informal and formal design information to establish a "shared understanding" of the design and design process. This paper presents the visions of SHARE, along with the research and strategies undertaken to build an infrastructure toward its realization. A preliminary prototype environment is being used by designers working on a variety of industry sponsored design projects. This testbed continues to inform and guide the development of NoteMail, MovieMail, and Xshare, as well as other components of the next generation SHARE environment that will help distributed design teams work together more effectively on the Internet.
Solvent-dependent fluorescence of pyrene-3-carboxaldehyde and its applications in the estimation of polarity at micelle-water interfaces (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolvent-dependent fluorescence of pyrene-3-carboxaldehyde and its applications in the estimation of polarity at micelle-water interfacesK. Kalyanasundaram and J. K. ThomasCite this: J. Phys. Chem. 1977, 81, 23, 2176–2180Publication Date (Print):November 1, 1977Publication History Published online1 May 2002Published inissue 1 November 1977https://pubs.acs.org/doi/10.1021/j100538a008https://doi.org/10.1021/j100538a008research-articleACS PublicationsRequest reuse permissionsArticle Views2466Altmetric-Citations329LEARN 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 options Get e-Alerts
Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression (2010)

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.
Sequential amplification of flanking sequences by Y-shaped adaptor dependent extension using multiple templates. (2007)

Y-shaped adaptor dependent extension (YADE) method is a useful tool to amplify the flanking sequence of a known DNA sequence, but its efficiency is frequently limited by the restriction sites around the known sequence. In this paper, we demonstrated that using multiple templates derived from several restrictions and ligations could dramatically increase the efficiency of YADE method and render it suitable for sequential amplification of flanking sequences. With templates originating from 7 digestions, a 2,228-bp 5'-upstream sequence of a cotton small GTPase gene was obtained by two rounds of sequential YADE amplifications. The results demonstrated that the YADE method with multiple templates may be a useful tool for sequential PCR walking in complex genomes.
Desulfonylative Radical Ring Closure onto Aromatics. A Modular Route to Benzazepin-2-ones and 5-Arylpiperidin-2-ones (2012)

Adducts from the intermolecular radical addition of N-xanthylacetyl-N-methanesulfanilides to Boc-protected allylamine undergo ring closure with loss of a methanesulfonyl radical to give benzazepin-2-ones. Upon deprotection and exposure to triethylamine, these compounds rearrange into 5-aryl-2-piperidones. This approach also represents a useful route to benzazepin-2-ones unsubstituted on the nitrogen atom of the azepinone ring.
Feedback Inhibition of Chorismate Mutase/Prephenate Dehydrogenase (TyrA) ofEscherichia coli: Generation and Characterization of Tyrosine-Insensitive Mutants (2005)

In order to get insights into the feedback regulation by tyrosine of the Escherichia coli chorismate mutase/prephenate dehydrogenase (CM/PDH), which is encoded by the tyrA gene, feedback-inhibition-resistant (fbr) mutants were generated by error-prone PCR. The tyrA(fbr) mutants were selected by virtue of their resistance toward m-fluoro-D,L-tyrosine, and seven representatives were characterized on the biochemical as well as on the molecular level. The PDH activities of the purified His6-tagged TyrA proteins exhibited up to 35% of the enzyme activity of TyrA(WT), but tyrosine did not inhibit the mutant PDH activities. On the other hand, CM activities of the TyrA(fbr) mutants were similar to those of the TyrA(WT) protein. Analyses of the DNA sequences of the tyrA genes revealed that tyrA(fbr) contained amino acid substitutions either at Tyr263 or at residues 354 to 357, indicating that these two sites are involved in the feedback inhibition by tyrosine.
Polybenzimidazoles. II (1963)

Abstract A polybenzimidazole has been prepared from 3,3′‐diaminobenzidine and phthalic anhydride which has a high molecular weight and very good heat stability. Replacement of the hydrogen atoms on the nitrogen of the imidazole nuclei in a polybenzimidazole does not improve the heat stability as indicated by the properties of poly‐2,6‐( m ‐phenylene)‐3,5‐diphenyldiimidazobenzene. Polybenzimidazoles with aliphatic units have been prepared from 3,3′‐diaminobenzidine and the diphenyl ester of succinic and glutaric acids. The diphenyl esters of oxalic and malonic acids did not yield polymers presumably because cyclic amides were formed. Further hydrolytic stability tests on polybenzimidazoles have been reported. Some model compounds have been prepared for comparison of their melting points and absorption spectra with those of the corresponding polymer.
[Experimental investigations of osteogenesis and chondrogenesis by implant of BMP-fibrin glue mixture]. (1990)

The influence of fibrin glue on ectopic osteo-chondrogenesis induced by bone morphogenetic protein (BMP), which was extracted from decalcified rabbit long bones, was investigated histologically, radiographically, and electronmicroscopically. The mixtures, consisting of fibrin glue and BMP, were implanted between femoral biceps muscles of AKR mice. They were examined 3 days, 5 days, 1 week, and 2 weeks after implantation, respectively. The fibrin glue did not affect osteo-chondrogenesis by BMP under the mixture conditions, and new bone formation was seen almost in every implant. The fine network of fibrin glue seemed to be effective for adhesion, differentiation of BMP responding cells and was well cooperated on BMP. Fibrin glue network could control the area of osteo-chondrogenesis by BMP. It might be due to restriction of diffusion of BMP. In addition, the whole shape of the newly formed cartilage and bone was influenced by the quantity of Aprotinin administered to fibrin glue. Fibrin glue may be regarded as an effective cooperator of BMP in the case of clinical application of BMP in the future.
Isolation and characterization of 1.alpha.-hydroxy-23-carboxytetranorvitamin D: a major metabolite of 1,25-dihydroxyvitamin D3 (1979)

The in vivo side-chain oxidation of 1 alpha,25-dihydroxyvitamin D3 was investigated by using a double-label radiotracer technique. Rats dosed with 1 alpha,25-dihydroxy-[3 alpha-3H]vitamin D3 and 1 alpha,25-dihydroxy[26,27-14C]vitamin D3 produced compounds with a high 3H/14C ratio. These compounds were found in sizable quantities in intestine and liver within 3 h after dosing. The major side-chain oxidized metabolite migrated as an acid on DEAE-Sephadex chromatography and contained no 14C. Methyl esterification of this compound with diazomethane proceeded in good yield and rendered the compound more amenable to chromatographic purification. The metabolite was isolated in several steps from rats dosed with 1 microgram of 1 alpha,25-dihydroxy[3 alpha-3H]vitamin D3. The metabolite was obtained in pure form as the methyl ester and was positively identified as 1 alpha,3 beta-dihydroxy-24-nor-9,10-seco-5,7,10(19)cholatrien-23-oic acid. The trivial name calcitroic acid is proposed for this major side-chain oxidized metabolite of 1,25-dihydroxyvitamin D3.
Yersinia enterocolitica and related species isolated from wildlife in New York State (1986)

Fecal specimens for Yersinia screening were obtained from a variety of wild mammals, birds, reptiles, fish, and invertebrates throughout New York State. One specimen from each of 1,426 animals was examined. A total of 148 isolates of Yersinia enterocolitica and related species were obtained from 133 (9.3%) of the animals. Y. enterocolitica was isolated from 100 (7%) of the animals tested, including 81 (10%) of 812 mammals and 19 (3.3%) of 573 birds. Y. intermedia, Y. frederiksenii, and Y. kristensenii were isolated from 39 (2.7%), 5 (0.35%), and 4 (0.28%) animals, respectively. The 81 Y. enterocolitica isolates from mammals belonged to 15 serogroups and included three pathogens: two isolates of typical serogroup 0:8, the "American strain," one from a gray fox (Urocyon cinereoargenteus) and one from a porcupine (Erethizon dorsatum); and one isolate of serogroup 0:3, bacteriophage type IXb, the "Canadian strain," from a gray fox. The most prevalent serogroups recovered from mammals were 0:6,31 (16 isolates) and 0:5,27 (6 isolates). The 19 isolates of Y. enterocolitica from birds belonged to nine serogroups and included one serogroup 0:6,31 isolate from a common grackle (Quiscalus quiscula) and two serogroup 0:5,27 isolates from great horned owls (Bubo virginianus).
Maleimide-Functionalized Self-Assembled Monolayers for the Preparation of Peptide and Carbohydrate Biochips (2002)

This paper reports a convenient method for immobilizing biologically active ligands to self-assembled monolayers of alkanethiolates on gold (SAMs). This methodology is based on monolayers that present maleimide and penta(ethylene glycol) groups. The maleimide groups react efficiently with thiol-terminated ligands, whereas the penta(ethylene glycol) groups prevent the nonspecific adsorption of protein to the substrate. The rate and selectivity of the immobilization of a ferrocene-thiol conjugate were characterized using cyclic voltammetry. This paper presents three examples of biochips prepared using this methodology. In the first example, four carbohydrate-thiol conjugates were immobilized to monolayers and the lectin-binding properties of the substrates were examined using fluorescence and surface plasmon resonance spectroscopy. The second biochip was used to study the enzymatic phosphorylation of the immobilized peptide IYGEFKKKC by the tyrosine kinase c-src. Monolayers presenting this peptide were then used to study the inhibition of the enzyme in an array format. The final class of substrates, which presents the tripeptide Arg-Gly-Asp, was used for studies of integrin-mediated cell adhesion. The immobilization methodology described here, which combines the structural order and inert properties of SAMs with the efficient reaction between soluble thiol and surface-bound maleimide groups, will be useful for preparing substrates for a wide range of applications in basic science and biotechnology.
The Puzzle of RNAs that Target Gene Promoters (2009)

Setting the right target: Most researchers who use small RNAs in mammalian cells assume that mRNA will be the target. Recent studies suggest that small RNAs can also target chromosomal DNA. Few discoveries have had the impact of RNAi. Most researchers who use small RNAs to control gene expression in mammalian cells assume that mRNA will be the target. Recent studies, however, have suggested that small RNAs can also target chromosomal DNA.
The Structure of NRRL B-512 Dextran. Methylation Studies2 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Structure of NRRL B-512 Dextran. Methylation Studies2J. W. Van Cleve, W. C. Schaefer, and C. E. RistCite this: J. Am. Chem. Soc. 1956, 78, 17, 4435–4438Publication Date (Print):September 1, 1956Publication History Published online1 May 2002Published inissue 1 September 1956https://pubs.acs.org/doi/10.1021/ja01598a064https://doi.org/10.1021/ja01598a064research-articleACS PublicationsRequest reuse permissionsArticle Views209Altmetric-Citations109LEARN 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
Micro-RNA： A New Kind of Gene Regulators (2006)

一组小 RNA 分子，从，但是与 siRNAs (小干扰 RNA ) 有关不同在许多有机体被识别了。这些小 RNA，叫的 microRNAs (miRNAs ) ，内长地被编码约 20 24 nt 长搁浅单人赛的 RNA。他们通常被表示在一高度 tissue-stage-specific 或 developmental-stage-specific 时尚并且是在动物和植物的基因表示的 post-transcriptional 管理者。这篇文章关于 miRNAs 总结特性，机制和分析方法。当前的看法那 miRNAs 表示基因规定的最新发现的、隐藏的层在 miRNAs，他们的目标，行动的表示机制和分析方法的发现在研究人员之中导致了高兴趣。
June Consultation # 6 (2006)

Journal of Cataract & Refractive Surgery 32(6):p 910-912, June 2006. | DOI: 10.1016/j.jcrs.2006.03.027
Microarray Analysis Reveals Glucocorticoid-Regulated Survival Genes That Are Associated With Inhibition of Apoptosis in Breast Epithelial Cells (2004)

Activation of the glucocorticoid receptor (GR) results in diverse physiological effects depending on cell type. For example, glucocorticoids (GC) cause apoptosis in lymphocytes but can rescue mammary epithelial cells from growth factor withdrawal-induced death. However, the molecular mechanisms of GR-mediated survival remain poorly understood. In this study, a large-scale oligonucleotide screen of GR-regulated genes was performed. Several of the genes that were found to be induced 30 min after GR activation encode proteins that function in cell survival signaling pathways. We also demonstrate that dexamethasone pretreatment of breast cancer cell lines inhibits chemotherapy-induced apoptosis in a GR-dependent manner and is associated with the transcriptional induction of at least two genes identified in our screen, serum and GC-inducible protein kinase-1 (SGK-1) and mitogen-activated protein kinase phosphatase-1 (MKP-1). Furthermore, GC treatment alone or GC treatment followed by chemotherapy increases both SGK-1 and MKP-1 steady-state protein levels. In the absence of GC treatment, ectopic expression of SGK-1 or MKP-1 inhibits chemotherapy-induced apoptosis, suggesting a possible role for these proteins in GR-mediated survival. Moreover, specific inhibition of SGK-1 or MKP-1 induction by the introduction of SGK-1- or MKP-1-small interfering RNA reversed the anti-apoptotic effects of GC treatment. Taken together, these data suggest that GR activation in breast cancer cells regulates survival signaling through direct transactivation of genes that encode proteins that decrease susceptibility to apoptosis. Given the widespread clinical administration of dexamethasone before chemotherapy, understanding GR-induced survival mechanisms is essential for achieving optimal therapeutic responses.
Repeatability of kinematic, kinetic, and electromyographic data in normal adult gait (1989)

The repeatability of gait variables is an important consideration in the clinical use of results of quantitative gait analysis. Statistical measures were used to evaluate repeatability of kinematic, kinetic, and electromyographic data waveforms and spatiotemporal parameters of 40 normal subjects. Subjects were evaluated three times on each test day and on three different test days while walking at their preferred or natural speed. Intrasubject repeatability was excellent for kinematic data in the sagittal plane both within a test day as well as between test days. For joint angle motion in the frontal and transverse planes, the repeatability was good within a test day and poor between test days. Poor between-day repeatability of joint angle motion in the frontal and transverse planes was noted to be partly due to variabilities in the alignment of markers. Vertical reaction and fore-aft shear forces were more repeatable than the mediolateral shear force. Sagittal plane joint moments were more repeatable than frontal or transverse plane moments. For electromyographic data, repeatability within a day was slightly better than between test days. In general, the results demonstrate that with the subjects walking at their natural or preferred speed, the gait variables are quite repeatable. These observations suggest that it may be reasonable to base significant clinical decisions on the results of a single gait evaluation.
Pharmaceutical development of anticancer agents derived from marine sources (2000)

The marine ecosystem is more and more acknowledged as a source of potential anticancer agents. After the identification of a potential substance several hurdles have to be overcome before a marine candidate can enter the clinic. Amongst these are the establishment of a method which ensures sufficient supply and, which is the focus of this review, the development of a clinically useful pharmaceutical formulation. General issues with respect to the pharmaceutical development of marine anticancer agents will be discussed, which will be illustrated by highlighting aspects of the pharmaceutical development and clinical use of some representative compounds.