gebhart/patrepeval huggingface dataset:
Accelerated aging for testing polymeric biomaterials and medical devices (2008)

Elevated temperature is frequently used to accelerate the aging process in polymers that are associated with medical devices and other applications. A common approach is to assume that the rate of aging is increased by a factor of 2(DeltaT/10), where DeltaT is the temperature increase. This result is a mathematical expression of the empirical observation that increasing the temperature by about 10 degrees C roughly doubles the rate of many polymer reactions. It is equivalent to assuming that the aging process is a first order chemical reaction with an activation energy of 10R/log(e)2, where R is the universal gas constant. A better approach would be to determine the activation energy for the process being considered but this is not always practicable. The simple approach does not depend on the temperature increase, provided that it is not so great that it initiates any physical or chemical process that is unlikely to be involved in normal aging. If a temperature increment theta were to increase a given polymer reaction rate n times, then an elevated temperature would increase the rate of aging by a factor of n(DeltaT/theta).
Synthesis of Amino- and Guanidino-G-Clamp PNA Monomers (2002)

Syntheses of the protected amino- and guanidino-G-clamp PNA monomers, 9a and 9b, respectively, have been accomplished in eight steps from 5-bromouracil. Enhanced stacking interactions and additional hydrogen bonds with guanine should increase the affinity of PNAs incorporating these cytosine analogues for their complementary strands. [reaction: see text]
Culture, Politeness and Directive Compliance: Does Saying "Please" Make a Difference? (2008)

Abstract : We argue that traditional cultural factors (from Hofstede, Nisbett, etc.) are too abstract to provide good, predictive models of important human performance behaviours such as compliance with directives. Instead, we focus on culture-specific social interaction behaviours in language, gesture, etc. (i.e., etiquette) as a more concrete and quantifiable bridge between abstract cultural factors and human performance. We describe a computational model of etiquette and face threat perception we have developed, called CECAEDA (Computational Effects of Cultural Attributes and Etiquette on Directive Adherence).
Involvement of NFκB in the Production of Chemokines by Rat and Human Conjunctival Cells Cultured Under Allergenic Conditions (2013)

Activated NFκB was found to be a major transcription factor for the release of cytokines from conjunctival cells and intensification of the allergic response. Inhibition of the NFκB pathway by therapeutic drugs may be an important objective for the treatment of human allergic conjunctivitis.
Formation of epoxyalcohols by a purified allene oxide synthase. Implications for the mechanism of allene oxide synthesis. (1993)

The allene oxide synthase (hydroperoxide dehydrase) of flaxseed is a cytochrome P450 that exhibits an exceptionally high catalytic turnover (> or = 1000/s) for hydroperoxy substrates. In a previous study, using a crude extract of flaxseed, we detected a secondary activity that could offer an insight into the mechanism of the enzymatic transformation of hydroperoxides. We observed that the substrate 8R-hydroxy-15S-hydroperoxyeicosa-5,9,11,13,17-pentaenoic acid is converted not only to allene oxide, but also to epoxyalcohol derivatives (Brash, A. R., Baertschi, S. W., and Harris, T. M. (1990) J. Biol. Chem. 265, 6705-6712). The transformation of hydroperoxides to epoxyalcohols has been investigated extensively in other systems, and heterolytic or homolytic cleavage of the hydroperoxide is associated with characteristic rearrangements and stereochemistry of the epoxyalcohol products. Using the purified enzyme, we established that the epoxyalcohols are products of the allene oxide synthase. Their structures were determined by UV, gas chromatography-mass spectrometry, and NMR. The major epoxyalcohol is 8R,13R-dihydroxy-14R,15S-epoxyeicosa-5Z,9E ,11Z,17Z-tetraenoic acid, a trans-epoxide with an alpha-hydroxyl in the relative threo configuration. Two minor products are the corresponding 11E isomer and a cis-epoxide identified as 8R,13-dihydroxy-14S,15S-epoxyeicosa-5Z,9E,11E,++ +17Z-tetraenoic acid. Gas chromatography-mass spectrometry analysis of a reaction with [18O2]hydroperoxide substrate indicated complete retention of the hydroperoxy oxygens in the epoxyalcohol products. Mechanistic precedents support a homolytic hydroperoxide cleavage as the initial step in the synthesis of these epoxyalcohols. We suggest that the same process initiates allene oxide synthesis, a conclusion that is also most compatible with the known chemistry of cytochromes P450.
Gold/Iron Oxide Core/Hollow‐Shell Nanoparticles (2008)

Gold/iron oxide core/hollow-shell composite nanoparticles (NPs) with controllable shell thicknesses are synthesized (see figure). The gap between the Au core and iron oxide shell is formed as a result of different outward and inward diffusion rates of Fe and O, respectively. Control over interparticle interactions allows encapsulation of several Au cores inside one iron oxide shell. Superparamagnetic measurements of the NPs at room temperature demonstrate the plasmon resonance at 565 nm. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Demonstration of Germacrene A as an Intermediate in 5-Epi-aristolochene Synthase Catalysis (2000)

Sesquiterpene synthases are a family of enzymes that catalyze farnesyl pyrophosphate (FPP) cyclization via alternative pathways to produce a variety of cyclic sesquiterpene products. Catalysis by several of these enzymes, including tobacco 5-epi-aristolochene synthase (TEAS), has been proposed to include the formation of germacrene A as a stable intermediate. Neither germacrene A nor any other intermediate is released from sesquiterpene synthase active sites during normal catalysis. Evidence to support the intermediacy of germacrene A has been derived from investigations of aristolochene synthases from Aspergillus terreus and Penicillium roquefortii (Cane, D. E. Chem. Rev. 1990, 90, 1089−1103 and references therein. Cane, D. E.; Bryant, C. J. Am. Chem. Soc. 1994, 116, 12063−12064. Cane, D. E.; Tsantrizos, Y. S. J. Am. Chem. Soc. 1996, 118, 10037−10040). However, until the present investigations of TEAS, formation of this postulated intermediate has never been directly demonstrated. TEAS catalyzes the cyclization of FPP to 5-epi-aristolochene, a precursor of a tobacco phytoalexin, capsidiol. Based upon the three-dimensional structure of TEAS, a detailed mechanism has been proposed for TEAS catalysis that includes the prediction that proton donation by Y520 is responsible for the activation of germacrene A to a eudesmane cation (Starks, C. M.; Back, K.; Chappell, J.; Noel, J. P. Science 1997, 277, 1815−1820). In the present investigation, a Y520F point mutation is introduced into TEAS (TEAS-Y520F) by site-directed mutagenesis. In the presence of 3H−FPP, TEAS-Y520F produces hexanes−extractable 3H with a catalytic efficiency approximately 3% that of nonmutated, recombinant TEAS. The hexanes−extractable 3H is identified as germacrene A, m/z 204, through direct GC-MS comparison to an authentic sample. This observation confirms the intermediacy of germacrene A in TEAS catalysis, supports the postulated production of germacrene A by a variety of other sesquiterpene synthases, and also confirms the proposed role of Y520 in TEAS catalysis.
The work done by an external electromagnetic field (2011)

Ehrenfest's theorem is used to derive the rate of change of kinetic energy induced by an external field. The expression for the power is valid for any electromagnetic field in arbitrary gauge. We discuss the applicable conditions for the Mott-Davis and Moseley-Lukes form of the Kubo-Greenwood formula (KGF) for the electrical conductivity which has been implemented in ab initio codes. We show that the conventional KGF does not satisfy gauge invariance, and is suitable only for computing the ac conductivity at sufficiently high frequency and when the gradient of the carrier density is small.
Graphene and carbon nanotube composite electrodes for supercapacitors with ultra-high energy density (2011)

We describe a graphene and single-walled carbon nanotube (SWCNT) composite film prepared by a blending process for use as electrodes in high energy density supercapacitors. Specific capacitances of 290.6 F g(-1) and 201.0 F g(-1) have been obtained for a single electrode in aqueous and organic electrolytes, respectively, using a more practical two-electrode testing system. In the organic electrolyte the energy density reached 62.8 Wh kg(-1) and the power density reached 58.5 kW kg(-1). The addition of single-walled carbon nanotubes raised the energy density by 23% and power density by 31% more than the graphene electrodes. The graphene/CNT electrodes exhibited an ultra-high energy density of 155.6 Wh kg(-1) in ionic liquid at room temperature. In addition, the specific capacitance increased by 29% after 1000 cycles in ionic liquid, indicating their excellent cyclicity. The SWCNTs acted as a conductive additive, spacer, and binder in the graphene/CNT supercapacitors. This work suggests that our graphene/CNT supercapacitors can be comparable to NiMH batteries in performance and are promising for applications in hybrid vehicles and electric vehicles.
Endoplasmic Reticulum and Golgi Localization Sequences for Mammalian Target of Rapamycin (2007)

Mammalian target of rapamycin (mTOR) forms two complexes, mTORC1 and mTORC2, that play central roles in cell growth and functions. Only mTORC1 is directly inhibited by the immunosuppressive drug rapamycin. Despite recent progress in identifying new components and functions of the mTOR pathway, relatively little is known about the spatial arrangement of mTOR signaling and the underlying mechanisms. In a previous study, we showed that a large proportion of mTOR is localized to the endoplasmic reticulum (ER) and Golgi in many common cell lines. Here, we report the identification of an internal mTOR sequence that contains two HEAT (HT) repeats, HT18 and HT19, and two intervening interunit spacers (IUSs), IUS17 and IUS18, which is sufficient to target enhanced green fluorescent protein to the Golgi. Surprisingly, deletion of IUS17 from this Golgi localization sequence (GLS) converts it to an ER localization sequence (ELS). Deletion of HT19, a common element of both GLS and ELS from the full-length mTOR, causes delocalization of mTOR and inhibits the ability of mTOR to promote S6 phosphorylation. Moreover, overexpression of GLS and ELS inhibits both mTOR complexes. Together, our results reveal unusual ER- and Golgi-targeting sequences and suggest that anchoring to these organelles is important for the functions of mTOR complexes.
A natural language understanding system combining syntactic and semantic techniques. (1994)

A large proportion of the medical record currently available in computerized medical information systems is in the form of free text reports. While the accessibility of this source of data is improved through inclusion in the computerized record, it remains unavailable for automated decision support, medical research, and management of medical delivery systems. Natural language understanding systems (NLUS) designed to encode free text reports represent one approach to making this information available for these uses. Below we describe an experimental NLUS designed to parse the reports of chest radiographs and store the clinical data extracted in a medical data base.
Requirement for Ca2+/calmodulin–dependent kinase II in the transition from pressure overload–induced cardiac hypertrophy to heart failure in mice (2009)

Ca2+/calmodulin-dependent kinase II (CaMKII) has been implicated in cardiac hypertrophy and heart failure. We generated mice in which the predominant cardiac isoform, CaMKIIdelta, was genetically deleted (KO mice), and found that these mice showed no gross baseline changes in ventricular structure or function. In WT and KO mice, transverse aortic constriction (TAC) induced comparable increases in relative heart weight, cell size, HDAC5 phosphorylation, and hypertrophic gene expression. Strikingly, while KO mice showed preserved hypertrophy after 6-week TAC, CaMKIIdelta deficiency significantly ameliorated phenotypic changes associated with the transition to heart failure, such as chamber dilation, ventricular dysfunction, lung edema, cardiac fibrosis, and apoptosis. The ratio of IP3R2 to ryanodine receptor 2 (RyR2) and the fraction of RyR2 phosphorylated at the CaMKII site increased significantly during development of heart failure in WT mice, but not KO mice, and this was associated with enhanced Ca2+ spark frequency only in WT mice. We suggest that CaMKIIdelta contributes to cardiac decompensation by enhancing RyR2-mediated sarcoplasmic reticulum Ca2+ leak and that attenuating CaMKIIdelta activation can limit the progression to heart failure.
Transthoracic Ventricular Defibrillation in the Dog with Truncated and Untruncated Exponential Stimuli (1971)

From 10 560 transthoracic fibrillation-defibrillation episodes in large anesthetized dogs, the effectiveness of 88 types of untruncated and truncated exponential waveforms in reversing ventricular fibrillation was evaluated. The study involved waveforms which could be generated with stored energy levels (in the simple capacitor-switch sense) of 60, 90, 120, and 180 J and initial current levels of 10, 20, 30, 40, 60, 80, and 100 A. The 10-A waveforms were untruncated or truncated at final current values of 5, 7.5, and 9 A. The 20-, 30-, and 40-A waveforms were untruncated or truncated at 5, 10, and 15 A. The 60-, 80-, and l00-A waveforms were untruncated or truncated at the 15-A level.
Internal Ribosome Entry in the Coding Region of Murine Hepatitis Virus mRNA 5 (1994)

The unique region of murine hepatitis virus (MHV) mRNA 5 has two open reading frames. ORF 5a and ORF 5b, that encode small proteins of unknown function. In the experiments described here, we have used the in vitro translation of synthetic mRNAs to examine the expression of these ORFs. Our results show that a synthetic mRNA containing both ORFs is functionally bicistronic. More importantly, the expression of ORF 5b, but not ORF 5a, is maintained in a tricistronic mRNA containing an additional 5'-proximal ORF. Thus, in the context of the MHV mRNA 5 unique region, the initiation of protein synthesis on ORF 5b can occur independently of ribosomes that enter from the 5' end of the mRNA. We conclude that the translation of ORF 5b is mediated by the internal entry of ribosomes.
Monoclonal antibodies to CD44 and their influence on hyaluronan recognition. (1995)

Antibodies to CD44 have been used to inhibit a variety of processes which include lymphohemopoiesis, lymphocyte migration, and tumor metastasis. Some, but not all, CD44-mediated functions derive from its ability to serve as a receptor for hyaluronan (HA). However, sites on CD44 that interact with either ligands or antibodies are poorly understood. Interspecies rat/mouse CD44 chimeras were used to analyze the specificity of 25 mAbs and to determine that they recognize at least seven epitopes. Amino acid substitutions that resulted in loss of antibody recognition were all located in the region of homology to other cartilage link family proteins. While at least five epitopes were eliminated by single amino acid replacements, multiple residues had to be changed to destroy binding by other antibodies. One antibody was sensitive to changes in any of three separate parts of the molecule and some antibodies to distinct epitopes cross-blocked each other. Certain antibodies had the ability to increase HA binding by lymphocytes but this did not correlate absolutely with antibody specificity and was only partially attributable to CD44 cross-linking. Antibodies that consistently blocked HA recognition were all sensitive to amino acid changes within a short stretch of CD44. Such blocking antibodies interacted with CD44 more strongly than ligand in competition experiments. One large group of antibodies blocked ligand binding, but only with a particular cell line. This detailed analysis adds to our understanding of functional domains within CD44 and requirements for antibodies to influence recognition of one ligand.
Identification of a high-affinity receptor for native human interleukin 1 beta and interleukin 1 alpha on normal human lung fibroblasts. (1987)

Native human IL-1 beta and IL-1 alpha stimulated prostaglandin E2 secretion by human embryonic lung fibroblasts at half-maximal concentrations of 3 +/- 1.2 pM (+/- SEM) and 10 +/- 2.3 pM, respectively. In contrast to the 20-50-fold lower affinities previously found for IL-1-R on 3T3 cells as well as murine and human lymphoblastoid lines, monoiodo 125I-IL-1 beta bound to normal human fibroblasts with a Kd of 8.4 +/- 4.1 pM in direct binding experiments, and with a Ki of 11.2 +/- 2.8 pM in competitive binding experiments. IL-1 alpha bound to the receptor identified by 125I-IL-1 beta with a Ki of 50 +/- 18 pM. The receptor exhibited homogeneous affinity for IL-1 beta or IL-1 alpha. The receptor did not recognize IL-2, IFN-gamma, tumor necrosis factor alpha, a functionally related monokine, or bovine acidic fibroblast growth factor, a structurally related mediator. Comparison of the biological response curves and binding curves obtained for IL-1 alpha and IL-1 beta showed that they were parallel and that 10-15% occupancy of the estimated 3,000 sites by either species of IL-1 was sufficient to give half-maximal stimulation of prostaglandin E2 secretion. Thus, the amount of apparent signal amplification observed on fibroblasts was considerably lower than the 100-100,000 fold amplification previously reported for lymphoid lines. Crosslinking experiments revealed a major band with a corrected molecular mass of approximately 80 kD and a minor band of approximately 200 kD. Labeling of these bands was blocked by IL-1 beta and IL-1 alpha but not by IL-2, IFN-gamma, or tumor necrosis factor alpha. These results demonstrate that normal human embryonic lung fibroblasts bear IL-1-R of sufficiently high affinity to mediate their biological responsiveness to low picomolar concentrations of IL-1 beta and IL-1 alpha and are consistent with the existence of a single receptor mediating the biological properties of both human IL-1 species.
Synthesis and Properties of Alternating Fluorene‐Based Oligomers for Sub‐µm Photopatterning (2010)

Abstract The synthesis of alternating photo‐crosslinkable fluorene co‐oligomers via Suzuki cross coupling is reported. The co‐oligomers were characterized using NMR and GPC, the results showing effective control of molecular weight. The oligomers have low T g s of 53–63 °C and are thermally stable up to ≈300 °C. Using TPD as co‐monomer, a blue‐emitting oligomer was obtained, a yellow‐fluorescent material for benzothiadiazole, and a red (film) and yellow‐green (solution) emitting material for bithiophene. The energy levels are very similar to those of randomly linked oligomers. The photo‐crosslinking behavior was studied and under optimized conditions a lateral resolution of 600 nm was obtained. magnified image
Serum vascular endothelial growth factor as a tumour marker in soft tissue sarcoma (2004)

Serum VEGF expression correlated with grade in soft tissue sarcoma and reflected response to treatment.
Mobisaic: An Information System for a Mobile Wireless Computing Environment (1994)

Mobisaic is a World Wide Web information system designed to serve users in a mobile wireless computing environment. Mobisaic extends the Web by allowing documents to both refer and react to potentially changzng contextual information, such as current location in the wireless network. Mobisaic relies on clientside processing of HTML documents that support two new concepts: Dynamic Uniform Resource Locators (URLs) and Active Documents. A dynamic URL is one whose results depend upon the state of the user's mobile context at the time it is resolved, An active document is one that automatically updates its contents in response to changes in a user's mobile context. This paper describes the design of Mobisaic, the mechanism it uses for representing a user's mobile content. and the extensions made to the syntax and function of Uniform Resource Locators and HyperText Markup Language documents to support mobility.
Atomic Layer Deposition of Hafnium Dioxide Films from Hafnium Tetrakis(ethylmethylamide) and Water (2002)

HfO2 films were produced from Hf[N(CH3)(C2H5)]4 and H2O, on borosilicate glass, indium-tin-oxide (ITO), and Si(100) substrates, in the temperature range 150–325 °C, using atomic layer deposition (ALD). In the temperature range 200–250 °C, the growth rate of the HfO2 films was 0.09 nm per cycle, but increased with both increasing and decreasing temperatures. The self-limiting adsorption of Hf[N(CH3)(C2H5)]4 at 250 °C was verified. The films were stoichiometric dioxides with an O/Hf ratio of 2.0 ± 0.1. The concentrations of residual carbon, nitrogen, and hydrogen, determined using ion beam analysis, were 0.3–0.6 at.-%, 0.1–0.2 at.-%, and 2–3 at.-%, respectively. The films crystallized at growth temperatures exceeding 150–175 °C, and consisted mainly of the monoclinic HfO2 phase. The refractive index of the films varied between 2.08 and 2.10. The effective permittivities of the HfO2 films grown in the temperature range 200–300 °C varied between 11 and 14.
Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. (2002)

Recent studies have suggested that information from gene expression profiles could be used to develop molecular classifications of cancer. We hypothesized that expression levels of specific genes in operative specimens could be correlated to recurrence risk in non-small cell lung cancer (NSCLC). We performed expression profiling using 19.2 K cDNA microarrays on tumor specimens from a total of 39 NSCLC patients with known clinical follow-up information. Statistical analysis and clustering approaches were used to determine patterns of gene expression segregating with clinical outcome. The results provide evidence that molecular subtyping of NSCLC can identify distinct profiles of gene expression correlating with disease-free survival.