gebhart/patrepeval huggingface dataset:
The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition (2006)

Most eukaryotic mRNAs are monocistronic and translated by cap-dependent initiation. LINE-1 RNA is exceptional because it is naturally dicistronic, encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Here, we show that sequences upstream of ORF1 and ORF2 in mouse L1 function as internal ribosome entry sites (IRESes). Deletion analysis of the ORF1 IRES indicates that RNA structure is critical for its function. Conversely, the ORF2 IRES localizes to 53 nt near the 3' end of ORF1, and appears to depend upon sequence rather than structure. The 40 nt intergenic region (IGR) is not essential for ORF2 IRES function or retrotransposition. Because of strong cis-preference for both proteins during L1 retrotransposition, correct stoichiometry of the two proteins can only be achieved post-transcriptionally. Although the precise stoichiometry is unknown, the retrotransposition intermediate likely contains hundreds of ORF1ps for every ORF2p, together with one L1 RNA. IRES-mediated translation initiation is a well-established mechanism of message-specific regulation, hence, unique mechanisms for the recognition and control of these two IRESes in the L1 RNA could explain differences in translational efficiency of ORF1 and ORF2. In addition, translational regulation may provide an additional layer of control on L1 retrotransposition efficiency, thereby protecting the integrity of the genome.
A first step towards automatic application of power analysis countermeasures (2011)

In cryptography, side channel attacks, such as power analysis, attempt to uncover secret information from the physical implementation of cryptosystems rather than exploiting weaknesses in the cryptographic algorithms themselves. The design and implementation of physically secure cryptosystems is a challenge for both hardware and software designers. Measuring and evaluating the security of a system is manual and empirical, which is costly and time consuming; this work demonstrates that it is possible to automate these processes. We introduce a systematic methodology for automatic application of software countermeasures and demonstrate its effectiveness on an AES software implementation running on an 8-bit AVR microcontroller. The framework identifies the most vulnerable instructions of the implementation to power analysis attacks, and then transforms the software using a chosen countermeasure to protect the vulnerable instructions. Lastly, it evaluates the security of the system using an information-theoretic metric and a direct attack.
Chemosensitization of glioblastoma cells to bis-dichloroethyl-nitrosourea with tyrphostin AG17. (1998)

Recent data have suggested that mitochondria play a supportive role in maintaining the tumorigenic phenotype. Indeed, antimitochondrial agents have been hypothesized to be potential chemosensitizers to human malignancy. We assessed the utility of this approach by characterizing the antimitochondrial activity of 3,5-di-tert-butyl-4-hydroxybenzylidene-malononitrile (AG17), in combination with 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) in two human glioblastoma cell lines. AG17 (NSC 242557) is a tyrphostin that has been thought to have some antimitochondrial activity, with limited tyrosine kinase antagonism, and was used at noncytotoxic and nongrowth-inhibitory concentrations (0.25 microM). Glioblastoma cells were incubated in AG17, and changes in mitochondrial activity were determined. Tumor cells became auxotrophically dependent on uridine and pyruvate, indicating the lack of a functioning respiratory chain. Despite this, cells continued to exhibit no growth-inhibitory effects. Exposure to AG17 was associated with significant depolarization of the mitochondrial membrane potential and decreases in mitochondrial mass in both glioblastoma cell lines, correlating with the finding of auxotrophic dependence. In contrast, normal human astrocytes treated with the same dose of AG17 did not show changes in growth, mitochondrial membrane potential, or mass. Indeed, auxotrophic dependence on uridine and pyruvate could not be established in these cells. Glioblastoma cells became significantly more responsive to BCNU chemotherapy with AG17 pretreatment; a linear relationship was noted that correlated the number as well as percentage of polarized mitochondria with glioblastoma cell survival at the highest dose of BCNU used (144 microg/ml). Normal human astrocytes did not change with regard to the dose response to BCNU with previous incubation with AG17. No difference was found in the type of cellular death (apoptosis) in either of the glioblastoma cell lines, with BCNU treatment alone, or with the combination AG17 and BCNU, despite the decrease in polarized mitochondria and mitochondrial mass. AG17 has antimitochondrial properties when used at low dose in human glioblastoma, which are relatively specific to tumor cells when compared with normal astrocytes. The use of AG17 as a chemosensitizer, with drugs such as BCNU, offers a new and possibly effective approach to be developed in patients with glial tumors.
Core/Rim Structure of Liquid‐Phase‐Sintered Silicon Carbide (1993)

Plasma etching in conjunction with scanning and analytical transmission electron microscopy was used to characterize the microstructure and microchemistry of silicon carbide sintered with yttrium‐aluminum garnet (YAG). The SiC grains comprise a core/rim structure with small amounts of excess yttrium, aluminum, and oxygen being present in the rim while these elements are missing in the core. The core/rim interface was found to be coherent, and both the core and the rim are composed of the same polytype, predominantly the 6H structure. These results suggest that Ostwald ripening by solution and reprecipitation controls the sintering mechanism in this system.
Measuring the human pelvis: A comparison of direct and radiographic techniques using a modern United States–based sample (1997)

Seven measurements were taken on a sample of 50 human cadaveric pelves, all white Texans born in the 20th century. Two separate methodologies were used to obtain these data: radiographs and direct measurements. These two methodologies were compared and contrasted, with the relative advantages and disadvantages of each explored. Results indicate that significant differences exist between the two methodologies. Pelvic height, breadth of symphysis, sacro-iliac breadth (P = 0.0001) and anterior upper spinal breadth (P = 0.0002) were larger when measured directly. Pelvic breadth, transverse diameter of the pelvic brim, and height of the ilium did not significantly differ between methodologies (P = 0.2037, P = 0.5253, P = 0.1752). Due to secular changes and inherent intrapopulational variation, taking measurements either directly from modern cadaveric specimens or radiographically on living volunteers in a limited geographic or socioeconomic grouping, rather than from skeletal collections or archived radiographs, may be more appropriate for providing data for current anthropometric applications.
ARAUCARIA: SOFTWARE FOR ARGUMENT ANALYSIS, DIAGRAMMING AND REPRESENTATION (2004)

Argumentation theory involves the analysis of naturally occurring argument, and one key tool employed to this end both in the academic community and in teaching critical thinking skills to undergraduates is argument diagramming. By identifying the structure of an argument in terms of its constituents and the relationships between them, it becomes easier to critically evaluate each part of an argument in turn. The task of analysis and diagramming, however, is labor intensive and often idiosyncratic, which can make academic exchange difficult. The Araucaria system provides an interface which supports the diagramming process, and then saves the result using AML, an open standard, designed in XML, for describing argument structure. Araucaria aims to be of use not only in pedagogical situations, but also in support of research activity. As a result, it has been designed from the outset to handle more advanced argumentation theoretic concepts such as schemes, which capture stereotypical patterns of reasoning. The software is also designed to be compatible with a number of applications under development, including dialogic interaction and online corpus provision. Together, these features, combined with its platform independence and ease of use, have the potential to make Araucaria a valuable resource for the academic community.
Maintenance of windup of second pain requires less frequent stimulation in fibromyalgia patients compared to normal controls (2004)

Many chronic pain syndromes, including fibromyalgia (FM), show evidence of central nervous system hyperexcitability related to central sensitization. Windup (WU) of second pain reflects increased excitability of spinal cord neurons that is related to central sensitization. Psychophysical testing can help characterize this important central nervous system phenomenon because of the parallels between electrophysiological WU and WU of second pain. Animal experiments have shown that once WU has been established, only low frequency tonic nociceptive input is required to maintain the sensitized state of dorsal horn neurons (WU-maintenance or WU-M). The stimulus frequency necessary to maintain the hyperexcitability of spinal cord neurons can provide a measure of central sensitization. Because central sensitization plays an important role in many chronic pain syndromes including FM, we compared WU-M in 72 normal controls (NC) and 104 FM subjects. WU of second pain was produced by a train of 0.7 s duration thermal pulses applied to the glabrous surface of the hands at a frequency of 0.3 Hz. Enhanced second pain associated with WU could, thereafter, be maintained in FM but not NC subjects for up to 120 s by stimuli delivered at 0.16 and 0.08 Hz (WU-M stimuli). These two frequencies of stimulation do not produce WU when delivered alone. Thus, unlike NC subjects, FM subjects showed enhanced second pain during WU-M stimuli at very low stimulus frequencies, indicating central sensitization. Increased WU sensitivity, enhanced WU-M, and increased WU-related aftersensations help account for persistent pain conditions in FM subjects. In addition to WU, WU-M appears to be a useful tool to study mechanisms of pain in patients with characteristics of central sensitization.
MULTI-BAND AND POLARIZATION INSENSITIVE METAMATERIAL ABSORBER (2011)

The design and realization of a multi-band and polarization insensitive metamaterial absorber is presented. The structure with thickness 1.1 mm consists of six close rings which distribute in two metallic layers separated by FR4 fiber glass PCB substrates. Experimental results show that over 93.3% absorption can be achieved in this metamaterial absorber at multiple frequency bands (more than two). Due to the rotational symmetric pattern of the metamaterial, the performance of the absorber is insensitive to the polarization of the incident waves, indicating the superiority of the structure in the application.
X-ray zone plate fabrication using a focused ion beam (2000)

An x-ray zone plate was fabricated using the novel approach of focused ion beam (FIB) milling. The FIB technique was developed in recent years, it has been successfully used for transmission electron microscopy (TEM) sample preparation, lithographic mask repair, and failure analysis of semiconductor devices. During FIB milling, material is removed by the physical sputtering action of ion bombardment. The sputter yield is high enough to remove a substantial amount of material, therefore FIB can perform a direct patterning with submicron accuracy. The authors succeeded in fabricating an x-ray phase zone plate using the Micrion 9500HT FIB station, which has a 50 kV Ga{sup +} column. Circular Fresnel zones were milled in a 1.0-{micro}m-thick TaSiN film deposited on a silicon wafer. The outermost zone width of the zone plate is 170 nm at a radius of 60 {micro}m. An achieved aspect ratio was 6:1.
Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field (2004)

The generalized Born/surface area (GB/SA) model of Still and co-workers was originally developed using partial atomic charges for organic molecules and ions from the OPLS united-atom force field. An efficient implementation of the GB/SA approach with the OPLS-AA (all-atom) force field is described here. Migration to the OPLS-AA model allows much broader application, and it also yields improved accuracy in predicting free energies of hydration. For 75 diverse, neutral organic molecules, the mean unsigned error is 0.6 kcal/mol with the OPLS-AA GB/SA model. Furthermore, effects of hydration on conformational equilibria are shown to be well represented, and results for free energies of hydration of a wide variety of ions are also in close accord with experimental data. As an even more general alternative, the use of partial charges from the CM1A procedure of Cramer, Truhlar, and co-workers has been tested on more than 400 organic molecules and ions. OPLS-AA force field parameters are also reported for primary alkyl halides, halobenzenes, and numerous ions.
Natural killer cells in HIV-1 infection: a double-edged sword. (2011)

In order to propagate and persist within the host, HIV-1 subverts a variety of checkpoints of innate and adaptive viral immunosurveillance. Many of these are related to natural killer cells, which bridge innate and adaptive immunity and play a major role in defeating virus infections. HIV-1 affects cytotoxicity of natural killer cells towards infected cells and natural killer cell-mediated priming of effector cells of the adaptive immune system. Moreover, a subpopulation of natural killer cells was found sensitive to infection by HIV-1. Consequently, an efficient immune response against HIV-1 cannot be mounted in most patients. The current review highlights the molecular interplay between HIV-1 and effector cells of the host immune system with a focus on natural killer cells, and summarizes strategies of HIV-1 to escape from natural killer cell immunosurveillance. A detailed knowledge of these immune escape strategies might lead to the identification of access points for intervention in order to block infection and progression to AIDS.
MHC-antigen-T cell interactions: an overview. (1991)

We describe the establishment and validation, both at the biochemical and biological levels, of direct assays to measure the interactions between synthetic peptides and purified HLA class II molecules. The results of several independent approaches to define the structural requirements for the interaction of peptide-class II molecules are also described. Such approaches include random screening, sequence analysis, and site-directed mutagenesis. Finally, in vivo data illustrating the possibility that the competition at the level of the interactions between autoantigenic peptides and class II molecules could be a useful tool in the treatment of T cell-mediated autoimmune diseases are presented.
CHRISTIAN THOUGHT (1973)

CHRISTIAN THOUGHT A History of Christian Thought. By JUSTO L. GONZALEZ. Vol. I: From the Beginnings to the Council of Charlcedon. New York. Abingdon Press, 1970. 409 pp. $9.00. Vol II. From Augustine to the Eve of the Reformation. New York: Abingdon Press, 1971. 352 pp $8.00. DOUGLAS JOHNSON DOUGLAS JOHNSON Claflin CollegeOrangeburg, S. Carolina Search for other works by this author on: Oxford Academic Google Scholar Journal of the American Academy of Religion, Volume XLI, Issue 1, March 1973, Pages 144–148, https://doi.org/10.1093/jaarel/XLI.1.144 Published: 01 March 1973
Efficient Temporal Compression of High Energy ns-Pulses Using Stimulated Brillouin Scattering (1996)

Simulated Brillouin Scattering (SBS) was used for the temporal compression of single mode Nd:YAG nanosecond laser pulses of 200 to 500 mJ energy. Compression factors of over 10 and energy conversion of 80% in the backscattered SBS beam were regularly obtained. The system consists of a simple SBS oscillator-amplifier setup which avoids the use of pump pulse splitting or pump beam attenuation techniques usually applied in high energy SBS compressors. Resulting SBS pulses were analyzed in the time domain by a fast oscilloscope and a streak camera, in the frequency domain by a pulsed spectrum analyzer. The experimental results were compared with extensive numerical simulations of the SBS-process in the multiple cell setup.
Projective Transformations of I C I Color Specifications (1937)

The use of the I. C. I. 1931 Standard Observer and Coordinate System for Colorimetry for all general color specifications and calculations is urged for the elimination of confusion in the field of colorimetry. Methods for constructing other coordinate systems are exhibited, and interpretations are given for the eight independent constants in the equations for transformation from the I. C. I. to other coordinate systems. Expressions are derived for the luminosity coefficients in terms of the constants of the equations for the transformation of coordinates. The possibility of assigning luminosity coefficients without restricting the shape of the spectrum locus is discussed, and an example is given. The assignment of luminosity coefficients interferes with the assignment of the shape of the spectrum locus only in the case of three equal luminosity coefficients. In general, two of the eight degrees of freedom which are available in the defining equations of a trichromatic coordinate system are eliminated by the assignment of the luminosity coefficients. Except in the case of three equal luminosity coefficients, four of the six remaining degrees of freedom are eliminated when the shape of the spectrum locus is established. One additional degree of freedom is eliminated when the size of the spectrum locus is assigned. The final degree of freedom is most profitably used for the purpose of simplifying the transformation equations. The entire discussion is based on well-known principles of transformation of color mixture data and projective geometry; no assumptions other than those underlying standard trichromatic color specification are made, and no conclusions of physiological or psychological import are justified.
A Plastidial Lysophosphatidic Acid Acyltransferase from Oilseed Rape1 (1999)

The biosynthesis of phosphatidic acid, a key intermediate in the biosynthesis of lipids, is controlled by lysophosphatidic acid (LPA, or 1-acyl-glycerol-3-P) acyltransferase (LPAAT, EC 2.3.1.51). We have isolated a cDNA encoding a novel LPAAT by functional complementation of the Escherichia coli mutant plsC with an immature embryo cDNA library of oilseed rape (Brassica napus). Transformation of the acyltransferase-deficient E. coli strain JC201 with the cDNA sequence BAT2 alleviated the temperature-sensitive phenotype of the plsC mutant and conferred a palmitoyl-coenzyme A-preferring acyltransferase activity to membrane fractions. The BAT2 cDNA encoded a protein of 351 amino acids with a predicted molecular mass of 38 kD and an isoelectric point of 9.7. Chloroplast-import experiments showed processing of a BAT2 precursor protein to a mature protein of approximately 32 kD, which was localized in the membrane fraction. BAT2 is encoded by a minimum of two genes that may be expressed ubiquitously. These data are consistent with the identity of BAT2 as the plastidial enzyme of the prokaryotic glycerol-3-P pathway that uses a palmitoyl-ACP to produce phosphatidic acid with a prokaryotic-type acyl composition. The homologies between the deduced protein sequence of BAT2 with prokaryotic and eukaryotic microsomal LAP acytransferases suggest that seed microsomal forms may have evolved from the plastidial enzyme.
Sequential model criticism in probabilistic expert systems (1993)

Probabilistic expert systems based on Bayesian networks require initial specification of both qualitative graphical structure and quantitative conditional probability assessments. As (possibly incomplete) data accumulate on real cases, the parameters of the system may adapt, but it is also essential that the initial specifications be monitored with respect to their predictive performance. A range of monitors based on standardized scoring rules that are designed to detect both qualitative and quantitative departures from the specified model is presented. A simulation study demonstrates the efficacy of these monitors at uncovering such departures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Prophylactic Effects of the Histamine H1 Receptor Antagonist Epinastine and the Dual Thromboxane A2 Receptor and Chemoattractant Receptor-Homologous Molecule Expressed on Th2 Cells Antagonist Ramatroban on Allergic Rhinitis Model in Mice (2011)

The prophylactic use of anti-allergic drugs has been proposed to be effective in the treatment of seasonal allergic rhinitis in humans. However, there is little information regarding the prophylactic effect of thromboxane A(2) (TXA(2)) receptor antagonist on allergic rhinitis. Recent studies revealed that a TXA(2) receptor antagonist ramatroban could block the prostaglandin D(2) (PGD(2)) receptor and chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2). In the present study, we investigated the prophylactic effects of the histamine H(1) receptor antagonist epinastine and the TXA(2) receptor antagonist ramatroban and seratrodast on mouse models of allergic rhinitis. Female BALB/c mice were sensitized by an intraperitoneal injection of ovalbumin and alum on days 0, 5, 14 and 21. Seven days later, mice were sensitized by intranasal application of ovalbumin thrice a week. Drugs were administered once a day from day 22. The severity of allergic rhinitis was assessed by determining the extent of 2 nasal allergic symptoms (sneezing and nasal rubbing). Histamine sensitivity and eosinophil infiltration into the nasal mucosa were also determined. Epinastine and ramatroban significantly reduced nasal symptoms and the number of eosinophils in the nasal mucosa. Seratrodast showed no effect on nasal symptoms and eosinophil infiltration into the nasal mucosa. In addition, histamine sensitivity was reduced by epinastine and ramatroban. These results indicate that epinastine and ramatroban induce the prophylactic effect on allergic rhinitis.