gebhart/patrepeval huggingface dataset:
Dual-work-function metal gates by full silicidation of poly-Si with Co-Ni bi-Layers (2005)

Dual-work-function metal gates fabricated by full silicidation (FUSI) of Co-Ni bi-layer with doped poly-Si were investigated for the first time, along with single-metal FUSI systems of CoSi/sub 2/ and NiSi. Complete conversion of poly-Si into Co-Ni alloy silicided metal gate (FUSI) Co/sub x/Ni/sub 1-x/Si/sub 2/ was demonstrated. Although a linear relationship between work function and Ni percentage was observed for FUSI of undoped poly-Si systems, the work functions of doped Co/sub x/Ni/sub 1-x/Si/sub 2/ are almost identical to those of doped NiSi FUSI metal gates. The alloy FUSI metal gates explored in this letter provide a new class of metal gates for CMOS devices that combine the advantages of both NiSi and CoSi/sub 2/, i.e., proper work function tunability of NiSi and high thermal stability of CoSi/sub 2/.
Cloning, expression, and sequencing of squalene-hopene cyclase, a key enzyme in triterpenoid metabolism (1992)

The pentacyclic hopanoids, a class of eubacterial lipids, are synthesized by squalene-hopene cyclase and side chain-elongating enzymes. With the aid of DNA probes based on the amino-terminal sequence of purified squalene-hopene cyclase from Bacillus acidocaldarius, clones of Escherichia coli that express this enzyme in the cytoplasmic membrane were isolated. According to the DNA sequence, the cyclase contained 627 amino acids with a molecular mass of 69,473 Da. A high percentage of the amino acids were basic. No significant similarity to existing sequenced proteins was found.
Combination of Baculovirus-Mediated Gene Delivery and Packed-Bed Reactor for Scalable Production of Adeno-Associated Virus (2007)

The production of recombinant adeno-associated virus (rAAV) commonly requires plasmid cotransfection, which hinders its mass production. Herein we describe the development of a novel process for rAAV production by combining the advantages of baculovirus-mediated gene delivery and BelloCell bioreactor (a novel packed-bed reactor for animal cell culture; CESCO Bioengineering, Hsinchu, Taiwan). We constructed three baculoviral vectors: Bac-LacZ carries the lacZ gene flanked by AAV inverted terminal repeats, Bac-RC harbors AAV rep and cap genes, and Bac-Helper carries helper genes derived from adenovirus. Cotransduction of HEK-293 cells with these three baculoviruses resulted in successful production of rAAV, and the protein and rAAV yield did not decrease with Bac-RC passage for up to four passages. By adjusting the dose ratio of Bac-LacZ to Bac-RC, adding sodium butyrate, and transferring the production process to the BelloCell-500-AP (500 ml), which allowed for high-density culture and effective baculovirus-mediated transduction of HEK-293 cells, the maximal specific rAAV yield reached approximately 3.8 x 10(4) vector genome (VG) or 247 infectious viral particles (IVP) per cell, which corresponded to approximately 1 x 10(14) VG or 8.5 x 10(11) IVP per reactor run. The yield was comparable or superior to those obtained with other production systems. Baculoviral transduction is simple and cost-effective and the BelloCell-500-AP offers high-density culture of HEK-293 cells. Altogether, the combination of baculoviral transduction and BelloCell reactor culture provides a novel and economically viable approach for rAAV production.
Location selection for active services (2002)

Active services are application-specified programs that are executed inside the network. The location where the active service is executed plays an important role. The dynamic behavior of networks requires that the selection of the most suitable location to instantiate a service is done at run time. To dynamically place an active service, information about the network (topology, bandwidth) and application (type of the service) is necessary. This paper describes a method to dynamically search for available active service locations in the Internet. To be deployed in the current Internet, a solution is required to (i) scale well to large networks, (ii) to demand as little changes to the Internet as possible, especially not at lower network layers. Finally, the solution must be flexible and customizable to take application requirements into account. The proposed solution makes use of the routing path between two end systems. Active service locations that are located close to the routing path are then found via DNS queries. The evaluation shows that the application pays an overhead at startup time. For applications that can tolerate a startup delay, we show with two experiments using a video application that the quality of the application can be increased by dynamic placement of active services.
Coculture of interleukin 3-dependent mouse mast cells with fibroblasts results in a phenotypic change of the mast cells. (1986)

The heparin-containing mast cells that reside in the connective tissue of the mouse, but not the chondroitin sulfate-containing mast cells in the gastrointestinal mucosa, stain with safranin when exposed to alcian blue/safranin. Mouse bone marrow-derived mast cells (BMMC), the probable in vitro counterparts of in vivo mucosal mast cells, were cultured for 14 days with mouse skin-derived 3T3 fibroblasts in RPMI 1640 medium containing 10% fetal calf serum and 50% WEHI-3 conditioned medium. Although the BMMC adhered to the fibroblast monolayer, they continued to divide, probably due to the presence of interleukin 3 in the conditioned medium. The mast cells remained viable throughout the period of coculture, since they failed to release lactate dehydrogenase and because they increased their histamine content approximately 15-fold. After 12-14 days of coculture, greater than 50% of the BMMC changed histochemically to become safranin+; 30-40% of the 35S-labeled glycosaminoglycans on the proteoglycans synthesized by these cocultured mast cells were heparin, whereas heparin was not detected in the initial BMMC. In the absence of WEHI-3 conditioned medium, BMMC adhered to the fibroblast monolayer, and after 8 days of coculture, the number of mast cells did not change and their histamine content remained the same. However, these mast cells also became safranin+ and synthesized 40% heparin glycosaminoglycans. Thus, coculture of BMMC with fibroblasts induces a phenotypic change so that the resulting mast cells stain safranin+ and synthesize heparin proteoglycans, whereas the presence of WEHI-3 conditioned medium stimulates proliferation and an increase in histamine content.
Multiplex PCR Assay for Direct Identification of Group B Streptococcal Alpha-Protein-Like Protein Genes (2004)

We developed a group B streptococcus multiplex PCR assay which allows, by direct analysis of the amplicon size, determination of the surface protein antigen genes of alpha-C protein, epsilon protein, Rib, Alp2, Alp3, and Alp4. The multiplex PCR assay offers a rapid and simple method of subtyping Streptococcus agalactiae based on surface protein genes.
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival (2005)

Perturbations of the p53 pathway are associated with more aggressive and therapeutically refractory tumors. However, molecular assessment of p53 status, by using sequence analysis and immunohistochemistry, are incomplete assessors of p53 functional effects. We posited that the transcriptional fingerprint is a more definitive downstream indicator of p53 function. Herein, we analyzed transcript profiles of 251 p53-sequenced primary breast tumors and identified a clinically embedded 32-gene expression signature that distinguishes p53-mutant and wild-type tumors of different histologies and outperforms sequence-based assessments of p53 in predicting prognosis and therapeutic response. Moreover, the p53 signature identified a subset of aggressive tumors absent of sequence mutations in p53 yet exhibiting expression characteristics consistent with p53 deficiency because of attenuated p53 transcript levels. Our results show the primary importance of p53 functional status in predicting clinical breast cancer behavior.
Drug delivery options to increase patient adherence and satisfaction in the management of rheumatoid arthritis &ndash; focus on subcutaneous tocilizumab (2014)

Rheumatoid arthritis (RA) is a chronic, progressive, inflammatory disease associated with joint destruction. Tocilizumab (TCZ) is a humanized monoclonal anti-interleukin-6 receptor antibody that was initially developed for use as an intravenous (IV) infusion. Previous studies have shown that TCZ-IV is an important treatment option in patients with moderate-to-severe RA. A subcutaneous (SC) formulation of 162 mg TCZ that was recently developed and approved provides an additional treatment option for RA patients. In the present review, we provide an update on the efficacy and safety of TCZ-SC, compared with TCZ-IV. The TCZ-SC doses of 162 mg every 2 weeks (q2w) or weekly (qw) were selected based on pharmacokinetic and pharmacodynamic studies. Both TCZ-SC q2w and qw regimens showed equivalent effects to TCZ-IV in most patients; however, the TCZ-SC qw regimen consistently showed a more rapid effect in terms of C-reactive protein normalization. Randomized controlled studies showed that TCZ-SC monotherapy or combined with disease-modifying antirheumatic drugs demonstrated comparable efficacy to TCZ-IV in patients who were both biologic-naïve and refractory to tumor necrosis factor inhibitors. TCZ-SC at both qw and q2w were generally well-tolerated for up to 24 weeks. There was a low rate of withdrawal due to adverse events, and their incidence was comparable with that seen with TCZ-IV. An injection site reaction was seen in approximately 10% of patients who received the subcutaneous formulation. In conclusion, although clinical results are still limited, the currently available evidence suggests that TCZ-SC is a promising treatment for moderate-to-severe RA, both as monotherapy and combination therapy. More data is needed to determine the optimal dosing schedule.
Imaging downgoing waves from ocean bottom stations (2005)

We present a method for imaging the downgoing waves recorded on the seabed. The first step in our method is a conventional combination of the hydrophone and the vertical geophone data to produce of up going and downgoing P waves. Conventionally one proceeds only with the upgoing waves, we proceed also with the downgoing waves, which contain no primary reflections. We migrate the downgoing waves by pretending that the data were acquired not on the seabed, but above the sea surface on top of an virtual water layer whose thickness is twice the sea depth. We applied this method to OBS data recorded in the North Sea and found that the downgoing waves provide a better image than the upgoing waves. We speculate that this is because of improved illumination and reduced exposure to shallow inhomogeneous anomalies directly below the seabed.
Anti-inflammatory benefits of tilmicosin in calves with Pasteurella haemolytica-infected lungs (1998)

By inducing neutrophil apoptosis, tilmicosin prevents further amplification of inflammatory injury in P haemolytica-infected lungs.
Updating quasi-Newton matrices with limited storage (1980)

We study how to use the BFGS quasi-Newton matrices to precondition minimization methods for problems where the storage is critical. We give an update formula which generates matrices using information from the last <italic>m</italic> iterations, where <italic>m</italic> is any number supplied by the user. The quasi-Newton matrix is updated at every iteration by dropping the oldest information and replacing it by the newest information. It is shown that the matrices generated have some desirable properties. The resulting algorithms are tested numerically and compared with several well-known methods.
P80, the HinT interacting membrane protein, is a secreted antigen of Mycoplasma hominis (2004)

Our model for secretion of the P80 protein of M. hominis implies a two-step process. In general the P80 protein is transported across the membrane and remains complexed to P60, surface-exposed and membrane anchored via the uncleaved signal sequence. Loss of the 4.7 kDa signal peptide seems to be a pre-requisite for P80 secretion, which is followed by a proteolytic process leading to a helical 74 kDa product. We propose that this novel form of two-step secretion is one of the solutions to a life with a reduced gene set.
Ligand variation and metal ion binding specificity in zinc finger peptides (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLigand variation and metal ion binding specificity in zinc finger peptidesBeth Allyn Krizek, Denise L. Merkle, and Jeremy M. BergCite this: Inorg. Chem. 1993, 32, 6, 937–940Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ic00058a030https://doi.org/10.1021/ic00058a030research-articleACS PublicationsRequest reuse permissionsArticle Views1493Altmetric-Citations192LEARN 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
High-Frequency TRNS Reduces BOLD Activity during Visuomotor Learning (2013)

Transcranial direct current stimulation (tDCS) and transcranial random noise stimulation (tRNS) consist in the application of electrical current of small intensity through the scalp, able to modulate perceptual and motor learning, probably by changing brain excitability. We investigated the effects of these transcranial electrical stimulation techniques in the early and later stages of visuomotor learning, as well as associated brain activity changes using functional magnetic resonance imaging (fMRI). We applied anodal and cathodal tDCS, low-frequency and high-frequency tRNS (lf-tRNS, 0.1-100 Hz; hf-tRNS 101-640 Hz, respectively) and sham stimulation over the primary motor cortex (M1) during the first 10 minutes of a visuomotor learning paradigm and measured performance changes for 20 minutes after stimulation ceased. Functional imaging scans were acquired throughout the whole experiment. Cathodal tDCS and hf-tRNS showed a tendency to improve and lf-tRNS to hinder early learning during stimulation, an effect that remained for 20 minutes after cessation of stimulation in the late learning phase. Motor learning-related activity decreased in several regions as reported previously, however, there was no significant modulation of brain activity by tDCS. In opposition to this, hf-tRNS was associated with reduced motor task-related-activity bilaterally in the frontal cortex and precuneous, probably due to interaction with ongoing neuronal oscillations. This result highlights the potential of lf-tRNS and hf-tRNS to differentially modulate visuomotor learning and advances our knowledge on neuroplasticity induction approaches combined with functional imaging methods.
A plant virus vector for systemic expression of foreign genes in cereals (2000)

Inserts bearing the coding sequences of NPT II and beta-glucuronidase (GUS) were placed between the nuclear inclusion b (NIb) and coat protein (CP) domains of the wheat streak mosaic virus (WSMV) polyprotein ORF. The WSMV NIb-CP junction containing the nuclear inclusion a (NIa) protease cleavage site was duplicated, permitting excision of foreign protein domains from the viral polyprotein. Wheat, barley, oat and maize seedlings supported systemic infection of WSMV bearing NPT II. The NPT II insert was stable for at least 18-30 days post-inoculation and had little effect on WSMV CP accumulation. Histochemical assays indicated the presence of functional GUS protein in systemically infected wheat and barley plants inoculated with WSMV bearing GUS. The GUS constructs had greatly reduced virulence on both oat and maize. RT-PCR indicated that the GUS insert was subject to deletion, particularly when expressed as a GUS-NIb protein fusion. Both reporter genes were expressed in wheat roots at levels comparable to those observed in leaves. These results clearly demonstrate the utility of WSMV as a transient gene expression vector for grass species, including two important grain crops, wheat and maize. The results further indicate that both host species and the nature of inserted sequences affect the stability and expression of foreign genes delivered by engineered virus genomes.
Immune response to nucleotide-supplemented infant formulae: systematic review and meta-analysis (2007)

Human milk is recommended as the only alimentary source for the first six months of life. Additionally there is a medical and social need for safe and effective alternative forms of nutrition for infants who cannot be fed with breast milk. Recently the safety and efficacy of some ingredients in infant formulae, such as nucleotides have been discussed. This systematic review analyzed the available evidence to establish the efficacy, safety and dose-response effect of ribonucleotide-supplemented infant formulae (RSIFs). Randomised controlled clinical trials (RCTs) comparing RSIFs to formulae without nucleotides or breast milk were considered in this review. Outcome measures were: antibody titres to common paediatric vaccinations, total lymphocytes, lymphocyte subclasses and NK-cells, episodes of diarrhoea and acute respiratory infection. Publication quality was determined using Jadad and CONSORT guidelines. Results were combined using a random effects model and reported through standardised mean differences (WMD) or risk ratio (RR). Systematic review and meta-analysis showed that RSIFs were associated with a better antibody response to immunisation with Haemopillus influenzae vaccine [SMD 1.74 (99%CI 1.43-2.05), P=0.001], diphtheria toxoid [SMD 0.94 (0.75-1.12), P=0.001], oral polio vaccine [SMD 0.73 (0.51-0.95), P=0.001], and fewer episodes of diarrhoea [RR 0.67 (0.58-0.76), P=0.02]. We did not find a major risk of upper respiratory infections [RR 1.11 (0.90-1.36), P=0.50]. Available evidence suggests a positive benefit of RSFIs on infant health without any risk. These benefits begin with nucleotide addition of 1.9 mg/418.4 kJ and are maintained or increased with 10.78 mg/418.4 kJ.
PAR-Aware Large-Scale Multi-User MIMO-OFDM Downlink (2013)

We investigate an orthogonal frequency-division multiplexing (OFDM)-based downlink transmission scheme for large-scale multi-user (MU) multiple-input multiple-output (MIMO) wireless systems. The use of OFDM causes a high peak-to-average (power) ratio (PAR), which necessitates expensive and power-inefficient radio-frequency (RF) components at the base station. In this paper, we present a novel downlink transmission scheme, which exploits the massive degrees-of-freedom available in large-scale MU-MIMO-OFDM systems to achieve low PAR. Specifically, we propose to jointly perform MU precoding, OFDM modulation, and PAR reduction by solving a convex optimization problem. We develop a corresponding fast iterative truncation algorithm (FITRA) and show numerical results to demonstrate tremendous PAR-reduction capabilities. The significantly reduced linearity requirements eventually enable the use of low-cost RF components for the large-scale MU-MIMO-OFDM downlink.
Site-Directed Mutagenesis of Tyr354 in Geobacillus stearothermophilus Alanine Racemase Identifies a Role in Controlling Substrate Specificity and a Possible Role in the Evolution of Antibiotic Resistance (2002)

Mechanism of alanine racemase specificity resolved: Site-directed mutagenesis has identified active site residue Tyr354 as a critical determinant of substrate specificity in the Geobacillus stearothermophilus alanine racemase, despite the fact it plays no direct role in catalysis. Mutation to asparagine imparts significant serine racemisation activity, which suggests that this was an important step in the evolution of serine racemases such as VanT, required for vancomycin resistance in Enterococcus gallinarum.
Better Science Needed for Restoration in the Gulf of Mexico (2011)

In the wake of the BP oil spill, U.S. agencies need research plans to collect data that will aid in managing and assessing marine species and ecosystems.
Monoclonal antibodies distinguish synthetic peptides that differ in one chemical group. (1987)

By using human calcitonin (hCT), human calcitonin-gene-related peptide (hCGRP), and a synthetic peptide with a sequence analogous to the 34 C-terminal amino acids of human preprocalcitonin (designated as PQN-34) as haptens in the generation of monoclonal antibodies, we assessed the role of amido and amino groups in paratope-epitope binding. By using peptide inhibition experiments and solid-phase immunoassays, monoclonal anti-hCT antibody CT07 and monoclonal anti-hCGRP antibody CGR01 were found to bind to an antigenic determinant located in the C-terminal segment of the hormones. These epitopes comprise the seven C-terminal amino acids of the hormones, and the presence of the hormone-ending carboxamide group was found to be essential for antibody binding. The corresponding heptapeptides, either bearing a carboxyl group or else linked to a glycine residue at their C-terminal part, failed to react with the antibodies. Moreover, these monoclonal antibodies did not bind to synthetic peptides analogous to the C-terminal region of the hormone precursor molecules that comprised the epitope site flanked by a peptide sequence. In an attempt to assess whether amido groups when present on the side-chain of amino acids may also modulate antibody binding, a monoclonal antibody referred to as QPO1 was produced and was found to recognize an antigenic determinant localized in the N-terminal region of the PQN-34 peptide bearing a glutamine residue as the N-terminal amino acid. The epitope was found to correspond to a topographic assembled site, and binding of QPO1 was found to be substantially dependent on the presence of the free amino and the side-chain amido groups borne by the N-terminal glutamine residue of this peptide PQN-34. In contrast to these findings, an antigenic determinant located in the internal sequence of calcitonin and recognized by monoclonal anti-hCT antibody CT08 was found to be expressed on the mature form of the hormone, as well as on synthetic peptides with sequence mimicking that of preprocalcitonin. These data should guide the choice of synthetic peptide haptens for the production of anti-protein antibodies.
Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria (2011)

Bacteria become highly tolerant to antibiotics when nutrients are limited. The inactivity of antibiotic targets caused by starvation-induced growth arrest is thought to be a key mechanism producing tolerance. Here we show that the antibiotic tolerance of nutrient-limited and biofilm Pseudomonas aeruginosa is mediated by active responses to starvation, rather than by the passive effects of growth arrest. The protective mechanism is controlled by the starvation-signaling stringent response (SR), and our experiments link SR-mediated tolerance to reduced levels of oxidant stress in bacterial cells. Furthermore, inactivating this protective mechanism sensitized biofilms by several orders of magnitude to four different classes of antibiotics and markedly enhanced the efficacy of antibiotic treatment in experimental infections.