gebhart/patrepeval huggingface dataset:
Selective Translation of Eukaryotic mRNAs: Functional Molecular Analysis of GRSF-1, a Positive Regulator of Influenza Virus Protein Synthesis (2002)

To understand the regulation of cap-dependent translation initiation mediated by specific 5' untranslated region (UTR) RNA-protein interactions in mammalian cells, we have studied the selective translation of influenza virus mRNAs. Previous work has shown that the host cell mRNA binding protein guanine-rich sequence factor 1 (GRSF-1) bound specifically to conserved viral 5' UTR sequences and stimulated translation of viral 5' UTR-driven mRNAs in vitro. In the present study, we have characterized the functional domains of GRSF-1 and mapped the RNA binding activity of GRSF-1 to RRM 2 (amino acids 194 to 275) with amino-terminal deletion glutathione S-transferase (GST)-GRSF-1 proteins. When these mutants were assayed for functional activity in vitro, deletion of an Ala-rich region (Delta[2-94]) appeared to diminish translational stimulation, while deletion of the Ala-rich region in addition to RRM 1 (Delta[2-194]) resulted in a 4-fold increase in translational activation over wild-type GRSF-1 (an overall 20-fold increase in activity). We have also mapped the GRSF-1 RNA binding site on influenza virus NP and NS1 5' UTRs, which was determined to be the sequence AGGGU. With polysome fractionation and cDNA microarray analysis, we have identified cellular and viral mRNAs containing putative GRSF-1 binding sites that were transcriptionally up-regulated and selectively recruited to polyribosomes following influenza virus infection. Taken together, these studies demonstrate that RRM 2 is critical for GRSF-1 RNA binding and translational activity. Further, our data suggest GRSF-1 functions by selectively recruiting cellular and viral mRNAs containing 5' UTR GRSF-1 binding sites to polyribosomes, which is mediated through interactions with cellular proteins.
Scheme for Demonstration of Fractional Statistics of Anyons in an Exactly Solvable Model (2007)

We propose a scheme to demonstrate fractional statistics of anyons in an exactly solvable lattice model proposed by Kitaev that involves four-body interactions. The required many-body ground state, as well as the anyon excitations and their braiding operations, can be conveniently realized through dynamic laser manipulation of cold atoms in an optical lattice. Because of the perfect localization of anyons in this model, we show that a quantum circuit with only six qubits is enough for demonstration of the basic braiding statistics of anyons. This opens up the immediate possibility of proof-of-principle experiments with trapped ions, photons, or nuclear magnetic resonance systems.
Structure-Activity Relationships of N6-Benzyladenosine-5'-uronamides as A3-Selective Adenosine Agonists (1994)

Adenosine analogues modified at the 5'-position as uronamides and/or as N6-benzyl derivatives were synthesized. These derivatives were examined for affinity in radioligand binding assays at the newly discovered rat brain A3 adenosine receptor and at rat brain A1 and A2a receptors. 5'-Uronamide substituents favored A3 selectivity in the order N-methyl > N-ethyl approximately unsubstituted carboxamide > N-cyclopropyl. 5'-(N-Methylcarboxamido)-N6-benzyladenosine was 37-56-fold more selective for A3 receptors. Potency at A3 receptors was enhanced upon substitution of the benzyl substituent with nitro and other groups. 5'-N-Methyluronamides and N6-(3-substituted-benzyl)adenosines are optimal for potency and selectivity at A3 receptors. A series of 3-(halobenzyl)-5'-N-ethyluronamide derivatives showed the order of potency at A1 and A2a receptors of I approximately Br > Cl > F. At A3 receptors the 3-F derivative was weaker than the other halo derivatives. 5'-N-Methyl-N6-(3-iodobenzyl)adenosine displayed a Ki value of 1.1 nM at A3 receptors and selectivity versus A1 and A2a receptors of 50-fold. A series of methoxybenzyl derivatives showed that a 4-methoxy group best favored A3 selectivity. A 4-sulfobenzyl derivative was a specific ligand at A3 receptors of moderate potency. An aryl amino derivative was prepared as a probe for radioiodination and receptor cross-linking.
Management Guidelines for Mucopolysaccharidosis VI (2007)

Mucopolysaccharidosis VI (Maroteaux-Lamy syndrome) is a lysosomal storage disease that is characterized by systemic clinical manifestations and significant functional impairment. Diagnosis and management are often challenging because of the considerable variability in symptom presentation and rate of progression. The optimal standard of care should be based on evidence from randomized, controlled trials, meta-analyses, systematic reviews, and expert opinion. In support of this goal, comprehensive management guidelines have been drafted by an international group of experts in the management of patients with mucopolysaccharidosis VI. The guidelines provide a detailed outline of disease manifestations by body system, recommendations for regular assessments, and an overview of current treatment options.
WE-E-J-6B-02: Image-Guided Minimally Invasive Robotic Surgery (2005)

Image-guided surgery allows surgeons to specifically target diseased tissue while sparing healthy tissue, reducing morbidity and improving patient outcomes. Minimally invasive surgical techniques deliver specific intervention without the morbidity associated with large open incisions. Image-guidance technology has the potential to provide significant benefits for minimally invasive surgery, where surgeons must usually cope with difficult access and reduced visualization. A new generation of minimally invasive surgery has emerged that uses a robot to hold surgical tools during laparoscopy or thoracoscopy, under direct control by the surgeon. Surgical robots offer an excellent platform upon which to fuse the benefits of image-guided and minimally invasive surgery. The da Vinci surgical robot system has a high-fidelity video display, a stereo endoscope, and sensors to track the position of each surgical instrument and the endoscope, offering a potentially ready-made stream of data for registration and tracking. The proposed project involved an academic/industry collaboration to give da Vinci the fundamentally new capability of steering to a specific point in the patient's frame of reference. Using the traditional da Vinci control paradigm, the robot simply follows the surgeon's relative motions and has no concept of the patient's frame of reference. With the new ability to navigate through the patient's frame of reference as described by preoperative imagery data sets registered to the patient during surgery, da Vinci will enable surgeons to more accurately perform targeted tasks such as biopsy, tumor ablation, resection planning, and gene therapy in a minimally invasive manner. The project used liver surgery as a motivating application. This work addressed three feasibility milestones: Establishing communication between the surgical robot and existing image-guidance software, establishing robot tracking error under 2 mm, and establishing surface registration errors under 5 mm.
Pharmacokinetic Properties of 2nd-Generation Fibroblast Growth Factor-1 Mutants for Therapeutic Application (2012)

Fibroblast growth factor-1 (FGF-1) is an angiogenic factor with therapeutic potential for the treatment of ischemic disease. FGF-1 has low intrinsic thermostability and is characteristically formulated with heparin as a stabilizing agent. Heparin, however, adds a number of undesirable properties that negatively impact safety and cost. Mutations that increase the thermostability of FGF-1 may obviate the need for heparin in formulation and may prove to be useful "2nd-generation" forms for therapeutic use. We report a pharmacokinetic (PK) study in rabbits of human FGF-1 in the presence and absence of heparin, as well as three mutant forms having differential effects upon thermostability, buried reactive thiols, and heparin affinity. The results support the hypothesis that heparan sulfate proteoglycan (HSPG) in the vasculature of liver, kidney and spleen serves as the principle peripheral compartment in the distribution kinetics. The addition of heparin to FGF-1 is shown to increase endocrine-like properties of distribution. Mutant forms of FGF-1 that enhance thermostability or eliminate buried reactive thiols demonstrate a shorter distribution half-life, a longer elimination half-life, and a longer mean residence time (MRT) in comparison to wild-type FGF-1. The results show how such mutations can produce useful 2nd-generation forms with tailored PK profiles for specific therapeutic application.
Oxidation of LDL by Myeloperoxidase and Reactive Nitrogen Species (2000)

Oxidative modification of low density lipoprotein (LDL) appears to play an important role in atherogenesis. Although the precise mechanisms of LDL oxidation in vivo are unknown, several lines of evidence implicate myeloperoxidase and reactive nitrogen species, in addition to ceruloplasmin and 15-lipoxygenase. Myeloperoxidase generates a number of reactive species, including hypochlorous acid, chloramines, tyrosyl radicals, and nitrogen dioxide. These reactive species oxidize the protein, lipid, and antioxidant components of LDL. Modification of apolipoprotein B results in enhanced uptake of LDL by macrophages with subsequent formation of lipid-laden foam cells. Nitric oxide synthases produce nitric oxide and, under certain conditions, superoxide radicals. Numerous other sources of superoxide radicals have been identified in the arterial wall, including NAD(P)H oxidases and xanthine oxidase. Nitric oxide and superoxide readily combine to form peroxynitrite, a reactive nitrogen species capable of modifying LDL. In this review, we examine the reaction pathways involved in LDL oxidation by myeloperoxidase and reactive nitrogen species and the potential protective effects of the antioxidant vitamins C and E.
High-Speed Circuit Designs for Transmitters in Broadband Data Links (2006)

Various high-speed techniques including internal peaking, differentially stacked inductor, and dual-loop PLL for wireline communications are proposed,analyzed, and verified by means of three independent circuits. A multiplexer incorporates multiple peaking techniques and gate control switching to achieve an operation speed of 20 Gb/s while consuming 22 mW from a 1.8-V supply. A voltage-controlled oscillator employing differentially stacked inductor accomplishes a phase noise of -90dBc/Hzat 1-MHz offset with a minimum power of 1 mW. A clock multiplication unit utilizes dual-loop architecture as well as a third-order loop filter, arriving at an output jitter of 0.2 ps, rms (0.87 ps, rms de-embedding 0.84 ps, rms from the instruments) and 4.5 ps, pp while consuming 40 mW from a 1.8-V supply.
Submicron area NbN/MgO/NbN tunnel junctions for SIS mixer applications (1991)

The development of submicron area mixer elements for operation in the submillimeter wave range is discussed. High-current-density NbN/MgO/NbN tunnel junctions with areas down to 0.1 mu m/sup 2/ have been fabricated in both planar and edge geometries. The planar junctions were fabricated from in situ deposited trilayers using electron-beam lithography to pattern submicron area mesas. Modifications of fabrication techniques used in larger-area NbN tunnel junctions are required and are discussed. The NbN/MgO/NbN edge junction process using sapphire substrates has been transferred to technologically important quartz substrates using MgO buffer layers to minimize substrate interactions. The two junction geometries are compared and contrasted in the context of submillimeter wave mixer applications.
Spectrally efficient direct-detected OFDM transmission employing an iterative estimation and cancellation technique (2009)

We demonstrate a linearly field-modulated, direct-detected virtual SSB-OFDM (VSSB-OFDM) transmission with an RF tone placed at the edge of the signal band. By employing the iterative estimation and cancellation technique for the signal-signal beat interference (SSBI) at the receiver, our approach alleviates the need of the frequency gap, which is typically reserved for isolating the SSBI, and saves half the electrical bandwidth, thus being very spectrally efficient. We derive the theoretical model for the VSSB-OFDM system and detail the signal processing for the iterative approach conducted at the receiver. Possible limitations for this iterative approach are also given and discussed. We successfully transmit a 10 Gbps, 4-quadrature-amplitude-modulation (QAM) VSSB-OFDM signal through 340 km of uncompensated standard single mode fiber (SSMF) with almost no penalty. In addition, the simulated results show that the proposed scheme has an approximately 2 dB optical-signal-to-noise-ratio (OSNR) gain and has a better chromatic dispersion (CD) tolerance compared with the previous intensity-modulated SSB-OFDM system.
Sequence patterns produced by incomplete enzymatic digestion or one‐step Edman degradation of peptide mixtures as probes for protein database searches (1996)

Mass spectrometric peptide mapping of proteins isolated by polyacrylamide gel electrophoresis is a rapid method for identifying proteins in sequence databases. A majority of tryptic peptide maps were found to contain pairs of peptide ion peaks separated by the molecular weight of the lysyl or arginyl residue. These peaks originate from amino acid sequence patterns such as Lys-Lys where trypsin has cleaved C-terminals to either one of the lysines. The peptide mass and the pattern define an N- or C-terminal sequence tag. Searching sequence databases by such a sequence tag results in only a moderate number of matches and significantly reduces the number of database matches when used in combination with a peptide mass map. Two N- or C-terminal sequence tags alone unambiguously identify a protein in most cases. The technique discussed here is simple, does not require additional measurements, and increases the percentage of protein samples that can be identified by their mass maps alone. N-Terminal peptide sequence tags for database searching can also be generated by manual one-step Edman degradation of the unseparated peptide mixture.
Conducting‐Polymer Nanotubes for Controlled Drug Release (2006)

Controlled release of an anti-inflammatory drug from PEDOT nanotubes using electrical stimulation is demonstrated (see Figure and Inside Cover). The fabrication process includes electrospinning of a biodegradable polymer into which the drug has been incorporated, followed by electrochemical deposition of the conducting polymer around the drug-loaded electrospun nanoscale fibers.
Biochemical Characterization of β-Lactamases Bla1 and Bla2 from Bacillus anthracis (2003)

The Sterne and Ames strains of Bacillus anthracis carry chromosomal genes bla1 and bla2, which confer beta-lactam resistance when expressed in Escherichia coli. MIC measurements and steady-state kinetic analyses indicate that Bla1 possesses penicillinase activity while Bla2 possesses penicillinase, cephalosporinase, and carbapenem-hydrolyzing activities.
Biostimulatory Windows in Low-Intensity Laser Activation: Lasers, Scanners, and NASA's Light-Emitting Diode Array System (2001)

This independence is of practical importance, at least for the medical application of photobiological effects achieved at low-energy density levels, accounting for the success and the failure in most of the cold laser uses since Mester's pioneering work.
Review Networks for Caption Generation (2016)

We propose a novel extension of the encoder-decoder framework, called a review network. The review network is generic and can enhance any existing encoder- decoder model: in this paper, we consider RNN decoders with both CNN and RNN encoders. The review network performs a number of review steps with attention mechanism on the encoder hidden states, and outputs a thought vector after each review step; the thought vectors are used as the input of the attention mechanism in the decoder. We show that conventional encoder-decoders are a special case of our framework. Empirically, we show that our framework improves over state-of- the-art encoder-decoder systems on the tasks of image captioning and source code captioning.
Fiber-Optic Crossbar Switch With Broadcast Capability (1988)

An all-optical fiber-optic crossbar switch capable of interconnecting N input fibers to M output fibers with an arbitrary interconnect pattern has been constructed. The switch can use any 1-D or 2-D spatial light modulator capable of realizing N X M pixels and can be configured for permutations, full or partial broadcast, or "wired-oring" of several inputs to a given output. Values of N and M achievable depend on the light efficiency of the switch components and the data rate. A 4X4 switch has been built; in a computer switching environment, the approach is capable of realizing a 16 X16 switch at 1 Gb/s and a 32 X32 switch at >100 Mb/s. The development of the switch has included construction of both a PLZT switch array and a magneto-optic switch array. We report on the investigations of both technologies. Reconfiguration times in the range of a few microseconds to a few tens of microseconds are of interest. A reconfiguration time shorter than 20 ps was actually achieved.
Preparing to Capture Carbon (2007)

Carbon sequestration from large sources of fossil fuel combustion, particularly coal, is an essential component of any serious plan to avoid catastrophic impacts of human-induced climate change. Scientific and economic challenges still exist, but none are serious enough to suggest that carbon capture and storage will not work at the scale required to offset trillions of tons of carbon dioxide emissions over the next century. The challenge is whether the technology will be ready when society decides that it is time to get going.
Attenuated T 2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution (1997)

Fast transverse relaxation of 1H, 15N, and 13C by dipole-dipole coupling (DD) and chemical shift anisotropy (CSA) modulated by rotational molecular motions has a dominant impact on the size limit for biomacromolecular structures that can be studied by NMR spectroscopy in solution. Transverse relaxation-optimized spectroscopy (TROSY) is an approach for suppression of transverse relaxation in multidimensional NMR experiments, which is based on constructive use of interference between DD coupling and CSA. For example, a TROSY-type two-dimensional 1H,15N-correlation experiment with a uniformly 15N-labeled protein in a DNA complex of molecular mass 17 kDa at a 1H frequency of 750 MHz showed that 15N relaxation during 15N chemical shift evolution and 1HN relaxation during signal acquisition both are significantly reduced by mutual compensation of the DD and CSA interactions. The reduction of the linewidths when compared with a conventional two-dimensional 1H,15N-correlation experiment was 60% and 40%, respectively, and the residual linewidths were 5 Hz for 15N and 15 Hz for 1HN at 4 degrees C. Because the ratio of the DD and CSA relaxation rates is nearly independent of the molecular size, a similar percentagewise reduction of the overall transverse relaxation rates is expected for larger proteins. For a 15N-labeled protein of 150 kDa at 750 MHz and 20 degrees C one predicts residual linewidths of 10 Hz for 15N and 45 Hz for 1HN, and for the corresponding uniformly 15N,2H-labeled protein the residual linewidths are predicted to be smaller than 5 Hz and 15 Hz, respectively. The TROSY principle should benefit a variety of multidimensional solution NMR experiments, especially with future use of yet somewhat higher polarizing magnetic fields than are presently available, and thus largely eliminate one of the key factors that limit work with larger molecules.
Capturing buried defects in metal interconnections with electron beam inspection system (2013)

In this paper we present a novel mode of electron beam inspection (EBI), entitled super wide optics (SWO) mode, which can effectively detect buried defects in tungsten (W) plugs and copper (Cu) wires. These defects are defects of interest (DOI) to integrated circuit (IC) manufacturers because they are not detectable in optical inspection, voltage contrast (VC) mode EBI or physical mode EBI. We used engineering systems to study two samples, a tungsten chemical mechanical polish (CMP) wafer and a copper CMP wafer with a silicon carbon nitride (SiCN) cap layer. EBI with our novel SWO mode was found to capture many dark defects on these two wafers. Furthermore, defect review with all three EBI modes found some of these dark defects were unique to SWO mode. For verification, physical failure analysis was performed on some SWO-unique DOI. The cross-sectional scanning electron microscope (SEM) images and transmission electron microscope (TEM) images confirmed that the unique DOI were buried voids in W-plugs and copper wire thinning caused by either buried particles or buried particle induced metal trench under-etch. These DOI can significantly increase the resistance of metal interconnects of IC chip and affect the chip yield. This new EBI mode can provide an in-line monitoring solution for these DOI, which does not exist before this study.
A new self-emulsifying formulation of mefenamic acid with enhanced drug dissolution (2014)

To enhance the dissolution of poorly soluble mefenamic acid, self-emulsifying formulation (SEF), composing of oil, surfactant and co-surfactant, was formulated. Among the oils and surfactants studied, Imwitor® 742, Tween® 60, Cremophore® EL and Transcutol® HP were selected as they showed maximal solubility to mefenamic acid. The ternary phase diagram was constructed to find optimal concentration that provided the highest drug loading. The droplet size after dispersion and drug dissolution of selected formulations were investigated. The results showed that the formulation containing Imwitor® 742, Tween® 60 and Transcutol® HP (10:30:60) can encapsulate high amount of mefenamic acid. The dissolution study demonstrated that, in the medium containing surfactant, nearly 100% of mefenamic acid were dissolved from SEF within 5 min while 80% of drugs were dissolved from the commercial product in 45 min. In phosphate buffer (without surfactant), 80% of drug were dissolved from the developed SEF within 5 min while only about 13% of drug were dissolved in 45 min, from the commercial product. The results suggested that the SEF can enhance the dissolution of poorly soluble drug and has a potential to enhance drug absorption and improve bioavailability of drug.