gebhart/patrepeval huggingface dataset:
Lactococcus lactis Lytic Bacteriophages of the P335 Group Are Inhibited by Overexpression of a Truncated CI Repressor (2002)

Phages of the P335 group have recently emerged as important taxa among lactococcal phages that disrupt dairy fermentations. DNA sequencing has revealed extensive homologies between the lytic and temperate phages of this group. The P335 lytic phage phi31 encodes a genetic switch region of cI and cro homologs but lacks the phage attachment site and integrase necessary to establish lysogeny. When the putative cI repressor gene of phage phi31 was subcloned into the medium-copy-number vector pAK80, no superinfection immunity was conferred to the host, Lactococcus lactis subsp. lactis NCK203, indicating that the wild-type CI repressor was dysfunctional. Attempts to clone the full-length cI gene in Lactococcus in the high-copy-number shuttle vector pTRKH2 were unsuccessful. The single clone that was recovered harbored an ochre mutation in the cI gene after the first 128 amino acids of the predicted 180-amino-acid protein. In the presence of the truncated CI construct, pTRKH2::CI-per1, phage phi31 was inhibited to an efficiency of plaquing (EOP) of 10(-6) in NCK203. A pTRKH2 subclone which lacked the DNA downstream of the ochre mutation, pTRKH2::CI-per2, confirmed the phenotype and further reduced the phi31 EOP to <10(-7). Phage phi31 mutants, partially resistant to CI-per, were isolated and showed changes in two of three putative operator sites for CI and Cro binding. Both the wild-type and truncated CI proteins bound the two wild-type operators in gel mobility shift experiments, but the mutated operators were not bound by the truncated CI. Twelve of 16 lytic P335 group phages failed to form plaques on L. lactis harboring pTRKH2::CI-per2, while 4 phages formed plaques at normal efficiencies. Comparisons of amino acid and DNA level homologies with other lactococcal temperate phage repressors suggest that evolutionary events may have led to inactivation of the phi31 CI repressor. This study demonstrated that a number of different P335 phages, lytic for L. lactis NCK203, have a common operator region which can be targeted by a truncated derivative of a dysfunctional CI repressor.
Control of Turf grass Weeds (1994)

Weeds most often become established in a weakened turf; thus, knowing turf weaknesses often helps to understand the reason for weed encroachment and how it may be reduced (Color Plate 8-1). Weak turf and bare areas exist because of: (i) improper turf species for a given area; (ii) damage from pests such as diseases, insects, nematodes, and animals; (iii) environmental stresses such as excessive shade, drought, heat, cold, and poor drainage; (iv) improper turf management practices such as misuse of fertilizer and chemicals, improper mowing height or frequency and lack of proper soil aeration; and (v) physical damage and compaction from concentrated traffic. Unless factors contributing to turf decline are corrected, continued weed encroachment should be expected. Weed control techniques include prevention, as well as cultural, mechanical, biological, and chemical control.
Text categorization for multiple users based on semantic features from a machine-readable dictionary (1994)

The text categorization module described here provides a front-end filtering function for the larger DR-LINK text retrieval system [Liddy and Myaeing 1993]. The model evaluates a large incoming stream of documents to determine which documents are sufficiently similar to a profile at the broad subject level to warrant more refined representation and matching. To accomplish this task, each substantive word in a text is first categorized using a feature set based on the semantic Subject Field Codes (SFCs) assigned to individual word senses in a machine-readable dictionary. When tested on 50 user profiles and 550 megabytes of documents, results indicate that the feature set that is the basis of the text categorization module and the algorithm that establishes the boundary of categories of potentially relevant documents accomplish their tasks with a high level of performance. This means that the category of potentially relevant documents for most profiles would contain at least 80% of all documents later determined to be relevant to the profile. The number of documents in this set would be uniquely determined by the system's category-boundary predictor, and this set is likely to contain less than 5% of the incoming stream of documents.
Inhaled Nitric Oxide for Preterm Infants: A Systematic Review (2007)

Inhaled nitric oxide as rescue therapy for very ill preterm infants undergoing ventilation does not seem to be effective and may increase severe intracranial hemorrhage. Later use of inhaled nitric oxide to prevent bronchopulmonary dysplasia does not seem to be effective. Early routine use of inhaled nitric oxide for mildly sick, preterm infants seems to decrease the risk of serious brain injury and may improve rates of survival without bronchopulmonary dysplasia.
CpG-Containing Oligonucleotides Are Efficient Adjuvants for Induction of Protective Antiviral Immune Responses with T-Cell Peptide Vaccines (1999)

Synthetic nonmethylated oligonucleotides containing CpG dinucleotides (CpG-ODNs) have been shown to exhibit immunostimulatory activity. CpG-ODNs have the capacity to directly activate B cells, macrophages, and dendritic cells, and we show here that this is reflected by cell surface binding of oligonucleotides to these cell subsets. However, T cells are not directly activated by CpG-ODNs, which correlates with the failure to bind to the T-cell surface. Efficient competition for CpG-induced B-cell activation by non-CpG-containing oligonucleotides suggests that oligonucleotides might bind to an as yet undefined sequence-nonspecific receptor prior to cellular activation. Induction of protective T-cell responses against challenge infection with lymphocytic choriomeningitis virus (LCMV) or with recombinant vaccinia virus expressing the LCMV glycoprotein was achieved by immunizing mice with the immunodominant major histocompatibility complex class I-binding LCMV glycoprotein-derived peptide gp33 together with CpG-ODNs. In these experiments, B cells, potentially serving as CpG-ODN-activated antigen-presenting cells (APCs), were not required for induction of protective immunity since CpG-ODN-gp33-immunized B-cell-deficient mice were equally protected against challenge infection with both viruses. This finding suggested that macrophages and/or dendritic cells were sufficiently activated in vivo by CpG-ODNs to serve as potent APCs for the induction of naive T cells. Furthermore, treatment with CpG-ODN alone induced protection against infection with Listeria monocytogenes via antigen-independent activation of macrophages. These data suggest that CpG activation of macrophages and dendritic cells may provide a critical step in CpG-ODN adjuvant activity.
Extraordinary Electroconductance in In-GaAs Metal-Semiconductor Hybrid Structures (2007)

In‐GaAs metal‐semiconductor hybrids (MSHs) are found to exhibit enhanced room‐temperature electroconductance in the presence of an external electric field. The lowering effect of the Schottky barrier that forms at the MS interface plays a key role in the extraordinary electroconductance (EEC) effects. At room temperature and a field 12kV/cm, we obtained EEC∼ 20% without bias voltage.
Application of Solid Phase Micro‐Extraction (SPME) to the analysis of pesticide residues in vegetables (2000)

Solid Phase Micro-Extraction (SPME) is a new analytical technique, based on capturing the analytes by adsorption onto an organic phase coating a glass fibre, and subsequent direct desorption into the injector of a gas chromatograph. This technique has been successfully applied in the analysis of organic contaminants in water, giving linear responses and, in some cases, high sensitivities. The present paper reports data about the application of SPME to the analysis of pesticide residues in a vegetable matrix, testing over nearly one hundred active compounds, with two types of adsorbent phase (polydimethylsiloxane and Carbowax/divinylbenzene). A vegetable matrix spiked with pesticides was analyzed by SPME and by a traditional multi-residue method; recoveries were determined and compared for the two cases. The behaviour of the analytical response by SPME was studied in the range 0.01–1 mg kg−1 by adding increasing amounts of given pesticide mixtures to the vegetable matrix. The procedure was further tested by analyzing real samples, and gave some difficulties in recovering the whole amount of some of the residues present (in comparison with the traditional method). The SPME method was then improved by pre-extracting with acetone and sonicating before the extraction/adsorption step. The results obtained were satisfactory (some certified matrices were also tested) with good accordance between the two methods. Nevertheless some active compounds showed very low responses or remained undetectable by SPME in our experimental conditions. © 2000 Society of Chemical Industry
Properties and Synthetic Applications of Ammonia-Lyases (2003)

Ammonia-lyases catalyze a wide range of processes leading to α,β-unsaturated compounds by elimination of ammonia having few features in common. They utilize an extraordinary range of prosthetic groups; e.g. coenzyme B12, dipyrromethane cofactor, pyridoxal-phosphate, or the 3,5-dihydro-5-methylidene-4H-imidazol- 4-one (MIO) prosthetic groups. In this work, ammonia-lyases are reviewed with major emphasis on various aspects of biotransformations, covering topics from the fundamental biochemistry of ammonia-lyases to their structure determined by protein crystallography. Keywords: Ammonia-Lyases, dipyrromethane cofactor, biotransformations
Autocrine production of IL-1 beta by human osteoarthritis-affected cartilage and differential regulation of endogenous nitric oxide, IL-6, prostaglandin E2, and IL-8. (1998)

Interleukin-1 beta (IL-1 beta) plays a central role in the pathophysiology of cartilage damage and degradation in arthritis. In noninflammatory arthropathies such as osteoarthritis (OA), the synovial-derived IL-1 beta has been implicated in the disease process. In this study, we report that human OA-affected cartilage demonstrates upregulated IL-1 beta mRNA not seen in normal cartilage. The OA-affected cartilage in ex vivo conditions spontaneously releases detectable amounts of autocrine IL-1 beta, nitric oxide (NO), and prostaglandin E2 (PGE2), known to be involved in cartilage damage and inflammation, that cannot be detected in normal cartilage. The autocrine IL-1 beta released by the OA-affected cartilage (for at least 72 hr in ex vivo conditions) is present in sufficient quantities to modulate NO and PGE2 production because addition of recombinant soluble IL-1 beta receptor (but not soluble tumor necrosis factor-alpha receptor) and cytokine-suppressive antiinflammatory drugs (CSAIDs) significantly attenuates the spontaneous release of NO and PGE2. Furthermore, OA-affected cartilage releases significant amounts of IL-6 and IL-8 in ex vivo conditions. Addition of CSAIDs to OA-affected cartilage differentially regulates IL-6 and IL-8 production by inhibiting the spontaneous release of IL-6 but not IL-8 in ex vivo conditions. These experiments demonstrate that the human OA-affected cartilage itself releases sufficient amounts of functionally active autocrine IL-1 beta that can modulate endogenous NO, PGE2, and IL-6, but not IL-8, all of which are known to be stimulated by IL-1 beta in vitro. These IL-1 beta induced pleotropic inflammatory mediators in OA-affected cartilage may be sufficient to facilitate or augment cartilage degradation and inhibit cartilage repair, and therefore lead the cartilage into an autodestructive pathway in osteoarthritis.
Role of Farnesyltransferase in ABA Regulation of Guard Cell Anion Channels and Plant Water Loss (1998)

Desiccation of plants during drought can be detrimental to agricultural production. The phytohormone abscisic acid (ABA) reduces water loss by triggering stomatal pore closure in leaves, a process requiring ion-channel modulation by cytoplasmic proteins. Deletion of the Arabidopsis farnesyltransferase gene ERA1 or application of farnesyltransferase inhibitors resulted in ABA hypersensitivity of guard cell anion-channel activation and of stomatal closing. ERA1 was expressed in guard cells. Double-mutant analyses of era1 with the ABA-insensitive mutants abi1 and abi2 showed that era1 suppresses the ABA-insensitive phenotypes. Moreover, era1 plants exhibited a reduction in transpirational water loss during drought treatment.
Uptake of disodium cromoglycate in obstructive airways disease (1973)

Summary The urinary excretion of disodium cromoglycate (DSCG) was used as an index of the amount reaching the lungs in nine normal subjects and in fifteen patients with obstructive airways disease. Vital capacity (VC), forced expiratory volume in one second (FEV 1 ) and peak inspiratory flow rate (PIF) through the spinhaler were also measured. The amount of DSCG detected in urine varied considerably. It was correlated with the physiological measures and with age. The usual DSCG excretion pattern was of a declining excretion rate from 0 to 3 hr following the dose, but certain individuals showed a rise to the second hour, before a fall occurred in the third hour. The occurrence of a rise was associated with a very low reading in the first hour, which in turn was associated with severe obstructive airways disease. Overall, the lowest excretion rates, and the poorest scores for VC, FEV 1 and PIF were recorded in a sub‐group of five chronic bronchitics, who were also the oldest group. In one chronic bronchitic no drug was detected. The highest excretion rates and best physiological scores were recorded in the normal subjects, who were also the youngest group.
Delays and Diversions Mark the Development of B Cell Responses to Borrelia burgdorferi Infection (2012)

B cell responses modulate disease during infection with Borrelia burgdorferi, the causative agent of Lyme disease, but are unable to clear the infection. Previous studies have demonstrated that B. burgdorferi infection induces predominantly T-independent B cell responses, potentially explaining some of these findings. However, others have shown effects of T cells on the isotype profile and the magnitude of the B. burgdorferi-specific Abs. This study aimed to further investigate the humoral response to B. burgdorferi and its degree of T cell dependence, with the ultimate goal of elucidating the mechanisms underlying the failure of effective immunity to this emerging infectious disease agent. Our study identifies distinct stages in the B cell response using a mouse model, all marked by the generation of unusually strong and persistent T-dependent and T-independent IgM Abs. The initial phase is dominated by a strong T-independent accumulation of B cells in lymph nodes and the induction of specific Abs in the absence of germinal centers. A second phase begins around week 2.5 to 3, in which relatively short-lived germinal centers develop in lymph nodes, despite a lymph node architecture that lacks clearly demarcated T and B cell zones. This response failed, however, to generate appreciable numbers of long-lived bone marrow plasma cells. Finally, there is a slow accumulation of long-lived Ab-secreting plasma cells in bone marrow, reflected by a strong but ultimately ineffective serum Ab response. Overall, the study indicates that B. burgdorferi might evade B cell immunity by interfering with its response kinetics and quality.
Polymer monolayers prepared by the spontaneous adsorption of sulfur-functionalized polystyrene on gold surfaces (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer monolayers prepared by the spontaneous adsorption of sulfur-functionalized polystyrene on gold surfacesJan M. Stouffer and Thomas J. McCarthyCite this: Macromolecules 1988, 21, 5, 1204–1208Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/ma00183a003https://doi.org/10.1021/ma00183a003research-articleACS PublicationsRequest reuse permissionsArticle Views1099Altmetric-Citations97LEARN 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
A 9-pJ/Pulse 1.42-Vpp OOK CMOS UWB Pulse Generator for the 3.1–10.6-GHz FCC Band (2009)

This paper presents the design of a fully integrated ultra-wideband (UWB) pulse generator for the Federal Communications Commission (FCC) 3.1-10.6-GHz band. This generator is reserved for medium rate applications and achieves pulses for an on-off keying (OOK) modulation, pulse position modulation, or pulse interval modulation. This UWB transmitter is based on the impulse response filter method, which uses an edge combiner in order to excite an integrated bandpass filter. The circuit has been integrated in an ST-Microelectronics CMOS 0.13-¿m technology with 1.2-V supply voltage and the die size is 0.54 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The pulse generator power consumption is 9 pJ per pulse and achieves a peak to peak magnitude of 1.42 V. The pulse is FCC compliant and the generator can be used with a rate up to 38 Mbs <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> with an OOK modulation. Based on the FCC power spectral density limitation, a sizing method is also presented.
Measuring long-range dependence under changing traffic conditions (1999)

Previous measurements of various types of network traffic have shown evidence consistent with long-range dependence and self-similarity. However, an alternative explanation for these measurements is non-stationarity. Standard estimators of LRD parameters such as the Hurst parameter H assume stationarity and are susceptible to bias when this assumption does not hold. Hence LRD may be indicated by these estimators when none is present, or alternatively LRD taken to be non-stationarity. The Abry-Veitch (see IEEE Trans. on on Info. Theory, vol.44, no.1, p.2-15, 1998) joint estimator has much better properties when a time-series is non-stationary. In particular the effect of polynomial trends in data may be intrinsically eliminated from the estimates of LRD parameters. This paper investigates the behavior of the AV estimator when there are non-stationarities in the form of a level shift in the mean and/or the variance of a process. We examine cases where the change occurs both gradually or as a single jump discontinuity, and also examine the effect of the size of the shift. In particular we show that although a jump discontinuity may cause bins in the estimates of the H, the bias is negligible except when the jump is sharp, and large compared with the standard deviation of the process. We explain these effects and suggest how any introduced errors might be minimized. We define a broad class of non-stationary LRD processes so that LRD remains well defined under time varying mean and variance. The results are tested by applying the estimator to a real data set which contains a clear non-stationary event falling within this class.
Variance Reduction Techniques for Gradient Estimates in Reinforcement Learning (2004)

Policy gradient methods for reinforcement learning avoid some of the undesirable properties of the value function approaches, such as policy degradation (Baxter and Bartlett, 2001). However, the variance of the performance gradient estimates obtained from the simulation is sometimes excessive. In this paper, we consider variance reduction methods that were developed for Monte Carlo estimates of integrals. We study two commonly used policy gradient techniques, the baseline and actor-critic methods, from this perspective. Both can be interpreted as additive control variate variance reduction methods. We consider the expected average reward performance measure, and we focus on the GPOMDP algorithm for estimating performance gradients in partially observable Markov decision processes controlled by stochastic reactive policies. We give bounds for the estimation error of the gradient estimates for both baseline and actor-critic algorithms, in terms of the sample size and mixing properties of the controlled system. For the baseline technique, we compute the optimal baseline, and show that the popular approach of using the average reward to define the baseline can be suboptimal. For actor-critic algorithms, we show that using the true value function as the critic can be suboptimal. We also discuss algorithms for estimating the optimal baseline and approximate value function.
Identification of Amino Acids in the Factor XI Apple 3 Domain Required for Activation of Factor IX (1999)

Activated coagulation factor XI (factor XIa) proteolytically cleaves its substrate, factor IX, in an interaction requiring the factor XI A3 domain (Sun, Y., and Gailani, D. (1996) J. Biol. Chem. 271, 29023-29028). To identify key amino acids involved in factor IX activation, recombinant factor XIa proteins containing alanine substitutions for wild-type sequence were expressed in 293 fibroblasts and tested in a plasma clotting assay. Substitutions for Ile(183)-Val(191) and Ser(195)-Ile(197) at the N terminus and for Ser(258)-Ser(264) at the C terminus of the A3 domain markedly decreased factor XI coagulant activity. The plasma protease prekallikrein is structurally homologous to factor XI, but activated factor IX poorly. A chimeric factor XIa molecule with the A3 domain replaced with A3 from prekallikrein (FXI/PKA3) activated factor IX with a K(m) 35-fold greater than that of wild-type factor XI. FXI/PKA3 was used as a template for a series of proteins in which prekallikrein A3 sequence was replaced with factor XI sequence to restore factor IX activation. Clotting and kinetics studies using these chimeras confirmed the results obtained with alanine mutants. Amino acids between Ile(183) and Val(191) are necessary for proper factor IX activation, but additional sequence between Ser(195) and Ile(197) or between Phe(260) and Ser(265) is required for complete restoration of activation.