gebhart/patrepeval huggingface dataset:
Mutational analysis of structure—activity relationships in human tumor necrosis factor-alpha (1990)

To determine the region of human tumor necrosis factor-alpha (TNF-alpha), essential for cytotoxic activity against mouse L-M cells, single amino-acid-substituted TNF-alpha mutant proteins (muteins) were produced in Escherichia coli by protein engineering techniques. An expression plasmid for TNF-alpha was mutagenized by passage through an E. coli mutD5 mutator strain and by oligonucleotide-directed mutagenesis. Approximately 100 single amino-acid-substituted TNF-alpha muteins were produced and assayed for cytotoxic activity. The cytotoxic activities of purified TNF-alpha muteins, e.g. TNF-31T, -32Y, -82D, -85H, -115L, -141Y, -144K and -146E, were less than 1% of that of parent TNF-alpha. These results indicate that the integrity of at least four distinct regions of the TNF-alpha molecule is required for full biological activity. These regions are designated as follows: region I, from position 30 to 32; region II, from position 82 to 89; region III, from position 115 to 117; region IV, from position 141 to 146. In addition, TNF-141Y could not completely compete with parent TNF-alpha for binding to the receptor. This demonstrates that region IV, and at least aspartic acid at position 141, must be involved in the TNF receptor binding site.
Size-Tunable Synthesis of Metallic Nanoparticles in a Continuous and Steady-Flow Reactor (2006)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTSize-Tunable Synthesis of Metallic Nanoparticles in a Continuous and Steady-Flow ReactorChunwei Wu and Taofang ZengView Author Information Mechanical and Aerospace Engineering Department, North Carolina State University, Raleigh, North Carolina 27695-7910 Cite this: Chem. Mater. 2007, 19, 2, 123–125Publication Date (Web):December 23, 2006Publication History Received1 October 2006Revised2 December 2006Published online23 December 2006Published inissue 1 January 2007https://pubs.acs.org/doi/10.1021/cm062344fhttps://doi.org/10.1021/cm062344frapid-communicationACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views708Altmetric-Citations9LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Metal nanoparticles,Metals,Nanoparticles,Nucleation,Redox reactions Get e-Alerts
Variation of cofactor levels in Escherichia coli. Sequence analysis and expression of the pncB gene encoding nicotinic acid phosphoribosyltransferase. (1990)

The pncB gene from Escherichia coli, which encodes nicotinic acid phosphoribosyltransferase (EC 2.4.2.11), was cloned on a 1.5-kilobase TaqI-EcoRI fragment. Its position on the E. coli chromosome was determined at 20.8 min between the asnS and pepN loci. The nucleotide sequence of the gene and the transcription and translation initiation sites were determined. Expression of pncB on a multicopy plasmid leads to a 25-fold increase in nicotinic acid phosphoribosyltransferase activity. Growth of E. coli in the presence of nicotinic acid leads to strong repression of nicotinic acid phosphoribosyltransferase activity, indicating that the cloned pncB sequence contains its own control sequences. It is shown that increased nicotinic acid phosphoribosyltransferase activity effects a 5-fold increase in the intracellular concentration of NAD. The cloned pncB gene can therefore be used as a tool to raise intracellular cofactor levels.
High‐Moment Antiferromagnetic Nanoparticles with Tunable Magnetic Properties (2008)

Synthetic antiferromagnetic (SAF) nanoparticles are fabricated by a combination of nanoimprint lithography and ferromagne tic multilayer structures, followed by release and stabilization of nanoparticles in solution. The SAF nanoparticles have desirable magnetic properties with respect to multiplex magnetic labeling and sorting, and can be functionalized with fluorescent dyes. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200703077_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Influence of agr on fibrinogen binding in Staphylococcus aureus Newman (1996)

The ability of Staphylococcus aureus to bind fibrinogen is believed to be important in promoting bacterial adherence to both intravascular catheters and host tissues during infection. We investigated the influence of the global regulator agr on the fibrinogen binding capacity and its relationship to the expression of coagulase (encoded by coa) and clumping factor (encoded by clfA) in strain Newman. Strains were obtained by transducing site-specific mutations of clfA, coa, and agr into strain Newman to obtain single, double, and triple mutants of the respective genes. As expected, the clfA mutant bound less soluble 125I-labeled fibrinogen than the corresponding coa mutant in agr+ strains; however, with agr mutant strains, the upregulation in fibrinogen binding capacity correlated mostly with the increased expression and transcription of coagulase as shown by Western (immunoblot) and Northern (RNA) blot analysis. In particular, the coa agr double mutant resulted in a significant reduction in fibrinogen binding compared with that of the agr mutant. The contribution of clfA to fibrinogen binding in agr-negative strains was less than that of coa (32,740 +/- 1,189 versus 18,141 +/- 334 and 38,919 +/- 1,021 cpm for clfA agr, coa agr, and the single agr mutant, respectively). Thus, coagulase is a major binding protein for soluble fibrinogen in the agr-negative background. In in vitro microtiter and catheter adherence assays with solid-phase fibrinogen, clumping factor, but not coagulase, plays a major role in binding to immobilized fibrinogen. coa transcription was negatively modulated by agr and occurred mainly during the exponential growth phase. In contrast, clfA transcription was agr independent and was strongest during the postexponential phase. Although an agr coa clfA triple mutant bound less soluble fibrinogen than the agr coa double mutant (8,504 +/- 831 versus 18,141 +/- 334 cpm), significant residual fibrinogen binding capacity remained in the triple mutant, thus suggesting an additional fibrinogen binding component. By using direct ligand affinity blotting with 125I-fibrinogen, we could identify coagulase and an additional unidentified 52-kDa protein as a fibrinogen binding component in cell extracts. This band was absent in the extract of the coa clfA double mutant.
The Georgia Tech aware home (2008)

The Aware Home Research Initiative (AHRI) at Georgia Tech is devoted to the multidisciplinary exploration of emerging technologies and services based in the home. Starting in 1998, our collection of faculty and students has created a unique research facility that allows us to simulate and evaluate user experiences with off-the-shelf and state-of-the-art technologies. With specific expertise in health, education, entertainment and usable security, we are able to apply our research to problems of significant social and economic impact.
XPS Study of Copper-Doped Carbon Aerogels (2002)

Copper-doped carbon aerogels were investigated by X-ray photoelectron spectroscopy to determine the chemical nature and distribution of the copper species in the aerogel framework. The Cu2p spectra of both the organic and carbon aerogels show a fairly uniform distribution of copper species in the aerogel network, with a slight increase in copper content going from the edge to the center of the monolith. The O1s spectra of the copper-doped organic aerogel indicate that both the carboxyl and hydroxyl groups of the aerogel framework are involved in chelation of the copper ions. After carbonization, the content of the copper detected by XPS decreases significantly as the copper ions are reduced into metallic copper nanoparticles. These nanoparticles are difficult to detect by XPS because they are coated by a thin carbon layer and migrate into the carbon matrix. The carbon skeleton of the copper-doped carbon aerogels is mainly composed of a uniform micro-graphite-like crystalline network, and no copper−carbon bonds were detectable in the aerogel.
Design and analysis of a query processor for brick (2017)

Brick is a recently proposed metadata schema and ontology for describing building components and the relationships between them. It represents buildings as directed labeled graphs using the RDF data model. Using the SPARQL query language, building-agnostic applications query a Brick graph to discover the set of resources and relationships they require to operate. Latency-sensitive applications, such as user interfaces, demand response and model-predictive control, require fast queries --- conventionally less than 100ms.
DNA-Level Splice Junction Prediction using Deep Recurrent Neural Networks (2015)

A eukaryotic gene consists of multiple exons (protein coding regions) and introns (non-coding regions), and a splice junction refers to the boundary between a pair of exon and intron. Precise identification of spice junctions on a gene is important for deciphering its primary structure, function, and interaction. Experimental techniques for determining exon/intron boundaries include RNA-seq, which is often accompanied by computational approaches. Canonical splicing signals are known, but computational junction prediction still remains challenging because of a large number of false positives and other complications. In this paper, we exploit deep recurrent neural networks (RNNs) to model DNA sequences and to detect splice junctions thereon. We test various RNN units and architectures including long short-term memory units, gated recurrent units, and recently proposed iRNN for in-depth design space exploration. According to our experimental results, the proposed approach significantly outperforms not only conventional machine learning-based methods but also a recent state-of-the-art deep belief network-based technique in terms of prediction accuracy.
Antisoiling technology: theories of surface soiling and performance of antisoiling surface coatings (1984)

Physical examination of surfaces undergoing natural outdoor soiling suggests that soil matter accumulates in up to three distinct layers. The first layer involves strong chemical attachment or strong chemisorption of soil matter on the primary surface. The second layer is physical, consisting of a highly organized arrangement of soil creating a gradation in surface energy from a high associated with the energetic first layer to the lowest possible state on the outer surface of the second layer. The lowest possible surface energy state is dictated by the chemical and physical nature of the regional atmospheric soiling materials. These first two layers are resistant to removal by rain. The third layer constitutes a settling of loose soil matter, accumulating in dry periods and being removed during rainy periods. Theories and evidence suggest that surfaces that should be naturally resistant to the formation of the first two rain-resistant layers should be hard, smooth, hydrophobic, free of first-period elements, and have the lowest possible surface energy. These characteristics, evolving as requirements for low-soiling surfaces, suggest that surfaces or surface coatings should be of fluorocarbon chemistry. Evidence for the three-soil-layer concept, and data on the positive performance of candidate fluorocarbon coatings on glass and transparent plastic films after 28 months of outdoor exposure, are presented.
Pre-clinical evaluation of the Gastrimmune immunogen alone and in combination with 5-fluorouracil/leucovorin in a rat colorectal cancer model (1998)

Mature and post-translational precursor gastrin forms are growth factors for colorectal tumours. The immunogen Gastrimmune is composed of the amino terminus of gastrin-17 linked to diphtheria toxoid and raises antibodies in situ which neutralise amidated and glycine-extended gastrin-17. The aim of the study was to determine the effect of treatment with 5-fluorouracil(5-FU)/leucovorin on the antibody titres induced by Gastrimmune and the effect of combination therapy on the growth of the rat colon tumour DHDK12. Gastrimmune was administered to rats s.c. at 3 weekly intervals. The rat colon tumour line DHDK12 was injected into the abdominal wall of BDIX rats. Combinations of 5-FU/leucovorin were injected i.v. on days 1, 3 and 5, with the cycle repeated every 4 weeks. Antibody titres were measured by an ELISA technique. Antibody titres were followed for 40 weeks after Gastrimmune (500 microg.ml(-1)) immunization, with titres peaking between 10 and 20 weeks after a single immunisation and falling by week 30. At termination, no effect was observed on either the histological appearance of the gastro-intestinal tract or the proliferation of the colonic mucosa. Pre- and post-treatment with 5-FU/leucovorin (30 mg.kg(-1)) had no effect on the kinetics and level of antibody response to Gastrimmune. Gastrimmune (200 microg.ml(-1)) and 5-FU/leucovorin combinations (12.5 and 20 mg.kg(-1)) increased the therapeutic effects on the in vivo growth of DHDK12 tumors when compared to the agents given singly. Gastrimmune immunisation may be a therapeutic option for the treatment of colorectal cancer in combination with 5-FU/leucovorin.
CT determination of femoral torsion (1981)

Femoral torsion has been measured in infants and children by computed tomography. The method requires two scans, one through the femoral neck, another through the femoral condyles. A specially designed device and packing about the knees assures immobilization of the legs. Slight variations in the positions of the sections in the neck and condyles do not alter the measurement significantly. Intraobserver and interobserver errors are low, 2 degrees and 3 degrees mean error, respectively. The radiation required involves small tissue volumes at about 1.7 R (4.4 x 10(-4) C/kg). Measurements are more difficult when the femoral necks are short or vertically oriented. The method appears to have sufficient accuracy for clinical purposes.
Three-Dimensional Substrate Impedance Engineering Based on&lt;tex&gt;$hbox p ^-$&lt;/tex&gt;/&lt;tex&gt;$hbox p ^+$&lt;/tex&gt;Si Substrate for Mixed-Signal System-on-Chip (SoC) (2005)

A novel approach for three-dimensional substrate impedance engineering of p/sup -//p/sup +/ Si substrate is described for mixed-signal integrated circuit applications. This technology requires minimum intrusion to conventional Si CMOS processing, but offers astounding improvements with regard to radio frequency (RF) crosstalk via substrate and on-chip inductor performance. Electroless plating or electro-plating is used to fabricate Faraday cage for crosstalk isolation as well as to provide "true ground" contacts. A self-limiting porous Si (PS) formation process is employed to allow the insertion of PS regions from the backside of the wafer, eliminating completely the waste of chip surface area. On-chip inductors are situated above the semi-insulating PS regions allowing for greatly increased Q-factor and resonance frequency (f/sub r/). RF crosstalk is reduced to the level limited by that across the air gap between the measurement probes.
Azaindolizines with Two Nitrogen Atoms in the Five‐Membered Ring (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Podoplanin: A Novel Marker for Oral Cancer Risk in Patients With Oral Premalignancy (2008)

Podoplanin is frequently expressed in OPL. Together with histology, podoplanin may serve as a powerful biomarker to predict the risk for oral cancer development in patients with OPL.
Real-Time View Independent Rasterization for Multi-View Rendering (2017)

Existing graphics hardware parallelizes view generation poorly, placing many multi-view effects - such as soft shadows, defocus blur, and reflections - out of reach for real-time applications. We present emerging solutions that address this problem using a high density point set tailored per frame to the current multi-view configuration, coupled with relatively simple reconstruction kernels. Points are a more flexible rendering primitive, which we leverage to render many high resolution views in parallel. Preliminary results show our approach accelerates point generation and the rendering of multi-view soft shadows up to 9x.
Sampling-based selectivity estimation for joins using augmented frequent value statistics (2002)

We compare empirically the cost of estimating the selectivity of a star join using the sampling-based t-cross procedure to the cost of computing the join and obtaining the exact answer. The relative cost of sampling can be excessive when a join attribute value exhibits "heterogeneous skew." To alleviate this problem, we propose Algorithm TCM, a modified version of t-cross that incorporates "augmented frequent value" (AFV) statistics. We provide a sampling-based method for estimating AFV statistics that does not require indexes on attribute values, requires only one pass though each relation, and uses an amount of memory much smaller than the size of a relation. Our experiments show that the use of estimated AFV statistics can reduce the relative cost of sampling by orders of magnitude. We also show that use of estimated AFV statistics can reduce the relative error of the classical System R selectivity formula.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Methanolysis of Dimethyl (1-Diazo-2-oxopropyl) Phosphonate: Generation of Dimethyl (Diazomethyl) Phosphonate and Reaction with Carbonyl Compounds (1989)

Abstract Dimethyl (1-diazo-2-oxopropyl) phosphonate (3) was transformed to dimethyl (diazomethyl)—phosphonate (4), which was used for the synthesis of enol ether or alkyne without isolation.
The Potential Impact of Droplet Microfluidics in Biology (2013)

Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, is an active research endeavor that evolved out of the larger field of microfluidics. Recently, this subfield of microfluidics has started to attract greater interest because researchers have been able to demonstrate applications of droplets as miniaturized laboratories for biological measurements. This perspective explores the recent developments and the potential future biological applications of droplet microfluidics.
Teplizumab Preserves C-Peptide in Recent-Onset Type 1 Diabetes (2013)

Protégé was a phase 3, randomized, double-blind, parallel, placebo-controlled 2-year study of three intravenous teplizumab dosing regimens, administered daily for 14 days at baseline and again after 26 weeks, in new-onset type 1 diabetes. We sought to determine efficacy and safety of teplizumab immunotherapy at 2 years and to identify characteristics associated with therapeutic response. Of 516 randomized patients, 513 were treated, and 462 completed 2 years of follow-up. Teplizumab (14-day full-dose) reduced the loss of C-peptide mean area under the curve (AUC), a prespecified secondary end point, at 2 years versus placebo. In analyses of prespecified and post hoc subsets at entry, U.S. residents, patients with C-peptide mean AUC >0.2 nmol/L, those randomized ≤6 weeks after diagnosis, HbA1c <7.5% (58 mmol/mol), insulin use <0.4 units/kg/day, and 8-17 years of age each had greater teplizumab-associated C-peptide preservation than their counterparts. Exogenous insulin needs tended to be reduced versus placebo. Antidrug antibodies developed in some patients, without apparent change in drug efficacy. No new safety or tolerability issues were observed during year 2. In summary, anti-CD3 therapy reduced C-peptide loss 2 years after diagnosis using a tolerable dose.
Particle Size Distribution of Food Boluses after Mastication of Six Natural Foods (2004)

There is a large variability between and among individuals in the physiology of mastication, but it is not known whether this produces a similar variability in the particle sizes of food boluses at the end of the chewing process. Food boluses obtained just before swallowing were analyzed in ten subjects (aged 36.7 +/- 9.5 yrs) with normal dentition. Food samples of 3 nuts (peanut, almond, pistachio) and 3 vegetables (cauliflower, radish, and carrot) were chewed and expectorated after self-estimated complete mastication. Measurements with sieving and laser diffraction methods indicated that particles were much larger in vegetables than in nuts. Particle size distributions were similar among nuts and among vegetables. Surprisingly, no inter-individual variability was observed in the particle distributions for the 6 foods, although several sequence variables differed markedly. A need for a bolus to be prepared with a precisely determined texture before it can be swallowed may explain the inter-subject variability of the masticatory function.
Enhancement of Electrochemical Activity of LiFePO4 (olivine) by Amphiphilic Ru-bipyridine Complex Anchored to a Carbon Nanotube (2007)

Single walled carbon nanotubes (SWNTs) were dissolved in an acetonitrile + tert-butanol mixture, using the amphiphilic Ru-bipyridine complex NaRu(4-carboxylic acid-4‘-carboxylate)(4,4‘-dinonyl-2,2‘bipyridine)(NCS)2 as a surfactant. The assembly of the SWNT/Ru-bipyridine complex was adsorbed on the surface of LiFePO4 (olivine), providing a material with approximately monolayer coverage by the Ru-bipyridine complex and ca. 0.04 wt % of SWNT. Electrodes fabricated from the surface-derivatized LiFePO4 exhibited greatly enhanced activity for electrochemical Li+ extraction/insertion compared to electrodes from commercial carbon-coated LiFePO4 or from LiFePO4 derivatized either by adsorption of sole Ru-bipyridine complex or by carbon nanotubes dispersed with the redox inactive pyrene butanoic acid. The SWNT backbone promotes the interfacial charge transfer between LiFePO4 and the Ru-complex, whose redox potentials closely match each other. The nanotube-mediated redox wiring of virtually insulating electrode materials such as LiFePO4 presents a novel strategy for application in high-energy lithium-ion batteries.