gebhart/patrepeval huggingface dataset:
Assembly of Mesoscale Particles over Large Areas and Its Application in Fabricating Tunable Optical Filters (1998)

This paper describes a method for the crystallization of mesoscale particles over areas as large as ∼1 cm2. We injected an aqueous dispersion of spherical particles into a cell formed by two glass substrates and a square frame of photoresist that had been patterned on the surface of one of the substrates. One side of the frame had channels on its surface that could retain the particles while letting the solvent flow through. External gas pressure and sonication drove the particles into a cubic-close-packed (ccp) assembly with the (111) face parallel to the surfaces of the glass substrates. The smallest particles that have been crystallized by this method are polystyrene beads of ∼60 nm in diameter. The procedure presented here offers a number of attractive features: (i) It is relatively fast. For example, polystyrene beads of 0.48 μm in diameter can be crystallized into a 25 layer assembly over an area of ∼1 cm2 in ∼48 h. (ii) It has a tight control over the surface morphology and the number of layers of the crystalline assemblies. (iii) It works for aqueous dispersions of a wide range of spherical particles regardless of their chemical compositions and/or surface properties (such as charge densities and chemical functional groups). We have also demonstrated fabrication of tunable optical filters from these crystalline assemblies of particles. Each crystalline assembly effectively rejects a narrow wavelength interval (as determined by the Bragg condition) in the spectral region ranging from ultraviolet to near-infrared. The tunability (in terms of wavelength) of the filter can be achieved by changing the angle between the incident light and the normal to the surface of the filter, or by using particles with different diameters.
Synthetic peptides as antigens (1986)

Symposium on Synthetic Peptides as Antigens, held at the Ciba Foundation, London, 4 6 June 1985. The subject of this symposium was proposed by P. Dukor and D. G. Braun. Editors: Ruth Porter (Organizer) and Julie Whelan. G. L. Ada Introduction. J. H. Humphrey Regulation of in vivo immune responses: few principles and much ignorance. Discussion. P. J. Lachmann, L. Strangeways, A. Vyakarnam and G. I. Evan Raising antibodies by coupling peptides to PPD and immunizing BCG-sensitized animals. Discussion. H. J. Dyson, K. J. Cross, J. Ostresh, R. A. Houghten, I. A. Wilson, P. E. Wright and R. A. Lerner Selection by site-directed antibodies of small regions of peptides which are ordered in water. Discussion. M. H. V. Van Regenmortel, D. Altschuh and A. Klug Influence of local structure on the location of antigenic determinants in tobacco mosaic virus protein. Discussion. M. J. Crumpton The importance of conformation and of equilibria in the interaction of globular proteins and their fragments with antibodies. Discussion. A. B. Edmundson and K. R. Ely Three-dimensional analyses of the binding of synthetic chemotactic and opioid peptides in the Mcg light chain dimer. Discussion. H. M. Geysen, S. J. Rodda and T. J. Mason The delineation of peptides able to mimic assembled epitopes. Discussion. V. Nussenzweig and R. S. Nussenzweig Experimental basis for the development of a synthetic vaccine against Plasmodium falciparum malaria sporozoites. Discussion. R. F. Anders, P-T. Shi, D. B. Scanlon, S. J. Leach, R. L. Coppel, G. V. Brown, H-D. Stahl and D. J. Kemp Antigenic repeat structures in proteins of Plasmodium falciparum. Discussion. M. Sela, R. Arnon and C. O. Jacob Synthetic peptides with antigenic specificity for bacterial toxins. Discussion. V. C. Stevens Use of synthetic peptides as immunogens for developing a vaccine against human chorionic gonadotropin. Discussion. D. R. Stanworth, D. S. Butt and G. Z. Hastings The use of synthetic peptides in the delineation of immunoglobulin antigenic epitopes and Fc effector functions. Discussion. G. I. Evan, D.C. Hancock, T. Littlewood and C. D. Pauza Characterization of the human c-myc protein using antibodies prepared against synthetic peptides. Discussion. S. S. Alkan and D. G. Braun Epitope mapping of human recombinant interferon alpha molecules by monoclonal antibodies. Discussion. Final general discussion Reactivity of anti-peptide antibodies with the parent proteins. The proportion of monoclonal antibodies reactive to conformational or other linear sequences. High and low affinity antibodies and their roles. T-dependent and T-independent antigen presentation. G. L. Ada Chairman's summing-up. Index of contributors. Subject index
The Cell Cycle Checkpoint Gene Rad9 Is a Novel Oncogene Activated by 11q13 Amplification and DNA Methylation in Breast Cancer (2005)

Human Rad9 (hRad9), a structural homologue of yeast Schizosaccharomyces pombe rad9, is involved in cell cycle checkpoints and apoptosis. hRad9 can serve as a corepressor of androgen receptor in prostate cancer cells, but little is known about its role in the development of breast or other cancers. In the present study, semiquantitative reverse transcription-PCR showed that Rad9 mRNA levels were up-regulated in 52.1% (25 of 48) of breast tumors, and this up-regulation correlated with tumor size (P = 0.037) and local recurrence (P = 0.033). Overexpression of Rad9 mRNA was partly due to an increase in Rad9 gene number as measured by quantitative PCR. In other breast tumors with Rad9 mRNA overexpression but without increase in gene number, there was differential methylation of two putative Sp1/3 binding sites within the first and second introns of the Rad9 gene, which was similarly found in MCF-7 breast cancer cell line with increased Rad9 mRNA. Silencing Rad9 expression by RNA interference in MCF-7 cell line inhibited its proliferation in vitro. Promoter assays indicated that the Sp1/3 site in intron 2 may act as a silencer. In vivo binding of Sp3 to intron 2 was shown by chromatin immunoprecipitation assays. Treatment of MCF-7 cell line with 5'-aza-2'-deoxycytidine reduced Rad9 mRNA expression and also increased binding of Sp3 to the demethylated intron 2 region. Collectively, these findings suggest that Rad9 is a novel oncogene candidate activated by 11q13 amplification and DNA hypermethylation in breast cancer and may play a role in tumor proliferation and local invasion.
Real-Time Tracking of Multiple People Using Continuous Detection (1999)

Recent investigations have shown the advantages of keeping multiple hypotheses during visual tracking. In this paper we explore an alternative method that keeps just a single hypothesis per tracked object for computational efficiency, but displays robust performance and recovery from error by employing continuous detection during tracking. The method is implemented in the domain of people-tracking, using a novel combination of stereo information for continuous detection and intensity image correlation for tracking. Real-time stereo provides extended information for 3D detection and tracking, even in the presence of crowded scenes, obscuring objects, and large scale changes. We are able to reliably detect and track people in natural environments, on an implemented system that runs at more than 10 Hz on standard PC hardware. 1 Introduction Our goal is to simulataneously track a number of people in crowded natural environments. A system of this sort would be useful in a number of applic...
Orally Fast Disintegrating Tablets: Developments, Technologies, Taste-Masking and Clinical Studies (2004)

Fast disintegrating tablets (FDTs) have received ever-increasing demand during the last decade, and the field has become a rapidly growing area in the pharmaceutical industry. Upon introduction into the mouth, these tablets dissolve or disintegrate in the mouth in the absence of additional water for easy administration of active pharmaceutical ingredients. The popularity and usefulness of the formulation resulted in development of several FDT technologies. This review describes various formulations and technologies developed to achieve fast dissolution/dispersion of tablets in the oral cavity. In particular, this review describes in detail FDT technologies based on lyophilization, molding, sublimation, and compaction, as well as approaches to enhancing the FDT properties, such as spray-drying, moisture treatment, sintering, and use of sugar-based disintegrants. In addition, taste-masking technologies, experimental measurements of disintegration times, and clinical studies are also discussed.
Maximum tolerable dose and low-dose metronomic chemotherapy have opposite effects on the mobilization and viability of circulating endothelial progenitor cells. (2003)

There is growing evidence that vasculogenesis (progenitor cell-derived generation of new blood vessels) is required for the growth of some neoplastic diseases. Here we show that the administration of cyclophosphamide (CTX) at the maximum tolerable dose with 21-day breaks or at more frequent low-dose (metronomic) schedules have opposite effects on the mobilization and viability of circulating endothelial progenitors (CEPs) in immunodeficient mice bearing human lymphoma cells. Animals treated with the maximum tolerable dose CTX experienced a robust CEP mobilization a few days after the end of a cycle of drug administration, and tumors rapidly became drug resistant. Conversely, the administration of metronomic CTX was associated with a consistent decrease in CEP numbers and viability and with more durable inhibition of tumor growth. Our findings suggest that metronomic low-dose chemotherapy regimens are particularly promising for avoiding CEP mobilization and, hence, to potentially reduce vasculogenesis-dependent mechanisms of tumor growth.
<title>Image quality of endoscopes</title> (2001)

Medical endoscopy has become a key technology for the purposes of minimally invasive diagnostic and therapeutic procedures. With the aid of an endoscope, and external observation of a location inside the human body which may be difficult or dangerous to reach or which should be subjected to minimal traumatization associated with the intended medical treatment is facilitated through a viewing channel. A television camera is usually attached to the distal end of an endoscope for image presentation. Of primary importance for the user are image quality, ease of application and safety. This communication is primarily concerned with aspects relating to image quality. First, the optical properties of various types of endoscopes are analyzed and their spatial resolution is determined. Second, it is shown that the inherent optical quality in terms of spatial, temporal and contrast resolution of most endoscopes exceeds the performance limits of presently used standard TV systems in part substantially. Accordingly, a special purpose advanced digital television system exhibiting high spatial resolution, furthermore true color and high contrast dynamics has been developed. Since endoscopic images usually are circular, its aspect ratio is quadratic with a spatial resolution of 1000 x 1000 pixels. The framing rate is variable from 1 Hz to 30 Hz noninterlaced. Some design aspects and the performance of the system are shown and further applications are indicated.
Cloning of the Vibrio harveyi luciferase genes: use of a synthetic oligonucleotide probe. (1983)

A mixed-sequence synthetic oligonucleotide probe was used to isolate a clone containing the gene encoding the alpha subunit of bacterial luciferase from Vibrio harveyi and part of the gene coding for the beta subunit. DNA sequence analysis has allowed us to determine that the genes are closely linked on the bacterial chromosome and transcribed in the same direction. Comparison of the sequences in the regions preceding the two structural genes has revealed considerable homology and has identified sites that may be involved in the expression of the genes. Identification of a clone from a clone bank of total genomic DNA from this organism shows that mixed probes can be successfully used to isolate a gene of interest from any bacterium provided some protein sequence for the gene product is available.
Comparison of the relative recovery of polyphenolics in two fruit extracts from a model of degradation during digestion and metabolism (2007)

To simulate the effects of digestion and metabolism on the survival of different polyphenolic compounds, extracts of blueberry and apple were deglycosylated by acid hydrolysis, followed by enzymic glucuronidation under neutral conditions, yielding approximately 5% overall recovery of polyphenolics. The major polyphenolics before and after the treatment were compared, to estimate which species are likely to be present in the intestinal lumen, undegraded and available for absorption, after consumption of the fruit. Whereas blueberry extract consisted predominantly of anthocyanins, epicatechin and caffeoyl quinate esters, the major components of the treated extract were quercetin glucuronides and (unglucuronidated) caffeoyl quinates, with only traces of anthocyanidin derivatives. In apple extract, compositional changes were less marked, but caffeoyl quinates, procyanidins and quercetin were enriched at the expense of caffeic acid, epicatechin and catechin. Hydrophobic compounds like phloretin and quercetin were extensively glucuronidated, whereas caffeic acid and caffeoyl quinate were not. These results suggest that the major polyphenolic components of a fruit are not necessarily the most important contributors to any health benefits because the polyphenolic composition in the intestinal lumen and consequently, in the circulation, may be considerably different.
Photonic Papers and Inks: Color Writing with Colorless Materials (2003)

A photonic paper/ink system for color writing on and with colorless materials is described. The “paper” is a 3D crystal of polymer beads embedded in an elastomer matrix made of poly(dimethylsiloxane) (PDMS), and the “ink” is a liquid (e.g., a silicone fluid or organic solvent) capable of swelling the matrix, changing the lattice constant and hence wavelength of light diffracted (see Figure and cover).
Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors (2007)

Very little is known regarding regulation of microRNA (miRNA) biogenesis in normal tissues, tumors, and cell lines. Here, we profiled the expression of 225 precursor and mature miRNAs using real-time PCR and compared the expression levels to determine the processing patterns. RNA from 22 different human tissues, 37 human cancer cell lines, and 16 pancreas and liver tissues/tumors was profiled. The relationship between precursor and mature miRNA expression fell into the following four categories: (1) a direct correlation exists between the precursor and mature miRNA expression in all cells/tissues studied; (2) direct correlation of the precursor and mature miRNA exists, yet the expression is restricted to specific cell lines or tissues; (3) there is detectable expression of mature miRNA in certain cells and tissues while the precursor is expressed in all or most cells/tissues; or (4) both precursor and mature miRNA are not expressed. Pearson correlation between the precursor and mature miRNA expression was closer to one for the tissues but was closer to zero for the cell lines, suggesting that processing of precursor miRNAs is reduced in cancer cell lines. By using Northern blotting, we show that many of these miRNAs (e.g., miR-31, miR-105 and miR-128a) are processed to the precursor, but in situ hybridization analysis demonstrates that these miRNA precursors are retained in the nucleus. We provide a database of the levels of precursor and mature miRNA in a variety of cell types. Our data demonstrate that a large number of miRNAs are transcribed but are not processed to the mature miRNA.
A Large-Insert Porcine Library with Sevenfold Genome Coverage: a Tool for Positional Cloning of Candidate Genes for Major Quantitative Traits (2003)

A porcine genomic bacterial artificial chromosome (BAC) library was constructed by cloning partial EcoRI-digested high-molecular-weight DNA from a Korean native boar into the EcoRI site of the pBACe3.6 vector. The library consists of about 165,000 clones with an average insert size of 125 kb, representing about seven genome equivalents of coverage. About 130,000 clones (corresponding to fivefold genome coverage) were arrayed in 14 superpools which were organized as four dimensional pools. The library was further characterized by PCR screening of 38 microsatellite probes. An average of 4.84 positive clones were selected per marker. This indicates that the library is unbiased and will be useful for initiating fine scale physical mapping of major QTL in pigs. The library is being used to isolate specific clones by screening with type I and type II marker clones located in the QTL region affecting intramuscular fat content on SSC6.
Differential induction of glutathione transferase isoenzymes of mice stomach by diallyl sulfide, a naturally occurring anticarcinogen (1991)

Diallyl sulfide (DAS), an organosulfur compound identified as the flavor component in garlic, has been shown to inhibit chemically induced neoplasia of forestomach and lung in mice. Even though the exact mechanism(s) of anti-neoplastic activity of DAS is not known, several independent studies suggest that this effect may, at least in part, be due to the elevation of glutathione-S-transferase (GST) activity. To gain further insight into the mechanism(s) of anti-carcinogenic activity of DAS, we have determined effect of orally administered DAS (25, 50 and 75 mumol) on levels of alpha, mu and pi class GSTs and glutathione (GSH) peroxidase and GSH reductase activities of female A/J mice stomach. Western blotting revealed presence of alpha, mu and pi class GSTs in mice stomach. A significant increase in all the three classes of GSTs was observed in the stomach of mice treated with DAS. Maximum increase in GST alpha and pi was evident by treating the animals with 75 mumol DAS whereas maximum induction of GST mu occurred after treating mice with 50 mumol DAS. GSH peroxidase activity towards t-butyl-hydroperoxide increased in a dose-dependent fashion in the mice stomach treated with DAS. Even though this activity towards hydrogen peroxide was similar in mice treated with 50 or 75 mumol DAS, these values were significantly higher than that of the control. GSH reductase was also elevated in the stomach of mice treated with 75 mumol DAS. These results suggest that DAS may exert anti-neoplastic effect by modulating GSH dependent detoxification enzymes.
Phosphorylation of the carboxy‐terminal repeat domain in RNA polymerase II by cyclin‐dependent kinases is sufficient to inhibit transcription (1997)

Cdc2 kinase triggers the entry of mammalian cells into mitosis, the only cell cycle phase in which transcription is globally repressed. We show here that Cdc2 kinase phosphorylates components of the RNA polymerase II transcription machinery including the RNA polymerase II carboxy-terminal repeat domain (CTD). To test specifically the effect of CTD phosphorylation by Cdc2 kinase, we used a yeast in vitro transcription extract that is dependent on exogenous RNA polymerase II that contains a CTD. Phosphorylation was carried out using immobilized Cdc2 so that the kinase could be removed from the phosphorylated polymerase. ATPγS and Cdc2 kinase were used to produce an RNA polymerase 110 that was not detectably dephosphorylated in the transcription extract. RNA polymerase 110 produced in this way was defective in promoter-dependent transcription, suggesting that phosphorylation of the CTD by Cdc2 kinase can mediate transcription repression during mitosis. In addition, we show that phosphorylation of pol II with the human TFIIH-associated kinase Cdk7 also decreases transcription activity despite a different pattern of CTD phosphorylation by this kinase. These results extend previous findings that RNA polymerase 110 is defective in preinitiation complex formation. Here we demonstrate that phosphorylation of the CTD by cyclin-dependent kinases with different phosphoryl acceptor specificities can inhibit transcription in a CTD-dependent transcription system. J. Cell. Biochem. 64:390–402. © 1997 Wiley-Liss, Inc.
Lipid-Based Nanoparticles in The Systemic Delivery of siRNA (2013)

RNAi therapeutics are believed to be the future of personalized medicine and have shown promise in early clinical trials. However, many physiological barriers exist in the systemic delivery of siRNAs to the cytoplasm of targeted cells to perform their function. To overcome these barriers, many siRNA delivery systems have been developed. Among these, lipid-based nanoparticles have great potential owing to their biocompatibility and low toxicity in comparison with inorganic nanoparticles and viral systems. This review discusses the hurdles of systemic siRNA delivery and highlights the recent progress made in lipid-based nanoparticles, which are categorized based on their key lipid components, including cationic lipid, lipoprotein, lipidoid, neutral lipid and anionic lipid-based nanoparticles. It is expected that these lipid nanoparticle-based siRNA delivery systems will have an enabling role for personalized cancer medicine, where siRNA delivery will join forces with genetic profiling of individual patients to achieve the best treatment outcome.
Characterization of a Negative Retinoic Acid Response Element in the Murine Oct4 Promoter (1994)

Expression of Oct4 in embryonic stem cells is controlled by a distal upstream stem cell-specific enhancer that is deactivated during retinoic acid (RA)-induced differentiation by an indirect mechanism not involving binding of RA receptors (H. Okazawa, K. Okamoto, F. Ishino, T. Ishino-Kaneko, S. Takeda, Y. Toyoda, M. Muramatsu, and H. Hamada, EMBO J. 10:2997-3005, 1991). Here we report that in RA-treated P19 embryonal carcinoma cells the Oct4 promoter is also subject to negative regulation by RA. The minimal Oct4 promoter sequence mediating repression consists of a promoter-proximal sequence containing a GC-rich SP1 consensus-like sequence and several hormone response element half-sites that can be arranged into direct repeats with different spacing. The GC box binds a nuclear factor that is invariably present in undifferentiated and RA-treated differentiated P19 cells. By contrast, the hormone response element-containing sequence binds factors that are induced following RA treatment. Mutational analysis and competition experiments show that the functional entity binding the RA-induced factor is a direct repeat sequence with a spacing of one nucleotide, previously shown to be a binding site for COUP transcription factors (COUP-TFs). Cotransfected orphan receptors COUP-TF1, ARP-1, and EAR-2 were able to repress the activity of Oct4 promoter-driven reporters in P19 EC cells, albeit with different efficiencies. Furthermore, the negative transcriptional effect of COUP-TFs is dominant over the activating effect of the Oct4 embryonic stem cell-specific enhancer. These results show that negative regulation of Oct4 expression during RA-induced differentiation of embryonic stem cells is controlled by two different mechanisms, including deactivation of the embryonic stem cell-specific enhancer and promoter silencing by orphan nuclear hormone receptors.
Hepatitis C Virus IRES RNA-Induced Changes in the Conformation of the 40 S Ribosomal Subunit (2001)

Initiation of protein synthesis in eukaryotes requires recruitment of the 40S ribosomal subunit to the messenger RNA (mRNA). In most cases, this depends on recognition of a modified nucleotide cap on the 5' end of the mRNA. However, an alternate pathway uses a structured RNA element in the 5' untranslated region of the messenger or viral RNA called an internal ribosomal entry site (IRES). Here, we present a cryo-electron microscopy map of the hepatitis C virus (HCV) IRES bound to the 40S ribosomal subunit at about 20 A resolution. IRES binding induces a pronounced conformational change in the 40S subunit and closes the mRNA binding cleft, suggesting a mechanism for IRES-mediated positioning of mRNA in the ribosomal decoding center.