gebhart/patrepeval huggingface dataset:
A binding protein-dependent transport system in Streptococcus mutans responsible for multiple sugar metabolism. (1992)

An 11-kilobase gene region of Streptococcus mutans has been identified which contains eight contiguous genes involved with the uptake and metabolism of multiple sugars (the msm system). Sequence analysis of this region indicates that several of these genes specify proteins with strong homology to components of periplasmic binding protein-dependent transport systems of Gram-negative bacteria. Additionally, this operon is controlled by a regulatory gene (msmR) that acts as a positive effector. The proteins specified by the structural genes of the msm operon include alpha-galactosidase (aga), a "periplasmic-like" sugar-binding protein (msmE), two membrane proteins (msmF, msmG), sucrose phosphorylase (gtfA), an ATP-binding protein (msmK), and dextran glucosidase (dexB). Insertional inactivation of each of these genes along with uptake data indicate that this system is responsible for the uptake of melibiose, raffinose, and isomaltotriose and the metabolism of melibiose, sucrose, and isomaltosaccharides.
High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray (2009)

Gut microbiota carry out key functions in health and participate in the pathogenesis of a growing number of diseases. The aim of this study was to develop a custom microarray that is able to identify hundreds of intestinal bacterial species. We used the Entrez nucleotide database to compile a data set of bacterial 16S rRNA gene sequences isolated from human intestinal and fecal samples. Identified sequences were clustered into separate phylospecies groups. Representative sequences from each phylospecies were used to develop a microbiota microarray based on the Affymetrix GeneChip platform. The designed microbiota array contains probes to 775 different bacterial phylospecies. In our validation experiments, the array correctly identified genomic DNA from all 15 bacterial species used. Microbiota array has a detection sensitivity of at least 1 pg of genomic DNA and can detect bacteria present at a 0.00025% level of overall sample. Using the developed microarray, fecal samples from two healthy children and two healthy adults were analyzed for bacterial presence. Between 227 and 232 species were detected in fecal samples from children, whereas 191 to 208 species were found in adult stools. The majority of identified phylospecies belonged to the classes Clostridia and Bacteroidetes. The microarray revealed putative differences between the gut microbiota of healthy children and adults: fecal samples from adults had more Clostridia and less Bacteroidetes and Proteobacteria than those from children. A number of other putative differences were found at the genus level.
Translational research with pemetrexed in breast cancer. (2004)

Pemetrexed (Alimta) is a novel folate antimetabolite that primarily inhibits the enzymes thymidylate synthase (TS), dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyl transferase (GARFT), all of which are involved in pyrimidine and purine synthesis. In a phase II trial of patients with T3/4, N0-2 breast cancer, expression of thymidylate synthase (TS), dihydrofolate reductase (DHFR), glycinamide ribonucleotide formyltransferase (GARFT), p53, and c-erb-B2 (at the mRNA or protein level) was examined in tumor biopsy specimens before and 24 hours after the first dose of pemetrexed and after three cycles of single-agent treatment to establish correlations of biomarker levels and changes with clinical outcome and toxicity. Although final data are not available, initial indications are that clinical response may correlate with decreased or low TS expression. The results obtained from clinical data are supported by laboratory results in three cell lines (MDA-231, MCF-7, and ZR-75). These results suggest that in vitro transcript profiling to identify which genes are important predictors of successful cytotoxic chemotherapy, followed by a focused clinical trial to confirm the in vitro results, may be the best approach for translational research.
Hyperinsulinemia as an Independent Risk Factor for Ischemic Heart Disease (1996)

High fasting insulin concentrations appear to be an independent predictor of ischemic heart disease in men.
Electrically Controlled Birefringence of Thin Nematic Films (1972)

This paper reports field-induced realignment of a nematic liquid crystal. A thin nematic film, which has a negative dielectric anisotropy, is initially homeotropic. Application of a threshold field parallel to the optic axis distorts the nematic ordering and increases the film's birefringence in certain light-propagation directions. Experimental results are given for threshold voltage, threshold width, optical contrast ratio, frequency response, angular field of view, electrical power consumption, and transient response. Light-valve applications are described.
From Isocyanides <i>via</i> Four‐Component Condensations to Antibiotic Syntheses (1982)

Abstract The four‐component condensation of amines and carbonyl compounds with isocyanides Previously, isocyanides were almost always referred to as isonitriles. However, according to IUPAC Rule C‐833.1 only the name “isocyanides” is permissible. and suitable acid components (water, thiosulfuric acid, hydrogen selenide, hydrogen azide, cyanic acid, thiocyanic acid, carboxylic acids, methyl hydrogen carbonate) to form α‐amino acid derivatives was discovered in 1959. This reaction principle shares some features with the Strecker synthesis and the Passerini reaction. The four‐component condensation affords easy and effective one‐pot synthesis of complex molecules from simple building blocks. Only in recent years, however, have the preparative advantages of the four‐component condensation been exploited by numerous authors in the synthesis of diverse natural products and related compounds, although many of the possibilities opened by this principle were recognized more than two decades ago. In this progress report some instructive syntheses of various antibiotics are reviewed. The design of each of these syntheses involves a four‐component condensation as key step, by means of which lengthy sequences of reactions are avoided, which otherwise would be required to achieve the synthetic goal.
Modeling shape variability for full heart segmentation in cardiac computed-tomography images (2006)

An efficient way to improve the robustness of the segmentation of medical images with deformable models is to use <i>a priori </i>shape knowledge during the adaptation process. In this work, we investigate how the modeling of the shape variability in shape-constrained deformable models influences both the robustness and the accuracy of the segmentation of cardiac multi-slice CT images. Experiments are performed for a complex heart model, which comprises 7 anatomical parts, namely the four chambers, the myocardium, and trunks of the aorta and the pulmonary artery. In particular, we compare a common shape variability modeling technique based on principal component analysis (PCA) with a more simple approach, which consists of assigning an individual affine transformation to each anatomical subregion of the heart model. We conclude that the piecewise affine modeling leads to the smallest segmentation error, while simultaneously offering the largest flexibility without the need for training data covering the range of possible shape variability, as required by PCA.
A 550-$\mu\hbox{W}$ 10-b 40-MS/s SAR ADC With Multistep Addition-Only Digital Error Correction (2011)

A speed-enhanced 10-b asynchronous SAR ADC with multistep addition-only digital error correction (ADEC) is presented with a straightforward DAC switching algorithm. The capacitor DAC is virtually divided into three sub-DACs for ADEC with negligible hardware overhead. The redundant decision cycles between stages reconfigure the capacitor connection of the DAC. These redundancies guarantee 10-b linearity under 4-b-accurate DAC settling in the MSB decision and the optimally designed ADC enhances the conversion speed by 37%. A prototype ADC was implemented in a CMOS 0.13-μm technology. The chip consumes 550 μW and achieves a 50.6-dB SNDR at 40 MS/s under a 1.2-V supply. The figure-of-merit (FOM) is 50 fJ/conversion-step.
Thermochemical processes for the production of hydrogen from water (1976)

The following aspects of thermochemical production of hydrogen are discussed: efficiency; single stage process; multistage processes; two-stage process; cycle evaluation; a hybrid cycle; and a sulfur cycle. (LK)
Topology-aware overlay networks for group communication (2002)

We propose an application level multicast approach, Topology Aware Grouping (TAG), which exploits underlying network topology information to build efficient overlay networks among multicast group members. TAG uses information about path overlap among members to construct a tree that reduces the overlay relative delay penalty, and reduces the number of duplicate copies of a packet on the same link. We study the properties of TAG, and model and experiment with its economies of scale factor to quantify its benefits compared to unicast and IP multicast. We also compare the TAG approach with the ESM approach in a variety of simulation configurations including a number of real Internet topologies and generated topologies. Our results indicate the effectiveness of the algorithm in reducing delays and duplicate packets, with reasonable algorithm time and space complexities.
Cell and Protein Compatibility of Parylene-C Surfaces (2007)

Parylene-C, which is traditionally used to coat implantable devices, has emerged as a promising material to generate miniaturized devices due to its unique mechanical properties and inertness. In this paper we compared the surface properties and cell and protein compatibility of parylene-C relative to other commonly used BioMEMS materials. We evaluated the surface hydrophobicity and roughness of parylene-C and compared these results to those of tissue culture-treated polystyrene, poly(dimethylsiloxane) (PDMS), and glass. We also treated parylene-C and PDMS with air plasma, and coated the surfaces with fibronectin to demonstrate that biochemical treatments modify the surface properties of parylene-C. Although plasma treatment caused both parylene-C and PDMS to become hydrophilic, only parylene-C substrates retained their hydrophilic properties over time. Furthermore, parylene-C substrates display a higher degree of nanoscale surface roughness (>20 nm) than the other substrates. We also examined the level of BSA and IgG protein adsorption on various surfaces and found that surface plasma treatment decreased the degree of protein adsorption on both PDMS and parylene-C substrates. After testing the degree of cell adhesion and spreading of two mammalian cell types, NIH-3T3 fibroblasts and AML-12 hepatocytes, we found that the adhesion of both cell types to surface-treated parylene-C variants were comparable to standard tissue culture substrates, such as polystyrene. Overall, these results indicate that parylene-C, along with its surface-treated variants, could potentially be a useful material for fabricating cell-based microdevices.
1,25-dihydroxyvitamin D3 prevents the in vivo induction of murine experimental autoimmune encephalomyelitis. (1991)

The hormone, 1,25-dihydroxyvitamin D3 (1,25-[OH]2-D3), inhibits lymphocyte activation in vitro. We studied the ability of the vitamin D metabolite to interfere in vivo with a primary T cell-mediated model of autoimmunity, murine experimental autoimmune encephalomyelitis (EAE). Within 2 wk of antigenic challenge, immunized animals will develop acute paralysis with central nervous tissue inflammation. If mice survive, a rise in antibody titer develops within a month. The administration of 0.1 microgram 1,25-(OH)2-D3 i.p. given every other day for 15 d, starting 3 d before immunization, significantly prevented the development of EAE. The rise in antibody titer to myelin basic protein was also abrogated. Histopathologic lesions of EAE were inhibited by treatment with the sterol. These results suggest a potent immunosuppressive role for 1,25-(OH)2-D3 in vivo in the modulation of a cell-mediated model of autoimmunity.
Control of the Translational Regulators PHAS-I and PHAS-II by Insulin and cAMP in 3T3-L1 Adipocytes (1996)

The eukaryotic initiation factor 4E (eIF-4E)-binding proteins PHAS-I and PHAS-II were found to have overlapping but different patterns of expression in tissues. Both PHAS proteins were expressed in 3T3-L1 adipocytes, in which insulin stimulated their phosphorylation, promoted dissociation of PHAS.eIF-4E complexes, and decreased the ability of both to bind exogenous eIF-4E. The effects of insulin were attenuated by rapamycin and wortmannin, two agents that block activation of p70(S6K). Unlike PHAS-I, PHAS-II was readily phosphorylated by cAMP-dependent protein kinase in vitro; however, the effects of insulin on both PHAS proteins were attenuated by agents that increase intracellular cAMP, by cAMP derivatives, and by phosphodiesterase inhibitors. These agents also markedly inhibited the activation of p70(S6K). In summary, our results indicate that PHAS-I and -II are controlled by the mammalian target of rapamycin and p70(S6K) signaling pathway and that in 3T3-L1 adipocytes this pathway is inhibited by increased cAMP.
Serotonin promotes the proliferation of serum-deprived hepatocellular carcinoma cells via upregulation of FOXO3a (2013)

This study demonstrates that FOXO3a functions as a growth factor in serum-deprived HCC cells and serotonin promotes the proliferation of serum-deprived HCC cells via upregulation of FOXO3a, in the presence of sufficient levels of the serotonin receptor 5-HT2BR. Drugs targeting the serotonin-5-HT2BR-FOXO3a pathway may provide a novel target for anticancer therapy.
Lysine post-translational modifications of collagen (2012)

Type I collagen is the most abundant structural protein in vertebrates. It is a heterotrimeric molecule composed of two α1 chains and one α2 chain, forming a long uninterrupted triple helical structure with short non-triple helical telopeptides at both the N- and C-termini. During biosynthesis, collagen acquires a number of post-translational modifications, including lysine modifications, that are critical to the structure and biological functions of this protein. Lysine modifications of collagen are highly complicated sequential processes catalysed by several groups of enzymes leading to the final step of biosynthesis, covalent intermolecular cross-linking. In the cell, specific lysine residues are hydroxylated to form hydroxylysine. Then specific hydroxylysine residues located in the helical domain of the molecule are glycosylated by the addition of galactose or glucose-galactose. Outside the cell, lysine and hydroxylysine residues in the N- and C-telopeptides can be oxidatively deaminated to produce reactive aldehydes that undergo a series of non-enzymatic condensation reactions to form covalent intra- and inter-molecular cross-links. Owing to the recent advances in molecular and cellular biology, and analytical technologies, the biological significance and molecular mechanisms of these modifications have been gradually elucidated. This chapter provides an overview on these enzymatic lysine modifications and subsequent cross-linking.
Incorporation of deuterium-labeled trans- and cis-13-octadecenoic acids in human plasma lipids (1983)

The absorption and distribution of deuterated trans- and cis-13-octadecenoic acid (13t-18:1 and 13c-18:1) in plasma lipids were compared to deuterated cis-9-octadecenoic acid (9c-18:1) in two young adult male subjects. A mixture of triglycerides was fed in a multiple-labeled experiment where each triglyceride contained a fatty acid labeled with a different number of deuterium atoms. Analysis of human plasma lipids by mass spectroscopy allowed the distribution of the two 13-octadecenoic acid isomers to be directly compared to cis-9-octadecenoic acid. Plasma lipids selectively excluded both the 13t-18:1 and 13c-18:1 isomers relative to 9c-18:1 in all neutral and phospholipid fractions. Discrimination against incorporation of the 13t-18:1 isomer into plasma cholesteryl ester and 2-acyl phosphatidylcholine was nearly absolute. The 1-acyl phosphatidylcholine fraction exhibited a large positive selectivity for the 13t-18:1 isomer. Differences in the relative distribution of the trans and cis 13-18:1 isomers vs. 9c-18:1 in the various lipoprotein lipid classes were found. Analysis of the chylomicron triglyceride component of the plasma lipids indicated all three fatty acids were equally well absorbed.
Release of Signal Peptide Fragments into the Cytosol Requires Cleavage in the Transmembrane Region by a Protease Activity That Is Specifically Blocked by a Novel Cysteine Protease Inhibitor (2000)

Signal peptides of secretory and membrane proteins are generated by proteolytic processing of precursor proteins after insertion into the endoplasmic reticulum membrane. Liberated signal peptides can be further processed, and the resulting N-terminal fragments are released toward the cytosol, where they may interact with target proteins like calmodulin. We show here that the processing of signal peptides requires a protease activity distinct from signal peptidase. This activity is inhibited specifically with a newly developed cysteine protease inhibitor, 1, 3-di-(N-carboxybenzoyl-l-leucyl-l-leucyl)amino acetone ((Z-LL)(2) ketone). Inhibitor studies revealed that the final, (Z-LL)(2) ketone-sensitive cleavage event occurs within the hydrophobic transmembrane region of the signal peptide, thus promoting the release of an N-terminal fragment into the cytosol.
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data (2007)

In this report, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information and high-throughput phenotyping experiments is presented. The initial reconstruction was converted into an in silico model and expanded in a four-step iterative fashion. First, network gap analysis was used to identify 48 missing reactions that are needed for growth but were not found in the genome annotation. Second, the computed growth rates under aerobic conditions were compared with high-throughput phenotypic screen data, and the initial in silico model could predict the outcomes qualitatively in 140 of 271 cases considered. Detailed analysis of the incorrect predictions resulted in the addition of 75 reactions to the initial reconstruction, and 200 of 271 cases were correctly computed. Third, in silico computations of the growth phenotypes of knock-out strains were found to be consistent with experimental observations in 720 of 766 cases evaluated. Fourth, the integrated analysis of the large-scale substrate utilization and gene essentiality data with the genome-scale metabolic model revealed the requirement of 80 specific enzymes (transport, 53; intracellular reactions, 27) that were not in the genome annotation. Subsequent sequence analysis resulted in the identification of genes that could be putatively assigned to 13 intracellular enzymes. The final reconstruction accounted for 844 open reading frames and consisted of 1020 metabolic reactions and 988 metabolites. Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes.
Introduction to Computer Methods for Microwave Circuit Analysis and Design (1991)

Fundamental principles and overview doppler radar waveform design and filtering doppler radar performance measures clutter properties and data theory of optimum radar doppler processing MTI systems pulsed doppler systems appendices.
Mobile phone based AR scene assembly (2005)

In this paper we describe a mobile phone based Augmented Reality application for 3D scene assembly. Augmented Reality on mobile phones extends the interaction capabilities on such handheld devices. It adds a 6 DOF isomorphic interaction technique for manipulating 3D content. We give details of an application that we believe to be the first where 3D content can be manipulated using both the movement of a camera tracked mobile phone and a traditional button interface as input for transformations. By centering the scene in a tangible marker space in front of the phone we provide a mean for bimanual interaction. We describe the implementation, the interaction techniques we have developed and initial user response to trying the application.
Hydroformylation of myrcene: metal and ligand effects in the hydroformylation of conjugated dienes (2003)

The hydroformylation of myrcene catalyzed by Rh and Pt/Sn catalysts containing different P-donor ligands leads to the formation of a number of mono- and dialdehydes. Nine major products of the reaction have been characterized, showing that they arise from the n-alkyl and η3-allyl intermediates, formed through the reaction of the metal catalysts with the less substituted CC bond of the substrate. Thus, 4-methylene-8-methyl-7-nonenal is the major aldehyde formed with Pt/Sn catalysts, regardless of the P-donor ligand used. This aldehyde is also the main product of the reaction catalyzed by the Rh/xantphos system (xantphos = 9,9-dimethyl-4,6-bis(diphenylphosphino)xantene). However, with ligands such as bisbi (bisbi = 2,2′-bis((diphenylphosphino)methyl)-1,1′-biphenyl), also with bite angles around 120°, but with more flexible backbones than xantphos, rhodium catalysts yield mainly cis- and trans-3-ethylidene-7-methyl-6-octenal. These two aldehydes are also formed in the reactions catalyzed by Rh and P-donor monodentate ligands or the bidentante ones with bite angles around 90° (dppe, dppp). For the last type of ligands, an increase in the flexibility of the backbone reduces the selectivity for the β,γ-unsaturated aldehydes.
Aperture Averaging of Scintillation (1967)

The relationship between the statistics of log-amplitude fluctuations and irradiance fluctuations due to atmospheric turbulence is derived. This is used to evaluate the effect of use of a large aperture diameter in reducing the variance of a fluctuating signal. Curves for the reduction factor are presented. From these, an irradiance-fluctuation correlation distance is evaluated. This distance, unlike the correlation distance for log-amplitude fluctuations, is found to be a function of the log-amplitude variance. A particular example of the application of these results to a space-to-ground communications systems performance is worked out.
Non‐carbon nanotubes (1996)

Nanotube formation is not limited to carbon , and in fact seems to be a general feature of layered materials. The classes of new nanotubes that have been synthesized, e.g., boron‐nitride‐containing compounds and transition‐metal dichalcogenides, are briefly reviewed. Theoretical predictions, such as the type II BC 2 N nanocoil, the smallest possible solenoid, point to enticing research and application opportunities, for example miniature transformers and magnetic storage or on‐nanotube devices (pn junctions, etc.).