gebhart/patrepeval huggingface dataset:
Arylamine N-acetyltransferase from chicken liver II. Cloning of cDNA and expression in Chinese hamster ovary cells. (1988)

A cDNA clone encoding the full coding region of chicken liver arylamine acetyltransferase (EC 2.3.1.5) was isolated from lambda gt10 cDNA library by screening with the 32P-labeled oligonucleotide deduced from the amino acid sequence reported in the preceding paper. The complete nucleotide sequence of the cDNA was determined, from which the amino acid sequence of N-acetyltransferase was deduced. It consisted of 1,302 nucleotides including a 861-nucleotide region coding for 287 amino acids with a molecular weight of 32,914. Two methods were applied to confirm that the cDNA encoded arylamine N-acetyltransferase. First, mRNA was synthesized in vitro by Bluescript and subsequently translated in vitro. The molecular mass of the translation product was 34 kDa consistent with that of the enzyme purified from the chicken liver. The translated protein was immunoprecipitated by a monoclonal antibody to N-acetyltransferase. Second, the cDNA was inserted into an expression vector pcDL1 and introduced into Chinese hamster ovary cells. The supernatant of the homogenate of transfected cells showed a high level of N-acetyltransferase activity with a substrate specificity comparable to that of the liver enzyme. Northern blot analysis revealed three mRNAs corresponding to 4.7, 2.0, and 1.4 kilobases. The levels of N-acetyltransferase mRNAs were relatively high in the liver and distributed in various tissues. Genomic Southern blot analysis indicated the presence of only one gene in the chicken haploid genome.
Improvement of Peripheral Endothelial Dysfunction by Protein Tyrosine Phosphatase Inhibitors in Heart Failure (2006)

Our results demonstrate for the first time that PTP1B inhibitors may be potent treatments for endothelial dysfunction.
A reactive ion etch study for producing patterned platinum structures (1997)

Abstract Various high-density DRAM and FRAM technologies currently under investigation utilize high-dielectric constant materials requiring noble metal or refractory metal oxide electrodes. In this paper we describe a study of platinum patterning by reactive ion etching (RIE). Platinum films were etched in a rf diode parallel plate RIE tool with a grounded upper electrode and a 13.56 rf powered lower electrode upon which substrates were processed. The removal characteristics of blanket platinum films and platinum films with a patterned photoresist etch mask were investigated as a function of gas chemistry (Ar, CF4, SF6, and Cl2), rf power (100 to 680 W), gas pressure (5 to 100 mTorr), total gas flow (5 to 80 scan), and substrate temperature (21 to 300°C). The platinum etch was characterized in terms of etch rate, amount of redeposited material observed on the photoresist etch sidewalls (‘fencing'), and etch scale-up non-uniformity versus small size and feature size. Platinum etch rates from 80 to 1250 Å/minute were observed with corresponding substrate dc bias voltages of -500 to -1600 V. A computer program was developed to model the etch process. Computer modeling results were correlated with etched structures to optimize the etch process conditions. Optical emission spectroscopy (OES) was utilized to observe gas phase plasma species for chemical etching determination, and optimized as an optical endpoint monitor. Auger electron spectroscopy (AES) was implemented in chemically analyzing the redeposited ‘fence’ material. Using selected RIE process conditions, platinum films with a patterned photoresist etch mask were etched resulting in clean, residue-free structures with sidewall angles approximately 29°. Best process to date using a post-RIE cleanup yields sidewall angles approximately 69°.
Properties of Natural and Hybrid Murine Alpha Interferons (1986)

Four natural murine interferon-alpha genes (MuIFN-alpha 1, -alpha 2, -alpha 4 and -alpha 6) and four hybrid genes (alpha 1 alpha 4, alpha 2 alpha 4, alpha 4 alpha 1 and alpha 4 alpha 2) were transiently expressed in monkey COS cells under the transcriptional control of the simian virus 40 early promoter. The proteins were labelled with [35S]methionine during a 16 h incubation and proteins secreted by the cells during this period were separated by polyacrylamide gel electrophoresis and subsequently visualized by fluorography. Under the conditions used, the IFNs represented 5 to 10% of the total amount of secreted proteins. All genes were found to encode biologically active IFN subspecies, including alpha 4 which has a deletion of five amino acids. When the specific activities of the proteins were compared, it appeared that the specific antiviral activity of alpha 4 on mouse cells was three- to sixfold higher than the activities of the other natural IFN subspecies. The specific activities of the hybrid proteins were similar to those of the natural proteins, except for the alpha 2 alpha 4 hybrid which had a higher specific activity than the original proteins. The ability of the natural and hybrid subspecies to protect hamster cells against viral infection was determined using MuIFN-alpha 1 as a standard. Large differences in activity were found, with alpha 6 as the most and alpha 4 as the least active subspecies.
An Introduction to the Helium Ion Microscope (2006)

Abstract In order to get high resolution images from any scanning beam microscope one must be able to produce a sufficiently small probe, have a small interaction volume in the substrate and have an abundance of information-rich particles to collect to create the image. A typical scanning electron microscope is able to meet all of these requirements to some degree. However, a helium ion microscope based on a Gas Field Ion Source (GFIS) has significant advantages over the SEM in all three categories.
Hybrid integration of VCSEL's to CMOS integrated circuits (1999)

Three hybrid integration techniques for bonding vertical-cavity surface-emitting lasers (VCSELs) to CMOS integrated circuit chips have been developed and compared in order to determine the optimum method of fabricating VCSEL based smart pixels for optical interconnects and free-space optical processing. Each of the three bonding techniques used different ways of attaching the VCSEL to the integrated circuit and making electrical contacts to the n- and p-mirrors. All three techniques remove the substrate from the VCSEL wafer leaving an array of individual VCSELs bonded to individual pixels. The 4/spl times/4 and/or 8/spl times/8 arrays of bonded VCSELs produced electrical and optical characteristics typical of unbonded VCSELs. Threshold voltages down to 1.5 V and dynamic resistance as low as 30 /spl Omega/ were measured, indicating good electrical contact was obtained. Optical power as high as /spl sim/10 mW for a VCSEL with a 20-/spl mu/m aperture and 0.7 mW with a 6-/spl mu/m aperture were observed. The VCSELs were operated at 200 Mb/s (our equipment limit) with the rise and fall times of the optical output <1 nS.
Hepatic activation and inactivation of clinically-relevant vitamin D analogs and prodrugs. (2006)

Like most pharmaceutical agents, vitamin D analogs are subject to hepatic metabolism by a variety of cytochrome P450 (CYP)-based systems. Metabolism can involve activation as well as inactivation of the vitamin D analog and one of the more successful families includes the 1alpha-hydroxyvitamin D prodrugs (1alpha-OH-D2, 1alpha-OH-D3, 1alpha-OH-D4, 1alpha-OH-D5), that all require a step of activation. Some of these prodrugs are in use or clinical trial because they have a therapeutic advantage over calcitriol. However, the nature of the activation of these molecules is poorly understood, particularly with regard to the CYP isoform involved. Various transfected CYPs and hepatic cell lines combined with tandem LC-MS analysis were used to investigate the metabolism of a spectrum of vitamin D analogs, including 1alpha-OH-Ds and the topical analog, calcipotriol. In the case of the 1alpha-OH-Ds, evidence was found of multiple sites of side-chain hydroxylation consistent with the generation of more than one active form. The potential involvement of CYP27A and other putative 25-hydroxylases in 1alpha-OH-D activation was also shown, as well as the potential for CYP24 activation and inactivation. In the case of calcipotriol, the respective roles of non-vitamin D-related CYPs and CYP24 in the catabolism of this anti-psoriatic drug were dissected out using cell lines with or without CYP24 expression, allowing us to demonstrate the potential contribution of CYP24 to "vitamin D resistance". The implications of hepatic metabolism in the context of other facets thought to play a role in the mechanism of action of anticancer and antiproliferative vitamin D analogs are discussed.
Hydrolysis of fluorescent pyrene‐acyl esters by human pancreatic carboxylic ester hydrolase and bile salt‐stimulated lipase (1990)

Fluorescent esters containing pyrenedecanoic acid (P10) or pyrenebutanoic (P4) acid (P4cholesterol, P10cholesterol, P4- and P10-containing triacylglycerols) were synthesized and used as substrates for human pancreatic carboxylic ester hydrolase and bile salt-stimulated lipase from human milk. Both enzymes were purified by immunoaffinity chromatography. All fluorescent pyrene derivatives were hydrolyzed by pancreatic carboxylic ester hydrolase and bile salt-stimulated lipase, but at different rates. The hydrolytic rates of the "short" acyl esters (P4-containing esters) were higher than those of the "long" ones (P10-containing esters). Conditions were optimized for sensitivity of the assay using fluorescent cholesteryl esters. The pH optimum was 7.5-8.0. Sodium cholate exhibited a stronger activating effect than taurocholate or taurodeoxycholate (maximal activation was achieved with 5 mmol/L cholate and with a molar ratio cholesteryl ester/cholate around 1:10). Both pancreatic carboxylic ester hydrolase and bile salt-stimulated lipase from milk were strongly inhibited by the other amphiphiles tested, namely phosphatidylcholine and Triton X-100, and were inactivated by low concentrations (10 mumol/L) of the serine-reactive diethyl-paranitrophenyl phosphate (E600). Both enzymes were strongly inhibited by relatively low concentrations of plasma low density lipoproteins. These studies indicate that the fluorescent esters containing pyrene fatty acids can be used as substrates for assaying and investigating the properties of pancreatic carboxylic ester hydrolase as well as bile salt-stimulated lipase from milk.
Monaural Sound Source Separation by Nonnegative Matrix Factorization With Temporal Continuity and Sparseness Criteria (2007)

An unsupervised learning algorithm for the separation of sound sources in one-channel music signals is presented. The algorithm is based on factorizing the magnitude spectrogram of an input signal into a sum of components, each of which has a fixed magnitude spectrum and a time-varying gain. Each sound source, in turn, is modeled as a sum of one or more components. The parameters of the components are estimated by minimizing the reconstruction error between the input spectrogram and the model, while restricting the component spectrograms to be nonnegative and favoring components whose gains are slowly varying and sparse. Temporal continuity is favored by using a cost term which is the sum of squared differences between the gains in adjacent frames, and sparseness is favored by penalizing nonzero gains. The proposed iterative estimation algorithm is initialized with random values, and the gains and the spectra are then alternatively updated using multiplicative update rules until the values converge. Simulation experiments were carried out using generated mixtures of pitched musical instrument samples and drum sounds. The performance of the proposed method was compared with independent subspace analysis and basic nonnegative matrix factorization, which are based on the same linear model. According to these simulations, the proposed method enables a better separation quality than the previous algorithms. Especially, the temporal continuity criterion improved the detection of pitched musical sounds. The sparseness criterion did not produce significant improvements
Prostate-Specific Membrane Antigen Protein Expression in Tumor Tissue and Risk of Lethal Prostate Cancer (2013)

PSMA is not a strong candidate biomarker for predicting prostate cancer-specific mortality in surgically treated patients.
Mechanism of Human Immunodeficiency Virus Type 1 Resistance to Monoclonal Antibody b12 That Effectively Targets the Site of CD4 Attachment (2009)

The region of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 that engages its primary cellular receptor CD4 forms a site of vulnerability to neutralizing antibodies. The monoclonal antibody b12 exploits the conservation and accessibility of the CD4-binding site to neutralize many, though not all, HIV-1 isolates. To understand the basis of viral resistance to b12, we used the atomic-level definition of b12-gp120 contact sites to study a panel of diverse circulating viruses. A combination of sequence analysis, computational modeling, and site-directed mutagenesis was used to determine the influence of amino acid variants on binding and neutralization by b12. We found that several substitutions within the dominant b12 contact surface, called the CD4-binding loop, mediated b12 resistance, and that these substitutions resided just proximal to the known CD4 contact surface. Hence, viruses varied in key b12 contact residues that are proximal to, but not part of, the CD4 contact surface. This explained how viral isolates were able to evade b12 neutralization while maintaining functional binding to CD4. In addition, some viruses were resistant to b12 despite minimal sequence variation at b12 contact sites. Such neutralization resistance usually could be reversed by alterations at residues thought to influence the quaternary configuration of the viral envelope spike. To design immunogens that elicit neutralizing antibodies directed to the CD4-binding site, researchers need to address the antigenic variation within this region of gp120 and the restricted access to the CD4-binding site imposed by the native configuration of the trimeric viral envelope spike.
Nitroxide-Mediated Controlled Free-Radical Emulsion Polymerization Using a Difunctional Water-Soluble Alkoxyamine Initiator. Toward the Control of Particle Size, Particle Size Distribution, and the Synthesis of Triblock Copolymers (2005)

A novel dialkoxyamine bearing two carboxylic acid groups was synthesized by the addition of a high dissociation rate constant alkoxyamine onto tri(ethylene glycol) diacrylate. This dialkoxyamine was first successfully used as an initiator for the bulk polymerizations of n-butyl acrylate and styrene. Then the sodium salt counterpart was used as a water-soluble initiator in the emulsion polymerizations of n-butyl acrylate and styrene via a multistep process. Owing to its unique structure with two carboxylate salts remaining covalently bound to the chain and hence locked at the particle surface, very stable latexes were recovered with, for the first time, small particles and narrow particle size distributions. The emulsion process was successfully applied to the synthesis of well-defined poly(n-butyl acrylate) and polystyrene homopolymers as well as polystyrene-b-poly(n-butyl acrylate)-b-polystyrene triblock copolymer. This work represents the first successful attempt of the synthesis of a complex architecture together with the control of average diameter and particle size distribution in nitroxide-mediated polymerization in emulsion, which is of high industrial and academic interest.
A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods (2014)

Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.
Sequence of three bronze alleles of maize and correlation with the genetic fine structure. (1988)

The genomic sequences of three bronze alleles from Zea mays, Bz-McC, Bz-W22 and bz-R, are presented together with their flanking sequences. The bronze locus encodes UDPglucose flavonoid glucosyl-transferase (UFGT), an anthocyanin biosynthetic enzyme. The wild-type alleles Bz-McC and Bz-W22 condition purple phenotypes in the seed and plant, while bz-R conditions a bronze color. A full length cDNA corresponding to the Bz-McC allele was cloned and sequenced. Primer extension and RNase protection experiments were used to verify the 5' end of the bronze transcript. The Bz-McC allele has a 1416-bp coding region, a 100-bp intron and an approximately 83-bp 5' leader. Upstream of the message initiation site the sequences CTAACT and AATAAA occupy the positions where the eukaryotic consensus CCAAT and TATA boxes are normally found. The alleles Bz-McC and bz-R each have different large insertions with characteristics of transposable elements in their 5' flanking regions. The bz-R allele is distinguished by a 340-bp deletion starting within the intron and including 285 bp of the second exon. The Bz-McC and Bz-W22 isoalleles are known to differ in two genetically defined locations. The uts and uqv sites from the Bz-McC allele condition, respectively, lowered thermostability for the UFGT enzyme and increased amount of UFGT activity when compared with the corresponding sites in the Bz-W22 allele. The uts site maps to a region of the gene encoding two adjacent amino acid differences, either or both of which might alter the thermostability of the UFGT enzyme. The difference in UFGT levels conditioned by the uqv site is shown here to be correlated with variation in the bronze mRNA level. A likely cause of this decreased bronze mRNA level in Bz-W22 is a 6-bp duplication near the sequence CTAACT located 74 bp upstream of the bronze message initiation site. This region is therefore tentatively identified as the uqv site.
An invariant T cell receptor alpha chain is used by a unique subset of major histocompatibility complex class I-specific CD4+ and CD4-8- T cells in mice and humans. (1994)

The mouse thymus contains a mature T cell subset that is distinguishable from the mainstream thymocytes by several characteristics. It is restricted in its usage of T cell receptor (TCR) V beta genes to V beta 8, V beta 7, and V beta 2. Its surface phenotype is that of activated/memory cells. It carries the natural killer NK1.1 surface marker. Furthermore, though it consists entirely of CD4+ and CD4-8- cells, its selection in the thymus depends solely upon major histocompatibility complex (MHC) class I expression by cells of hematopoietic origin. Forced persistence of CD8, in fact, imparts negative selection. Here, we have studied the TCR repertoire of this subset and found that, whereas the beta chain V-D-J junctions are quite variable, a single invariant alpha chain V alpha 14-J281 is used by a majority of the TCRs. This surprisingly restricted usage of the V alpha 14-J281 alpha chain is dependent on MHC class I expression, but independent of the MHC haplotype. In humans, a similar unusual population including CD4-8- cells can also be found that uses a strikingly homologous, invariant alpha chain V alpha 24-JQ. Thus, this unique V alpha-J alpha combination has been conserved in both species, conferring specificity to some shared nonpolymorphic MHC class I/peptide self-ligand(s). This implies that the T cell subset that it defines has a specialized and important role, perhaps related to its unique ability to secrete a large set of lymphokines including interleukin 4, upon primary stimulation in vitro and in vivo.
Characterization of the Interaction between Tumor Necrosis Factor-stimulated Gene-6 and Heparin (2005)

TSG-6, the secreted product of tumor necrosis factor-stimulated gene-6, is not constitutively expressed but is up-regulated in various cell-types during inflammatory and inflammation-like processes. The mature protein is comprised largely of contiguous Link and CUB modules, the former binding several matrix components such as hyaluronan (HA) and aggrecan. Here we show that this domain can also associate with the glycosaminoglycan heparin/heparan sulfate. Docking predictions and site-directed mutagenesis demonstrate that this occurs at a site distinct from the HA binding surface and is likely to involve extensive electrostatic contacts. Despite these glycosaminoglycans binding to non-overlapping sites on the Link module, the interaction of heparin can inhibit subsequent binding to HA, and it is possible that this occurs via an allosteric mechanism. We also show that heparin can modify another property of the Link module, i.e. its potentiation of the anti-plasmin activity of inter-alpha-inhibitor (IalphaI). Experiments using the purified components of IalphaI indicate that TSG-6 only binds to the bikunin chain and that this is at a site on the Link module that overlaps the HA binding surface. The association of heparin with the Link module significantly increases the anti-plasmin activity of the TSG-6.IalphaI complex. Changes in plasmin activity have been observed previously at sites of TSG-6 expression, and the results presented here suggest that TSG-6 is likely to contribute to matrix remodeling, at least in part, through down-regulation of the protease network, especially in locations containing heparin/heparan sulfate proteoglycans. The differential effects of HA and heparin on TSG-6 function provide a mechanism for its regulation and functional partitioning in particular tissue microenvironments.