gebhart/patrepeval huggingface dataset:
Densification of Chemical Vapor Deposition Silicon Dioxide Film Using Ozone Treatment (2009)

Silicon dioxide (SiO2) films formed by chemical vapor deposition (CVD) have been treated with ozone (O3) or oxygen (O2) gas ambient at 450 °C. Density depth profiles of the SiO2 films were investigated using X-ray reflectivity analysis with synchrotron radiation. The density depth profile of the base CVD-SiO2 film without the O3 or O2 treatment is low (∼2.03 g/cm3) and constant. That of the CVD-SiO2 film with the O3 treatment is not constant. The O3-treated CVD-SiO2 film is composed of a middle-density top layer (∼2.13 g/cm3), a low-density center layer (∼2.03 g/cm3), and a high-density bottom layer (∼2.24 g/cm3). The density depth profile of the CVD-SiO2 film treated with O2 gas agrees with that of the base CVD-SiO2 film. The temperature or presence of O2 molecules during the O3 treatment at 450 °C does not affect the densification of the base CVD-SiO2 film. Therefore, the active species that densify the base CVD-SiO2 film during the O3 treatment are oxygen (O) radicals generated by the thermal decomposition of O3 molecules. The middle-density top layer near the SiO2 surface is formed by the reconstruction of a Si–O network with the oxidation of oxygen vacancies in the base CVD-SiO2 film with O radicals. The high-density bottom layer near the SiO2/Si interface is formed by the oxidation of the silicon substrate with O radicals that diffuse through the low-density base CVD-SiO2 film. The penetration length of O radicals in the base CVD-SiO2 film is very large because the thickness of the high-density bottom layer does not depend on the thickness of the base CVD-SiO2 film up to 16.8 nm at least. Therefore, this densification method for the CVD-SiO2 film with O3 treatment can be applied to the formation of either thin or thick SiO2 films.
Characterization of SSIIIa-Deficient Mutants of Rice: The Function of SSIIIa and Pleiotropic Effects by SSIIIa Deficiency in the Rice Endosperm (2007)

Starch synthase IIIa (SSIIIa)-deficient rice (Oryza sativa) mutants were generated using retrotransposon insertion and chemical mutagenesis. The lowest migrating SS activity bands on glycogen-containing native polyacrylamide gel, which were identified to be those for SSIIIa, were completely absent in these mutants, indicating that they are SSIIIa null mutants. The amylopectin B(2) to B(4) chains with degree of polymerization (DP) >/= 30 and the M(r) of amylopectin in the mutant were reduced to about 60% and 70% of the wild-type values, respectively, suggesting that SSIIIa plays an important part in the elongation of amylopectin B(2) to B(4) chains. Chains with DP 6 to 9 and DP 16 to 19 decreased while chains with DP 10 to 15 and DP 20 to 25 increased in the mutants amylopectin. These changes in the SSIIIa mutants are almost opposite images of those of SSI-deficient rice mutant and were caused by 1.3- to 1.7-fold increase of the amount of SSI in the mutants endosperm. Furthermore, the amylose content and the extralong chains (DP >/= 500) of amylopectin were increased by 1.3- and 12-fold, respectively. These changes in the composition in the mutants starch were caused by 1.4- to 1.7-fold increase in amounts of granules-bound starch synthase (GBSSI). The starch granules of the mutants were smaller with round shape, and were less crystalline. Thus, deficiency in SSIIIa, the second major SS isozyme in developing rice endosperm affected the structure of amylopectin, amylase content, and physicochemical properties of starch granules in two ways: directly by the SSIIIa deficiency itself and indirectly by the enhancement of both SSI and GBSSI gene transcripts.
A graphical environment to query XML data with XQuery (2004)

XQuery, the standard query language for XML, is increasingly popular among computer scientists with a SQL background, since queries in XQuery and SQL require comparable skills to be formulated. However, the number of these experts is limited, and the availability of easier XQuery "dialects" could be extremely valuable. With this motivation in mind, we designed XQBE, a dialect of XQuery inspired by the QBE language (query by example). QBE, initially proposed as an alternative to SQL, has then become popular as the user-friendly query language supported by MS Access. XQBE starts from hierarchical structures, coherent with the hierarchical nature of XML, and uses one or more structures to denote the input documents, and one structure to denote the XML document produced in output. These structures are annotated to express selection predicates; explicit bindings connecting the nodes of these structures visualize the input/output mappings.
Persistence of Human Papillomavirus Type 16 Infection Is Associated with Lack of Cytotoxic T Lymphocyte Response to the E6 Antigens (2000)

Our cross-sectional study suggested that cytotoxic T lymphocyte (CTL) responses have a protective effect in squamous intraepithelial lesion (SIL) development. More CTL responses in women with human papillomavirus type 16 (HPV 16) infection without SILs than with SILs were detected. In the current longitudinal study, the role of CTL in clearing HPV 16 infection in women without SILs was investigated. Women with HPV 16 infection (n=51) were enrolled, along with HPV 16-negative control women (n=3). Twenty-two (55%) of 40 women who cleared HPV 16 infection had an E6 CTL response at least once, compared with none of 9 women who had HPV 16 persistence (P=.003). Such a difference was not demonstrated for E7; 25 (63%) of 40 women who cleared HPV 16 infection responded, versus 5 (56%) of 9 women with persistence (P=.720). It appears that lack of response to E6 is important in the persistence of HPV 16 infection.
Identification of differentially expressed proteins in oral squamous cell carcinoma using a global proteomic approach (2005)

A number of protein markers for oral cancer are still not applicable in large populations. Proteomic technologies provide excellent tools for rapid screening of a large number of potential biomarkers in malignant cells. To gain insight into the molecular mechanisms of carcinogenesis and to identify potential biomarkers for oral squamous cell carcinomas (OSCCs), we performed proteomic profiling between human normal oral keratinocytes (HNOKs) and OSCC-derived cell lines (HSC-2 and HSC-3) using fluorescent two-dimensional difference in-gel electrophoresis. Proteins with a > or =2-fold change in expression were considered significant. The spots of interest were digested and identified by matrix-assisted laser desorption/ionization time-of-flight peptide mass finger-printing. Twenty-two proteins were identified as differentially expressed between the HNOKs and OSCC-derived cell lines. Of these, 9 spots were up-regulated and 13 were down-regulated in OSCC-derived cell lines compared to the HNOKs. These spots included the cancer-related proteins; annexin A1, heat shock protein 27, lamin A/C, interleukin 1 receptor antagonist, serine proteinase inhibitor clade B5, stathmin 1, and superoxide dismutase 2. Our results are a first step toward identifying a protein profile of HNOKs and OSCC-derived cell lines. The identified proteins in this experiment may be used in future studies of carcinogenesis or as diagnostic markers and therapeutic targets for OSCC.
Purification and characterization of recombinant human thyrotropin (TSH) isoforms produced by Chinese hamster ovary cells: the role of sialylation and sulfation in TSH bioactivity. (1993)

The biological significance of glycosylation variants of pituitary glycoprotein hormones remains controversial because of the indirect methods usually employed to determine carbohydrate composition or structure as well as the use of unreliable biological/immunological ratio to determine bioactivity. We have previously characterized recombinant human TSH (rhTSH) secreted by Chinese hamster ovary cells attached to microcarrier beads in a large scale bioreactor after stable transfection of hCG alpha and hTSH beta minigenes. In the present study rhTSH has been used as a model to determine structure-function relationships of different isoforms of glycoprotein hormones. We have now produced greater than 200 mg rhTSH using a hollow fiber bioreactor. The highly purified rhTSH produced in the hollow fiber bioreactor (rhTSH-N) as well as rhTSH commercially produced in a large scale bioreactor (rhTSH-G) were quantitated by immunoassays, receptor binding assay, and amino acid analysis and further characterized by a variety of physico-biochemical methods, including chromatofocusing and carbohydrate analysis. rhTSH-G, rhTSH-N, as well as pituitary human TSH (phTSH) have been separated by chromatofocusing on a Mono P column into several isoforms with different pI values. Compositional analysis of the fractions showed higher sialic acid content in the more acidic rhTSH-G fractions. phTSH acidic isoforms showed higher total sulfate and sialic acid contents than the more basic fractions. The bioactivities of various TSH isoforms based on rigorous quantitation of mass by amino acid analysis determined in three different FRTL-5 cell bioassays showed that the more basic and less sialylated fractions of rhTSH-G were more active than the more acidic fractions. In contrast to the in vitro data, highly sialylated and acidic rhTSH-G isoforms showed longer plasma half-lives and higher in vivo bioactivity than the basic forms. These results indicate that secreted rhTSH, similar to intrapituitary phTSH, exists as a mixture of charge isoforms that are related at least in part to the degree of sialylation. The degree of sialylation, highly dependent on the bioreactor production conditions, appears to be the major factor affecting the charge heterogeneity, MCR, and bioactivity of rhTSH.
Inhibition of T-cell responses by feeding peptides containing major and cryptic epitopes: studies with the Der p I allergen. (1994)

H-2b mice respond to the 222 residue allergen Der p I by producing T cells sensitized to the dominant epitopes encompassed in peptides 21-49, 78-100, 110-131 and 197-212. Immunization with the synthetic peptides 120-143 and 144-169, however, revealed cryptic epitopes which could sensitize T cells for responses to the respective peptides and, providing splenic adherent cells were added to lymph node cultures, to the whole allergen. It is shown that feeding recombinant fusion peptides can markedly inhibit the ability of the whole antigen to immunize mice, as measured by the in vitro interleukin-2 (IL-2) and granulocyte-macrophage colony-stimulating factor (GM-CSF)/IL-3 release on stimulation with protein or peptides, although inhibition measured by IL-2 release was more marked. The inhibition extended to epitopes other than those in the fusion peptides used for feeding. Thus feeding peptide 101-154 inhibited responses to 110-131 and 78-100. Fusion peptides 1-14 and 188-222 did not inhibit responses, although 188-222 did contain an epitope. Inhibition was also obtained when mice were fed a fusion containing the cryptic epitope 144-169. The ability of peptides containing the cryptic epitopes to inhibit responses has significant implications for peptide-based immunotherapy.
The axes of rotation of the knee. (1993)

Knee motion is believed to occur about a variable flexion-extension (FE) axis perpendicular to the sagittal plane and a longitudinal rotation (LR) axis. The authors used a mechanical device to locate the FE and the LR axes of six fresh anatomic specimen knees. The motion of points on the LR axis produced circular, planar paths about the fixed FE axis. Magnetic resonance (MR) images in planes perpendicular to the FE axis showed a circular profile for the femoral condyles. The FE axis is constant and directed from anterosuperior on the medial side to posteroinferior on the lateral side, passing through the origins of the medial and lateral collateral ligaments and superior to the crossing point of the cruciates. The LR axis is anterior and not perpendicular to the FE axis, the anatomic planes. This offset produces the valgus and external rotation observed with extension. The implications of two fixed offset axes for knee motion on prosthetic design, braces, gait analysis, and reconstructive surgery are profound.
Essential Roles of Sphingosine‐1‐Phosphate and Platelet‐Derived Growth Factor in the Maintenance of Human Embryonic Stem Cells (2005)

Human embryonic stem cells (hESCs) have great potential for use in research and regenerative medicine, but very little is known about the factors that maintain these cells in the pluripotent state. We investigated the role of three major mitogenic agents present in serum--sphingosine-1-phosphate (S1P), lysophosphatidic acid (LPA), and platelet-derived growth factor (PDGF)--in maintaining hESCs. We show here that although LPA does not affect hESC growth or differentiation, coincubation of S1P and PDGF in a serum-free culture medium successfully maintains hESCs in an undifferentiated state. Our studies indicate that signaling pathways activated by tyrosine kinase receptors act synergistically with those downstream from lysophospholipid receptors to maintain hESCs in the undifferentiated state. This study is the first demonstration of a role for lysophospholipid receptor signaling in the maintenance of stem cell pluri-potentiality.
What determines the lateral bonding speed in silicon wafer bonding? (1995)

In silicon wafer bonding, the initial contact area spreads laterally with a typical speed on the order of 10 mm/s. We observed that this lateral bonding speed increases with decreasing ambient pressure, and is independent of the distance of the contact front to the rim of the wafers and independent of wafer thickness. From these results, we conclude that the lateral bonding speed is mainly determined by pressing the ambient gas out between the two wafers from a very localized area close to the propagating bonding front.
A Single Additive Non-ionic System for Frac Packing Offers Operators a Small Equipment Footprint and High Compatibility with Brines and Crude Oils (2003)

Abstract There are many advantages to using a single component, non- ionic viscoelastic surfactant gel (VES) for sand control and stimulation applications. The VES is highly compatible with a wide range of completion brines and crude oils, is virtually non-damaging to the formation and demonstrates shale- stabilizing characteristics with many types of shale. Another advantage of having a single additive VES system is that it requires a small equipment footprint. With this combination of compact equipment set-up and simplified fluid mixing, complex, high rate, high sand concentration frac jobs are possible where rig space is limited or equipment is limited because of the remote location from full stimulation service. A treatment using a single additive system can typically be performed with only one or two frac pumps, a frac blender, proppant silo or a modified sand infuser and data acquisition equipment. Many offshore facilities have commingled gathering systems many of which must be treated for emulsions with chemicals. This treatment process may be substantially reduced or simplified when a non-ionic VES fluid is used for stimulation compared to a crosslinked gel fluid. The high compatibility with completion brines and crude oils, coupled with the non- damaging nature of the VES itself, reduces the likelihood of formation damage in the well. The VES promotes a fast and more thorough recovery of the stimulation fluid from the formation and if emulsions are generated, it will allow for easier treatment in the surface facility. Since December 2000, non-ionic VES gels have been used in over 30 applications in the Adriatic Sea and in the Gulf of Mexico in brines ranging from seawater with varying amounts of KCl to 10.5 ppg CaCl2. Each application has resulted in enhanced production due to the excellent performance of the fluid. Clean-up rates have been directly related to bottom hole pressure, and have not been complicated with typical clean-up problems such as clay swelling, water blocks, and filter cake plugging of proppant packs. This type of treatment with a minimum equipment set-up has made high rate/volume frac treatments possible without the need of a stimulation vessel.
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR (2006)

We advocate use of sequence-based background adjustment in lieu of mismatch adjustment to achieve the best results across the intensity spectrum. No method of normalization or probeset summary showed any consistent advantages.
A Time Reversal Transmission Approach for Multiuser UWB Communications (2006)

We propose and evaluate the performance of the time reversal technique in impulse radio ultrawideband (UWB) communications. The evaluation was based on measured channel impulse responses of a 4times1 multiple input single output (MISO) system in the UWB frequency bandwidth of 3 to 5 GHz with both vertical and horizontal polarization at the receiver. The results show that there is a great potential in combining time reversal and UWB technique with respect to both reducing the receiver complexity and improving the system performance. Simultaneous communication is illustrated with 5 users, each with a bit error rate (BER) of less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> at an average signal to noise ratio (SNR) of 15 dB
Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen (2001)

AlphaScreen technology allows the development of high-throughput homogeneous proximity assays. In these assays, signal is generated when 680 nm laser light irradiates a donor bead in close proximity to an acceptor bead. For the detection of nucleic acids, donor and acceptor beads are brought into proximity by two bridging probes that hybridize simultaneously to a common target and to the generic oligonucleotides attached covalently to the beads. This method allows the detection of as little as 10 amole of a single-stranded DNA target. The combination of AlphaScreen with allele-specific amplification (ASA) and allele-specific hybridization (ASH) has allowed the development of two homogenous single-nucleotide polymorphism (SNP) genotyping platforms. Both types of assay are very robust, routinely giving accurate genotyping results with &lt; 2 ng of genomic DNA per genotype. An AlphaScreen validation study was performed for 12 SNPs by using ASA assays and seven SNPs by using ASH assays. More than 580 samples were genotyped with accuracy &gt;99%. The two assays are remarkably simple, requiring no post-PCR manipulations. Genotyping has been performed successfully in 96- and 384-well formats with volumes as small as 2 μL, allowing a considerable reduction in the amount of reagents and genomic DNA necessary for genotyping. These results show that the AlphaScreen technology can be successfully adapted to high-throughput genotyping.
Peripheral inflammation facilitates Abeta fiber-mediated synaptic input to the substantia gelatinosa of the adult rat spinal cord. (1999)

Whole-cell patch-clamp recordings were made from substantia gelatinosa (SG) neurons in thick adult rat transverse spinal cord slices with attached dorsal roots to study changes in fast synaptic transmission induced by peripheral inflammation. In slices from naive rats, primary afferent stimulation at Abeta fiber intensity elicited polysynaptic EPSCs in only 14 of 57 (25%) SG neurons. In contrast, Abeta fiber stimulation evoked polysynaptic EPSCs in 39 of 62 (63%) SG neurons recorded in slices from rats inflamed by an intraplantar injection of complete Freund's adjuvant (CFA) 48 hr earlier (p < 0.001). Although the peripheral inflammation had no significant effect on the threshold and conduction velocities of Abeta, Adelta, and C fibers recorded in dorsal roots, the mean threshold intensity for eliciting EPSCs was significantly lower in cells recorded from rats with inflammation (naive: 33.2 +/- 15.1 microA, n = 57; inflamed: 22.8 +/- 11.3 microA, n = 62, p < 0.001), and the mean latency of EPSCs elicited by Abeta fiber stimulation in CFA-treated rats was significantly shorter than that recorded from naive rats (3.3 +/- 1.8 msec, n = 36 vs 6.0 +/- 3.5 msec, n = 12; p = 0.010). Abeta fiber stimulation evoked polysynaptic IPSCs in 4 of 25 (16%) cells recorded from naive rat preparations and 14 of 26 (54%) SG neurons from CFA-treated rats (p < 0.001). The mean threshold intensity for IPSCs was also significantly lower in CFA-treated rats (naive: 32.5 +/- 15.7 microA, n = 25; inflamed: 21. 9 +/- 9.9 microA, n = 26, p = 0.013). The facilitation of Abeta fiber-mediated input into the substantia gelatinosa after peripheral inflammation may contribute to altered sensory processing.
Pattern discovery from audio recordings by Variable Markov Oracle: A music information dynamics approach (2015)

In this paper, a framework for automatic pattern discovery within an audio recording is proposed. The concept of the proposed framework stems from music information dynamics and is realized by Variable Markov Oracle. Music information dynamics is the research area focusing on information theoretic measures describing musical structure and is thus closely related to the field of music pattern discovery. Variable Markov Oracle is a data structure that provides both fast retrieval of repeated sub-clips from a signal and efficient calculation of music information dynamics measures. Evaluation of the proposed framework is performed on the JKU Patterns Development Dataset with significantly improved performance of the current state of the art.
Tautoméric entre structures α‐aleoxy énaminocétone et β‐céto iminoéther présentée par les pipéridéines résultant de la semihydrogénation d'alcoxy‐2 acyl‐3 pyridines (1979)

Abstract L'hydrogénation partielle, en présence de palladium ou de platine, d'alcoxy‐2 acyl‐3 pyridines a été réalisée en vue d'étudier la tautoméric des tétrahydropyridines résultantes. La réduction en pipéridéine se produit sélectivement pour les composés bicycliques 2 et 3, tandis que la réduction du groupe carbonyle devient prépondérante dans le cas du dérivé 1 présentant le groupe acyle dans une chaǐne ouverte. Cetle différence de comportement est interprétée à I'aide du concept de contrainte interne (“I‐strain” effect). Alors que les tétrahydropyridines bicycliques 6 et 7 possèdent exclusivement une structure d'α‐alcoxy ènaminocétone, la pipéridéine 5 qui est substituée par des chaǐnes ouvertes existe uniquement sous forme de β‐céto iminoéther, comme le montrenl les études spectrographiques ir et de rmn. L'analyse des interactions susceptibles de se produire entre les doublets libres des hétéroalomes permet de rendre compte du déplacement total des équilibres de tautoméric vers I'une ou I'autre de ces deux structures: dans le cas des dérivés bicycliques, I'interaction destabilisante que présenterait I'iminoéther, fait place au sein de la structure ènaminocétone, à une interaction stabilisante entre le doublet de I'oxygène et la liaison N‐II, sans qu'il y ait accroissement des contraintes stériques.