gebhart/patrepeval huggingface dataset:
Sam68 up‐regulation correlates with, and its down‐regulation inhibits, proliferation and tumourigenicity of breast cancer cells (2010)

The biosynthesis and metabolism of RNA play important roles in regulating gene expression. On the other hand, it has been shown that RNA expression profiling is differentially distinct between cancer and normal cells, suggesting the possibility that aberrant regulation of RNA metabolism might be associated with the development and progression of cancer. In the current study, we found that Sam68, an RNA-binding protein that links cellular signalling to RNA processing, was markedly overexpressed in breast cancer cells and tissues. Immunohistochemical analysis showed that the expression and cytoplasmic localization of Sam68 significantly correlated with clinical characteristics of patients, including clinical stage, tumour-nodule-metastasis (TNM) classification, histological grade, and ER expression. Univariate and multivariate analyses showed that the expression level and cytoplasmic localization of Sam68 were identified as independent prognostic factors. Furthermore, we found that siRNA knockdown of endogenous Sam68 inhibited cell proliferation and tumourigenicity of breast cancer cells in vitro, through blocking the G1 to S phase transition. Moreover, we demonstrated that the anti-proliferative effect of silencing Sam68 on breast cancer cells was associated with up-regulation of cyclin-dependent kinase inhibitor p21(Cip1) and p27(Kip1), enhanced transactivation of FOXO factors, and attenuation of Akt/GSK-3β signalling. Taken together, our results suggest that Sam68 might play an important role in promoting the proliferation and carcinogenesis of human breast cancer, and thereby might be a novel and useful prognostic marker and a potential target for human breast cancer treatment.
Heterocyclic systems related to pyrrocoline. Part I. 2: 3a-Diazaindene (1955)

J. D. Bower and G. R. Ramage, J. Chem. Soc., 1955, 2834 DOI: 10.1039/JR9550002834
Detection of fungi in blood cultures (1975)

In a retrospective study covering the period January 1972 to June 1974, recovery rates of bacteria and of fungi were generally equivalent with tryptic soy broth, Thiol, thioglycolate, and Columbia broth media (all under vacuum with carbon dioxide and sodium polyanetholesulfonate). An additional biphasic medium consisting of brain heart infusion broth and a brain heart infusion agar slant, which was inoculated only where fungal sepsis was suspected clinically, yielded significantly higher recovery rates of fungi. There were 29 instances of cultures with fungi in both the biphasic and broth media, 80 instances of cultures with fungi only in the biphasic medium, and no instances of fungi only in the broth media. The isolates were as follows: Candida albicans, 74; C. parapsilosis, 20; C. tropicalis, 16; Torulopsis glabrata, 18; Torulopsis sp., 1; Cryptococcus neoformans, 12; C. laurentii, 2; and Histoplasma capsulatum, 16. Despite routine subcultures of the broth media to chocolate blood agar within 24 h of inoculation and after 5 days of incubation, detection of fungemia was significantly improved by the use of a biphasic medium.
DNA-Protein Cross-link Formation Mediated by Oxanine (2003)

Chronic inflammation is a risk factor for many human cancers, and nitric oxide (NO) produced in inflamed tissues has been proposed to cause DNA damage via nitrosation or oxidation of base moieties. Thus, NO-induced DNA damage could be relevant to carcinogenesis associated with chronic inflammation. In this report, we report a novel genotoxic mechanism of NO that involves DNA-protein cross-links (DPCs) induced by oxanine (Oxa), a major NO-induced guanine lesion. When a duplex DNA containing Oxa at the site-specific position was incubated with DNA-binding proteins such as histone, high mobility group (HMG) protein, and DNA glycosylases, DPCs were formed between Oxa and protein. The rate of DPC formation with DNA glycosylases was approximately two orders of magnitude higher than that with histone and HMG protein. Analysis of the reactivity of individual amino acids to Oxa suggested that DPC formation occurred between Oxa and side chains of lysine or arginine in the protein. A HeLa cell extract also gave rise to two major DPCs when incubated with DNA-containing Oxa. These results reveal a dual aspect of Oxa as causal damage of DPC formation and as a suicide substrate of DNA repair enzymes, both of which could pose a threat to the genetic and structural integrity of DNA, hence potentially leading to carcinogenesis.
Synthetic studies on indoles and related compounds. XXV. The Friedel-Crafts acylation of ethyl 1H-indole-2-carboxylate. (2). (1990)

The Friedel-Crafts acylation of ethyl 1H-indole-2-carboxylate (1) with various acylating reagents having a functional group or hetero atom and the acylation of some derivatives (6, 7, 8, and 9) of ethyl 1H-indole-2-carboxylate (1) with simple acylating reagents are described. Acylation occurred at the C3-position or on the benzene moiety (mainly at the C5-position) of the indole nucleus. The regioselectivity of the above acylation of indoles (1, 6, 7, 8, and 9) is discussed.
Determination of swelling behavior and morphological properties of poly(acrylamide‐<i>co</i>‐itaconic acid) and poly(acrylic acid‐<i>co</i>‐itaconic acid) copolymeric hydrogels (2006)

Abstract Poly(acrylamide‐ co ‐itaconic acid) (PAAmIA) and poly(acrylic acid‐ co ‐itaconic acid) (PAAIA) copolymeric hydrogels were prepared with different compositions via free‐radical polymerization. Ethylene glycol dimethacrylate (EGDMA) was used as an original crosslinker for these monomers. Gelation percentages of the monomers were studied in detail and it was found that addition of IA into the monomer mixture decreased the gelation percentage. The variation in swelling values (%) with time, temperature, and pH was determined for all hydrogels. PAA, which is the most swollen hydrogel, has the swelling percentage value of 2000% at pH = 7.4, 37°C. Swelling behaviors were explained with detailed SEM micrographs, which show the morphologic differences between dry and swollen hydrogels. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 5994–5999, 2006
An apparatus for the measurement of the second virial coefficients of vapours; the second virial coefficients of some <i>n</i> -alkanes and of some mixtures of <i>n</i> -alkanes (1962)

Abstract An apparatus for the measurement of the second virial coefficients of vapours is described. It is designed so that a sample of the gas under investigation can be compared directly with a reference gas (nitrogen). This differential method has practical advantages over direct methods. The apparatus has been used to measure the second virial coefficients of the series of n-alkanes from propane to n-octane from near room temperature to about 140 °C. The results form a family showing deviations from the principle of corresponding states which increase regularly with increasing chain length. A simple formula based on the principle of corresponding states has been found to fit not only the present measurements, but also, previous measurements by other workers at higher temperatures on these substances, and also previous measurements on methane and on ethane. Measurements have also been made on equimolar mixtures of propane + n-heptane and of propane + n-octane. The results are in much better agreement with a slight extension of a rule of Guggenheim & McGlashan (1951) based on the principle of corresponding states than with the rule of Lewis & Randall (1923)-
Increased expression of pro-inflammatory cytokines and metalloproteinase-1 by TGF-<b>β</b>1 in synovial fibroblasts from rheumatoid arthritis and normal individuals (2002)

Transforming growth factor (TGF)-beta1 is expressed abundantly in the rheumatoid synovium. In this study, the inflammatory effect of TGF-beta1 in rheumatoid arthritis (RA) was investigated using cultured fibroblast-like synoviocytes (FLS) from RA and osteoarthritis (OA) patients, as well as non-arthritic individuals. mRNA expressions of IL-1beta, tumour necrosis factor (TNF)-alpha, IL-8, macrophage inflammatory protein (MIP)-1alpha and metalloproteinase (MMP)-1 were increased in RA and OA FLS by TGF-beta1 treatment, but not in non-arthritic FLS. Enhanced protein expression of IL-1beta, IL-8 and MMP-1 was also observed in RA FLS. Moreover, TGF-beta1 showed a synergistic effect in increasing protein expression of IL-1beta and matrix metalloproteinase (MMP)-1 with TNFalpha and IL-1beta, respectively. Biological activity of IL-1 determined by mouse thymocyte proliferation assay was also enhanced by 50% in response to TGF-beta1 in the culture supernatant of RA FLS. DNA binding activities of nuclear factor (NF)-kappaB and activator protein (AP)-1 were shown to increase by TGF-beta1 as well. These results suggest that TGF-beta1 contributes for the progression of inflammation and joint destruction in RA, and this effect is specific for the arthritic synovial fibroblasts.
Synthesis and Preclinical Evaluation of<sup>11</sup>C-UCB-J as a PET Tracer for Imaging the Synaptic Vesicle Glycoprotein 2A in the Brain (2016)

(11)C-UCB-J exhibited excellent characteristics as an SV2A PET radiotracer in nonhuman primates. The radiotracer is currently undergoing first-in-human evaluation.
Does CTCF mediate between nuclear organization and gene expression? (2009)

The multifunctional zinc-finger protein CCCTC-binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three-dimensional position in the nucleus, apparently responding to a "code" in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF-DNA interactions, the CTCF-binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three-dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the "CTCF code," explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.
A 768-lane microfabricated system for high-throughput DNA sequencing (2005)

A 768-lane DNA sequencing system based on microfluidic plates has been designed as a near-term successor to 96-lane capillary arrays. Electrophoretic separations are implemented for the first time in large-format (25 cm x 50 cm) microdevices, with the objective of proving realistic read length, parallelism, and the scaled sample requirements for long-read de novo sequencing. Two 384-lane plates are alternatively cycled between electrophoresis and regeneration via a robotic pipettor. A total of greater than 172000 bases, 99% accuracy (corresponding to quality score 20) is achieved for each iteration of a 384 lane plate. At current operating conditions, this implies a system throughput exceeding 4 megabases of raw sequence (Phred 20) per day on the new platform. Standard operation is at "1/32x" Sanger chemistry, equal to typical genome center operation on mature capillary array machines, and a 16-fold improvement in scaling relative to previous microfabricated devices. Experiments provide evidence that sample concentration can be further reduced to 1/256x Sanger chemistry in the microdevice. Life-testing indicates a usable life of >150 hours (more than 50 runs) for the 384 lane plates. The combined advances, particularly those in read length and sample requirement, directly address the cost model requirements for adaptation of the new technology as the next step beyond capillary array instruments.
The Cubli: A reaction wheel based 3D inverted pendulum (2013)

The Cubli is a 15×15×15 cm cube with reaction wheels mounted on three of its faces. By applying controlled torques to the reaction wheels the Cubli is able to balance on its corner or edge. This paper presents the development of the Cubli. First, the mechatronic design of the Cubli is presented. Then the multi-body system dynamics are derived. The parameters of the nonlinear system are identified using a frequency domain based approach while the Cubli is balancing on its edge with a nominal controller. Finally, the corner balancing using a linear feedback controller is presented along with experimental results.
Office (2014)

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Estrogen and Related Compounds: Biphasic Dose Responses (2001)

This article documents and quantitatively assesses the capacity of estrogen, phytoestrogens, and antiestrogens to affect biphasic dose-response relationships in animal/human models and across a broad range of cell types, affecting multiple endpoints. The range of endpoints displaying such biphasic dose responses includes plasminogen activation, oxytocin secretion, angiogenesis, cell proliferation, bone growth, monocyte chemotaxis, secretion of various cytokines, and other effects. The quantitative features of the dose response relationships revealed that the magnitude of the stimulatory responses was typically less than twofold, whereas the stimulatory responses were markedly variable ranging from about 5- to 10(6)-fold. Mechanistic explanations of the biphasic responses are addressed.
Identification of <scp>d</scp> -Peptide Ligands Through Mirror-Image Phage Display (1996)

Genetically encoded libraries of peptides and oligonucleotides are well suited for the identification of ligands for many macromolecules. A major drawback of these techniques is that the resultant ligands are subject to degradation by naturally occurring enzymes. Here, a method is described that uses a biologically encoded library for the identification of D-peptide ligands, which should be resistant to proteolytic degradation. In this approach, a protein is synthesized in the D-amino acid configuration and used to select peptides from a phage display library expressing random L-amino acid peptides. For reasons of symmetry, the mirror images of these phage-displayed peptides interact with the target protein of the natural handedness. The value of this approach was demonstrated by the identification of a cyclic D-peptide that interacts with the Src homology 3 domain of c- SRC. Nuclear magnetic resonance studies indicate that the binding site for this D-peptide partially overlaps the site for the physiological ligands of this domain.
Development of Porous Metal Mold Material using Vacuum Sintering Method (2008)

The porous metal material is used for injection metal mold with a great deal of gas production because it makes plenty of gas exhausted through pores formed in the metal mold. A canning HIP method was conventionally used for manufacturing of porous metals, but because of difficulty of process control and high cost of production its application was limited. In this experiment, porous metal mold material was produced by an enhanced vacuum sintering method with simply controlled and economical process and porosities/mechanical properties with variation of sintering temperature and duration time during vacuum sintering were studied. As a result, quality goods were obtained at optimized conditions as follows: sintering temperature of <TEX>$1230^{\circ}C$</TEX>, duration time of 2 hr and showed superior properties in wear loss and thermal conductivity and the same properties in hardness, TRS (Transverse Rupture Strength), and thermal expansion coefficient in comparison with those under canning HIP.
Still Image Objective Segmentation Evaluation using Ground Truth (2003)

In this paper, an objective segmentation evaluation metric suitable for the evaluation of still image segmentation results is proposed. The proposed metric is based on the spatial accuracy approach, originally proposed for the evaluation of foreground/backgroung segmentation masks generated from video sequences. This approach is extended to still image segmentation evaluation, where both the estimated segmentation masks and the ground truth mask typically contain multiple regions. The proposed method takes into account, using a single metric, not only the accuracy of the boundary localization of the created segments but also the under-segmentation and over-segmentation effects, which can hinder the performance of any segmentation algorithm and decrease the usability of the segmentation results in content-based applications. Several experiments have shown the potential of this approach.
The R‐type pyocin of <i>Pseudomonas aeruginosa</i> is related to P2 phage, and the F‐type is related to lambda phage (2000)

Pseudomonas aeruginosa produces three types of bacteriocins: R-, F- and S-type pyocins. The S-type pyocin is a colicin-like protein, whereas the R-type pyocin resembles a contractile but non-flexible tail structure of bacteriophage, and the F-type a flexible but non-contractile one. As genetically related phages exist for each type, these pyocins have been thought to be variations of defective phage. In the present study, the nucleotide sequence of R2 pyocin genes, along with those for F2 pyocin, which are located downstream of the R2 gene cluster on the chromosome of P. aeruginosa PAO1, was analysed in order to elucidate the relationship between the pyocins and bacteriophages. The results clearly demonstrated that the R-type pyocin is derived from a common ancestral origin with P2 phage and the F-type from lambda phage. This notion was supported by identification of a lysis gene cassette similar to those for bacteriophages. The gene organization of the R2 and F2 pyocin gene cluster, however, suggested that both pyocins are not simple defective phages, but are phage tails that have been evolutionarily specialized as bacteriocins. A systematic polymerase chain reaction (PCR) analysis of P. aeruginosa strains that produce various subtypes of R and F pyocins revealed that the genes for every subtype are located between trpE and trpG in the same or very similar gene organization as for R2 and F2 pyocins, but with alterations in genes that determine the receptor specificity.
Securing position and distance verification in wireless networks (2004)

Approximately one third of individuals who experience a severe traumatic event will develop posttraumatic stress disorder (PTSD). It is crucial to identify what factors may be associated with increased or decreased risk for PTSD. We conducted an umbrella review of systematic reviews and meta-analyses of risk/protective factors for PTSD and assessed and graded the evidence of the association between each factor and PTSD. Thirty-three systematic reviews and meta-analyses were included and 130 potential risk factors were identified. Of those, 57 showed a significant association with PTSD. Being female or being indigenous people of the Americas, among the sociodemographic factors; history of physical disease and family history of psychiatric disorder, among the pretrauma factors; and cumulative exposure to potentially traumatic experiences, trauma severity, and being trapped during an earthquake, among the peritrauma factors, showed convincing or highly suggestive evidence of an association with PTSD. Data from prospective studies were less conclusive. Our results have the potential of helping refine PTSD prediction models and contributing to the design of prevention strategies.
Quantitative Elisa for Human Lactate Dehydrogenase Isoenzyme 5 (1988)

Four monoclonal antibodies (Mab) derived from mice immunized with lactate dehydrogenase 5 (LDH5) react strongly with LDH5, but weakly with LDH2 which contains a single subunit of type M. Experimental evidence suggest that these antibodies are directed to an antigenic determinant in the interface between two subunits of type M. A sandwich ELISA procedure was devised, using these Mabs to identify and quantify LDH5. The procedure involves immobilization of one of these Mabs by its adsorption onto polyclonal anti-mouse IgG coated polystyrene plates, adsorption of LDH5, its identification by the same Mab as that used in the immobilization step, and finally color development by an enzyme labeled rabbit anti-mouse IgG antiserum. The method enables LDH5 to be assayed at a concentration range of 0-5 micrograms/ml.
Immunization with Leishmania receptor for macrophages protects mice against cutaneous leishmaniasis. (1985)

The Leishmania major receptor for macrophages is a lipid-containing glycoconjugate that is recognized by the monoclonal antibody WIC-79.3. When L. major promastigotes were incubated with Fab fragments of WIC-79.3 prior to injection into genetically susceptible mice, their infectivity was decreased. Fab fragments from an irrelevant control antibody of the same class had no effect. The L. major glycolipid was purified from detergent-solubilized promastigotes by affinity chromatography on immobilized WIC-79.3 and used to vaccinate mice that are genetically resistant or susceptible to disease. Genetically resistant mice could be protected totally from cutaneous disease with as little as 5 micrograms of glycolipid. A high but not absolute level of resistance was also induced in the susceptible mice, in which the disease is otherwise fatal. No protection was obtained with the carbohydrate fragment of the glycolipid alone or by injection of the glycolipid in the absence of adjuvant. Genetically susceptible mice, immunized and protected from disease as a result of multiple injections of live avirulent cloned promastigotes of L. major, produced antibodies to the glycolipid of L. major. No antibodies were detected in serum from chronically diseased mice. The data suggest that this functionally important antigen of L. major is a candidate vaccine against cutaneous leishmaniasis.
The regulation of biofilm development by quorum sensing in <i>Aeromonas hydrophila</i> (2002)

Aeromonas hydrophila is an opportunistic Gram-negative pathogen that readily attaches to stainless steel to produce a thin biofilm with a complex 3D structure covering 40-50% of the available surface and producing large microcolonies. As A. hydrophila possesses an N-acylhomoserine lactone (AHL)-dependent quorum-sensing system based on the ahyRI locus, the presence of the AhyI protein and C4-HSL within the biofilm phase was first established by Western blot and AHL biosensor analysis respectively. The ability of the A. hydrophila AH-1 N strain to form biofilms in a continuous-flow chamber was compared with isogenic ahyI and ahyR mutants. The ahyI mutant, which cannot produce C4-HSL, failed to form a mature biofilm. In addition, the viable count of biofilm, but not planktonic phase ahyI mutants, was significantly lower that the parent or ahyR mutant. This defect in the differentiation of the ahyI mutant biofilm could be partially restored by the addition of exogenous C4-HSL. A mutation in ahyR increased coverage of the available surface to around 80% with no obvious effect upon biofilm microcolony formation. These data support a role for AHL-dependent quorum sensing in A. hydrophila biofilm development. Exposure of the A. hydrophila AH-1N biofilm to N-(3-oxodecanoyl)homoserine lactone, which inhibits exoprotease production in planktonic cells, however, had no effect on biofilm formation or architecture within the continuous-flow chamber.
Electromagnetic Prospect Scanning—Seabed Logging Moves from Risk Reduction to Value Creation (2007)

Abstract Seabed logging is an emerging technology that measures subsurface resistivity prior to drilling. The technique has been commercially available for over 5 years, and has been proven to reduce drilling risk in many offshore geologic environments. Electromagnetic scanning is a new application of this proven technology. Sparse spatial sampling and wide azimuth geometry can be used to apply seabed logging to find and accelerate delivery of new prospects in frontier areas. In this paper, we evaluate the costs and benefits of various geometries and show results from the Campos basin in Brasil.