gebhart/patrepeval huggingface dataset:
Velocity update for pre‐stack time migration (2008)

We present a new approach for updating velocity models for ray traced pre‐stack time migration (PreSTM). Our approach is based on automated structural dip and residual‐ move‐out (RMO) picking from locally coherent events in time migrated images. For each locally coherent event (characterized by its dip and RMO curve) of a given Common Image Gather we optimize, using a slope tomographic approach, a local 1D velocity profile with the objective to flatten the CIG. Since local 1D velocity updates are performed independently, editing and smoothing of the updated velocity model is required before the final pre‐stack time migration. The use of the dip information in the proposed flow is the main improvement compared to conventional approaches where only the NMO or RMO are taken into account with a zero dip assumption. This improvement leads to more accurate velocity estimation for ray traced PreSTM.
TOPO-MLP : A Simplicial Network without Message Passing (2023)

Due to their ability to model meaningful higher order relations among a set of entities, higher order network models have emerged recently as a powerful alternative for graph-based network models which are only capable of modeling binary relationships. Message passing paradigm is still dominantly used to learn representations even for higher order network models. While powerful, message passing can have disadvantages during inference, particularly when the higher order connectivity information is missing or corrupted. To overcome such limitations, we propose Topo-MLP, a purely MLP-based simplicial neural network algorithm to learn the representation of elements in a simplicial complex without explicitly relying on message passing. Our framework utilizes a novel Higher Order Neighborhood Contrastive (HONC) loss which implicitly incorporates the simplicial structure into representation learning. Our proposed model’s simplicity makes it faster during inference. Moreover, we show that our model is robust when faced with missing or corrupted connectivity structure.
The 1′,4′-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes (2006)

Thiamin diphosphate, a key coenzyme in sugar metabolism, is comprised of the thiazolium and 4'-aminopyrimidine aromatic rings, but only recently has participation of the 4'-aminopyrimidine moiety in catalysis gained wider acceptance. We report the use of electronic spectroscopy to identify the various tautomeric forms of the 4'-aminopyrimidine ring on four thiamin diphosphate enzymes, all of which decarboxylate pyruvate: the E1 component of human pyruvate dehydrogenase complex, the E1 subunit of Escherichia coli pyruvate dehydrogenase complex, yeast pyruvate decarboxylase, and pyruvate oxidase from Lactobacillus plantarum. It is shown that, according to circular dichroism spectroscopy, both the 1',4'-iminopyrimidine and the 4'-aminopyrimidine tautomers coexist on the E1 component of human pyruvate dehydrogenase complex and pyruvate oxidase. Because both tautomers are seen simultaneously, these two enzymes provide excellent evidence for nonidentical active centers (asymmetry) in solution in these multimeric enzymes. Asymmetry of active centers can also be induced upon addition of acetylphosphinate, an excellent electrostatic pyruvate mimic, which participates in an enzyme-catalyzed addition to form a stable adduct, resembling the common predecarboxylation thiamin-bound intermediate, which exists in its 1',4'-iminopyrimidine form. The identification of the 1',4'-iminopyrimidine tautomer on four enzymes is almost certainly applicable to all thiamin diphosphate enzymes: this tautomer is the intramolecular trigger to generate the reactive ylide/carbene at the thiazolium C2 position in the first fundamental step of thiamin catalysis.
Design of highly sensitive and selective Au@NiO yolk–shell nanoreactors for gas sensor applications (2014)

Au@NiO yolk-shell nanoparticles (NPs) were synthesized by simple solution route and applied for efficient gas sensor towards H₂S gas. Carbon encapsulated Au (Au@C core-shell) NPs were synthesized by glucose-assisted hydrothermal method, whereas Au@NiO yolk-shell NPs were synthesized by precipitation method using Au@C core-shell NPs as a template. Sub-micrometer Au@NiO yolk-shell NPs were formed having 50-70 nm Au NPs at the periphery of NiO shell (10-20 nm), which was composed of 6-12 nm primary NiO particles. Au@NiO yolk-shell NPs showed higher response for H2S compared to other interfering gases (ethanol, p-xylene, NH₃, CO and H₂). The maximum response was 108.92 for 5 ppm of H₂S gas at 300 °C, which was approximately 19 times higher than that for the interfering gases. The response of Au@NiO yolk-shell NPs to H₂S was approximately 4 times higher than that of bare NiO hollow nanospheres. Improved performance of Au@NiO yolk-shell NPs was attributed to hollow spaces that allowed the accessibility of Au NPs to gas molecules. It was suggested that adsorption of H₂S on Au NPs resulted in the formation of sulfide layer, which possibly lowered its work function, and therefore tuned the electron transfer from Au to NiO rather NiO to Au, which leaded to increase in resistance and therefore response.
Temperature and wall coating dependence of alkali vapor transport speed in micron-scale capillaries (2017)

The impact of storage temperature and wall coatings on alkali vapor transport through micron-scale glass capillaries is analyzed. Glass microbore tubing, chromatography vials, and copper tubing are assembled into closed atomic spectroscopy units with varying capillary lengths and inner diameters. Such devices serve as valuable test models for integrated atomic spectroscopy platforms that rely on hollow-core optical waveguides for chip-scale implementation of quantum coherence phenomena such as slow and stopped light. The inside surface of the systems are coated with dimethyldichlorosilane (DMDCS) after which the system is loaded with rubidium vapor and hermetically sealed. The loaded units are stored in a tube furnace at elevated temperatures and tested daily for absorption over several weeks. Both a wall coating of DMDCS and higher storage temperature increases the transport speed of Rb vapor. The limits and implications of these results are discussed and compared to an expected theoretical model. Suggestions for increasing transport speed are given.
Adaptive State Estimation Over Lossy Sensor Networks Fully Accounting for End-To-End Distortion (2018)

This paper investigates state estimation with wireless sensors communicating over unreliable bandwidth-limited networks. Specifically, we consider so-called smart sensors equipped with simple processing units, which enable predictive coding at the sensor side, to meet the bandwidth constraint. While predictive coding significantly reduces the bit-rate by removing temporal redundancies, it exacerbates the impact of packet loss, due to error propagation through the prediction loop, potentially causing significant degradation of the reconstructed signal. To fully account for and control the conflict between coding efficiency and robustness to packet loss, we propose a coding approach that explicitly optimizes the tradeoff between rate and end-to-end distortion (EED). The proposed method determines optimal switching decisions between available coding modes, offering different compression-robustness operating points, based on EED that is optimally estimated at the encoder (sensor), in order to realize the best rate-distortion tradeoff. Simulation results demonstrate that the proposed approach achieves considerable gains in signal-to-noise ratio for state estimation over lossy sensor networks.
OFDM versus Single Carrier: A Realistic Multi-Antenna Comparison (2004)

There is an ongoing discussion in the broadband wireless world about the respective benefits of orthogonal frequency division multiplexing (OFDM) and single carrier with frequency domain equalization (SC-FD). SC-FD allows for more relaxed front-end requirements, of which the power amplifier efficiency is very important for battery-driven terminals. OFDM, on the other hand, can yield improved BER performance at low complexity. Both schemes have extensions to multiple antennas to enhance the spectral efficiency and/or the link reliability. Moreover, both schemes have nonlinear versions using decision feedback equalization (DFE) to further improve performance of the linear equalizers. In this paper, we compare these high-performance OFDM and SC-FD schemes using multiple antennas and DFE, while also accounting for the power amplifier efficiency. To make a realistic comparison, we also consider most important digital imperfections, such as channel and noise estimation, transmit and receive filtering, clipping and quantization, as well as link layer impact. Our analysis shows that for frequency-selective channels the relative performance impact of the power amplifier is negligible compared to the frequency diversity impact. The higher frequency diversity exploitation of SC-FD allows it to outperform OFDM in most cases. Therefore, SC-FD is a suitable candidate for broadband wireless communication.
ChemInform Abstract: Chiral Toluene‐2,α‐sultam Auxiliaries: Asymmetric Alkylations, Acylations, and Aldolizations of N‐Acyl Derivatives. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile (2020)

The World health organization (WHO) declared Coronavirus disease 2019 (COVID-19) a global pandemic and a severe public health crisis. Drastic measures to combat COVID-19 are warranted due to its contagiousness and higher mortality rates, specifically in the aged patient population. At the current stage, due to the lack of effective treatment strategies for COVID-19 innovative approaches need to be considered. It is well known that host cellular miRNAs can directly target both viral 3'UTR and coding region of the viral genome to induce the antiviral effect. In this study, we did <i>in silico</i> analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. We found 848 common miRNAs targeting the SARS genome and 873 common microRNAs targeting the COVID-19 genome. Out of a total of 848 miRNAs from SARS, only 558 commonly present in all COVID-19 isolates. Interestingly, 315 miRNAs are unique for COVID-19 isolates and 290 miRNAs unique to SARS. We also noted that out of 29 COVID-19 isolates, 19 isolates have identical miRNA targets. The COVID-19 isolates, Netherland (EPI_ISL_422601), Australia (EPI_ISL_413214), and Wuhan (EPI_ISL_403931) showed six, four, and four unique miRNAs targets, respectively. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Recent studies also suggested that some of the human miRNAs targeting COVID-19 decreased with aging and underlying conditions. GO and KEGG identified impaired signaling pathway may be due to low abundance miRNA which might be one of the contributing factors for the increasing severity and mortality in aged individuals and with other underlying conditions. Further, <i>in vitro</i> and <i>in vivo</i> studies are needed to validate some of these targets and identify potential therapeutic targets.
Spectres, virtual ghosts, and hardware support (2018)

Side-channel attacks, such as Spectre and Meltdown, that leverage speculative execution pose a serious threat to computing systems. Worse yet, such attacks can be perpetrated by compromised operating system (OS) kernels to bypass defenses that protect applications from the OS kernel.
Anchoring Ceria Nanoparticles on Reduced Graphene Oxide and Their Electronic Transport Properties (2011)

We report a simple scheme of anchoring crystalline ceria nanoparticles (CNPs) onto reduced graphene oxide (RGO) sheets. Two types of CNPs, consisting of predominantly either Ce(3+) or Ce(4+) valence states, were mixed with GO suspended in water, with simultaneous reduction using hydrazine to yield CNP/RGO composite. Structural and surface characterizations reveal a strong electrostatic interaction between the CNPs and the RGO. Electrical characterizations show that with increased oxygen vacancies from Ce(4+) to Ce(3+) states the predominantly ambipolar RGO transforms to n-type CNP/RGO composites due to the electrostatic interaction between the localized electrons in oxygen vacancy sites of CNPs and mobile holes in RGO.
Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays (2004)

Scanning arrays of antisense DNA oligonucleotides provide a novel and systematic means to study structural features within an RNA molecule. We used this approach to probe the structure of the untranslated leader of the human immunodeficiency virus type 1 (HIV-1) RNA genome. This 335 nt RNA encodes multiple important replication signals and adopts two mutually exclusive conformations. The poly(A) and the dimer initiation signal (DIS) sequences of the leader RNA are base-paired in the long-distance interaction (LDI) conformation, but both domains form distinct hairpins in the branched multiple hairpins (BMH) conformation. An RNA switch mechanism has been proposed to regulate the activity of the DIS dimerization signal that is masked in one, yet exposed in the other conformation. The two RNA conformations demonstrate discrete differences in the array-based hybridization patterns. LDI shows increased hybridization in the poly(A) region and decreased hybridization in the DIS region when compared with BMH. These results provide additional evidence for the structure models of the two alternative leader RNA conformations. We also found a correlation between the efficiency of oligonucleotide hybridization and the accessibility of the RNA structure as determined by chemical and enzymatic probing in previous studies. The array approach therefore provides a very sensitive method to detect structural differences in related transcripts.
Quantum Policy Iteration via Amplitude Estimation and Grover Search -- Towards Quantum Advantage for Reinforcement Learning (2022)

We present a full implementation and simulation of a novel quantum reinforcement learning method. Our work is a detailed and formal proof of concept for how quantum algorithms can be used to solve reinforcement learning problems and shows that, given access to error-free, efficient quantum realizations of the agent and environment, quantum methods can yield provable improvements over classical Monte-Carlo based methods in terms of sample complexity. Our approach shows in detail how to combine amplitude estimation and Grover search into a policy evaluation and improvement scheme. We first develop quantum policy evaluation (QPE) which is quadratically more efficient compared to an analogous classical Monte Carlo estimation and is based on a quantum mechanical realization of a finite Markov decision process (MDP). Building on QPE, we derive a quantum policy iteration that repeatedly improves an initial policy using Grover search until the optimum is reached. Finally, we present an implementation of our algorithm for a two-armed bandit MDP which we then simulate.
Coupled Nd and B' spin ordering in the double perovskites Nd2NaB'O6 (B' = Ru, Os) (2013)

We present a neutron powder diffraction study of the monoclinic double perovskite systems Nd2NaB'O6 (B' = Ru, Os), with magnetic atoms occupying both the A and B' sites. Our measurements reveal coupled spin ordering between the Nd and B' atoms with magnetic transition temperatures of 14 K for Nd2NaRuO6 and 16 K for Nd2NaOsO6. There is a Type I antiferromagnetic structure associated with the Ru and Os sublattices, with the ferromagnetic planes stacked along the c-axis and [110] direction respectively, while the Nd sublattices exhibit complex, canted antiferromagnetism with different spin arrangements in each system.
Anterior Segment Prosthesis Development (1997)

Replacement of the entire anterior segment of the eye is a very ambitious and complex endeavor and it is not known whether the retina remains functional when the anterior structures have been removed. We used routine histo-pathologic evaluation and electroretinographic measurements to determine the structural and functional status of rabbit retinas following surgical removal of the internal anterior structures (iris, ciliary body, and lens) and replacement of the vitreous with silicone oil. In some cases, we were able to record both a scotopic and a photopic electroretinographic response as long as 15 weeks after complete removal of the internal anterior segment structures. Although many hurdles remain and more efficacious surgical techniques and biomaterials need to be developed, our results suggest that, in the rabbit, the retina may continue to function in the absence of critical anterior segment structures.
MR imaging of pelvic floor continence mechanisms in the supine and sitting positions. (1998)

Changes of pelvic floor laxity related to incontinence can be seen with subjects in both the supine and the sitting positions but are increased in the sitting position.
Projective representations of the inhomogeneous symplectic group: Quantum symmetry origins of the Heisenberg commutation relations (2019)

Quantum symmetries that leave invariant physical transition probabilities are described by projective representations of Lie groups. The mathematical theory of projected representations for topologically connected Lie groups is reviewed and applied to the inhomogeneous symplectic group ISp(2n). The projective representations are given in terms of the ordinary unitary representations of the central extension of the group with respect to its first homotopy group direct product with its second cohomology group. The second cohomology group of ISp(2n) is the one dimensional abelian group and the central extension turns the 2n dimension abelian normal subgroup of translations of ISp(2n) into the Weyl-Heisenberg group. This is the quantum symmetry origin of the Heisenberg commutation relations that are the Hermitian representation of the Lie algebra of the Weyl-Heisenberg group.
Tunable, narrow, and directional luminescence from porous silicon light emitting devices (1999)

Controlled room-temperature photoluminescence (PL) and electroluminescence (EL) from porous silicon (PSi) multilayer structures are achieved. The basic structure is composed of two PSi multilayer mirrors sandwiching a highly luminescent PSi film. This creates an active microcavity resonator, in which a significant PL and EL line narrowing is observed. EL from a microcavity resonator is shown to have a high angular concentration of the output emission (30° around the normal axis). A tunable and narrow EL device, from an all-PSi microcavity resonator is presented, which offers the possibility for high spectral purity, flat-panel displays.
79664 Complement Driven Auto-Reactive Antibodies in Lung Transplantation (2021)

ABSTRACT IMPACT: Our work unveils a novel mechanism of ischemia repurfusion injury driven by pre-existing autoimmunity following lung transplant and a potential therapeutic strategy for blocking complement-dependent injury thereby reducing risk of lung transplant rejection. OBJECTIVES/GOALS: Our goal was to determine if pre-existing autoimmune autoantibodies, such as those resulting from cigarette smoke (CS), contribute to graft rejection in lung transplantation (LTx) and if autoreactive-mediated graft injury is complement-dependent. METHODS/STUDY POPULATION: For in vivo experiments, we utilized our emphysema mouse model. Briefly, eight-week-old C57BL/6J mice are exposed to 3R4F reference cigarette smoke 5 hours per day, 5 days a week for 6 months. Upon completion, cigarette smoked (CS) mice and control (NS) mice received syngeneic orthotopic left-lung transplant from age-matched C57BL/6J donors. To determine if pre-existing autoreactivity mediated graft injury was complement-dependent we treated CS-LTx mice with a novel, bifunctional complement inhibitor. Autoantibody levels were measured by ELISA and lung injury was assessed by blinded histopathological analyses. Complement inhibition was verified by immunofluorescence. RESULTS/ANTICIPATED RESULTS: We found that CS-exposure leads to production of autoreactive antibodies towards extracellular matrix (ECM) components and contributes to graft injury. Interestingly, LTx into CS exposed mice further increased de-novo ECM autoantibody development. Lastly, treatment with our novel, bifunctional complement inhibitor blocked autoantibody spreading and significantly reduced graft rejection. DISCUSSION/SIGNIFICANCE OF FINDINGS: These data demonstrate that smoking induces pre-LTx autoreactivity to ECM proteins that promotes graft injury following LTx. Furthermore, complement inhibition reduces autoantibody production and protects the graft from injury.
Acute and Chronic Response of Articular Cartilage to Holmium (1995)

A Ho:YAG (holmium-yttrium-aluminum-garnet) laser system operating at a wavelength of 2.1 microns has been introduced recently for use in arthroscopic surgery. The acceptability of this new tool will be determined not only by its ability to resect tissue, but also by its long-term effects on articular surfaces. Two studies were performed to evaluate the acute and chronic effects of the laser on cartilaginous tissue. The acute in vitro effects of 2.1-micron laser irradiation were evaluated, including measurement of ablation efficiency, ablation threshold, and thermal damage in meniscal and articular cartilage. To document the chronic effects on articular cartilage in vivo, a 10-week healing study was performed. Eight sheep weighing 30 to 40 kg underwent bilateral arthrotomy procedures. Multiple full-thickness and partial-thickness defects were created. Animals were euthanized at 0, 2, 4, and 10 weeks. The results of the healing study showed (1) no healing of full- or partial-thickness defects in hyaline cartilage at 10 weeks; (2) fibrocartilaginous granulation tissue filling full-thickness defects at 2 and 4 weeks that was no longer evident at 10 weeks; (3) chondrocyte necrosis extending to > 900 microns distal to ablation craters at 4 weeks, with no evidence of repair at later dates; (4) chondrocyte hyperplasia at the borders of the damage zone at 2 weeks but not at euthanization occurring at later periods.