gebhart/patrepeval huggingface dataset:
Polymer Gel Rheology and Adhesion (2012)

Polymer gels are found in many applications ranging from foods (Ross-Murphy, 1995; Tunick, 2010) and drug delivery (Andrews & Jones, 2006) to adhesives (Creton, 2003) and consumer products (Solomon & Spicer, 2010). By manipulating the gel’s microstructure, a wide variety of physical properties can be achieved ranging from hard rubbery plastics to soft hydrogels. Silicone-based polymer gels in particular have found wide utilization in consumer products ranging from medical implants to cooking utensils. Here we will discuss methods of characterizing polymer gels using rheological techniques to probe their adhesion and mechanical response. Further, we will link the observed adhesion and mechanical behavior to the gel microstructure.
Second-order Volterra filtering and its application to nonlinear system identification (1985)

Some recent results on the design and implementation of second-order Volterra filters are presented. The (second-order) Volterra filter is a nonlinear filter with the filter structure of (second-order) Volterra series. A simple minimum mean-square error solution for the Volterra filter is derived, based on the assumption that the filter input is Gaussian. Also, we propose an iterative factorization technique to design a subclass of the Volterra filters, which can alleviate the complexity of the filtering operations considerably. Furthermore, an adaptive algorithm for the Volterra filter is investigated along with its mean convergence and asymptotic excess mean-square error. Finally, the utility of the Volterra filter is demonstrated by utilizing it in studies of nonlinear drift oscillations of moored vessels subject to random sea waves.
Microbial degradation of chloroaromatics: use of the meta-cleavage pathway for mineralization of chlorobenzene (1997)

Pseudomonas putida GJ31 is able to simultaneously grow on toluene and chlorobenzene. When cultures of this strain were inhibited with 3-fluorocatechol while growing on toluene or chlorobenzene, 3-methylcatechol or 3-chlorocatechol, respectively, accumulated in the medium. To establish the catabolic routes for these catechols, activities of enzymes of the (modified) ortho- and meta-cleavage pathways were measured in crude extracts of cells of P. putida GJ31 grown on various aromatic substrates, including chlorobenzene. The enzymes of the modified ortho-cleavage pathway were never present, while the enzymes of the meta-cleavage pathway were detected in all cultures. This indicated that chloroaromatics and methylaromatics are both converted via the meta-cleavage pathway. Meta cleavage of 3-chlorocatechol usually leads to the formation of a reactive acylchloride, which inactivates the catechol 2,3-dioxygenase and blocks further degradation of catechols. However, partially purified catechol 2,3-dioxygenase of P. putida GJ31 converted 3-chlorocatechol to 2-hydroxy-cis,cis-muconic acid. Apparently, P. putida GJ31 has a meta-cleavage enzyme which is resistant to inactivation by the acylchloride, providing this strain with the exceptional ability to degrade both toluene and chlorobenzene via the meta-cleavage pathway.
Total Synthesis of (−)-Steganone Utilizing a Samarium(II) Iodide Promoted 8-Endo Ketyl−Olefin Cyclization (1999)

A six-step synthesis of (±)-steganone from commercially available 3,4,5-trimethoxybenzyl alcohol features a samarium(II) iodide promoted 8-endo ketyl−olefin coupling to install, in a single transformation, the 8,5 ring system common to the lignan lactones. The racemic synthesis provided the basis for the construction of (−)-steganone, which exploited a chromium tricarbonyl moiety both to establish and protect the desired absolute stereochemistry through key transformations, including a SmI2-promoted 8-endo radical cyclization and two palladium-catalyzed couplings.
An overhanging 3' terminus is a conserved feature of telomeres. (1989)

The reactivity of single-stranded thymidines with osmium tetraoxide was used to demonstrate the existence of a terminal overhang of the G-rich strand of telomeres from two distantly related eucaryotes, the ciliated protozoan Tetrahymena spp. and the acellular slime mold Didymium spp. Conservation of a G-strand overhang at the molecular terminus of telomeres is consistent with our suggestion that an unusual DNA structure formed by the G-strand overhang is important for telomere function (E. Henderson, C. C. Hardin, S. K. Wolk, I. Tinoco Jr., and E. H. Blackburn, Cell 51:899-908, 1987).
Cutting Edge: Receptor-Mediated Endocytosis of Heat Shock Proteins by Professional Antigen-Presenting Cells (1999)

Immunization with heat shock proteins (HSPs) induces Ag-specific CTL responses. The specificity of the immune response is based on peptides associated with HSPs. To investigate how exogenous HSP/peptide complexes gain access to the MHC class I-restricted Ag presentation pathway, we incubated the monocytic cell line P388D1 and the dendritic cell line D2SC/1 with gold-labeled HSPs gp96 and HSC70. We show that HSPs bind specifically to the surface of these APCs and are internalized spontaneously by receptor-mediated endocytosis, demonstrating the existence of specific receptors for HSPs on these cells. In addition, we observe colocalization of internalized HSPs and surface MHC class I molecules in early and late endosomal structures. These findings provide possible explanations for the immunogenicity of HSP/peptide complexes and for the transfer of HSP-associated peptides onto MHC class I molecules.
Radical Migration Through the DNA Helix: Chemistry at a Distance (2018)

This chapter focuses on experiments employing probes intercalated or stacked within the double helix of DNA. The reaction of the DNA bases with radical species generated by radiation, carcinogens, or oxidative stress can lead to mutagenic damage. The efficiency and dynamics of radical transport through the DNA helix therefore hold profound biological implications. The chapter addresses the concerning charge migration through DNA arises that can by using well-defined chemical experiments. Efficient long-range charge transport over remarkable molecular distances has been elucidated in diverse systems utilizing spectroscopy, electrochemistry, and the visualization of chemical reactions. In reactions monitored spectroscopically, electrochemically, and chemically, now demonstrated that a whole series of intercalated reactants with different structural properties can undergo remarkably efficient electron transfer over long molecular distances through the DNA helix. The base stack therefore serves as a bridging medium that is particularly favorable for facilitating long-range electronic coupling.
Electricity Production byGeobacter sulfurreducensAttached to Electrodes (2003)

ABSTRACT Previous studies have suggested that members of the Geobacteraceae can use electrodes as electron acceptors for anaerobic respiration. In order to better understand this electron transfer process for energy production, Geobacter sulfurreducens was inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor. The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential). When a small inoculum of G. sulfurreducens was introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism. When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks. This represents the first report of microbial electricity production solely by cells attached to an electrode. Electrode-attached cells completely oxidized acetate to levels below detection (&lt;10 μM), and hydrogen was metabolized to a threshold of 3 Pa. The rates of electron transfer to electrodes (0.21 to 1.2 μmol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (E o ′ =+0.37 V). The production of current in microbial fuel cell (65 mA/m 2 of electrode surface) or poised-potential (163 to 1,143 mA/m 2 ) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds. Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells. These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such as G. sulfurreducens that can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.
Replicating Ad-recombinants encoding non-myristoylated rather than wild-type HIV Nef elicit enhanced cellular immunity (2006)

The results support the hypothesis that immunization with Ad-recombinants encoding HIVnefNM rather than HIVnefWT elicits enhanced cellular immunity resulting from improved antigen presentation and greater T-cell help.
Artificial Intelligence in Medicine (1987)

After hearing for several decades that computers will soon be able to assist with difficult diagnoses, the practicing physician may well wonder why the revolution has not occurred. Skepticism at this point is understandable. Few, if any, programs currently have active roles as consultants to physicians. The story behind these unfulfilled expectations is instructive and, we believe, offers hope for the future.Research on computer-aided diagnosis began in the 1960s with high hopes that difficult clinical problems might yield to mathematical formalisms. Most work therefore centered on the application of flow charts, Boolean algebra, pattern matching, and decision analysis to . . .
Synaptopodin: An Actin-associated Protein in Telencephalic Dendrites and Renal Podocytes (1997)

Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified rat kidney and forebrain synaptopodin and derived from human and mouse brain cDNA clones show no significant homology to any known protein. In particular, synaptopodin does not contain functional domains found in receptor-clustering PSD proteins. The open reading frame of synaptopodin encodes a polypeptide with a calculated Mr of 73.7 kD (human)/74.0 kD (mouse) and an isoelectric point of 9.38 (human)/9. 27 (mouse). Synaptopodin contains a high amount of proline ( approximately 20%) equally distributed along the protein, thus virtually excluding the formation of any globular domain. Sequence comparison between human and mouse synaptopodin revealed 84% identity at the protein level. In both brain and kidney, in vivo and in vitro, synaptopodin gene expression is differentiation dependent. During postnatal maturation of rat brain, synaptopodin is first detected by Western blot analysis at day 15 and reaches maximum expression in the adult animal. The exclusive synaptopodin synthesis in the telencephalon has been confirmed by in situ hybridization, where synaptopodin mRNA is only found in perikarya of the olfactory bulb, cerebral cortex, striatum, and hippocampus, i.e., the expression is restricted to areas of high synaptic plasticity. From these results and experiments with cultured cells we conclude that synaptopodin represents a novel kind of proline-rich, actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and podocyte foot processes.
Detection of circular and linear herpesvirus DNA molecules in mammalian cells by gel electrophoresis (1984)

A simple gel technique is described for the detection of large, covalently closed, circular DNA molecules in eucaryotic cells. The procedure is based on the electrophoretic technique of Eckhardt (T. Eckhardt, Plasmid 1:584-588, 1978) for detecting bacterial plasmids and has been modified for the detection of circular and linear extrachromosomal herpesvirus genomes in mammalian cells. Gentle lysis of suspended cells in the well of an agarose gel followed by high-voltage electrophoresis allows separation of extrachromosomal DNA from the bulk of cellular DNA. Circular viral DNA from cells which carry the genomes of Epstein-Barr virus, Herpesvirus saimiri, and Herpesvirus ateles can be detected in these gels as sharp bands which comigrate with bacterial plasmid DNA of 208 kilobases. Epstein-Barr virus producer cell lines also show a sharp band of linear 160-kilobase DNA. The kinetics of the appearance of this linear band after induction of viral replication after temperature shift parallels the known kinetics of Epstein-Barr virus production in these cell lines. Hybridization of DNA after transfer to filters shows that the circular and linear DNA bands are virus specific and that as little as 0.25 Epstein-Barr virus genome per cell can be detected. The technique is simple, rapid, and sensitive and requires relatively low amounts of cells (0.5 X 10(6) to 2.5 X 10(6)).
N ε -Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function (2007)

Post-translational modification of histones and other chromosomal proteins regulates chromatin conformation and gene activity. Methylation and acetylation of lysyl residues are among the most frequently described modifications in these proteins. Whereas these modifications have been studied in detail, very little is known about a recently discovered chemical modification, the N(epsilon)-lysine formylation, in histones and other nuclear proteins. Here we mapped, for the first time, the sites of lysine formylation in histones and several other nuclear proteins. We found that core and linker histones are formylated at multiple lysyl residues located both in the tails and globular domains of histones. In core histones, formylation was found at lysyl residues known to be involved in organization of nucleosomal particles that are frequently acetylated and methylated. In linker histones and high mobility group proteins, multiple formylation sites were mapped to residues with important role in DNA binding. N(epsilon)-lysine formylation in chromosomal proteins is relatively abundant, suggesting that it may interfere with epigenetic mechanisms governing chromatin function, which could lead to deregulation of the cell and disease.
Systolic architectures to evaluate polynomials of degree n using the Horner's rule (2013)

This paper presents the design of two systolic architectures to evaluate polynomials of degree n considering the Horner's rule. The systolic arrays are based on processing elements that process normalized and non-normalized data. The designed architectures are flexible, parameterized and described by using VHDL. This allows achieving a good trade-off between area, performance and flexibility. The synthesis results show that the proposed architectures can be used as coprocessors for high performance reconfigurable computing.
A mathematical framework to determine the temporal sequence of somatic genetic events in cancer (2010)

Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and represent promising targets for therapeutic intervention. Here we describe a computational approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to deduce the temporal sequence of genetic events during tumorigenesis from cross-sectional genomic data of tumors at their fully transformed stage. When applied to a dataset of 70 advanced colorectal cancers, our algorithm accurately predicts the sequence of APC, KRAS, and TP53 mutations previously defined by analyzing tumors at different stages of colon cancer formation. We further validate the method with glioblastoma and leukemia sample data and then apply it to complex integrated genomics databases, finding that high-level EGFR amplification appears to be a late event in primary glioblastomas. RESIC represents the first evolutionary mathematical approach to identify the temporal sequence of mutations driving tumorigenesis and may be useful to guide the validation of candidate genes emerging from cancer genome surveys.
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions (2007)

RNA viruses are responsible for a variety of human diseases, and the pathogenicity of RNA viruses is often attributed to a high rate of mutation. Self-cleavage activity of the wild-type hepatitis delta virus (HDV) ribozyme as measured in standard divalent ion renaturation assays is biphasic and mostly slow and can be improved by multiple rational changes to ribozyme sequence or by addition of chemical denaturants. This is unusual in the sense that wild type is the most catalytically active sequence for the majority of protein enzymes, and RNA viruses are highly mutable. To see whether the ribozyme takes advantage of fast-reacting sequence changes in vivo, we performed alignment of 76 genomic and 269 antigenomic HDV isolates. Paradoxically, the sequence for the ribozyme was found to be essentially invariant in nature. We therefore tested whether three ribozyme sequence changes that improve self-cleavage under standard divalent ion renaturation assays also improve self-cleavage during transcription. Remarkably, wild type was as fast, or faster, than these mutants under cotranscriptional conditions. Slowing the rate of transcription or adding the hepatitis delta antigen protein only further stimulated cotranscriptional self-cleavage activity. Thus, the relative activity of HDV ribozyme mutants depends critically on whether the reaction is assayed under in vivo-like conditions. A model is presented for how wild-type ribozyme sequence and flanking sequence work in concert to promote efficient self-cleavage during transcription. Wild type being the optimal ribozyme sequence under in vivo-like conditions parallels the behavior of most protein enzymes.
Periplasmic expression of human growth hormone via plasmid vectors containing the PL promoter: use of HPLC for product quantification (2003)

The influence of different factors acting on Escherichia coli periplasmic expression of recombinant human growth hormone (hGH) in shake flask cultures has been investigated. Bacterial vectors containing the phage lambdaP(L) promoter, which is temperature activated, were utilized. Four different signal peptides were compared: DsbA, npr, STII and one derived from the natural hGH signal peptide, this last used as a reference. Other factors such as medium composition, optimized induction and expression conditions, and different bacterial strains were also studied. The determination of hGH, carried out directly in osmotic shock fluids, was based on an isocratic reversed-phase high-performance liquid chromatography method, which allows direct, rapid evaluation of the quality and quantity of hGH being secreted in the bacterial periplasmic space immediately after or even during fermentation. The level of hGH production increased 2.5-fold compared with the reference vector, reaching a level of 3.9 +/- 0.63 micro g/ml/A(600) (n = 6; coefficient of variation = 16.2%). The expression level was affected by the signal peptide and by the induction conditions, being more effective when activation started in the early logarithmic phase which, however, exhibited remarkably different optical density (OD) according to medium composition. Our results thus indicate that 6 h activation at 40-42 degrees C, starting with an OD (A(600)) of approximately 3 in a very rich medium, were conditions capable of providing the maximum secretion level for a vector utilizing the DsbA signal sequence and E.coli W3110 or RB791 as host cells.
Magnetic Resonance Imaging of the Musculoskeletal System (1998)

Magnetic resonance imaging in the patient who has had surgery is discussed. The most common indication for postoperative imaging is in the distinction between postoperative fibrosis and recurrent disc herniation. Magnetic resonance imaging is invaluable in the assessment of potential causes of failed back surgery syndrome such as postoperative infection, arachnoiditis and adjacent segment degeneration. Magnetic resonance imaging assumes a less important role in postoperative patients with metal hardware owing to image degradation secondary to metal artifact. Magnetic resonance imaging has a complementary role with computed tomography evaluation of spinal trauma. It excels at the noninvasive evaluation of spinal deformities and neoplasms.
Deglycosylation of asparagine-linked glycans by peptide:N-glycosidase F (1985)

Endo-beta-N-acetylglucosaminidase F (Endo F) and peptide:N-glycosidase F (PNGase F) were purified from cultures of Flavobacterium meningosepticum by ammonium sulfate precipitation followed by gel filtration on TSK HW-55(S). This system separated the two enzymes and provided PNGase F in a high state of purity, but the basis for the resolution appeared to be hydrophobic interaction and not molecular size. Studies using purified Endo F and PNGase F with defined glycopeptides demonstrated that Endo F was somewhat similar to Endo H in that it hydrolyzed many, but not all, high-mannose and hybrid oligosaccharides, as well as complex biantennary oligosaccharides. PNGase F, in contrast, hydrolyzed all classes of asparagine-linked glycans examined, provided both the alpha-amino and carboxyl groups of the asparagine residue were in peptide linkage. Deglycosylation studies with PNGase F revealed that many proteins in their native conformation were susceptible to this enzyme but that prior denaturation in sodium dodecyl sulfate greatly decreased the amount of enzyme required for complete carbohydrate removal.
Resistance to BRAF Inhibition in Melanomas (2011)

PLX4032, an inhibitor of activated BRAF, has shown clinical efficacy in treating patients with melanomas carrying an activating mutation in BRAF, but resistance to the drug develops in some patients. Two recent studies show possible mechanisms of such resistance.
Long-Term Human B Cell Lines Dependent on Interleukin-4 and antibody to CD40 (1991)

CD40 is a 45- to 50-kilodalton transmembrane glycoprotein expressed on B lymphocytes, epithelial cells, and some carcinoma cell lines. Human resting B lymphocytes entered a state of sustained proliferation when incubated with both the mouse fibroblastic Ltk- cell line that had been transfected with the human Fc receptor (Fc gamma RII/CDw32) and monoclonal antibodies to CD40. In combination with interleukin-4, factor-dependent long-term normal human B cell lines were generated that were consistently negative for Epstein-Barr viral infection. Thus, cross-linking of CD40 is likely to represent an important phenomenon in the clonal expansion of B cells.