gebhart/patrepeval huggingface dataset:
Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. (1987)

An approximately 16-kilobase pair region of the Bacillus subtilis chromosome at 55 degrees containing genes for de novo purine nucleotide synthesis (Piggot, P. J., and Hoch, J. A. (1985) Microbiol. Rev. 49, 158-179) was cloned. The nucleotide sequence of over 13 kilobase pairs indicates that this region contains a cluster of 12 genes, 11 of which encode enzymes that catalyze the 10 reactions for de novo purine nucleotide synthesis from 5-phosphoribosyl 1-pyrophosphate to IMP. The genes were identified by complementation of Escherichia coli pur mutants and by sequence comparisons with homologous enzymes. The cluster is likely an operon and is organized into three groups of overlapping genes followed by the last gene: purEKB-purC(orf)QLF-purMNH(J)-purD. Sequence comparisons provide evidence for homology of monofunctional purine nucleotide biosynthetic enzymes from B. subtilis with the corresponding multifunctional enzymes from yeast and Drosophila. Sequence alignment of the phosphoribosylaminoimidazole carboxylase heterodimer from B. subtilis with the monomeric enzyme from Methanobrevibacter smithii indicates an evolutionary relationship between these two enzymes. S1 nuclease analysis was used to map the mRNA 5' and 3' ends and to estimate levels of mRNA. These experiments indicate that synthesis of purine nucleotides is regulated independently by adenine and guanine nucleotides. Adenine nucleotides regulate transcription initiation. Guanine nucleotides regulate transcription by a termination-antitermination mechanism in a 242-nucleotide 5' untranslated mRNA leader region. Groups of overlapping genes, regulated at least in part by transcription termination-antitermination is likely to be a common theme for genetic organization and regulation of biosynthetic genes in this Gram-positive organism.
Mass spectrometric profiling of oxidized lipid products in human nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (2010)

Oxidative stress is a core abnormality responsible for disease progression in nonalcoholic fatty liver disease (NAFLD). However, the pathways that contribute to oxidative damage in vivo are poorly understood. Our aims were to define the circulating profile of lipid oxidation products in NAFLD patients, the source of these products, and assess whether their circulating levels reflect histological changes in the liver. The levels of multiple structurally specific oxidized fatty acids, including individual hydroxy-eicosatetraenoic acids (HETE), hydroxy-octadecadenoic acids (HODE), and oxo-octadecadenoic acids (oxoODE), were measured by mass spectrometry in plasma at time of liver biopsy in an initial cohort of 73 and a validation cohort of 49 consecutive patients. Of the markers monitored, 9- and 13-HODEs and 9- and 13-oxoODEs, products of free radical-mediated oxidation of linoleic acid (LA), were significantly elevated in patients with nonalcoholic steatohepatitis (NASH), compared with patients with steatosis. A strong correlation was revealed between these oxidation products and liver histopathology (inflammation, fibrosis, and steatosis). Further analyses of HODEs showed equivalent R and S chiral distribution. A risk score for NASH (oxNASH) was developed in the initial clinical cohort and shown to have high diagnostic accuracy for NASH versus steatosis in the independent validation cohort. Subjects with elevated oxNASH levels (top tertile) were 9.7-fold (P < 0.0001) more likely to have NASH than those with low levels (bottom tertile). Collectively, these findings support a key role for free radical-mediated linoleic acid oxidation in human NASH and define a risk score, oxNASH, for noninvasive detection of the presence of NASH.
A 0.042-mm<sup>2</sup> fully integrated analog PLL with stacked capacitor-inductor in 45nm CMOS (2008)

We present a fully integrated Phase Locked Loop in an advanced 45nm CMOS technology. The loop filter is integrated on chip under the voltage-controlled oscillator inductor, resulting in significant area savings. The whole PLL measures only 280um by 150um. The PLL has a dual-band output for 2-2.5GHz and 4-5GHz. The circuit operates from a 0.85V supply and consumes 15.3mW for a −120dBc/Hz phase noise at a 1MHz offset from a 2.0 to 2.5GHz carrier.
ZnO/ZnS(O,OH)/Cu(In,Ga)Se/sub 2//Mo solar cell with 18.6% efficiency (2003)

We report on recent enhancements to device performance leading to a certified total-area energy conversion efficiency of 18.6% for Cu(In,Ga)Se/sub 2/ solar cells that incorporate a ZnS(O,OH) buffer layer as an alternative to CdS. Along with information on device fabrication and layer properties, we provide a comparative device analysis between this type of solar cell and the slightly more efficient ZnO/CdS/Cu(In,Ga)Se/sub 2//Mo solar cell structure. This comparative study allows us to elucidate the areas for optimization in the quest for conversion efficiency above 20% in thin-film polycrystalline solar cells. It quantifies the gains in current generation due to superior collection at short wavelengths, as well as the somewhat lower voltage and infrared response.
Biological activity of protein antigens isolated from Mycobacterium tuberculosis culture filtrate (1988)

Mycobacterium tuberculosis culture filtrate (MTCF) protein antigens were isolated from mid-logarithmic-phase cultures grown in liquid medium and examined by high-pressure liquid chromatography and Western blot (immunoblot) analysis. A major protein band with a molecular mass of about 68 kilodaltons (kDa) and several fainter bands in the 38- and 24-kDa range were observed. The MTCF protein produced a significant delayed footpad hypersensitivity response in Mycobacterium bovis BCG-vaccinated C57BL/6 mice, comparable to that observed with standard purified protein derivative (PPD). The same proteins induced a blastogenic response in tuberculin-sensitive human peripheral blood monocytes and in T-cell clones developed from these cells. The proliferative responses to the MTCF antigens were equivalent to those observed following stimulation with PPD or M. tuberculosis sonic extracts. However, the MTCF sensitins were not recognized by five monoclonal antibodies directed against killed M. tuberculosis antigens in an enzyme immunoassay, although some response was seen with a monoclonal antibody (ML34) directed against M. leprae antigens. The ability of the MTCF to stimulate T-cell responses both in vivo and in vitro while not being recognized by antibodies directed against dead mycobacterial antigens suggests that they may be of interest as potential protective immunogens.
A New Fabrication and Assembly Process for Ultrathin Chips (2009)

A new ultrathin chip fabrication and assembly process, consisting of a preprocess module Chipfilm and a postprocess module Pick, Crack, and Place, is presented. In contrast to the established wafer thinning technique, the preprocessed wafer substrates are prepared with extremely narrow buried cavities beneath the chip areas at a well-defined distance from the wafer surface, thus precisely defining the chip thickness <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">priori</i> . After CMOS integration on those dedicated wafer substrates, chips are detached from the wafer surface by etching trenches at the chip edges into the buried cavities and breaking of residual anchors by mechanical force in the postprocess. The feasibility of the new process is demonstrated through a mixed-signal circuit having 38 000 digital and 2700 analog transistors, showing full functionality within specifications for 20-mum-thin chips even under a bending stress of up to 110 MPa.
Distinct egg membrane vesicles differing in binding and fusion properties contribute to sea urchin male pronuclear envelopes formed in vitro (1996)

We have identified three distinct membrane vesicle populations from sea urchin egg cytoplasm that cooperate in assembling the male pronuclear envelope in vitro. Membranes from sea urchin egg homogenates were separated by buoyant density into five vesicle fractions, three of which bind to demembranated sperm nuclei. Each requires a membranous element (lipophilic structure) derived from the sperm nuclear envelope at the tip and base (poles) of the nucleus in order to bind. Binding is differentially sensitive to protease, high salt and N-ethyl maleimide treatment of the membrane vesicles. MV1 binds at the poles and is required for fusion of the membrane vesicle fractions to each other and to the lipophilic structures. MV2 beta binds over the entire chromatin surface and is enriched in an endoplasmic reticulum marker enzyme. MV2 alpha binds at the nuclear poles, is enriched in a Golgi enzyme marker and is required for fusion of MV2 beta. All three fractions are required for nuclear envelope formation in vitro. The results suggest a multistep process for nuclear envelope formation involving contributions from both sperm and egg, roles for both endoplasmic reticulum and non-endoplasmic reticulum-derived vesicles, and the localization of a critical element of the fusion machinery in MV1.
Curve analogies (2002)

This paper describes a method for learning statistical models of 2D curves, and shows how these models can be used to design line art rendering styles by example. A user can create a new style by providing an example of the style, e.g. by sketching a curve in a drawing program. Our method can then synthesize random new curves in this style, and modify existing curves to have the same style as the example. This method can incorporate position constraints on the resulting curves.
Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii (2002)

We demonstrate that two rhodopsins, identified from cDNA sequences, function as low- and high-light-intensity phototaxis receptors in the eukaryotic alga Chlamydomonas reinhardtii. Each of the receptors consists of an approximately 300-residue seven-transmembrane helix domain with a retinal-binding pocket homologous to that of archaeal rhodopsins, followed by approximately 400 residues of additional membrane-associated portion. The function of the two rhodopsins, Chlamydomonas sensory rhodopsins A and B (CSRA and CSRB), as phototaxis receptors is demonstrated by in vivo analysis of photoreceptor electrical currents and motility responses in transformants with RNA interference (RNAi) directed against each of the rhodopsin genes. The kinetics, fluence dependencies, and action spectra of the photoreceptor currents differ greatly in transformants in accord with the relative amounts of photoreceptor pigments expressed. The data show that CSRA has an absorption maximum near 510 nm and mediates a fast photoreceptor current that saturates at high light intensity. In contrast, CSRB absorbs maximally at 470 nm and generates a slow photoreceptor current saturating at low light intensity. The relative wavelength dependence of CSRA and CSRB activity in producing phototaxis responses matches precisely the wavelength dependence of the CSRA- and CSRB-generated currents, demonstrating that each receptor mediates phototaxis. The saturation of the two photoreceptor currents at different light fluence levels extends the range of light intensity to which the organism can respond. Further, at intensities where both operate, their light signals are integrated at the level of membrane depolarization caused by the two photoreceptor currents.
Protein Modification by Amino Acid Addition Is Increased in Crushed Sciatic But Not Optic Nerves (1986)

Rat optic and sciatic nerves were crushed, and 10 minutes to 3 days later nerve segments between the crushed site and the cell body were removed and assayed for posttranslational protein modification by amino acid addition. Protein modification was comparable in intact optic and sciatic nerves, but in sciatic nerves increased to 1.6 times control levels 10 minutes after crushing and reached a maximum of ten times control levels by 2 hours. In optic nerves activity was decreased throughout the time course studied. The results indicate that, in a nerve which is capable of regeneration (sciatic), protein modification by the addition of amino acids increases immediately after injury, but a nerve incapable of regeneration (optic) is incapable of activating the modification reaction. These findings may be important in understanding the reasons for the lack of a regenerative response after injury to central mammalian nerves.
Determination of pH with surface-enhanced Raman fiber optic probes (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of pH with surface-enhanced Raman fiber optic probesKen I. Mullen, DaoXin. Wang, L. Gayle. Crane, and Keith T. CarronCite this: Anal. Chem. 1992, 64, 8, 930–936Publication Date (Print):April 15, 1992Publication History Published online1 May 2002Published inissue 15 April 1992https://pubs.acs.org/doi/10.1021/ac00032a018https://doi.org/10.1021/ac00032a018research-articleACS PublicationsRequest reuse permissionsArticle Views481Altmetric-Citations53LEARN 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
Flavor Aspects of Pulse Ingredients (2016)

Pulses (Fabaceae) have regained interest for their high protein level. However, food application of pulses and pulse ingredients is hampered by several issues around their off‐flavor. Off‐flavors in pulses are partially inherent and partially produced during harvesting, processing, and storage. Generally, volatile off‐flavor compounds in pulses belong to the categories of aldehydes, alcohols, ketones, acids, pyrazines, sulfur compounds, and others, and off‐taste is strongly correlated to the presence of saponins, phenolic compounds, and sometimes alkaloids. No systematic studies have been performed on the identification of the off‐flavor compounds present in pulses in relation to their contribution to the overall perception of the pulses. This review article aims to provide a concise overview highlighting the most important aspects of the knowledge available on the off‐flavor compounds present in various pulses, their possible origins, and the technologies available to prevent, reduce, or mask these off‐flavor compounds. Rather than attempting to make a full inventory of the literature in the field, this paper addresses the most relevant topics referring to a selected set of relevant papers on each topic to substantiate the observations and conclusions that may guide the reader toward additional literature.
Mechanism of Reaction of Myeloperoxidase with Nitrite (2000)

Myeloperoxidase (MPO) is a major neutrophil protein and may be involved in the nitration of tyrosine residues observed in a wide range of inflammatory diseases that involve neutrophils and macrophage activation. In order to clarify if nitrite could be a physiological substrate of myeloperoxidase, we investigated the reactions of the ferric enzyme and its redox intermediates, compound I and compound II, with nitrite under pre-steady state conditions by using sequential mixing stopped-flow analysis in the pH range 4-8. At 15 degrees C the rate of formation of the low spin MPO-nitrite complex is (2.5 +/- 0.2) x 10(4) m(-1) s(-1) at pH 7 and (2.2 +/- 0.7) x 10(6) m(-1) s(-1) at pH 5. The dissociation constant of nitrite bound to the native enzyme is 2.3 +/- 0.1 mm at pH 7 and 31.3 +/- 0.5 micrometer at pH 5. Nitrite is oxidized by two one-electron steps in the MPO peroxidase cycle. The second-order rate constant of reduction of compound I to compound II at 15 degrees C is (2.0 +/- 0.2) x 10(6) m(-1) s(-1) at pH 7 and (1.1 +/- 0.2) x 10(7) m(-1) s(-1) at pH 5. The rate constant of reduction of compound II to the ferric native enzyme at 15 degrees C is (5.5 +/- 0.1) x 10(2) m(-1) s(-1) at pH 7 and (8.9 +/- 1.6) x 10(4) m(-1) s(-1) at pH 5. pH dependence studies suggest that both complex formation between the ferric enzyme and nitrite and nitrite oxidation by compounds I and II are controlled by a residue with a pK(a) of (4.3 +/- 0.3). Protonation of this group (which is most likely the distal histidine) is necessary for optimum nitrite binding and oxidation.
Software mitigations to hedge AES against cache-based software side channel vulnerabilities. (2006)

Hardware side channel vulnerabilities have been studied for many years in embedded silicon-security arena including SmartCards, SetTop-boxes, etc. However, because various recent security activities have goals of improving the software isolation properties of PC platforms, software side channels have become a subject of interest. Recent publications discussed cache-based software side channel vulnerabilities of AES and RSA. Thus, following the classical approach --- a new side channel vulnerability opens a new mitigation research path --- this paper starts to investigate e#cient mitigations to protect AES-software against side channel vulnerabilities. First, we will present several mitigation strategies to harden existing AES software against cache-based software side channel attacks and analyze their theoretical protection.
Resveratrol attenuates hyperoxia‐induced oxidative stress, inflammation and fibrosis and suppresses Wnt/β‐catenin signalling in lungs of neonatal rats (2015)

Although survival rate of infants born prematurely has been raised by supplemental oxygen treatment, it is followed by high morbidity of hyperoxia-induced bronchopulmonary dysplasia. In this study, the effect of resveratrol on the lung injury was evaluated in hyperoxia-exposed rats of preterm birth. The results demonstrated that hyperoxia led to thickened alveolar wall, simplified alveolar architecture and fibrosis. In addition, elevated methane dicarboxylic aldehyde level, decreased glutathione level and superoxide dismutase activity were also found in hyperoxic lungs, as well as the increased tumor necrosis factor-α, interleukin-1β and interleukin-6 in the bronchoalveolar lavage fluid. Fibrotic-associated proteins transforming growth factor-β1, α-smooth muscle actin, collagen I and fibronectin deposition were also found in interstitial substance of lungs. Furthermore, Wnt/β-catenin signalling was found to be active in hyperoxia-induced lungs. In addition, expression of SP-C was increased and T1α was decreased in hyperoxia-exposed lungs. Resveratrol intraperitoneal administration alleviated hyperoxia-induced histological injury of lungs, regulated redox balance, decreased pro-inflammatory cytokine release, and down-regulated expression of fibrotic-associated proteins. Furthermore, Wnt/β-catenin signalling was also suppressed by resveratrol, as represented by diminished expression of lymphoid enhancer factor-1, Wnt induced signalling protein-1 and cyclin D1. In addition, the increase of SP-C and decrease of T1α expression was prevented as well. The present study showed that resveratrol could protect lungs from hyperoxia-induced injury through its antioxidant, anti-inflammatory and anti-fibrotic effects. The transdifferentiation of alveolar epithelial type II cells to alveolar epithelial type I cells promotion and Wnt/β-catenin signalling suppression are also involved in the protective effect.
A 3-D differential coil design for localized magnetic stimulation (2001)

A novel three-dimensional (3-D) differential coil has been designed for improving the localization of magnetic stimulation. This new coil design consists of a butterfly coil with two additional wing units and an extra bottom unit, both perpendicular to the plane of the butterfly coil. The wing units produce opposite fields to restrict the spread of induced fields while the bottom unit enhances the induced fields at the excitation site. The peak induced field generated by this new design is located at the center of the coil, providing an easy identification of the excitation site. The field localization of the new coil is comparable with that of much smaller coils but with an inductance compatible to current magnetic stimulators. Numerical computations based on the principles of electromagnetic induction and using a human nerve model were performed to analyze the induced fields and the stimulation thresholds of new coil designs. The localization of the coil design was assessed by a half power region (HPR), within which the magnitude of the normalized induced field is greater than 1/square root of 2. The HPR for a 3-D differential coil built is improved (decreased) by a factor of three compared with a standard butterfly coil. Induced fields by this new coil were measured and in agreement with theoretical calculations.
Site-directed mutagenesis of monocyte chemoattractant protein-1 identifies two regions of the polypeptide essential for biological activity (1996)

Monocyte chemoattractant protein-1 (MCP-1) mediates monocyte migration into tissues in inflammatory diseases and atherosclerosis. We have investigated structure-activity relationships for human MCP-1. Mutations were introduced based upon differences between MCP-1 and the structurally related but functionally distinct molecule interleukin-8 (IL-8). Mutant proteins produced using the baculovirus/insect cell expression system were purified and their ability to stimulate monocyte chemotaxis and elevation of intracellular calcium in THP-1 monocytic leukaemia cells was measured. Two regions in MCP-1 were identified as important for its biological activity. One region consists of the sequence Thr-Cys-Cys-Tyr (amino acids 10-13). Point mutations of Thr-10 to Arg and Tyr-13 to Ile greatly lowered MCP-1 activity. The second functionally important region is formed by Ser-34 and Lys-35. Insertion of a Pro between these two residues, or their substitution by the sequence Gly-Pro-His, caused nearly complete loss of MCP-1 activity. Competition binding experiments showed that the mutations that affected activity also lowered the ability to compete with wild-type MCP-1 for receptors on THP-1 cells. Point mutations at positions 8, 15, 30, 37, 38 and 68 had little effect on MCP-1 activity. The important regions that we have identified in MCP-1 correspond with previously identified functionally important regions of IL-8, suggesting that the two molecules bind to their respective receptors by similar contacts.
Role of interleukin-28B polymorphisms in the treatment of hepatitis C virus genotype 2 infection in Asian patients (2010)

The rs8099917 TT genotype is significantly independently predictive of RVR, which is the single best predictor of SVR, in Asian HCV-2 patients.