gebhart/patrepeval huggingface dataset:
TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C <sub>5</sub> and C <sub>6</sub> Epimerization Reactions (2017)

There is currently little information on nonphosphorylated sugar epimerases, which are of potential interest for producing rare sugars. We found a gene (the TM0416 gene) encoding a putative d-tagatose-3-epimerase-related protein from the hyperthermophilic bacterium <i>Thermotoga maritima</i> We overexpressed the TM0416 gene in <i>Escherichia coli</i> and purified the resulting recombinant protein for detailed characterization. Amino acid sequence alignment and a structural similarity search revealed that TM0416 is a putative nonphosphorylated sugar epimerase. The recombinant enzyme exhibited maximal C-3 epimerization of l-ribulose to l-xylulose at ∼80°C and pH 7 in the presence of 1 mM Mn<sup>2+</sup> In addition, this enzyme showed unusually high activity for the epimerization of d-tagatose to d-sorbose, with a conversion yield of 20% after 6 h at 80°C. Remarkably, the enzyme catalyzed the isomerization of d-erythrose or d-threose to d-erythrulose significantly, with conversion yields of 71% and 54.5%, respectively, after 6 h at 80°C at pH 7. To further investigate the substrate specificity of TM0416, we determined its crystal structures in complex with divalent metal ions and l-erythrulose at resolutions of 1.5 and 1.6 Å. Detailed inspection of the structural features and biochemical data clearly demonstrated that this metalloenzyme, with a freely accessible substrate-binding site and neighboring hydrophobic residues, exhibits different and promiscuous substrate preferences, compared with its mesophilic counterparts. Therefore, this study suggests that TM0416 can be functionally classified as a novel type of l-ribulose 3-epimerase (R3E) with d-erythrose isomerase activity.<b>IMPORTANCE</b> Rare sugars, which occur naturally in small amounts, have attracted considerable attention in the food and drug industries. However, there is little information on nonphosphorylated sugar epimerases, which might potentially be applied for the production of rare sugars. This study describes the characterization and functional annotation of a putative nonphosphorylated sugar 3-epimerase from a hyperthermophilic bacterium. Furthermore, we determined its crystal structures in complex with divalent metal ions and l-erythrulose, highlighting its metal-dependent, bifunctional, sugar-isomerizing activity. This hyperthermophilic R3E exhibited d-erythrose/d-threose isomerase activity, with structural features near the substrate-binding site distinct from those of its mesophilic counterparts. Moreover, this metalloenzyme showed unusually high activity for the epimerization of d-tagatose to d-sorbose at 70°C. Therefore, TM0416 can be functionally classified as a novel type of promiscuous R3E with a potential for the production of rare sugars for the food and pharmaceutical industries.
Supplementary Materials and Methods, Supplementary Figure 1-8 from Harnessing the hERG1/β1 Integrin Complex via a Novel Bispecific Single-chain Antibody: An Effective Strategy against Solid Cancers (2023)

<p>Supplementary Table S1 shows nucleotide sequence of the scDb-hERG1-β1. Supplementary Table S2 reports a list of primers. Supplementary Figure S1 dot blot and Coomassie staining of different scDb-hERG1-β1 clones. Supplementary Figure S2 shows peptide ELISA assay performed using different peptides. Supplementary Figure S3 shows Figure S3 cell ELISA assay performed using different cancer cell lines. Supplementary Figure S4 shows dose-dependence curves of different cell lines treated with scDb-hERG1-β1. Supplementary Figure S5 shows cell cycle plots. Supplementary Figure S6 shows spheroid growth curves of different cancer cell lines. Supplementary Figure S7 shows microscopic appearance of spheroids of PANC-1, HCT116 and MIAPaca 2 cells. Supplementary Figure S8 shows sequence alignments</p>
Rotation of Characteristic Vectors with Piezoelectric Coupling (1974)

Acoustic ultrasonic waves are launched in a block of single-crystal mater, such as alpha-quartz, by means of a transducer fastened to one end of the block. The waves are steered by electrically altering the properties of the crystal between the piezoelectrically unstiffened and stiffened excitation modes.
Milestone Report - Complete New Adsorbent Materials for Marine Testing to Demonstrate 4.5 g-U/kg Adsorbent (2014)

This report describes work on the successful completion of Milestone M2FT-14OR03100115 (8/20/2014) entitled, “Complete new adsorbent materials for marine testing to demonstrate 4.5 g-U/kg adsorbent”. This effort is part of the Seawater Uranium Recovery Program, sponsored by the U.S. Department of Energy, Office of Nuclear Energy, and involved the development of new adsorbent materials at the Oak Ridge National Laboratory (ORNL) and marine testing at the Pacific Northwest National Laboratory (PNNL). ORNL has recently developed two new families of fiber adsorbents that have demonstrated uranium adsorption capacities greater than 4.5 g-U/kg adsorbent after marine testing at PNNL. One adsorbent was synthesized by radiation-induced graft polymerization of itaconic acid and acrylonitrile onto high surface area polyethylene fibers followed by amidoximation and base conditioning. This fiber showed a capacity of 4.6 g-U/kg adsorbent in marine testing at PNNL. The second adsorbent was prepared by atom-transfer radical polymerization of t-butyl acrylate and acrylonitrile onto halide-functionalized round fibers followed by amidoximation and base hydrolysis. This fiber demonstrated uranium adsorption capacity of 5.4 g-U/kg adsorbent in marine testing at PNNL.
Molecular genetics of primary congenital glaucoma in Brazil (2002)

Made available in DSpace on 2014-11-17T02:00:25Z (GMT). No. of bitstreams: 1 WOS000175927800020.pdf: 159851 bytes, checksum: 5b66edb304f234a77a5a7ac641fb0c4d (MD5) Previous issue date: 2002
The Use of a Spinning Dissipator for Attitude Stabilization of Earth-Orbiting Satellites (1973)

This paper considers a novel attitude stabilizing system which acts both as a passive nutation damper and a momentum source for an Earth-orbiting satellite. The system may be designed to use four identical wheels mounted coaxially with and at the ends of the arms of a cruciform structure. The structure may then be spun about the axis perpendicular to the arms to provide angular momentum along the spacecraft spin axis. The wheels experience torques produced by inertial forces. The necessary damping and restoring (spring) torques are provided by means of a torsional arrangement built around the center of each wheel. The performance characteristics of the proposed stabilizing unit are evaluated by considering spacecraft parameters used in one phase of development of the Communications Technology Satellite (CTS). The results obtained for a specific design of the stabilizer indicate that global stability of the desired attitude motion of the spacecraft can be guaranteed with associated damping time constant as low as one second.
Development of versatile allele-specific siRNAs able to silence all the dominant dynamin 2 mutations (2022)

Dominant centronuclear myopathy (CNM) is a rare form of congenital myopathy associated with a wide clinical spectrum, from severe neonatal to milder adult forms. There is no available treatment for this disease due to heterozygous mutations in the <i>DNM2</i> gene encoding Dynamin 2 (DNM2). Dominant <i>DNM2</i> mutations also cause rare forms of Charcot-Marie-Tooth disease and hereditary spastic paraplegia, and deleterious DNM2 overexpression was noticed in several diseases. The proof of concept for therapy by allele-specific RNA interference devoted to silence the mutated mRNA without affecting the normal allele was previously achieved in a mouse model and patient-derived cells, both expressing the most frequent <i>DNM2</i> mutation in CNM. In order to have versatile small interfering RNAs (siRNAs) usable regardless of the mutation, we have developed allele-specific siRNAs against two non-pathogenic single-nucleotide polymorphisms (SNPs) frequently heterozygous in the population. In addition, allele-specific siRNAs against the p.S619L DNM2 mutation, a mutation frequently associated with severe neonatal cases, were developed. The beneficial effects of these new siRNAs are reported for a panel of defects occurring in patient-derived cell lines. The development of these new molecules allows targeting the large majority of the patients harboring <i>DNM2</i> mutations or overexpression by only a few siRNAs.
Analysis and Mapping of Gene Families Encoding β-1,3-Glucanases of Soybean (1999)

Oligonucleotide primers designed for conserved sequences from coding regions of beta-1,3-glucanase genes from different species were used to amplify related sequences from soybean [Glycine max (L.) Merr.]. Sequencing and cross-hybridization of amplification products indicated that at least 12 classes of beta-1,3-glucanase genes exist in the soybean. Members of classes mapped to 34 loci on five different linkage groups using an F(2) population of 56 individuals. beta-1,3-Glucanase genes are clustered onto regions of five linkage groups. Data suggest that more closely related genes are clustered together on one linkage group or on duplicated regions of linkage groups. Northern blot analyses performed on total RNA from root, stem, leaf, pod, flower bud, and hypocotyl using DNA probes for the different classes of beta-1,3-glucanase genes revealed that the mRNA levels of all classes were low in young leaves. SGlu2, SGlu4, SGlu7, and SGlu12 mRNA were highly accumulated in young roots and hypocotyls. SGlu7 mRNA also accumulated in pods and flower buds.
Selective, Pulsed CVD of Platinum on Microfilament Gas Sensors (1996)

A post-processing, selective micro-chemical vapor deposition ("micro-CVD") technology for the deposition of catalytic films on surface-micromachined, nitride-passivated polysilicon filaments has been investigated. Atmospheric pressure deposition of platinum on microfilaments was accomplished by thermal decomposition of platinum acetylacetonate, an organometallic Pt precursor; deposition occurs selectively only on those filaments which are electrically heated.
P-B27 Targeting the binding interface on a shared receptor subunit of a cytokine family enables the inhibition of multiple member-cytokines with selectable target spectrum (2016)

The common gamma molecule (γc) is a shared signaling receptor subunit used by 6 γc-cytokines. These cytokines play crucial roles in the differentiation of mature immune system and are involved in many human diseases. Moreover, recent studies suggest that multiple γc- cytokines (IL-2, -4, -7, -9, -15, and -21) are pathogenically involved in a single disease, thus making the shared γc-molecule as a logical target for therapeutic intervention. However, the current therapeutic strategies seem to lack options to treat such cases, partly because of the lack of appropriate neutralizing antibodies recognizing the γc, and more importantly because of the inherent and practical limitations in the use of monoclonal antibodies. For example, combinatorial use of monoclonal antibodies (mAb) for clinical use becomes prohibitingly expensive. Moreover, a mixture of cytokines would be only marginally inhibitable by mAb against one of the mixtures (the experimenal demonstration will be shown in the presentation) so such inhibition targeting only one of the factors by mAb may generate a misleading conclusion that the relevant factor is not causing the disease. By targeting the binding interface of the γc and cytokines, we successfully designed peptides that can not only inhibit multiple γc-cytokines but with selectable target spectrum. Notably, the lead-peptide inhibited three γc-cytokines (IL-2, 15, and -9) without affecting other cytokines. Structural and mutational analyses of our peptide provide new insights to the current understanding on the binding geometry of γc-cytokines the γc-molecule. Furthermore, our peptide, when conjugated to polyethylene glycol to gain stability in vivo, efficiently block the action of IL-2 and IL-15 in multiple animal models. Collectively, our technology can be expandable to target various combinations of γc-cytokines and thereby provide a novel strategy to improve current anti- cytokine therapies against necrotizing diseases, including HAM/TSP, an HTLV-1 caused myelopathy as the primary target.
ChemInform Abstract: SYNTHESIS OF 1β‐HYDROXYVITAMIN D3 AND 1β,25‐DIHYDROXYVITAMIN D3 (1978)

Abstract Auf dem im Formelschema skizzierten Weg erhält man aus den Epimeren (I) die gesuchten Vitamine (V).
Camera-based video synchronization for a federation of mobile projectors (2011)

Ultra-portable projectors, called pico projectors, are now being embedded in mobile devices like cell-phones. Such mobile devices are projected to be the primary device to be used by younger people for ubiquitous sharing of all possible media initiating novel social interaction paradigms. Yet, the pico-projectors offer a much lower resolution and brightness than a standard projector. However, images displayed from multiple such mobile devices can be tiled to create a dramatically improved display in both brightness and resolution. This will allow multiple users to view and share media at a much higher quality. In this paper, we present a camera-based video synchronization algorithm that allows a federation of projection-enabled mobile devices to collaboratively present a synchronized video stream, though only a smaller part of the video comes from each device. Since, the synchronization does not use any wireless network infrastructure, it is independent of network congestion and connectivity. We combined our method with existing distributed registration techniques to demonstrate a synchronized video stream for a federation of four projectors arranged in a 2 × 2 array. To the best of our knowledge, this is the first time that a camera-based technique has been used to mitigate network uncertainties to achieve accurate video synchronization across multiple devices.
Powder Processing by Suspension Plasma Spraying (1997)

Abstract Suspension Plasma Spraying (SPS) is a thermal spray process based on a suspension of fine (&lt;10 μm) or even ultrafine (&lt;100 nm) powders which is axially fed into the induction plasma through an atomization probe. The atomization of the suspension results in microdroplets (20 μm in size). They are flash dried in the plasma, melted and finally can impact a substrate to build a coating or be cooled down and collected as a spheroidized powder. The large industrial potential of this technology results first from the use of fine powder or even sol-gel which is one of the starting step for many ceramic processes, and second from the various side benefits of the liquid phase in the SPS. Indeed, the liquid phase can be simply a carrier for ultrafine powder, or a protection against oxidation in the case of metals, or a protection for health in the case of whiskers, for instance. It can also take a part in chemical reactions when the liquid phase is a solution of chloride, nitrates... or it can be an organic liquid for the synthesis of carbide, where CO is a strong reducer. Furthermore the liquid phase can also release some energy because of its combustion at the very end of the process. It can also change the local atmosphere surrounding the in flight droplets in the plasma where it is possible to use H2O2 as a carrier in order to increase the oxygen partial pressure around sensitive to oxygen decomposition materials. The applications of SPS are in the powder synthesis (in R&D or production), in the spraying of metals, ceramics or composites directly synthesized, or in production of very reactive with air materials. Applications of SPS will be presented for hydroxyapatite (HA) and NiAlMo. Induction plasma SPS coatings and/or powders properties will be discussed as a function of the SPS process variables.
Emitter Localization and Visualization (ELVIS): A Backward Ray Tracing Algorithm for Locating Emitters (2007)

We present ELVIS, a new approach for localizing a first responder (e.g., firefighter) inside a building. We assume that the first responder emits RF energy, which undergoes multiple reflections with the walls, ceilings and floors of the building. There are K receivers, each of which receives ray(s) from the first responder. Each receiver estimates the AOA (angle of arrival), TOA (time of arrival) and power of each ray. We assume that the receivers know the blueprint of the building and the electromagnetic characteristics of the construction material used in the building. We show that, based on this information, the receivers can localize the first responder to a high degree of accuracy by applying ELVIS, which is based on backward ray tracing. We have evaluated the performance of ELVIS, using both single and multiple receivers, under a variety of channel and propagation conditions. We find that, the location prediction error depends mostly on the angular resolution of the receiver antennas. One advantage of ELVIS over other RF-based localization methods is that, if AOA is estimated with high degree of accuracy, a single receiver would be sufficient to do localization in 3D. In this case one could localize 100% of the Bell Labs, Crawford Hill building within 9 cm. With degraded accuracy, including fading and noise effects, plusmn10 degree angular error, and plusmn10 ns temporal error, one could localize 80% of the building within 10 m using multiple receivers.
High-efficiency, high-power mid-infrared quantum cascade lasers [Invited] (2018)

The step-taper active-region (STA) design concept is implemented for ~5.0 μm-emitting quantum cascade lasers (QCLs) grown by metal-organic chemical vapor deposition (MOCVD). Carrier-leakage suppression yields high characteristic temperatures for the threshold-current density Jth, T0, and for the slope efficiency ηsl, T1: 226 K and 653 K. Resonant-tunneling extraction from the lower level results in miniband-like extraction. In turn, the internal efficiency ηi is found, from a variable mirror-loss study, to be ~77%; thus approaching the ~90% upper limit, when employing only inelastic scattering. Considering interface-roughness and alloy-disorder scattering, the transition efficiency reaches values of ~95%. Then, the injection efficiency is ~81%, and, for λ = 4.6 μm, the wallplug-efficiency ηwp upper limit reaches 41.2%. Results include 4.2 W/A single-facet ηsl and 0.96 kA/cm2Jth values. Buried-heterostructure (BH) QCLs provide single-facet 2.6 W continuous-wave (CW) power and 12% CW ηwp. Optimized 8 μm-emitting, STA-design QCLs provide 2 W/A ηsl, and 1.1 kA/cm2Jth; and BH devices yield single-facet 1 W CW power and 6% CW ηwp.
Novel dual-rotor single-stator axial flux switching permanent magnet machine with even harmonic elimination topology (2015)

This paper proposes a novel 6 slot-4 pole axial flux switching permanent magnet machine using dual-rotor single-stator. The analytical method is used to find offset angle to eliminate even harmonics of flux linkage and back-EMF of a conventional 6 slot-4 pole topology. The analytical method is verified with finite element analysis. Proposed novel topology is also compared with a conventional dual-rotor single-stator 6 slot-4 pole axial flux switching machine. The simulation results prove that the proposed topology effectively eliminates even harmonics in the axial flux switching machine.
Extending Boolean Methods for Scalable Logic Synthesis (2020)

In recent years, Boolean methods in logic synthesis have been drawing the attention of EDA researchers due to the continuous push to advance quality of results. Boolean methods require high computational cost, as they rely on complete functional properties of a logic circuit (e.g., don't cares), but usually result in better optimization. In particular, Boolean resubstitution is considered one of the most powerful Boolean methods in logic synthesis. In this paper, we present three novel Boolean resubstitution algorithms designed to be scalable and runtime-effective in a modern synthesis flow. They make use of circuit partitioning techniques and Boolean filtering to be fast and computationally tractable. We also discuss different data structures and reasoning engines, namely truth tables, binary decision diagrams, and satisfiability, that are required to gather don't cares and functional information. As the choice of the engine determines the scalability of Boolean resubstitution we present different scenarios in which the Boolean methods are best driven by one or the other of these. We have implemented the presented resubstitution techniques together with state-of-the-art methods in an industrial logic optimization engine to create a novel resynthesis flow. Our global resynthesis flow achieves significant synthesis results: Within the EPFL synthesis competition, we improve the best-known area results when mapped into LUT-6; when embedded in a commercial EDA flow, the new Boolean resynthesis flow results in 3.12% combinational area savings and 1.34% WNS reduction after physical implementation, at contained (w.r.t. the time of the entire flow) runtime cost.
Deducing similarities in Java sources from bytecodes (1998)

Several techniques for detecting similarities of Java programs from bytecode files, without access to the source, are introduced in this paper. These techniques can be used to compare two files, to find similarities among thousands of files, or to compare one new file to an index of many old ones. Experimental results indicate that these techniques can be very effective. Even changes of 30 % to the source file will usually result in bytecode that can be associated with the original. Several applications are discussed.
Parallel connection control (PCC) algorithm for ATM networks (2002)

This paper describes a parallel connection control (PCC) algorithm for the setup, modification and release of ATM connections. The procedure for a basic two-party connection setup is first described. The extensions of this procedure for third-party connection control, the setup of unidirectional multicast connections, and the setup of multiparty-to-multiparty connections are then described. We make a novel, though simple, observation that multiparty-to-multiparty connections with multiple sending nodes can be realized as ATM layer connections without any application-layer special resources, such as bridges. We demonstrate two ways of realizing such connections. In the descriptions of the procedures for the different connection control tasks, we identify and solve several interesting problems.
On uplink non-orthogonal multiple access for 5g: opportunities and challenges (2017)

In this paper, the concept of grant-free non-orthogonal multiple access (NOMA) for uplink data transmission is elaborated. NOMA in combination with grant-free can be applied to ultra reliability low latency communication (URLLC), massive machine type communication (mMTC), enhanced mobile broadband (eMBB) small packet and two-step random-access channel (RACH) scenarios. The advantages of grant-free NOMA are low latency and signaling overhead, high access capability and efficient resource utilization. Candidate uplink NOMA schemes are summarized and preliminary comparison among a subset of schemes are presented. Furthermore, design aspects for grant-free NOMA are discussed, with special notes on particular issues such as blind UE identification and transmitter/ receiver (Tx/Rx) impairments in realistic deployment.