gebhart/patrepeval huggingface dataset:
In Vivo Quantification of Parallel and Bidirectional Fluxes in the Anaplerosis of Corynebacterium glutamicum (2000)

The C(3)-C(4) metabolite interconversion at the anaplerotic node in many microorganisms involves a complex set of reactions. C(3) carboxylation to oxaloacetate can originate from phosphoenolpyruvate and pyruvate, and at the same time multiple C(4)-decarboxylating enzymes may be present. The functions of such parallel reactions are not yet fully understood. Using a (13)C NMR-based strategy, we here quantify the individual fluxes at the anaplerotic node of Corynebacterium glutamicum, which is an example of a bacterium possessing multiple carboxylation and decarboxylation reactions. C. glutamicum was grown with a (13)C-labeled glucose isotopomer mixture as the main carbon source and (13)C-labeled lactate as a cosubstrate. 58 isotopomers as well as 15 positional labels of biomass compounds were quantified. Applying a generally applicable mathematical model to include metabolite mass and carbon labeling balances, it is shown that pyruvate carboxylase contributed 91 +/- 7% to C(3) carboxylation. The total in vivo carboxylation rate of 1.28 +/- 0.14 mmol/g dry weight/h exceeds the demand of carboxylated metabolites for biosyntheses 3-fold. Excess oxaloacetate was recycled to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase. This shows that the reactions at the anaplerotic node might serve additional purposes other than only providing C(4) metabolites for biosynthesis.
Conservation of orbital angular momentum in air-core optical fibers (2015)

Light's orbital angular momentum (OAM) is a conserved quantity in cylindrically symmetric media; however, it is easily destroyed by free-space turbulence or fiber bends, because anisotropic perturbations impart angular momentum. We observe the conservation of OAM even in the presence of strong bend perturbations, with fibers featuring air cores that appropriately sculpt the modal density of states. In analogy to the classical reasoning for the enhanced stability of spinning tops with increasing angular velocity, these states' lifetimes with OAM magnitude. Consequently, contrary to convention wisdom that ground states of systems are the most stable, OAM longevity in air-core fiber increases with mode order. Aided by conservation of this fundamental quantity, we demonstrate fiber propagation of 12 distinct higher-order OAM modes, of which 8 remain low-loss and >98% pure from near-degenerate coupling after km-length propagation. The first realization of long-lived higher-order OAM states, thus far posited to exist primarily in vacuum, is a necessary condition for achieving the promise of higher-dimensional OAM-based classical and quantum communications over practical distances.
Rapid increase in plasma tenascin‐C concentration after isolated limb perfusion with high‐dose tumor necrosis factor (TNF), interferon gamma (IFNγ) and melphalan for regionally advanced tumors (1995)

The matrix protein tenascin-C (TN-C) is present in the blood of healthy individuals at concentrations around 1 mg/l. Elevated serum levels have been reported in cancer patients. In this study we have measured the concentration of circulating TN-C in 40 patients with melanoma, soft-tissue sarcoma (STS) or squamous-cell carcinoma (SCC) of the limbs, and have found a minor increase in the mean concentration compared with healthy subjects. Only 10 patients had TN-C levels above the normal range. No correlation was observed between TN-C levels and tumor burden. Nineteen patients were treated by isolation limb perfusion (ILP) with TNF, IFN gamma, melphalan (11 melanoma, 2 SCC and I STS), melphalan alone (3 melanoma) or hyperthermia at 41.5 degrees C (2 melanoma). ILP with TNF, IFN gamma and melphalan induced a rapid increase in plasma TN-C levels, peaking in most patients between 24 or 48 hr after ILP. Two patients treated with hyperthermia only had a slow increase in TN-C concentration peaking at day 4, while the patients treated with melphalan alone had no significant change. In some cases elevated TN-C levels persisted for over 8 weeks after ILP. The early rise in TN-C concentration correlates with the increase in circulating C-reactive protein. Our findings suggest that circulating TN-C behaves, at least in part, as an acute-phase protein and that it may play a role in the inflammatory response.
Joint channel estimation and detection for interference cancellation in multi-channel systems (2002)

Interference from other users and interference due to multipath propagation limit the capacity of wireless communication networks. As the number of users and the demand for new services in the networks increases, co-channel interference will be a limiting factor. This paper proposes an iterative structured multichannel receiver algorithm that jointly estimates the communication channels and desired data while canceling interference. A general way of adding training redundancy to a data frame is also introduced. From simulations the proposed method is shown to achieve low bit error rates also in the presence of strong interference. These simulations also show that by distributing the training information in a data burst elaborately further improvements in performance are achievable.
Hybrid integration of 660/780 nm laser diodes on a Si-photodetector for the DVD-RAM/CD-R compatible optical disk head (2002)

Cost-effective optical-head was developed using hybrid integration of 660 nm and 780 nm laser-diodes on a Si-photodiode-plate for the DVD-RAM and CD-R compatibility. Its jitter and tilt characteristics satisfy the specifications with 325 /spl mu/m distance between the two lasers.
Initializing the flux state of multiwell inductively isolated Josephson junction qubits (2006)

We describe a technique for initializing the flux state of an inductively isolated Josephson junction, fulfilling an essential requirement for using the device as a qubit. By oscillating the applied magnetic flux with a specified amplitude and offset, we can select any of the allowed long-lived metastable flux states. We applied this technique to $\mathrm{Nb}\text{\ensuremath{-}}{\mathrm{Al}}_{2}{\mathrm{O}}_{3}\text{\ensuremath{-}}\mathrm{Nb}$ and $\mathrm{Al}\text{\ensuremath{-}}{\mathrm{Al}}_{2}{\mathrm{O}}_{3}\text{\ensuremath{-}}\mathrm{Al}$ devices with from 10 to over 100 distinct flux states at temperatures as low as $25\phantom{\rule{0.3em}{0ex}}\mathrm{mK}$. In a ten-state system with an initial probability $p=0.13$ to be in the desired flux state, we achieved $p=0.999\phantom{\rule{0.2em}{0ex}}96$ after 50 oscillations at $22.6\phantom{\rule{0.3em}{0ex}}\mathrm{kHz}$. The technique is generally applicable to other systems with multiple metastable wells (including rf SQUIDs), requires no additional readout or bias lines, involves minimal energy dissipation, and appears to scale favorably with the number of qubits.
Corrigendum: Implications of Seed Vault Storage Strategies for Conservation of Seed Bacterial Microbiomes (2022)

[This corrects the article DOI: 10.3389/fmicb.2021.784796.].
Desmotomy of the Accessory Ligament of the Superficial Digital Flexor Muscle in Equine Cadaver Limbs (1991)

Effects of longitudinal compression before and after transection of the accessory ligament of the superficial digital flexor (SDF) muscle were measured in eight equine cadaver forelimbs. When compression was increased from 890 N to 3115 N, the metacarpophalangeal (MCP) and carpal joints hyperextended 20 degrees and 4 degrees, respectively, and strain in the SDF and deep digital flexor tendons was increased 3.5% and 1.4%, respectively. The accessory ligament did not elongate. Immediately after transection of the accessory ligament at 3115 N load, a 2.8 mm gap formed between the transected ends of the accessory ligament, and the muscle belly of the SDF elongated and moved distad. The MCP joint hyperextended 15.8% further and strain of the SDF tendon increased 11.2% further. These results show that the accessory ligament transferred load in the SDF musculotendinous unit away from the muscle belly and that desmotomy altered this function. Decrease in the MCP joint angle indicated that the accessory ligament contributed to the support of the MCP joint under load. Increase in SDF strain after desmotomy was probably influenced by the change in the moment about the MCP joint and increased length of the SDF musculotendinous unit.
Advances in combat casualty care (2012)

From the US Army Institute of Surgical Research, Fort Sam Houston, Texas. Address for reprints: Lorne H. Blackbourne, MD, US Army Institute of Surgical Research, 3698 Chambers Pass, Fort Sam Houston, TX 78234-6315; email: [email protected].
Replication Data for: Dilute Pd/Au Alloy Nanoparticles Embedded in Colloid-Templated Porous SiO 2 : Stable Au-Based Oxidation Catalysts (2021)

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.
The effector mechanism of siRNA spherical nucleic acids (2020)

Spherical nucleic acids (SNAs) are nanostructures formed by chemically conjugating short linear strands of oligonucleotides to a nanoparticle template. When made with modified small interfering RNA (siRNA) duplexes, SNAs act as single-entity transfection and gene silencing agents and have been used as lead therapeutic constructs in several disease models. However, the manner in which modified siRNA duplex strands that comprise the SNA lead to gene silencing is not understood. Herein, a systematic analysis of siRNA biochemistry involving SNAs shows that Dicer cleaves the modified siRNA duplex from the surface of the nanoparticle, and the liberated siRNA subsequently functions in a way that is dependent on the canonical RNA interference mechanism. By leveraging this understanding, a class of SNAs was chemically designed which increases the siRNA content by an order of magnitude through covalent attachment of each strand of the duplex. As a consequence of increased nucleic acid content, this nanostructure architecture exhibits less cell cytotoxicity than conventional SNAs without a decrease in siRNA activity.
Table S1 and S2 from T-cell Responses to <i>TP53</i> “Hotspot” Mutations and Unique Neoantigens Expressed by Human Ovarian Cancers (2023)

&lt;p&gt;Clinical details (S1) and neoepitope details (S2).&lt;/p&gt;
The SKYNIVI Experience: Evoking Startle and Frustration in Dyads and Single Drivers (2019)

To study naturalistic in-cabin emotion we developed SKYNIVI, a modified open source driving simulator, with scenarios designed to elicit startle and frustration. We target generating these emotions because we believe that by detecting these it will be possible for autonomous vehicles to learn to drive better. We show how to use SKYNIVI to develop datasets that capture naturalistic emotions in drivers and passengers for algorithmic development. We recruited 51 participants as dyads and single drivers to participate in two different scenarios. We show that we were able to evoke hundreds of instances of our target emotions in this cohort and present an analysis of factors we found to impact emotional expression including: scenario design , demographic factors, personality and baseline affect . We find that having a second person in the vehicle impacts observed expressions of emotion even when no difference in baseline affect is reported.
Local evanescent, array coupled (LEAC) biosensor response to low index adlayers (2006)

Experiments on planar optical waveguide based local evanescent array coupled biosensors using low-index photoresist and polystyrene nanoparticle adlayers are reported. Near-field scanning optical microscopy measurements are in close agreement with beam propagation method simulations.
Cyclic Thiouronium Ionic Liquids: Physicochemical Properties and their Electronic Structure Probed by X‐Ray Induced Photoelectron Spectroscopy (2012)

Radiography of a structure skeleton: Cyclic thiouronium ionic liquids have been synthesized and characterized in such a way that the straightforward introduction of three different alkyl substituents at the cation has been realized. X-ray induced photoelectron spectroscopy studies indicated a significant electronic contribution of the free electrons at the sulfur to stabilize the cationic charge, leading to structures with peculiar physicochemical properties (see figure).
Microwave-Assisted Solid-Supported Alkyne Cyclotrimerization Reactions for Combinatorial Chemistry (2007)

ADVERTISEMENT RETURN TO ISSUEReportNEXTMicrowave-Assisted Solid-Supported Alkyne Cyclotrimerization Reactions for Combinatorial ChemistryDouglas D. Young, Lakshminath Sripada, and Alexander DeitersView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204 Cite this: J. Comb. Chem. 2007, 9, 5, 735–738Publication Date (Web):July 21, 2007Publication History Received4 May 2007Published online21 July 2007Published inissue 1 September 2007https://pubs.acs.org/doi/10.1021/cc070068bhttps://doi.org/10.1021/cc070068bbrief-reportACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views754Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Electromagnetic radiation,Hydrocarbons,Irradiation,Reactivity Get e-Alerts
Low‐silica Cu‐CHA Zeolite Enriched with Al Pairs Transcribed from Silicoaluminophosphate Seed: Synthesis and Ammonia Selective Catalytic Reduction Performance (2023)

Cu-exchanged low-silica CHA zeolites (Si/Al≤4) synthesized without organic templates are promising candidate catalysts for ammonia selective catalytic reduction of nitrogen oxides (NH<sub>3</sub> -SCR), but their practical application is restricted due to the low hydrothermal stability. Here, inspired by the transcription from duplex DNA to RNA, we synthesized Al pairs enriched low-silica CHA zeolite (CHA-SPAEI, Si/Al=3.7) by using silicoaluminophosphate (SAPO) featured by strict alternation of -Al-O-P(Si)-O-Al-O- tetrahedra as seed. The proportion of Al pairs in CHA-SPAEI is 78 %, which is much higher than that in the conventional low-silica CHA (CHA-LS, 52 %). After hydrothermal ageing at 800 °C for 6 h, Cu-exchanged CHA-SPAEI shows NO conversion above 90 % within 225-500 °C under a gas hourly space velocity of 200,000 h<sup>-1</sup> , which is much better than that of Cu-exchanged CHA-LS. The spatial close proximity of Al pairs in CHA-SPAEI is confirmed by the <sup>27</sup> Al double-quantum single-quantum two-dimensional NMR analyses. The strict -P(Si)-O-Al-O-P(Si)-O- sequence in the fragments from the dissolution of SAPO seed promotes the Al pairs with the -Al-O-Si-O-Al-O- sequence via a transcription process. The utilization of aluminophosphate-based zeolites as seeds opens up a new avenue for the regulation of the Al distribution in zeolites.
A stimulus/response system based on hierarchical timing diagrams (2002)

The authors present a tool that captures timing specifications from hierarchical timing diagrams and models them using hierarchical constraint graphs. The main contribution of the present work is a novel algorithm that traverses the graph during simulation to generate stimuli and to validate circuit responses. The system, implemented in VHDL (VHSIC hardware description language), interacts with the circuit during simulation, thus allowing the generation of stimuli that depend on circuit responses. Experimental results are presented, and areas of future work are identified, such as the extension of the model to include inter-TD constraints, conditional execution semantics, and early firing events.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the efficiency issues of virtual keyboard design (2012)

Virtual keyboards are useful tools, which ease effortless entry of textual data and enable typing with alternative input hardware such as a single switch. Early virtual keyboards are designed similar to physical keyboards in terms of appearance. Since a physical keyboard is designed for tactile-use; the usability of the first virtual keyboards comes up short in utilization with pointing devices. For this reason, more useful virtual keyboards are proposed with improvements in modal and functional properties. In this study, we examine a couple of design issues for virtual keyboards to provide their efficient utilization with pointing devices. We analyze the effects of visual key layout to the performance of virtual keyboards in connection with the statistical properties of the target language's vocabulary. We also propose a virtual keyboard design for a comfortable text entry experience based on our observations.
EUDOC on the IBM Blue Gene/L system: Accelerating the transfer of drug discoveries from laboratory to patient (2008)

EUDOC™ is a molecular docking program that has successfully helped to identify new drug leads. This virtual screening (VS) tool identifies drug candidates by computationally testing the binding of these drugs to biologically important protein targets. This approach can reduce the research time required of biochemists, accelerating the identification of therapeutically useful drugs and helping to transfer discoveries from the laboratory to the patient. Migration of the EUDOC application code to the IBM Blue Gene/L™ (BG/L) supercomputer has been highly successful. This migration led to a 200-fold improvement in elapsed time for a representative VS application benchmark. Three focus areas provided benefits. First, we enhanced the performance of serial code through application redesign, hand-tuning, and increased usage of SIMD (single-instruction, multiple-data) floating-point unit operations. Second, we studied computational load-balancing schemes to maximize processor utilization and application scalability for the massively parallel architecture of the BG/L system. Third, we greatly enhanced system I/O interaction design. We also identified and resolved severe performance bottlenecks, allowing for efficient performance on more than 4,000 processors. This paper describes specific improvements in each of the areas of focus.
Structural Mass Spectrometry of Matrix-Assisted Laser-Desorbed Biomolecules by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Photoionization and Photofragmentation (1993)

Laser desorption ionization of compounds that absorb 337 nm (e.g., vitamin B 12 and selected porphyrins) are examined by using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The experiments are performed by mixing the sample with a host compound that promotes desorption and/or ionization. The relative abundance of photofragment ions can be controlled by simple adjustments of parameters such as the laser power and matrix-to-analyte ratio. In addition, it is shown that gas-phase photoionization/photodissociation of laser-desorbed species by a second laser pulse provides structural information for both negative and positive ions.
invited) Carbon Wonderland from an Engineering Perspective (2014)

A fresh look on carbon-based materials like carbon nanotubes (CNTs) or graphene in microelectronic applications will be given. Graphene has just passed the peak of inflated expectations and is heading towards the trough of disillusionment from where CNTs are just recovering. In contrast to short scale SWCNTs, graphene nanoribbons - even with bandgap - are not promising candidates for a better transistor. However, interconnects made of multi-layer graphene show promise in a wide range of applications. Through-Silicon-Vias (TSV), capacitors, metal gate, diodes, membranes, memories and sensors will be discussed. These applications are heavily based on the direct deposition methods which we have developed over the past decade.
Differential Requirement for the IKKβ/NF-κB Signaling Module in Regulating TLR- versus RLR-Induced Type 1 IFN Expression in Dendritic Cells (2014)

Host innate-immune responses are tailored by cell type to control and eradicate specific infectious agents. For example, an acute RNA virus infection can result in high-level expression of type 1 IFNs by both conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs), but whereas cDCs preferentially use RIG-I-like receptor (RLR) signaling to produce type 1 IFNs, pDCs predominantly use TLRs to induce these cytokines. We previously found that the IκB kinase β (IKKβ)/NF-κB pathway regulates early IFN-β expression, but not the magnitude of type 1 IFN expression following RLR engagement. In this study, we use IKKβ inhibition and mice deficient in IKKβ or canonical NF-κB subunits (p50, RelA/p65, and cRel) to demonstrate that the IKKβ/NF-κB axis is critical for virus-induced type 1 IFN expression in pDCs, but not in cDCs. We also reveal a crucial and more general requirement for IKKβ/NF-κB in TLR- but not RLR-induced expression of type 1 IFNs and inflammatory cytokines. Together, these findings reveal a previously unappreciated specificity of the IKKβ/NF-κB signaling axis in regulation of antimicrobial responses by different classes of pattern recognition receptors, and therefore by individual cell types reliant on particular pattern recognition receptors for their innate-immune transcriptional responses.
On RF implementation of WINNER II channel model for MIMO OTA performance evaluations (2010)

The development of MIMO over-the-air (OTA) test methodology is an ongoing activity in 3GPP RAN4, CTIA and EU COST Action 2100. In this paper, the focus is on the anechoic chamber approach, which uses a uniform circular array of probe antennas to replicate directional channels for the device under test (DUT) at the array center. In particular, we study in simulation the complexity requirements of implementing the WINNER II clustered delay line (CDL) model in RF using off-the-shelf RF components. Our results reveal that a significant reduction in complexity of the CDL model can be achieved while keeping both ergodic and outage capacity to within 10% of the full model. This suggests that it is both feasible and cost effective in implementing state-of-the-art directional channel models in RF for MIMO OTA tests.
Cartilage Plate Tympanoplasty (2009)

On the basis of this study, we recommend the tuliplike arrangement of thin but large auricular cartilage slices for the reconstruction of tympanic membrane defects in high-risk ears. This combination proved its high stability and long-lasting vitality in our long-term study. These characteristics are crucial for permanent disease removal and for reducing the risk of recurrent pathologic abnormality.
TOWARDS IDENTIFICATION, ISOLATION AND CHARACTERIZATION OF DISEASE RESISTANT GENES FROM THE NATIVE NORTH AMERICAN GRAPE SPECIES VITIS SHUTTLEWORTHII (2007)

ISHS International Symposium on Biotechnology of Temperate Fruit Crops and Tropical Species TOWARDS IDENTIFICATION, ISOLATION AND CHARACTERIZATION OF DISEASE RESISTANT GENES FROM THE NATIVE NORTH AMERICAN GRAPE SPECIES VITIS SHUTTLEWORTHII