gebhart/patrepeval huggingface dataset:
Ultrafast Charge Separation in Multiexcited CdSe Quantum Dots Mediated by Adsorbed Electron Acceptors (2009)

Ultrafast ET with a characteristic time constant of approximately 70 fs between CdSe QDs (mean radii of 1.4 nm) photoexcited in the lowest 1S electron state (lambda(exc) = 539 nm), and the molecular electron acceptor MV(2+) adsorbed on the QD surface was observed. The photophysics of such a system was investigated by time-resolved transient absorbance spectroscopy in the UV-visible spectral region. Our studies for the coupled system as a function of excitation intensity at lambda(exc) = 387 nm show that the ET processes compete efficiently with Auger recombination in CdSe QDs and at least 4 e-h pairs can be separated by ET to the electron acceptor MV(2+).
THINC: A Remote Display Architecture for Thin-Client Computing (2004)

Rapid improvements in network bandwidth, cost, and ubiquity combined with the security hazards and high total cost of ownership of personal computers have created a growing market for thin-client computing. We introduce THINC, a remote display system architecture for high-performance thin-client computing in both LAN and WAN environments. THINC transparently maps high-level application display calls to a few simple low-level commands which can be implemented easily and efficiently. THINC introduces a number of novel latency-sensitive optimization techniques, including offscreen drawing awareness, command buffering and scheduling, non-blocking display operation, native video support, and server-side screen scaling. We have implemented THINC in an XFree86/Linux environment and compared its performance with other popular approaches, including Citrix MetaFrame, Microsoft Terminal Services, SunRay, VNC, and X. Our experimental results on web and video applications demonstrate that THINC can be as much as five times faster than traditional thin-client systems in high latency network environments and is capable of playing full-screen video at full frame rate.
The Wzz (Cld) Protein in Escherichia coli : Amino Acid Sequence Variation Determines O-Antigen Chain Length Specificity (1998)

The O antigen is a polymer with a repeated unit. The chain length in most Escherichia coli strains has a modal value of 10 to 18 O units, but other strains have higher or lower modal values. wzz (cld/rol) mutants have a random chain length distribution, showing that the modal distribution is determined by the Wzz protein. Cloned wzz genes from E. coli strains with short (7 to 16), intermediate (10 to 18), and long (16 to 25) modal chain lengths were transferred to a model system, and their effects on O111 antigen were studied. The O111 chain length closely resembled that of the parent strains. We present data based on the construction of chimeric wzz genes and site-directed mutagenesis of the wzz gene to show that the modal value of O-antigen chain length of E. coli O1, O2, O7, and O157 strains can be changed by specific amino acid substitutions in wzz. It is concluded that the O-antigen chain length heterogeneity in E. coli strains is the result of amino acid sequence variation of the Wzz protein.
mRNA secondary structure in an open reading frame reduces translation efficiency in Bacillus subtilis (1989)

The structural gene for thermostable neutral protease, nprM, has only one stacking region, whose energy is -16.3 kcal/mol (-68.2 kJ/mol). Mutations for increasing (-30.8 kcal/mol [128.9 kJ/mol] and decreasing (-5.0 kcal/mol [-20.9 kJ/mol]) the energy of the stacking region were introduced in nprM on the recombinant plasmid pMK1 by using site-directed mutagenesis without any amino acid substitutions. The resultant plasmids were designated pMK2 and pMK3, respectively. The enzyme productivity of the pMK2 carrier was about 40% lower than that of pMK1, whereas the productivity of the pMK3 carrier was about 5% higher. The higher the stability of the stacking regions, the lower the enzyme productivity that was observed. mRNA concentrations were almost the same in the cells harboring these three plasmids. These results indicate that the secondary structure of mRNA reduces the translation efficiency.
The Adaptor Protein Paxillin Is Essential for Normal Development in the Mouse and Is a Critical Transducer of Fibronectin Signaling (2002)

The integrin family of cell adhesion receptors are important for a diverse set of biological responses during development. Although many integrins have been shown to engage a similar set of cytoplasmic effector proteins in vitro, the importance of these proteins in the biological events mediated by different integrin receptors and ligands is uncertain. We have examined the role of one of the best-characterized integrin effectors, the focal adhesion protein paxillin, by disruption of the paxillin gene in mice. Paxillin was found to be critically involved in regulating the development of mesodermally derived structures such as heart and somites. The phenotype of the paxillin(−/−) mice closely resembles that of fibronectin(−/−) mice, suggesting that paxillin is a critical transducer of signals from fibronectin receptors during early development. Paxillin was also found to play a critical role in fibronectin receptor biology ex vivo since cultured paxillin-null fibroblasts display abnormal focal adhesions, reduced cell migration, inefficient localization of focal adhesion kinase (FAK), and reduced fibronectin-induced phosphorylation of FAK, Cas, and mitogen-activated protein kinase. In addition, we found that paxillin-null fibroblasts show some defects in the cortical cytoskeleton and cell spreading on fibronectin, raising the possibility that paxillin could play a role in structures distinct from focal adhesions. Thus, paxillin and fibronectin regulate some common embryonic developmental events, possibly due to paxillin modulation of fibronectin-regulated focal adhesion dynamics and organization of the membrane cytoskeletal structures that regulate cell migration and spreading.
Myosin VI Binds to and Localises with Dab2, Potentially Linking Receptor‐Mediated Endocytosis and the Actin Cytoskeleton (2002)

Myosin VI, an actin-based motor protein, and Disabled 2 (Dab2), a molecule involved in endocytosis and cell signalling, have been found to bind together using yeast and mammalian two-hybrid screens. In polarised epithelial cells, myosin VI is known to be associated with apical clathrin-coated vesicles and is believed to move them towards the minus end of actin filaments, away from the plasma membrane and into the cell. Dab2 belongs to a group of signal transduction proteins that bind in vitro to the FXNPXY sequence found in the cytosolic tails of members of the low-density lipoprotein receptor family. The central region of Dab2, containing two DPF motifs, binds to the clathrin adaptor protein AP-2, whereas a C-terminal region contains the binding site for myosin VI. This site is conserved in Dab1, the neuronal counterpart of Dab2. The interaction between Dab2 and myosin VI was confirmed by in vitro binding assays and coimmunoprecipitation and by their colocalisation in clathrin-coated pits/vesicles concentrated at the apical domain of polarised cells. These results suggest that the myosin VI-Dab2 interaction may be one link between the actin cytoskeleton and receptors undergoing endocytosis.
UV-curable polymers with chemically-bonded carbon nanotubes for MEMS applications (2002)

Current ultraviolet (UV) curable polymer techniques for MEMS fabrication pose certain challenges due to the electrical and mechanical properties of the polymer. A novel UV-curable polymer uniformly bonded with functionalized nanotubes was synthesized via a modified threestep in-situ polymerization. Purified multi-walled nanotubes, gained from the microwave chemical vapor deposition method, were functionalized by oxidation. X-ray photoelectron spectroscopy (XPS) was used to identify the —OH and —COOH groups attached to nanotube surface. The UV curable polymer was prepared from toluene diisocyanate (TDI), functionalized nanotubes, and 2-hydroxyethyl methacrylate (HEMA). The chemical bonds between —NCO groups of TDI and —OH, -COOH groups of functionalized nanotubes were confirmed by Fourier transform infrared (FTIR) spectra. This new UV-curable polymer is expected to be a costeffective solution with a variety of applications in UV coating, phase shifters for telecommunications and global positioning systems, and polymer and BioMEMS devices.
1H NMR structure of an antifungal γ-thionin protein SIα1: Similarity to scorpion toxins (1998)

The three-dimensional structure of the Sorghum bicolor seed protein gamma-thionin SIalpha1 has been determined by 2D 1H nuclear magnetic resonance (NMR) spectroscopy. The secondary structure of this 47-residue antifungal protein with four disulphide bridges consists of a three-stranded antiparallel sheet and one helix. The helix is tethered to the sheet by two disulphide bridges which link two successive turns of the helix to alternate residues i, i+2 in one strand. Possible binding sites for antifungal activity are discussed. The same fold has been observed previously in several scorpion toxins.
Characterization of a mouse interferon gene locus I. Isolation of a cluster of four α-interferon genes (1985)

A BALB/c mouse genomic library was screened with a murine interferon alpha 2 (MuIFN-alpha 2) cDNA coding region fragment. Eight clones were isolated which contain different mouse chromosomal segments related to the MuIFN-alpha 2 probe and a 28 kilobase (kb) region of mouse genomic DNA containing four different MuIFN-alpha genes (alpha 1, alpha 4, alpha 5 and alpha 6) was identified and characterized; an intergenic 1000 nucleotide long conserved sequence was found to be associated with three of these four alpha genes, indicating that this alpha-IFN gene cluster evolved through tandem duplications. Sequence analysis revealed the absence of a polyadenylation site in the 3' untranslated region of MuIFN-alpha 1, and showed that one of the genes (alpha 4) contains an internal deletion of 5 amino acids in the coding region.
Overexpression of keratinocyte growth factor in cancer cells and enterochromaffin cells in human colorectal cancer (2000)

Keratinocyte growth factor (KGF) is a mitogenic polypeptide that is mainly synthesized by mesenchymal cells. Its actions are dependent on its binding to a specific cell-surface KGF receptor (KGFR), which is localized in epithelial cells. In the present study, the expression level of KGF and KGFR messenger RNA (mRNA), and the localization of these mRNA and proteins in tumor specimens obtained from 12 human colorectal cancer cases were estimated. Competitive reverse transcriptase-polymerase chain reaction (RT-PCR) revealed the expression of KGF and KGFR mRNA in both colorectal cancer and normal colorectal tissues. In specimens from 10 of the 12 cancer cases, the KGF mRNA level was higher in the specimens obtained from the cancerous portions than in those obtained from non-cancerous tissues of the same cases. KGFR mRNA was higher in cancerous tissues in eight of 12 cases. To localize the KGF protein in normal and cancerous human colorectal tissues, immunohistochemistry was employed. In normal colorectal tissue, faint KGF immunoreactivity was present in a few fibroblasts. In contrast, strong KGF immunoreactivity was present in many of the neuroendocrine cells present in close proximity to cancer cells, and moderate immunoreactivity was recognized in the cancer cells themselves and adjacent fibroblasts. KGF-positive neuroendocrine cells also showed serotonin immunoreactivity, indicating that they were enterochromaffin cells. By in situ hybridization, both KGF and KGFR mRNA were co-overexpressed in these colorectal cancer cells, and KGF mRNA was recognized in neuroendocrine cells lying in close proximity to the cancer cells. These findings indicate the possibility that KGF acts in both a paracrine and autocrine manner to induce colorectal cancer cell growth in vivo.
Graphics rendering architecture for a high performance desktop workstation (1993)

Hundreds of commercial applications used in mainstream design activities have demonstrated proven demand for 3D graphics rendering products. The demand is for faster and more powerful renderers, thus creating the system design problem of how to achieve maximum rendering performance from the technology available to implement the system. This paper describes a graphics rendering architecture that takes advantage of several novel architectural features: a custom floating point processing core with tailored data stores and bussing structures, the arrangement of these cores into a SIMD processor for low overhead multiprocessing, and the hyperpipelining of the fixed point scan conversion units for low overhead, high bandwidth pixel generation into an interleaved frame buffer. These features combine to form a solution to the system design problem which distinguishes itself by its overall performance and its ability to maximize performance while minimizing system size. The resulting architecture is capable of over a half million gouraud shaded Z-buffered triangles per second, with a sustained fill rate for gouraud shaded and Z-buffered pixels of 80M pixels per second. The architecture fits in a desktop workstation.
Identification and molecular characterization of a Salmonella typhimurium gene involved in triggering the internalization of salmonellae into cultured epithelial cells. (1992)

Penetration of intestinal epithelial cells is an important step in the pathogenesis of Salmonella infections. We have characterized a gene, invE, that is necessary for Salmonella invasion of cultured epithelial cells. The predicted amino acid sequence of InvE showed significant homology to the Yersinia outer membrane protein YopN (LcrE). Strains of Salmonella carrying mutations in invE were unable to penetrate Henle-407 human intestinal cells and Madin-Darby canine kidney cells, although they were fully capable of attaching to the same cells. Unlike wild-type Salmonella typhimurium, invE mutants failed to change the intracellular free calcium levels or the distribution of polymerized actin in cultured epithelial cells; neither did they alter the normal architecture of the microvilli of polarized Madin-Darby canine kidney cells. Wild-type S. typhimurium was able to rescue the invasive phenotype of the invE mutants in simultaneous infections of cultured epithelial cells although it did not rescue the Escherichia coli strain RDEC-1. We hypothesize that invE mutants are deficient in triggering the intracellular events that lead to bacterial internalization.
Targeting Notch Signaling with a Notch2/Notch3 Antagonist (Tarextumab) Inhibits Tumor Growth and Decreases Tumor-Initiating Cell Frequency (2015)

These findings indicate that blockade of Notch2/3 signaling with this cross-reactive antagonist antibody may be an effective strategy for treatment of a variety of tumor types.
Epidemiology of Tetracycline Resistance Determinants in Shigella spp. and Enteroinvasive Escherichia coli : Characterization and Dissemination of tet (A)- 1 (2003)

To make a comprehensive study of tetracycline resistance determinant distribution in the genus Shigella, a collection of 577 clinical isolates of Shigella spp. and enteroinvasive Escherichia coli (EIEC) from a variety of geographical locations was screened to identify tetracycline-resistant strains. The 459 tetracycline-resistant isolates identified were then screened by PCR analysis to determine the distribution in these strains of tetracycline efflux resistance determinants belonging to classes A to E, G, and H that have been identified in gram-negative bacteria. Only classes A to D were represented in these strains. Although Tet B was the predominant determinant in all geographical locations, there were geographical and species differences in the distribution of resistance determinants. An allele of tet(A), designated tet(A)-1, was identified and sequenced, and the 8.6-kb plasmid containing determinant Tet A-1, designated pSSTA-1, was found to have homologies to portions of a Salmonella enterica cryptic plasmid and the broad-host-range resistance plasmid RSF1010. This allele and pSSTA-1 were used as epidemiological markers to monitor clonal and horizontal transmission of determinant Tet A-1. An analysis of serotype, distribution of tetracycline resistance determinants, and resistance profiles indicated that both clonal spread and horizontal transfer had contributed to the spread of specific tetracycline resistance determinants in these populations and demonstrated the use of these parameters as an epidemiological tool to follow the transmission of determinants and strains.
Organization of the neural cell adhesion molecule (N-CAM) gene: alternative exon usage as the basis for different membrane-associated domains. (1987)

The neural cell adhesion molecule, N-CAM, is expressed as at least three polypeptide chain, (ld, sd, and ssd chains) specified by a single gene and derived by alternative splicing and polyadenylation-site selection during RNA processing. We describe here the characterization of seven overlapping genomic phage clones reactive with N-CAM cDNA, indicating that the chicken N-CAM gene is more than 50 kilobases long. Analysis of the gene shows that there are at least 19 exons and that the coding sequences for the ld, sd, and ssd chains are assembled from 18, 17, and 15 exons, respectively. The first 14 exons appear to be common to all three chains and encode the amino-terminal portion of N-CAM, which contains five tandem homologous repeats resembling those seen in the immunoglobulin gene superfamily. In contrast to other genes containing such domains, each of these segments in N-CAM is specified by two exons. The carboxyl-terminal portion of each N-CAM chain is different as a result of the alternative use of exons. A single exon encodes the carboxyl-terminal 26 amino acids of the ssd chain and the 3' untranslated region of its mRNA, ending with a poly(A)-addition site. Two exons encode the transmembrane and cytoplasmic sequences common to the ld and sd chains, and another exon encodes the additional 261 amino acids found in the cytoplasmic domain of the ld chain. The carboxyl-terminal 21 amino acids common to the ld and sd chains and the 3' untranslated region common to their mRNAs are encoded by a single large exon of 3475 base pairs that ends with a second poly(A)-addition site. Sequences from the 13-kilobase intron that separates the exons encoding the amino-terminal and carboxyl-terminal regions of the molecule hybridize to a 2-kilobase poly(A)+ RNA transcript of unknown identity. This description of the chicken N-CAM gene provides a basis for determining the mechanisms that regulate the differential expression of the N-CAM polypeptide chains during development.
Comments on "A metrics suite for object oriented design (1995)

A suite of object oriented software metrics has recently been proposed by S.R. Chidamber and C.F. Kemerer (see ibid., vol. 20, p. 476-94, 1994). While the authors have taken care to ensure their metrics have a sound measurement theoretical basis, we argue that is premature to begin applying such metrics while there remains uncertainty about the precise definitions of many of the quantities to be observed and their impact upon subsequent indirect metrics. In particular, we show some of the ambiguities associated with the seemingly simple concept of the number of methods per class. The usefulness of the proposed metrics, and others, would be greatly enhanced if clearer guidance concerning their application to specific languages were to be provided. Such empirical considerations are as important as the theoretical issues raised by the authors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Serologic diagnosis of infectious cyclic thrombocytopenia in dogs using an indirect fluorescent antibody test (1983)

An indirect fluorescent antibody test was used for detection of serum antibodies to the platelet-specific rickettsial organism that is the causative agent of infectious cyclic thrombocytopenia (ICT) in dogs. The test converted from negative to positive in 7 of 7 experimentally inoculated dogs. One of 2 attempts to recover the rickettsial agent of ICT from naturally occurring seropositive dogs, by blood inoculation of experimental dogs, was successful. Seemingly, the test did not detect antibodies to Ehrlichia canis, nor did a similar test, using E canis antigen slides, detect antibodies to the rickettsial agent of ICT. The rickettsial agent of ICT has been classified tentatively as E platys. When applied to sera from a group of healthy random-source dogs, the test revealed a relatively low (5%) occurrence of positive reactions. A higher occurrence of positive reactions (35%) was noticed in sera from a group of thrombocytopenic dogs from the University of Florida. A majority of these positive sera were also positive for antibodies to E canis. The highest occurrence of positive reactions was found (greater than 50%) in E canis-positive sera from dogs at the University of Florida, as well as from dogs from 9 other states.
Dynamic Range of Optical Reflectometry with Spectral Interferometry (1999)

I present an optical reflectometry (OR) technique with spectral interferometry (SIOR) that realizes high dynamic range compared with a conventional OR system using the delayed heterodyne technique (DHOR), and report on the application of this system to noninvasive in vivo measurements of the structure of the skin and the nail of an index finger. The theoretically derived dynamic range of SIOR is m /4-times superior to that of DHOR, where m is the number of independent image pixels. A dynamic range of 105 db was experimentally realized, which is comparable to the theoretically expected dynamic range of 112 db.
Synthesis and cycloaddition reaction of 2-cyano-3-indoleacetonitriles. (1986)

The reactions of 3-acylindoles [3-indolecarbaldehyde (1), 3-acetylindole (12), 3-benzoylindole (13), and N-substituted 3-indolecarbaldehydes (20a-d)] with diethyl phosphorocyanidate (DEPC) in the presence of lithium cyanide (LiCN) are described. Treatment of 1 with DEPC and LiCN gave a mixture of (E)- and (Z)-3-cyanomethylene-1-diethylphosphono-2-hydroxyindolines (2 and 3). On the other hand, reaction of 12, 13 and 20a-d with DEPC and LiCN afforded 2-cyano-3-indoleacetonitrile derivatives (16, 19 and 21a-d). Strong base-induced cycloaddition reactions of 2-cyano-1-methyl-3-indoleacetonitrile (21a) with carbon-carbon triple bonds were carried out and gave the corresponding condensation products, 1-amino-4-cyanocarbazoles (22a-e), 6-amino-11-cyanobenzo[b]carbazole (23), pyrido[4, 3-b]carbazole (25), and pyrido[3, 4-b]carbazole (26), in moderate yields.