gebhart/patrepeval huggingface dataset:
Nucleotide sequence and molecular characterization of a gene encoding GTP-binding protein from Streptococcus gordonii (2006)

A 1286-bp fragment of chromosomal DNA from Streptococcus gordonii strain Challis was cloned and sequenced. The gene sgg consisted of 897-bp nucleotides encoding a 299-amino acid polypeptide (33,200 Da). The deduced amino acid sequence exhibited significant similarity to Era, G protein of Escherichia coli. The nucleotide binding assay demonstrated that recombinant Sgg bound [32P]GTP but not [32P]ATP, [32P]CTP, or [32P]UTP. These findings indicate that Sgg is a member of the G protein superfamily in the genus Streptococcus.
Optically-Driven Fast and Widely Wavelength-Swept Fiber Laser Based on Dispersion Tuning (2010)

We demonstrate optically-driven fast and wide wavelength-swept laser based on dispersion tuning via cross gain modulation of the SOA. We achieved the tuning range of 87.9 nm and the tuning rate of 200 kHz.
Telomerase Assays in the Diagnosis and Prognosis of Cancer (2007)

Telomerase activity is present in most primary human tumours but not in normal somatic tissues except for proliferative cells of renewal tissues (e.g. crypts of the intestine, basal layer of the epidermis, haemopoietic and inflammatory cells). In some instances telomerase activity is detected in preinvasive lesions, whereas in others it is only detected at later stages. Lower telomerase activity levels are detected in some specimens obtained from regions adjacent to primary tumours. The key clinical challenge is to determine if the presence or level of telomerase activity has diagnostic or prognostic utility. Almost any clinical specimen can be used to assay telomerase activity including frozen sections, fine needle aspirates, brushes, washes and sedimented cells in voided urine. In certain cancers increased telomerase activity levels may identify patients that will have either favourable or poor prognostic outcomes, whereas in other instances telomerase activity can distinguish between benign and malignant lesions. New approaches to improve the diagnostic value of telomerase determinations include application of in situ hybridization methods for detecting human telomerase RNA expression on archival paraffin-embedded material. Results show that this assay easily distinguishes cancer from normal cells, and thus may complement the telomerase activity assays.
Pharmacology of ginsenosides: a literature review (2010)

The therapeutic potential of ginseng has been studied extensively, and ginsenosides, the active components of ginseng, are shown to be involved in modulating multiple physiological activities. This article will review the structure, systemic transformation and bioavailability of ginsenosides before illustration on how these molecules exert their functions via interactions with steroidal receptors. The multiple biological actions make ginsenosides as important resources for developing new modalities. Yet, low bioavailability of ginsenoside is one of the major hurdles needs to be overcome to advance its use in clinical settings.
Hypoxia regulation of ATP13A2 (PARK9) gene transcription (2012)

Parkinson's disease (PD) is the second most common neurodegenerative disorders with a variable combination of motor and non-motor symptoms. Mutations in several genes including ATP13A2 (PARK9) are reported to be associated with PD. The underlying mechanism of PD is not well defined, however, both genetic and environmental causes contribute to it. ATP13A2 gene locates in chromosome 1 and contains 29 exons encoding for a protein of 1180 amino acids with 10 transmembrane domains. Abnormal gene expression has been implicated in neurodegenerative disorders. The transcriptional regulation of the ATP13A2 gene is unknown. In this report, we cloned and functionally characterized the human ATP13A2 gene promoter. We showed that the promoter region of the human ATP13A2 gene contains hypoxia response elements which can bind to transcription factor hypoxia-inducible factor 1α (HIF-1α). Hypoxia up-regulated ATP13A2 transcription via HIF-1α in HEK293 and dopaminergic MN9D cells. Our study indicates that hypoxia signaling plays a very important role in the regulation of human ATP13A2 gene expression. Further study is needed to determine the role of hypoxia in the pathogenesis of PD and its interaction with other PD causative genes, which will provide insights to the role of hypoxia and dysregulation of gene expression in Parkinson's disease.
Enhanced discriminability for nonbiological motion violating the two-thirds power law (2016)

The two-thirds power law describes the relationship between velocity and curvature in human motor movements. Interestingly, this motor law also affects visual motion perception, in which stimuli moving according to the two-thirds power law are perceived to have a constant velocity compared to stimuli actually moving at constant velocity. Thus, visual motion adhering to biological motion principles causes a kinematic illusion of smooth and velocity-invariant motion. However, it is yet unclear how this motion law affects the discrimination of visual stimuli and if its encoding requires attention. Here we tested the perceptual discrimination of stimuli following biological (two-thirds power law) or nonbiological movement under conditions in which the stimuli were degraded or masked through continuous flash suppression. Additionally, we tested subjective perception of naturalness and velocity consistency. Our results show that the discriminability of a visual target is inversely related to the perceived "naturalness" of its movement. Discrimination of stimuli following the two-thirds power law required more time than the same stimuli moving at constant velocity or nonecological variants of the two-thirds power law and was present for both masked and degraded stimuli.
Policosanol, α-Tocopherol, and Moisture Content as a Function of Timing of Harvest of Switchgrass (Panicum virgatum L.) (2009)

Using switchgrass ( Panicum virgatum L.) as a cellulosic feedstock for the production of ethanol could lead to the extraction of co-products prior to the pretreatment step, thereby adding value to the ethanol conversion process. Policosanols, registered as 142583-61-7, are present in Poaceae and are a mixture of long-chained primary alcohols. Policosanols are composed mainly of docosanol (C(22)), tetracosanol (C(24)), hexacosanol (C(26)), octacosanol (C(28)), triacontanol (C(30)), and dotriacontanol (C(32)). This study determined changes in moisture, policosanol, and alpha-tocopherol concentrations of Cave-in-Rock and Blackwell switchgrass cultivars during maturation from July to December in Arkansas and Oklahoma. Moisture content on a dry weight basis declined from 150 to 50% with progressive harvests. The total policosanol concentration ranged between 89 mg/kg for July harvested Cave-in-Rock switchgrass from Arkansas and 182 mg/kg for August harvested Cave-in-Rock switchgrass for Oklahoma, and these values remained relatively constant throughout the season. This is the first report on the presence of policosanols in switchgrass. Total switchgrass policosanol concentrations were lower than those typically reported for sorghum grains; however, switchgrass-extracted policosanols contained different policosanol ratios, wherein C(30) and C(32) alcohol ranges were 36-41 and 43-50%, respectively. alpha-Tocopherol extracted from both switchgrass cultivars varied between 320 and 400 mg/kg but decreased in the October harvest after frost.
Copper(I) catalysis of olefin photoreactions. 11. Synthesis of multicyclic furans and butyrolactones via photobicyclization of homoallyl vinyl and diallyl ethers (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCopper(I) catalysis of olefin photoreactions. 11. Synthesis of multicyclic furans and butyrolactones via photobicyclization of homoallyl vinyl and diallyl ethersSwadesh R. Raychaudhuri, Subrata Ghosh, and Robert G. SalomonCite this: J. Am. Chem. Soc. 1982, 104, 24, 6841–6842Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/ja00388a089https://doi.org/10.1021/ja00388a089research-articleACS PublicationsRequest reuse permissionsArticle Views343Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Efficient joint compensation of speech for the effects of additive noise and linear filtering (1992)

The authors describe two algorithms that provide robustness for automatic speech recognition systems in a fashion that is suitable for real-time environmental normalization for workstations of moderate size. The first algorithm is a modification of the SNR-dependent cepstral normalization (SDCN) and the fixed code-word dependent cepstral normalization (FCDCN) algorithms given by Acero and Stern (1990), except that unlike these algorithms it provides computationally-efficient environment normalization without prior knowledge of the acoustical characteristics of the environment in which the system will be operated. The second algorithm is a modification of the more complex CDCN algorithm that enables it to perform environmental compensation in better than real time. The authors compare the recognition accuracy, computational complexity, and amount of training data needed to adapt to new acoustical environments using these algorithms with several different types of headset-mounted and desktop microphones.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inkjet Printing of Ultrawideband (UWB) Antennas on Paper-Based Substrates (2011)

For the first time, we demonstrate the feasibility of realizing ultrawideband antennas through ink-jetting of conductive inks on commercially available paper sheets. The characterization of the conductive ink as well as of the electrical properties of the paper substrate are reported for frequencies up to 10 GHz. This letter is one step further toward the development of low-cost, environment-friendly conformal printed antennas/electronics for ad hoc wireless sensor networks operating in rugged environments.
UDPgalactose:glycoprotein–<i>N</i>‐acetyl‐<scp>d</scp>‐galactosamine 3‐β‐<scp>d</scp>‐galactosyltransferase activity synthesizing O‐glycan core 1 is controlled by the amino acid sequence and glycosylation of glycopeptide substrates (1994)

In order to investigate the role of the peptide moiety of glycoproteins in the control of O-glycan biosynthesis, UDPgalactose:glycoprotein-N-acetyl-D-galactosamine 3-beta-D-galactosyltransferase (core 1 beta 3-Gal-T) from rat liver was tested for its specificity towards GalNAc-containing glycopeptide substrates. Series of glycopeptides have been synthesized by solid-phase synthesis, protected with an acetyl group on the amino terminal and an amide group on the carboxy terminal, based on variations of the repeat sequences of human intestinal mucin. Most glycopeptides were excellent substrates for core 1 beta 3-Gal-T compared to benzyl alpha-D-galactosamine as indicated by their relatively high Vmax/Km. The enzyme preferred threonine alpha-D-galactosamine Thr(GalNAc) to serine alpha-D-galactosamine. Pro on the carboxy-terminal side adjacent to Thr(GalNAc) was inhibitory. Negatively charged amino acids on either side showed a low Km; substrates with negatively charged amino acids on the amino-terminal side were highly efficient substrates, suggesting charge-charge interactions between enzyme and substrate. Gal beta 1-3GalNAc alpha residues adjacent to Thr(GalNAc) reduced the activity. Product analysis using glycopeptide substrates with three adjacent GalNAc residues showed incorporation of one, two and a small amount of three Gal residues per molecule with an uneven distribution of the potential di-galactosylated isomers. These studies indicate that, in addition to initial glycosylation, the second step in the glycosylation pathways of O-glycans is also controlled by the structure and glycosylation of the peptide core of substrates.
Toward Black-Box Detection of Logic Flaws in Web Applications (2014)

Author(s): Giancarlo Pellegrino, Davide Balzarotti Download: Paper (PDF) Date: 22 Feb 2014 Document Type: Briefing Papers Additional Documents: Slides Associated Event: NDSS Symposium 2014 Abstract: In this paper we present a black-box testing technique to detect logic vulnerabilities in web applications. Our technique is based on the automatic identification of a number of behavioral patterns … Continued
Integral transforms, data compression, and automatic analysis of seismic sections (1990)

It is shown that seismic sections contain 10/sup 5/ times more data than is needed to fully describe a completely interpreted section. Three ways of reducing the size of a data set are suggested: mapping into subsets of smaller dimension; normalization providing a reduction factor of four or more; and conversion into zero crossings, further reducing the data by a factor of 20. If combined, these methods can reduce the data set by a factor of 100 or more and may also improve the S/N (signal/noise) of the data and their effective dynamic range. In implementing these methods, two families of transforms that are designed to extract the information from the data (integral and morphological transforms) are introduced. Interpretation by visual inspection is more of a pattern classification rather than quantified analysis of the data. Ways to identify such patterns using clustering algorithms are suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular Doping and Trap Filling in Organic Semiconductor Host–Guest Systems (2017)

We investigate conductivity and mobility of different hosts mixed with different electron-withdrawing guests in concentrations ranging from ultralow to high. The effect of the guest material on the mobility and conductivity of the host material varies systematically with the guests LUMO energy relative to the host HOMO, in quantitative agreement with a recently developed model. For guests with a LUMO within similar to 0.5 eV of the host HOMO the dominant process governing transport is the competition between the formation of a deep tail in the host DOS and state filling. In other cases, the interaction with the host is dominated by any polar side groups on the guest and changes in the host morphology. For relatively amorphous hosts the latter interaction can lead to a suppression of deep traps, causing a surprising mobility increase by 1-2 orders of magnitude. In order to analyze our data, we developed a simple method to diagnose both the presence and the filling of traps.
The L6 Protein TM4SF1 Is Critical for Endothelial Cell Function and Tumor Angiogenesis (2009)

Transmembrane-4-L-six-family-1 (TM4SF1) was originally described as a cancer cell protein. Here, we show that it is highly expressed in the vascular endothelium of human cancers and in a banded pattern in the filopodia of cultured endothelial cells (EC). TM4SF1 knockdown prevented filopodia formation, inhibited cell mobility, blocked cytokinesis, and rendered EC senescent. Integrin-alpha5 and integrin-beta1 subunits gave a similar staining pattern and interacted constitutively with TM4SF1, whereas integrin subunits often associated with angiogenesis (alphaV, beta3, beta5) interacted with TM4SF1 only after vascular endothelial growth factor (VEGF)-A or thrombin stimulation. TM4SF1 knockdown substantially inhibited maturation of VEGF-A(164)-induced angiogenesis. Thus, TM4SF1 is a key regulator of EC function in vitro and of pathologic angiogenesis in vivo and is potentially an attractive target for antiangiogenesis therapy.
Buffer layer strain transfer in AlN/GaN near critical thickness (1999)

X-ray diffraction has been employed to investigate the strain relaxation of both components of a GaN/AlN bilayer on sapphire (0001) as a function of the GaN layer thickness. Below a critical thickness, GaN and AlN both relax with the same in-plane lattice constant, consistent with the energy minimum condition of elasticity theory for a bilayer. Above the critical thickness, however, the strain relaxations in the two layers were different. We can fit this strain relaxation behavior with a free standing bilayer model with an additional term describing the interaction of dislocations.
[Gastritis associated with Gastrospirillum hominis--a zoonosis?]. (1991)

We found spiral bacteria (non-Helicobacter pylori, SB) in gastric biopsies of 5 patients corresponding to an incidence of 0.3%. The bacteria were found on the surface of the gastric mucosa and in part tightly packed within the crypts. Contrary to Helicobacter pylori, most of them had no direct contact to the surface and crypt epithelium. They are distinctly coiled, 3.6-5.5 microns in length and on average 0.5 microns thick. Ultrastructural studies revealed sheathed flagella at each pole. In one case the bacteria displayed periplasmic fibrils in pairs as also described in cultures of SB from cats' stomachs. In all 5 cases there was histological evidence of inflammation of the gastric mucosa, i.e. one acute diffuse gastritis, one case of granulomatous and three of slight to medium grade chronic gastritis. Biopsies of 2 patients showed a positive urease reaction in the CLO test. Morphologically very similar SB occur as commensals in the stomachs of various animals, in particular dogs and cats. We investigated the stomachs of four dogs and four cats and found all to be infested with SB. The bacteria were found not only on the surface of the mucosa and in crypts, but within the glands of the corpus and antrum and often also within parietal (oxyntic) cells. Yet despite bacterial colonization there was no evidence of gastritis in dogs. However, all of the cats' stomachs showed slight to medium grade chronic gastritis. Cultivation of SB has not been successful so far, with the exception of cats' stomachs. Since the germs have been defined only morphologically, the question as to how close the relationship is among SB of various origins must for the time being remain unanswered. Furthermore, species-specific pathogenicity and the possibility of contagion from animal to man has not yet been clarified.
Modified enhanced max-log-maximum a posteriori algorithm using variable scaling factor (2007)

Using a variable scaling factor (VSF), a modified enhanced max-log-maximum a posteriori (EMLMAP) algorithm is proposed to improve the performance of the conventional EMLMAP algorithm which uses a fixed SF. The VSF, maximising the mutual information exchanged between component decoders in a turbo decoder, is adaptively varied with a priori information of each component decoder. For a large size of interleaver, it is shown that the proposed algorithm improves the bit error rate performance and speed of decoding convergence of the conventional EMLMAP algorithm. The improved speed of the decoding convergence reduces the average number of iterations and results in low-power implementations of a turbo decoder.
Analysis of Transcription Factors Regulating Induction of Indoleamine 2,3-Dioxygenase by IFN- <i>gamma</i> (2000)

IFN-gamma treatment of the human carcinoma cell line ME180 causes cell death due to induction of indoleamine 2,3-dioxygenase (IDO) and resulting starvation for tryptophan. A mutant cell line 3B6A derived from ME180 was resistant to IFN-gamma because of loss of IDO activity. Cotransfecting an IDO promoter-chloramphenicol acetyl transferase (CAT) construct with IFN regulatory factor-1 (IRF-1) resulted in induction of CAT activity in both ME180 and 3B6A cells even in the absence of IFN-gamma. This induction was reduced by cotransfection with IRF-2. However, IRF-1 was not able to restore IDO activity, suggesting a possible repressor site outside the IDO promoter region. Stat1alpha (p91) restored both CAT and IDO activities in 3B6A cells following IFN-gamma treatment. 3B6A cells doubly treated with IFN-gamma and IFN-alpha or IFN-beta restored IDO activity, although neither cytokine on its own could induce IDO. Western blot analysis showed that both constitutive expression and induction of Stat1alpha by IFN-gamma were reduced in 3B6A cells, and double treatment of IFN-gamma with IFN-alpha or IFN-beta restored the expression level of Statla. Electrophoretic mobility shift assays indicated that Stat1 binds to the IFN-gamma-activated sequence (GAS) region in the IDO promoter in ME180 cells following IFN-gamma treatment. Our results indicated that the defect in 3B6A cells was reduced expression of Stat1alpha and that IRF-1, NF-kappaB, and PKR were all involved to some extent in the induction of IDO following IFN-gamma treatment.
Processing Path Model to Describe Texture Evolution during Mechanical Processing (2005)

Using a processing path model based on the conservation principle in the orientation space explicit solutions can be formed linking any final (desired) microstructure to a given initial state for polycrystalline materials. The model uses texture coefficients in spherical harmonics expansion to as materials descriptors to represent the texture state of polycrystalline materials. In this work, the effect of increasing the maximum number of texture coefficients used in the series expansion (represented by Lmax) on the prediction of texture and its accuracy is fully studied.