gebhart/patrepeval huggingface dataset:
Videoconferencing over packet-based networks (1997)

The Internet explosion is driving the need for new collaboration tools which will enable two or more users to share data, audio, and video. The real-time packet-based solutions which are emerging differ considerably from the circuit-switch solutions which have existed for some time now. In this paper, we present one such packet-based approach, the Multimedia Multiparty Teleconferencing (MMT) system, which was fully implemented as a research prototype. Using MMT as an example, we address some of the fundamental issues related to videoconferencing systems in a packet-based environment, and discuss the differences with the traditional circuit-switch approaches, namely, the ITU H.320 standard. In particular, MMT is a distributed solution, while H.320 is centralized. The use of multicast and a novel video-mixing technique to facilitate the distributed solution are presented. Furthermore, MMT audio and video streams are susceptible to congestion and packet loss in the shared media packet-based environment, while H.320 streams use dedicated connections. As such, synchronization, error resilience, and dynamic rate control schemes for the packet-based system are presented.
Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana (2002)

Regulation of gene expression at the post-transcriptional level is mainly achieved by proteins containing well-defined sequence motifs involved in RNA binding. The most widely spread motifs are the RNA recognition motif (RRM) and the K homology (KH) domain. In this article, we survey the complete Arabidopsis thaliana genome for proteins containing RRM and KH RNA-binding domains. The Arabidopsis genome encodes 196 RRM-containing proteins, a more complex set than found in Caenorhabditis elegans and Drosophila melanogaster. In addition, the Arabidopsis genome contains 26 KH domain proteins. Most of the Arabidopsis RRM-containing proteins can be classified into structural and/or functional groups, based on similarity with either known metazoan or Arabidopsis proteins. Approximately 50% of Arabidopsis RRM-containing proteins do not have obvious homologues in metazoa, and for most of those that are predicted to be orthologues of metazoan proteins, no experimental data exist to confirm this. Additionally, the function of most Arabidopsis RRM proteins and of all KH proteins is unknown. Based on the data presented here, it is evident that among all eukaryotes, only those RNA-binding proteins that are involved in the most essential processes of post-transcriptional gene regulation are preserved in structure and, most probably, in function. However, the higher complexity of RNA-binding proteins in Arabidopsis, as evident in groups of SR splicing factors and poly(A)-binding proteins, may account for the observed differences in mRNA maturation between plants and metazoa. This survey provides a first systematic analysis of plant RNA-binding proteins, which may serve as a basis for functional characterisation of this important protein group in plants.
Identification by Mass Spectrometry of a New α-Tubulin Isotype Expressed in Human Breast and Lung Carcinoma Cell Lines (2001)

The extensive C-terminal molecular heterogeneity of alpha- and beta-tubulin is a consequence of multiple isotypes, the products of distinct genes, that undergo several posttranslational modifications. These include polyglutamylation and polyglycylation of both subunits, reversible tyrosination and removal of the penultimate glutamate from alpha-tubulin, and phosphorylation of the beta III isotype. A mass spectrometry-based method has been developed for the analysis of the C-terminal diversity of tubulin from human cell lines. Total cell extracts are resolved by SDS--PAGE and transferred to nitrocellulose, and the region of the blot corresponding to tubulin (approximately 50 kDa) was excised and digested with CNBr to release the highly divergent C-terminal tubulin fragments. The masses of the human alpha- and beta-tubulin CNBr-derived C-terminal peptides are all in the 1500--4000 Da mass range and can be analyzed directly by MALDI-TOF mass spectrometry in the negative ion mode without significant interference from other released peptides. In this study, the tubulin isotype diversity in MDA-MB-231, a human breast carcinoma cell line, and A549, a human non-small lung cancer cell line, is reported. The major tubulin isotypes present in both cell lines are k-alpha 1 and beta 1. Importantly, we report a previously unknown alpha isotype present at significant levels in both cell lines. Moreover, the degree of posttranslational modifications to all isotypes was limited. Glu-tubulin, in which the C-terminal tyrosine of alpha-tubulin is removed, was not detected. In contrast to mammalian neuronal tubulin which exhibits extensive polyglutamylation, only low-level monoglutamylation of the k-alpha 1 and beta 1 isotypes was observed in these two human cell lines.
Radioiodinated biotin derivatives for in vitro radioassays. (1987)

The synthesis of two radioiodinated biotin derivatives with the biotin-ureido group intact is described. This synthesis was performed by coupling (pH 8.5, 20-22 degrees C, 90 min) N-hydroxysuccinimidobiotin to tyramine, which was radioiodinated prior to this using a modified chloramine-T method. Two derivatives were produced, the N-[beta-(4-OH-3-125I-phenyl)ethyl] and the N-[beta-(4-OH-3,5-di 125I-phenyl)ethyl] biotin amides, depending on the amount of tyramine used in the radioiodination reaction. The final products were separated by thin layer chromatography (n-butanol: 2N NH4OH: ethanol, 3:1:1, v/v/v). The radioiodinated derivatives that were synthesized or their resulting mixture were found to complete with biotin for the avidin-binding sites; thus, they were capable of being used as tracers in biotin radioassays. The specific activity of their mixture was high-greater than 350 Ci/mmol-and they were stable for 2 mo at 4 degrees C.
Interleaving syntax and semantics in an efficient bottom-up parser (1994)

We describe an efficient bottom-up parser that interleaves syntactic and semantic structure building. Two techniques are presented for reducing search by reducing local ambiguity: Limited left context constraints are used to reduce local syntactic ambiguity, and deferred sortal-constraint application is used to reduce local semantic ambiguity. We experimentally evaluate these techniques, and show dramatic reductions in both number of chart edges and total parsing time. The robust processing capabilities of the parser are demonstrated in its use in improving the accuracy of a speech recognizer.
Cell cycle-dependent expression of Nek2, a novel human protein kinase related to the NIMA mitotic regulator of Aspergillus nidulans. (1994)

The serine/threonine protein kinase NIMA of Aspergillus nidulans is required for entry into mitosis and may function in parallel to the universal mitotic inducer p34cdc2. Here, we report the isolation of complementary DNAs encoding Nek2 and Nek3, two novel human protein kinases structurally related to NIMA. Sequence comparisons revealed several unique features which may define a family of NIMA-related protein kinases. Nek2 was chosen for further study since it represents the closest known mammalian relative of NIMA. Chromosomal mapping of the nek2 gene identified two independent loci on chromosomes 1 and 14, and Northern blot analyses revealed the expression of two distinct mRNAs of approximately 2.4 and 4.7 kilobases in all human cell lines examined. In HeLa cells synchronized by both drug arrest and elutriation, a strikingly cell cycle-dependent pattern of Nek2 expression could be observed; Nek2 protein was almost undetectable during G1 but accumulated progressively throughout S, reaching maximal levels in late G2. These observations demonstrate that Nek2 resembles Aspergillus NIMA, not only in its catalytic domain, but also in its cell cycle-dependent expression. Hence, the human Nek2 protein kinase may also function at the onset of mitosis.
Visually-guided haptic object recognition (1987)

Sensory capabilities are vital if a robot is to function autonomously in unknown or partially specified environments, if it is to carry out complex, roughly detailed tasks, and if it is to interact with and to learn from the world around it. Perception forms the all important interface between the cogitative organism and the world in which it must act and survive. Hence the first step toward intelligent, autonomous robots is to develop this interface--to provide robots with perceptual capabilities. This work presents a model for robotic perception. Within the framework of this model, we have developed a system which utilizes passive vision and active touch for the task of object categorization. The system is organized as a highly modularized, distributed hierarchy of domain specific and informationally encapsulated knowledge-based experts. The visual subsystem is passive and consists of a two-dimensional region analysis and a three-dimensional edge analysis. The haptic subsystem is active and consists of a set of modules which either execute exploratory procedures to extract information from the world or which combine information from lower level modules into more complex representations. We also address the issues of visually-guided haptic exploration and intersensory integration. Finally, we establish representational and reasoning paradigms for dealing with generic objects. Both representation and reasoning are feature-based. The representation includes both definitional information in the form of a hierarchy of frames and spatial/geometric information in the form of the spatial polyhedron.
Growth factors in corneal wound healing following refractive surgery: A review (2002)

The first part of this review article aims to provide important basic definitions of growth factor terminology, and to put forward a model for understanding the role of growth factors in a wound healing context. In the second part of the paper, we review the literature on growth factors in the cornea, including that on changes associated with wound healing following refractive surgery in the epithelial, stromal, and endothelial layers. The role of growth factors in stromal removal, corneal neovascularization, corneal innervation and wound healing is considered. The importance of the epithelial-stromal interaction is discussed, including the role of growth factors in keratocyte apoptosis. In the final section, we review the current literature on endogenous and exogenous modulation of growth factors in corneal wound healing. This includes important in vitro work but aims to emphasize clinically relevant results. Photorefractive keratectomy (PRK) may have short-term complications such as pain and haze, whereas laser in situ keratomilieusis (LASIK) may have longer-term adverse effects on corneal biomechanics. The emerging technique of laser epithelial keratomilieusis (LASEK) provides an interesting alternative wound which may be less susceptible to the inherent complications of PRK and LASIK. At present, the phenomenon of iatrogenic keratectasia following LASIK is not fully understood, but these features of wound healing following PRK may be amenable to growth factor modulation.
An eight-issue tree-VLIW processor for dynamic binary translation (2002)

Presented is an 8-issue tree-VLIW processor designed for efficient support of dynamic binary translation. This processor confronts two primary problems faced by VLIW architectures: binary compatibility and branch performance. Binary compatibility with existing architectures is achieved through dynamic binary translation which translates and schedules PowerPC instructions to take advantage of the available instruction level parallelism. Efficient branch performance is achieved through tree instructions that support multi-way path and branch selection within a single VLIW instruction. The processor architecture is described, along with design details of the branch unit, pipeline, register file and memory hierarchy for a 0.25 micron standard-cell design. Performance simulations show that the simplicity of a VLIW architecture allows a wide-issue processor to operate at high frequencies.
Studies on Hydrogen Exchange. IX. Electrophilic Deuteration of 2-Pyridinol, 2-Quinolinol, and 1-Isoquinolinol (1968)

Acid-catalyzed deuterations of 2-pyridinol, 2-quinolinol, and 1-isoquinolinol were examined and their deuteration reactivities were discussed in connection with their electrophilic substitution reactions other than deuteration.
Modeling of low-temperature depolymerization of poly (methyl methacrylate) promoted by ion beam (1999)

The role played by the ion beam in the depolymerization of poly(methyl methacrylate) (PMMA) is the creation of initiators for the unzipping reaction at relatively low temperatures [lower than the ceiling temperature of PMMA (TC=220 °C)]. Monomer (MMA) evolution out of the polymeric film is thus governed by the kinetics of the chemical reaction and also by the diffusion of monomer inside the polymeric film. In this work this phenomenon has been described by using simple models in which both one- and two-dimension monomer diffusion is considered. Exact analytical solutions of the models are provided. The theory fit well the experimental data and allows for the determination of important parameters such as the kinetics constant of the depolymerization and the monomer diffusion coefficient, D, inside the polymer film. Thus, the pulsed ion beam technique, here modeled, is useful not only for extracting D values of slow diffusants in polymers, but even for measuring kinetics constants of depolymerization at a temperature well below that needed for the formation of suitable thermal initiators.
Severe ischemia of the lower limb and of the intestine associated with systemic vasoconstrictor therapy and femoral arterial catheterization (2006)

Arterial catheterization combined with the administration of vasoconstrictor drugs, particularly vasopressin or terlipressin, can lead to local ischemic complications and severe intestinal ischemia in infants in shock.
The Comparative Safety of Intravenous Iron Dextran, Iron Saccharate, and Sodium Ferric Gluconate (2000)

Intravenous iron treatment is an important component of anemia therapy for patients on dialysis. Until recently iron dextran was the only parenteral form of iron available in the United States. This drug has been associated with occasional serious adverse reactions, including full-blown anaphylaxis. In 1999 the Food and Drug Administration approved a second form of iron for intravenous administration, sodium ferric gluconate in sucrose. It is expected that by the time of this publication, a third agent, iron saccharate will also be approved. In this review the comparative safety of these three agents is critically evaluated.
Localization of the Rab3 Small G Protein Regulators in Nerve Terminals and Their Involvement in Ca2+-dependent Exocytosis (1998)

The Rab3 small G protein subfamily (Rab3) consists of four members, Rab3A, -B, -C, and -D. We have recently isolated and characterized the Rab3 regulators, GDP/GTP exchange protein (GEP) and GTPase activating protein (GAP), both of which are specific for the Rab3 subfamily. Rab3 GEP stimulates the conversion of the GDP-bound inactive form to the GTP-bound active form, whereas Rab3 GAP stimulates the reverse reaction. Of the four members of the Rab3 subfamily, evidence is accumulating that Rab3A is involved in Ca2+-dependent exocytosis, particularly in neurotransmitter release. We first analyzed the subcellular localization of Rab3 GEP and GAP in rat brain. Subcellular fractionation analysis showed that both Rab3 GEP and GAP were enriched in the synaptic soluble fraction. Immunocytochemical analysis in primary cultured rat hippocampal neurons showed that both Rab3 GEP and GAP were concentrated at the presynaptic nerve terminals. We then examined whether Rab3 GEP and GAP were involved in Ca2+-dependent exocytosis by use of human growth hormone (GH) co-expression assay system of cultured PC12 cells. Overexpression of the deletion mutant of Rab3 GEP possessing the catalytic activity reduced the high K+-induced GH release without affecting the basal GH release, whereas that of the deletion mutant lacking the catalytic activity showed no effect on the high K+-induced GH release. In contrast, overexpression of Rab3 GAP or its deletion mutant possessing the catalytic activity did not affect the high K+-induced GH release or the basal GH release. These results indicate that Rab3 GEP and GAP are colocalized with Rab3A at the synaptic release sites and suggest that they regulate the activity of Rab3A and are involved in Ca2+-dependent exocytosis.
Tunable High-Q N-Path Band-Pass Filters: Modeling and Verification (2011)

A differential single-port switched-RC N-path filter with band-pass characteristic is proposed. The switching frequency defines the center frequency, while the RC-time and duty cycle of the clock define the bandwidth. This allows for high-Q highly tunable filters which can for instance be useful for cognitive radio. Using a linear periodically time-variant (LPTV) model, exact expressions for the filter transfer function are derived. The behavior of the circuit including non-idealities such as maximum rejection, spectral aliasing, noise and effects due to mismatch in the paths is modeled and verified via measurements. A simple RLC equivalent circuit is provided, modeling bandwidth, quality factor and insertion loss of the filter. A 4-path architecture is realized in 65 nm CMOS. An off-chip transformer acts as a balun, improves filter-Q and realizes impedance matching. The differential architecture reduces clock-leakage and suppresses selectivity around even harmonics of the clock. The filter has a constant <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$-$</tex></formula> 3 dB bandwidth of 35 MHz and can be tuned from 100 MHz up to 1 GHz. Over the whole band, IIP3 is better than 14 dBm, <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm P}_{\rm 1dB}=2\ $</tex></formula> dBm and the noise figure is 3–5 dB, while the power dissipation increases from 2 mW to 16 mW (only clocking power).
Bexarotene Blocks Calcium-Permeable Ion Channels Formed by Neurotoxic Alzheimer’s β-Amyloid Peptides (2014)

The anticancer drug bexarotene has been shown to restore cognitive functions in animal models of Alzheimer's disease, but its exact mechanism of action remains elusive. In the present report, we have used a combination of molecular, physicochemical, and cellular approaches to elucidate the mechanisms underlying the anti-Alzheimer properties of bexarotene in neural cells. First of all, we noticed that bexarotene shares a structural analogy with cholesterol. We showed that cholesterol and bexarotene compete for the same binding site in the C-terminal region of Alzheimer's β-amyloid peptide 1-42 (Aβ1-42). This common bexarotene/cholesterol binding domain was characterized as a linear motif encompassing amino acid residues 25-35 of Aβ1-42. Because cholesterol is involved in the oligomerization of Alzheimer's β-amyloid peptides into neurotoxic amyloid channels, we studied the capability of bexarotene to interfere with this process. We showed that nanomolar concentrations of bexarotene efficiently prevented the cholesterol-dependent increase of calcium fluxes induced by β-amyloid peptides Aβ1-42 and Aβ25-35 in SH-SY5Y cells, suggesting a direct effect of the drug on amyloid channel formation. Molecular dynamics simulations gave structural insights into the role of cholesterol in amyloid channel formation and explained the inhibitory effect of bexarotene. Because it is the first drug that can both inhibit the binding of cholesterol to β-amyloid peptides and prevent calcium-permeable amyloid pore formation in the plasma membrane of neural cells, bexarotene might be considered as the prototype of a new class of anti-Alzheimer compounds. The experimental approach developed herein can be used as a screening strategy to identify such compounds.
Lensless digital holographic microscope with light-emitting diode illumination (2004)

We demonstrate the operation of a digital in-line microscope with LED illumination. We show with a practical example that, for typical setups, the limited temporal coherence and the spatial incoherence of the source do not affect the resolving power of the system. On the contrary, important advantages are obtained in terms of signal-to-noise ratio and alignment simplification.
12-O-tetradecanoyl-phorbol-13-acetate induction of the human collagenase gene is mediated by an inducible enhancer element located in the 5'-flanking region. (1987)

Genomic clones coding for human fibroblast collagenase were isolated. By constructing and transfecting mutants with 5' and 3' deletion mutations of the 5' control region of the gene into human or murine cells, we delimited a 32-base-pair sequence at positions -73 to -42 which is required for the induction of transcription by the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. The DNA element behaves as a 12-O-tetradecanoyl-phorbol-13-acetate-inducible enhancer: it mediates the stimulation of transcription to the heterologous herpes simplex virus thymidine kinase promoter and acts in a position- and orientation-independent manner. Differences in enhancer efficiency in different cell lines are interpreted to indicate differences in the activity of a trans-acting factor.
Designing dual-trench alternating phase-shift masks for 140-nm and smaller features using 248-nm KrF and 193-nm ArF lithography (1998)

One method for making the alternating phase-shift mask involves cutting a trench into the quartz of the mask using an anisotropic dry etch, followed by an isotropic etch to move the corners of the trench underneath the chrome to minimize problems caused by diffraction at the bottom corners of the phase-trench. This manufacturing method makes the addition of subresolution scattering bars and serifs problematic, because the amount of the undercut causes chrome lifting of these small features. Adding an additional anisotropically etched trench to both cut and uncut regions is helpful, but the etch does not move the trench corners under the chrome and result in a loss to intensity and image contrast. At 248 nm illumination and 4X magnification, our work shows that a combination of 240 nm dual-trench and 5 nm to 10 nm undercut produces images with equal intensity between shifted and unshifted regions without loss of image contrasts. This paper demonstrates optical proximity correction for doing 100 nm, 120 nm, 140 nm and 180 nm lines of varying pitch for a simple alternating phase-shift mask, with no dual-trench or undercut. Then the electromagnetic field simulator, TEMPEST, is used to find the best combination of dual-trench depth and amount of undercut for an alternating phase-shift mask. Phase measurement using 248 nm light and depth measurement of thirty-six unique combinations of dual-trench and phase-shift trench are shown. Based on modeling and experimental results, recommendations for making a fine tuned dual-trench 248 nm mask, as well as an extension of the dual-trench alternating phase-shift technique to 193 nm lithography, are made.
A Facile System for Encoding Unnatural Amino Acids in Mammalian Cells (2009)

A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl-tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl-tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal tRNA-aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins.