gebhart/patrepeval huggingface dataset:
Activation of human factor V by meizothrombin. (1994)

A recombinant human prothrombin was prepared in which Arg155 was replaced by Ala. The recombinant prothrombin was converted into a meizothrombin derivative (R155A meizothrombin) that was resistant to autocatalytic removal of the fragment 1 domain. R155A meizothrombin appeared to be a potent factor V activator in reaction mixtures that contained negatively charged phospholipid vesicles. Factor V activation by R155A meizothrombin was characterized by second-order rate constants of 0.06 x 10(6) M-1 S-1 in the absence of phospholipid and 18 x 10(6) M-1 S-1 in the presence of 60 microM phospholipid vesicles composed of a 10:90 mol/mol mixture of phosphatidylserine (PS) and phosphatidylcholine (PC). The rate constant for thrombin-catalyzed activation of factor V was hardly affected by the presence of phospholipid vesicles and was 4.0 x 10(6) M-1 S-1. The initial rate of activation of 3 nM factor V by R155A meizothrombin was a function of the concentration of PS/PC vesicles present in the reaction mixture, and the calculated rate constant reached a plateau value at > or = 50 microM PS/PC. Gel electrophoretic analysis of factor V activation showed that R155A meizothrombin and thrombin cleaved the susceptible peptide bonds in factor V at different rates. However, both activators finally generated a factor Va molecule composed of a heavy chain with an M(r) of 104,000 and a light chain doublet with M(r) values of 74,000 and 71,000. Since meizothrombin is one of the major reaction products formed during the initial phase of prothrombin activation, these findings are indicative of a significant contribution of meizothrombin to in vivo factor V activation.
Quantitative Analysis of HER2 Receptor Expression In Vivo by Near-Infrared Optical Imaging (2010)

Human epidermal growth factor receptor 2 (HER2) overexpression in breast cancers is associated with poor prognosis and resistance to therapy. Current techniques for estimating this important characteristic use ex vivo assays that require tissue biopsies. We suggest a novel noninvasive method to characterize HER2 expression in vivo, using optical imaging, based on HER2-specific probes (albumin-binding domain-fused-(ZHER2:342)2-Cys Affibody molecules [Affibody AB, Solna, Sweden], labeled with Alexa Fluor 750 [Molecular Probes, Invitrogen, Carlsbad, CA]) that could be used concomitantly with HER2-targeted therapy. Subcutaneous tumor xenografts, expressing different levels of HER2, were imaged with a near-infrared fluorescence small-animal imaging system at several times postinjection of the probe. The compartmental ligand-receptor model was used to calculate HER2 expression from imaging data. Correlation between HER2 amplification/overexpression in tumor cells and parameters, directly estimated from the sequence of optical images, was observed (eg, experimental data for BT474 xenografts indicate that initial slope, characterizing the temporal dependence of the fluorescence intensity detected in the tumor, linearly depends on the HER2 expression, as measured ex vivo by an enzyme-linked immunosorbent assay for the same tumor). The results obtained from tumors expressing different levels of HER2 substantiate a similar relationship between the initial slope and HER2 amplification/overexpression. This work shows that optical imaging, combined with mathematical modeling, allows noninvasive monitoring of HER2 expression in vivo.
A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide (2002)

Alignment of the protein sequence of DNA-dependent DNA polymerases has allowed the definition of a new motif, lying adjacent to motif B in the direction of the N-terminus and therefore named pre-motif B. Both motifs are located in the fingers subdomain, shown to rotate towards the active site to form a dNTP-binding pocket in several DNA polymerases in which a closed ternary complex pol:DNA:dNTP has been solved. The functional significance of pre-motif B has been studied by site-directed mutagenesis of phi29 DNA polymerase. The affinity for nucleotides of phi29 DNA polymerase mutant residues Ile364 and Lys371 was strongly affected in DNA- and terminal protein-primed reactions. Additionally, mutations in Ile364 affected the DNA-binding capacity of phi29 DNA polymerase. The results suggest that Lys371 of phi29 DNA polymerase, highly conserved among families A and B, interacts with the phosphate groups of the incoming nucleotide. On the other hand, the role of residue Ile364 seems to be structural, being important for both DNA and dNTP binding. Pre-motif B must therefore play an important role in binding the incoming nucleotide. Interestingly, the roles of Lys371 and Ile364 were also shown to be important in reactions without template, suggesting that phi29 DNA polymerase can achieve the closed conformation in the absence of a DNA template.
An Aluminum Ate Base:  Its Design, Structure, Function, and Reaction Mechanism (2007)

An aluminum ate base, i-Bu(3)Al(TMP)Li, has been designed and developed for regio- and chemoselective direct generation of functionalized aromatic aluminum compounds. Direct alumination followed by electrophilic trapping with I(2), Cu/Pd-catalyzed C-C bond formation, or direct oxidation with molecular O(2) proved to be a powerful tool for the preparation of 1,2- or 1,2,3-multisubstituted aromatic compounds. This deprotonative alumination using i-Bu3Al(TMP)Li was found to be effective in aliphatic chemistry as well, enabling regio- and chemoselective addition of functionalized allylic ethers and carbamates to aliphatic and aromatic aldehydes. A combined multinuclear NMR spectroscopy, X-ray crystallography, and theoretical study showed that the aluminum ate base is a Li/Al bimetallic complex bridged by the nitrogen atom of TMP and the alpha-carbon of an i-Bu ligand and that the Li exclusively serves as a recognition point for electronegative functional groups or coordinative solvents. The mechanism of directed ortho alumination reaction of functionalized aromatic compounds has been studied by NMR and in situ FT-IR spectroscopy, X-ray analysis, and DFT calculation. It has been found that the reaction proceeds with facile formation of an initial adduct of the base and aromatic, followed by deprotonative formation of the functionalized aromatic aluminum compound. Deprotonation by the TMP ligand rather than the isobutyl ligand was suggested and reasoned by means of spectroscopic and theoretical study. The remarkable regioselectivity of the ortho alumination reaction was explained by a coordinative approximation effect between the functional groups and the counter Li(+) ion, enabling stable initial complex formation and creation of a less strained transition state structure.
Ultrasensitive broadband infrared 4 × 4 Mueller-matrix ellipsometry for studies of depolarizing and anisotropic thin films (2019)

The authors present a second-generation broadband 4×4 Mueller-matrix (MM) ellipsometer for ultrasensitive infrared-spectroscopic (8000−800cm−1) studies of complex nanometer-thin films. In a modular design, the instrument employs retractable achromatic retarders and various sets of tandem polarizers. Using high-transmittance free-standing wire-grid polarizers, the device reaches an unparalleled precision of up to 5⋅10−5 in the important fingerprint region, even for block-offdiagonal MM elements. Broadband and signal-to-noise optimized access to the full 4×4 MM provides in-depth information on the sample’s polarimetric properties and opens the door for detailed explorations of depolarizing and anisotropic materials. The authors discuss examples of highly depolarizing nonuniform polyimide membranes, uniaxial-to-biaxial anisotropy changes in ultrathin polymer films, and azimuthal off-axis effects in 2D-structured silica arrays. Diverse optical modeling approaches based upon anisotropic layer stacks and rigorous coupled-wave analysis are used to quantify the optical, structural, and chemical properties of the sample.
Induction of differentiation of the human histiocytic lymphoma cell line U-937 by retinoic acid and cyclic adenosine 3':5'-monophosphate-inducing agents. (1982)

The monoblast-like human histiocytic lymphoma cell line, U-937, is induced to differentiate into monocyte-like cells by incubation with 0.1 to 1.0 microM retinoic acid (RA). These induced cells are phagocytic, reduce nitroblue tetrazolium, and show an increased hexose monophosphate shunt activity, consistent with monocyte-like cells. Prostaglandin E, cholera toxin, or dibutyryl cyclic adenosine 3':5'-monophosphate, all inactive alone, increased markedly the extent of RA-induced differentiation of U-937. These data suggest that the intracellular level of cyclic adenosine 3':5'-monophosphate is of importance for expression of the RA-induced effect. Responsiveness to RA seems to be limited to those leukemic myeloid cells blocked at a relatively late stage of maturation, like the promyelocytic HL-60 and the monoblast-like U-937 cell lines.
A 0.18-&lt;tex&gt;$muhboxm$&lt;/tex&gt;CMOS 3.5-Gb/s Continuous-Time Adaptive Cable Equalizer Using Enhanced Low-Frequency Gain Control Method (2004)

This paper describes a high-speed CMOS adaptive cable equalizer using an enhanced low-frequency gain control method. The additional low-frequency gain control loop enables the use of an open-loop equalizing filter, which alleviates the speed bottleneck of the conventional adaptation method. In addition, combined adaptation of low-frequency gain and high-frequency boosting improves the adaptation accuracy while supporting high-frequency operation. The open-loop equalizing filter incorporates a merged-path topology and offers infinite input impedance, which are suitable for higher frequency operation and cascaded design. This equalizing filter controls its common-mode output voltage level in a feedforward manner, thereby improving bandwidth. A prototype chip was fabricated in 0.18-/spl mu/m four-metal mixed-mode CMOS technology. The realized active area is 0.48/spl times/0.73 mm/sup 2/. The prototype adaptive equalizer operates up to 3.5 Gb/s over a 15-m RG-58 coaxial cable with 1.8-V supply and dissipates 80 mW. Moreover, the equalizing filter in manual adjustment mode operates up to 5 Gb/s over a 15-m RG-58 coaxial cable.
Increased serum interleukin‐17 and peripheral Th17 cells in children with acute Henoch–Schönlein purpura (2011)

The increased frequency of peripheral Th17 cells and serum IL-17 levels are shown in childhood HSP that may in part contribute to vascular inflammation, suggesting cellular immunity is likely to be involved in the process of HSP.
Effectiveness of Mupirocin and Polymyxin B in Experimental Staphylococcus aureus, Pseudomonas aeruginosa, and Serratia marcescens Keratitis (2002)

The mupirocin:polymyxin B combination was effective in treating experimental, and keratitis.
Improvements in Fabrication Process for Nb-Based Single Flux Quantum Circuits in Japan (2008)

We developed an Nb-based fabrication process for single flux quantum (SFQ) circuits in a Japanese government project that began in September 2002 and ended in March 2007. Our conventional process, called the Standard Process (SDP), was improved by overhauling all the process steps and routine process checks for all wafers. Wafer yield with the improved SDP dramatically increased from 50% to over 90%. We also developed a new fabrication process for SFQ circuits, called the Advanced Process (ADP). The specifications for ADP are nine planarized Nb layers, a minimum Josephson junction (JJ) size of 1×1μm, a line width of 0.8μm, a JJ critical current density of 10kA/cm2, a 2.4Ω Mo sheet resistance, and vertically stacked superconductive contact holes. We fabricated an eight-bit SFQ shift register, a one million SQUID array and a 16-kbit RAM by using the ADP. The shift register was operated up to 120GHz and no short or open circuits were detected in the one million SQUID array. We confirmed correct memory operations by the 16-kbit RAM and a 5.7 times greater integration level compared to that possible with the SDP.
Optimizing 10-Gigabit Ethernet for Networks of Workstations, Clusters, and Grids (2003)

This paper presents a case study of the 10-Gigabit Ethernet (10GbE) adapter from Intel R . Specifically, with appropriate optimizations to the configurations of the 10GbE adapter and TCP, we demonstrate that the 10GbE adapter can perform well in local-area, storage-area, system-area, and wide-area networks. For local-area, storage-area, and system-area networks in support of networks of workstations, network-attached storage, and clusters, respectively, we can achieve over 7-Gb/s end-to-end throughput and 12-µs end-to-end latency between applications running on Linux-based PCs. For the wide-area network in support of grids, we broke the recently-set Internet2 Land Speed Record by 2.5 times by sustaining an end-to-end TCP/IP throughput of 2.38 Gb/s between Sunnyvale, California and Geneva, Switzerland (i.e., 10,037 kilometers) to move over a terabyte of data in less than an hour. Thus, the above results indicate that 10GbE may be a cost-effective solution across a multitude of computing environments.
Finding the right RNA: Identification of cellular mRNA substrates for RNA-binding proteins (1999)

Defects in RNA-binding proteins have been implicated in human genetic disorders. However, efforts in understanding the functions of these proteins have been hampered by the inability to obtain their mRNA substrates. To identify cognate cellular mRNAs associated with an RNA-binding protein, we devised a strategy termed isolation of specific nucleic acids associated with proteins (SNAAP). The SNAAP technique allows isolation and subsequent identification of these mRNAs. To assess the validity of this approach, we utilized cellular mRNA and protein from K562 cells and αCP1, a protein implicated in α-globin mRNA stability, as a model system. Immobilization of an RNA-binding protein with the glutathione-S-transferase (GST) domain enables isolation of mRNA within an mRNP context and the identity of the bound mRNAs is determined by the differential display assay. The specificity of protein–RNA interactions was considerably enhanced when the interactions were carried out in the presence of cellular extract rather than purified components. Two of the mRNAs specifically bound by αCP1 were mRNAs encoding the transmembrane receptor protein, TAPA-1, and the mitochondrial cytochrome c oxidase subunit II enzyme, coxII. A specific poly(C)-sensitive complex formed on the TAPA-1 and coxII 3′ UTRs consistent with the binding of αCP1. Furthermore, direct binding of purified αCP proteins to these 3′ UTRs was demonstrated and the binding sites determined. These results support the feasibility of the SNAAP technique and suggest a broad applicability for the approach in identifying mRNA targets for clinically relevant RNA-binding proteins that will provide insights into their possible functions.
Purification and Characterization of a Protein That Permits Early Detection of Lung Cancer (1996)

We have reported that a mouse monoclonal antibody 703D4, detects lung cancer 2 years earlier than routine chest x-ray or cytomorphology. We purified the 703D4 antigen to elucidate its role in early lung cancer biology, using Western blot detection after SDS-polyacrylamide gel electrophoresis. Purification steps included anion exchange chromatography, preparative isoelectric focusing, polymer-based C18-like, and analytical C4 reverse phase high performance liquid chromatography. After 25-50,000-fold purification, the principal immunostaining protein was > 95% pure by Coomassie staining. The NH2 terminus was blocked, so CNBr digestion was used to generate internal peptides. Three sequences, including one across a site of alternate exon splicing, all identified a single protein, heterogeneous nuclear ribonucleoprotein-A2 (hnRNP-A2). A minor co-purifying immunoreactive protein resolved at the final C4 high performance liquid chromatography step is the splice variant hnRNP-B1. Northern analysis of RNA from primary normal bronchial epithelial cells demonstrated a low level of hnRNP-A2/B1 expression, consistent with immunohistochemical staining of clinical samples, and increased hnRNP-A2/B1 expression was found in lung cancer cells. hnRNP-A2/B1 expression is under proliferation-dependent control in normal bronchial epithelial cell primary cultures, but not in SV40-transformed bronchial epithelial cells or tumor cell lines. With our clinical data, this information suggests that hnRNP-A2/B1 is an early marker of lung epithelial transformation and carcinogenesis.
Genetics of human prion disease. (1993)

Prion diseases are fatal neurodegenerative disorders in which an abnormal isoform of prion protein (PrPSc) accumulates in brain. Prion disease is either inherited as an autosomal dominant disorder with very high penetrance, sporadic, where no epidemiological association with other human or animal prion diseases can be demonstrated or acquired, where disease results from contamination with PrPSc from another case of prion disease. No human case of prion disease is known to have been acquired from an animal but about 50 cases have been acquired from contaminated growth hormone or gonadotrophin prepared from human pituitaries, from human meningeal transplants or other neuro-surgical procedures. Several thousand cases of the prion disease, kuru, occurred in Papua New Guinea, mainly during the first half of this century. This epidemic probably started with a sporadic case of Creutzfeldt-Jakob disease but was transmitted through funerary practices which are though to have involved endo-cannibalism. Inherited cases of prion disease are associated with mutations in the PrP gene. There are at least five point mutations and a further five mutations involving five to nine extra repeats of the five octapeptide repeat sequence in the PrP gene, all of which may lead to one of the forms of human prion disease i.e. Creutzfeldt-Jakob disease, Gerstmann-Sträussler syndrome and atypical prion dementia. In addition there is a common polymorphism at codon 129 of the PrP gene. This may affect age at onset and duration of illness in inherited and sporadic cases.(ABSTRACT TRUNCATED AT 250 WORDS)
Identification of the 170-kDa Melanoma Membrane-bound Gelatinase (Seprase) as a Serine Integral Membrane Protease (1997)

The 170-kDa membrane-bound gelatinase, seprase, is a cell surface protease, the expression of which correlates with the invasive phenotype of human melanoma and carcinoma cells. We have isolated seprase from cell membranes and shed vesicles of LOX human melanoma cells. The active enzyme is a dimer of N-glycosylated 97-kDa subunits. Sequence analysis of three internal proteolytic fragments of the 97-kDa polypeptide revealed up to 87.5% identity to the 95-kDa fibroblast activation protein alpha (FAPalpha), the function of which is unknown. Thus, we used reverse transcription-polymerase chain reaction to generate a 2.4-kilobase cDNA from LOX mRNA with FAPalpha primers. COS-7 cells transfected with this cDNA expressed a 170-kDa gelatinase that is recognized by monoclonal antibodies directed against seprase. Sequence analysis also showed similarities to the 110-kDa subunit of dipeptidyl peptidase IV (DPPIV). Like DPPIV, the gelatinase activity of seprase was completely blocked by serine-protease inhibitors, including diisopropyl fluorophosphate. Seprase could be affinity-labeled by [3H]diisopropyl fluorophosphate, but the proteolytically inactive 97-kDa subunit could not, confirming the existence of a serine protease active site on the dimeric form. Proteolytic activity is lost upon dissociation into its 97-kDa subunit following treatment with acid, heat, or cysteine and histidine-modifying agents. We conclude that seprase, FAPalpha, and DPPIV are related serine integral membrane proteases and that seprase is similar to DPPIV, the proteolytic activities of which are dependent upon subunit association.
Image and Video Coding Standards (1993)

Most image or video applications involving transmission or storage require some form of data compression to reduce the otherwise inordinate demand on bandwidth and storage. Compatibility among different applications and manufacturers is very desirable, and often essential. This paper describes several standard compression algorithms developed in recent years.
Human T lymphocytes and monocytes bear the same Leu-3(T4) antigen. (1986)

An analysis of the cellular distribution, biosynthesis, and structure of the human T lymphocyte antigen Leu-3(T4) was performed. By using a sensitive ELISA as well as FACS analysis, relative quantities of the Leu-3(T4) antigen from whole cell lysates and from cell surfaces of six cell lines were determined. The T-T hybrid cell line 255.88, and the monocyte/macrophage cell line U937, proved to be high producers of the antigen and were chosen for additional investigation. The Leu-3(T4) antigens from the T lymphocyte cell line and the monocyte/macrophage cell were shown to be identical by SDS-PAGE. Leu-3(T4) was a polypeptide of 55,000 AMW under reducing conditions, and 63,000 AMW under nonreducing conditions. In the 255.88 cell line, a second band of 41,000 AMW was associated with the true Leu-3(T4) molecule. The 55,000 AMW Leu-3(T4) molecule was shown to possess a high mannose sugar side chain, and to contain few accessible tyrosine residues. These studies demonstrate that human T lymphocytes and monocytes produce and process similar molecules that react with the anti-Leu-3(T4) monoclonal antibody. They also characterize this important associative antigen recognition structure and suggest that cells other than the T lymphocyte may be targets for the retrovirus HTLV-III.
Single nucleotide polymorphisms : methods and protocols (2003)

Single nucleotide polymorphisms (SNPs) have become the markers of choice in elucidating the relationship between DNA sequence variation and susceptibility to disease and have clearly become the focus of the next phase of the human genome project. In Single Nucleotide Polymorphisms: Methods and Protocols, Pui-Yan Kwok, MD, PhD, has assembled a collection of robust techniques for the difficult process of SNP discovery and genotyping. These cutting-edge protocols for mutation/SNP detection utilize denaturing high-performance liquid chromatography (dHPLC), single-strand conformation polymorphism (SSCP), conformation-sensitive gel electrophoresis (CSGE), chemical cleavage, and direct sequencing. Equally powerful and up-to-date methods are given for genotyping SNPs, including molecular beacons, the Taqman assay, single-base extension approaches, pyrosequencing, ligation, the Invader assay, and primer extension with mass spectrometry detection. Described in step-by-step detail by their inventors, each method provides extensive notes on the technical steps critical for experimental success, time-saving techniques, and tips on avoiding pitfalls. Comprehensive and authoritative, Single Nucleotide Polymorphisms: Methods and Protocols provides in a readily reproducible format all the major SNP discovery and genotyping techniques in use today, whether for using DNA diagnostics to identify a pathogen, for studying the genetic basis of human disease, or for molecular breeding programs in agriculture