cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains
Creators: name: Ke, Ruian
name: Lemon, Stanley M.
name: Yamane, Daisuke
name: Benzine, Tiffany
name: Brandt, Ryan
name: De Francesco, Raffaele
name: Lovell, William C.
name: McGivern, David R.
name: Perelson, Alan S.
name: Neddermann, Petra
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Hepatitis C virus (HCV) RNA is synthesized by the replicase complex (RC), a macromolecular assembly composed of viral non-structural proteins and cellular co-factors. Inhibitors of the HCV NS5A protein block formation of new RCs but do not affect RNA synthesis by pre-formed RCs. Without new RC formation, existing RCs turn over and are eventually lost from the cell. We aimed to use NS5A inhibitors to estimate the half-life of the functional RC of HCV. We compared different cell culture-infectious strains of HCV that may be grouped based on their sensitivity to lipid peroxidation: robustly replicating, lipid peroxidation resistant (LPOR) viruses (e.g. JFH-1 or H77D) and more slowly replicating, lipid peroxidation sensitive (LPOS) viruses (e.g. H77S.3 and N.2). In luciferase assays, LPOS HCV strains declined under NS5A inhibitor therapy with much slower kinetics compared to LPOR HCV strains. This difference in rate of decline was not observed for inhibitors of the NS5B RNA-dependent RNA polymerase suggesting that the difference was not simply a consequence of differences in RNA stability. In further analyses, we compared two isoclonal HCV variants: the LPOS H77S.3 and the LPOR H77D that differ only by 12 amino acids. Differences in rate of decline between H77S.3 and H77D following NS5A inhibitor addition were not due to amino acid sequences in NS5A but rather due to a combination of amino acid differences in the non-structural proteins that make up the HCV RC. Mathematical modeling of intracellular HCV RNA dynamics suggested that differences in RC stability (half-lives of 3.5 and 9.9 hours, for H77D and H77S.3, respectively) are responsible for the different kinetics of antiviral suppression between LPOS and LPOR viruses. In nascent RNA capture assays, the rate of RNA synthesis decline following NS5A inhibitor addition was significantly faster for H77D compared to H77S.3 indicating different half-lives of functional RCs.
Algebraic equations for the exceptional eigenspectrum of the generalised Rabi model
Creators: name: Li, Zi-Min
name: Batchelor, Murray T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We obtain the exceptional part of the eigenspectrum of the generalised Rabi model, also known as the driven Rabi model, in terms of the roots of a set of algebraic equations. This approach provides a product form for the wavefunction components and allows an explicit connection with recent results obtained for the wavefunction in terms of truncated confluent Heun functions. Other approaches are also compared. For particular parameter values the exceptional part of the eigenspectrum consists of doubly degenerate crossing points. We give a proof for the number of roots of the constraint polynomials and discuss the number of crossing points.
description: 14 pages, 3 figures. One figure replaced. Degenerate atomic limit covered. Proof for the number of roots clarified and expanded
Measurability of neutron star tidal deformability from merging neutron star-black hole binaries
Creators: name: Cho, Hee-Suk
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The neutron star-black hole binary (NSBH) system has been considered one of the promising detection candidates for ground-based gravitational-wave (GW) detectors such as LIGO and Virgo. The tidal effects of neutron stars (NSs) are imprinted on the GW signals emitted from NSBHs as well as binary neutron stars. In this work, we study how accurately the parameter $λ_{\rm NS}$ can be measured in GW parameter estimation for NSBH signals. We set the parameter range for the NSBH sources to $[4M_{\odot}, 10M_{\odot}]$ for the black hole mass, $[1M_{\odot}, 2M_{\odot}]$ for the NS mass, and $[-0.9, 0.9]$ for the dimensionless black hole spin. For realistic populations of sources distributed in different parameter spaces, we calculate the measurement errors of $λ_{\rm NS}$ ($σ_{λ_{\rm NS}}$) using the Fisher matrix method. In particular, we perform a single-detector analysis using the advanced LIGO and the Cosmic Explorer detectors and a multi-detector analysis using the 2G (advanced LIGO-Hanford, advanced LIGO-Livingstone, advanced Virgo, and KAGRA) and the 3G (Einstein Telescope and Cosmic Explorer) networks. We show the distribution of $σ_{λ_{\rm NS}}$ for the population of sources as a one-dimensional probability density function. Our result shows that the probability density function curves are similar in shape between advanced LIGO and Cosmic Explorer, but Cosmic Explorer can achieve $\sim 15$ times better accuracy overall in the measurement of $λ_{\rm NS}$. In the case of the network detectors, the probability density functions are maximum at $σ_{λ_{\rm NS}} \sim 130$ and $\sim 4$ for the 2G and the 3G networks, respectively, and the 3G network can achieve $\sim 10$ times better accuracy overall.
description: 16 pages, 19 figures, accepted for publication in PRD
A Review on the Use of Blockchain for the Internet of Things
Creators: name: Fernandez-Carames, Tiago M.
name: Fraga-Lamas, Paula
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: The paradigm of Internet of Things (IoT) is paving the way for a world, where many of our daily objects will be interconnected and will interact with their environment in order to collect information and automate certain tasks. Such a vision requires, among other things, seamless authentication, data privacy, security, robustness against attacks, easy deployment, and self-maintenance. Such features can be brought by blockchain, a technology born with a cryptocurrency called Bitcoin. In this paper, a thorough review on how to adapt blockchain to the specific needs of IoT in order to develop Blockchain-based IoT (BIoT) applications is presented. After describing the basics of blockchain, the most relevant BIoT applications are described with the objective of emphasizing how blockchain can impact traditional cloud-centered IoT applications. Then, the current challenges and possible optimizations are detailed regarding many aspects that affect the design, development, and deployment of a BIoT application. Finally, some recommendations are enumerated with the aim of guiding future BIoT researchers and developers on some of the issues that will have to be tackled before deploying the next generation of BIoT applications.
description: Accepted version of IEEE Access journal paper
Exploring the Fundamental Mechanism in Driving Highest-velocity Ionized Outflows in Radio AGNs
Creators: name: Ayubinia, Ashraf
name: Xue, Yongquan
name: Woo, Jong-Hak
name: Le, Huynh Anh Nguyen
name: He, Zhicheng
name: Miraghaei, Halime
name: Lin, Xiaozhi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We investigate the ionized gas kinematics relationship with X-ray, radio and accreting properties using a sample of 348 nearby ($z < 0.4$) SDSS-FIRST-X-ray detected AGNs. X-ray properties of our sample are obtained from XMM-$Newton$, $Swift$ and $Chandra$ observations. We unveil the ionized gas outflows in our sample manifested by the non-gravitational broad component in [OIII] $λ$5007$\overset{\circ}{A}$. emission line profiles. From the comparison of the correlation of non-parametric outflow velocities (i.e., the velocity width, the maximal velocity of outflow and line dispersion) with X-ray luminosity and radio luminosity, we find that outflow velocities have similarly positive {correlations} with both X-ray and radio luminosity. After correcting for the gravitational component, we find that the [OIII] velocity dispersion normalized by stellar mass also increases with both X-ray luminosity and radio luminosity. We also find that for a given X-ray (radio) luminosity, radio (X-ray) luminous AGNs have higher outflow velocities than non-radio (non-X-ray) luminous AGNs. Therefore, we find no clear preference between X-ray luminosity and radio luminosity in driving high-velocity ionized outflows and conclude that both AGN activity and small-scale jets contribute comparably. Moreover, there is no evidence that our obscured AGNs are preferentially associated with higher velocity outflows. Finally, we find a turning point around log$(λ_{Edd}) \simeq -1.3$ when we explore the dependency of outflow velocity on Eddington ratio. It can be interpreted considering the role of high radiation pressure (log$(λ_{Edd}) \gtrsim -1.3$) in drastic reduction in the covering factor of the circumnuclear materials.
description: 23 pages, 14 figures, Accepted to Universe
Simulating Brownian suspensions with fluctuating hydrodynamics
Creators: name: Delmotte, Blaise
name: Keaveny, Eric E
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Fluctuating hydrodynamics has been successfully combined with several computational methods to rapidly compute the correlated random velocities of Brownian particles. In the overdamped limit where both particle and fluid inertia are ignored, one must also account for a Brownian drift term in order to successfully update the particle positions. In this paper, we present an efficient computational method for the dynamic simulation of Brownian suspensions with fluctuating hydrodynamics that handles both computations and provides a similar approximation as Stokesian Dynamics for dilute and semidilute suspensions. This advancement relies on combining the fluctuating force-coupling method (FCM) with a new midpoint time-integration scheme we refer to as the drifter-corrector (DC). The DC resolves the drift term for fluctuating hydrodynamics-based methods at a minimal computational cost when constraints are imposed on the fluid flow to obtain the stresslet corrections to the particle hydrodynamic interactions. With the DC, this constraint need only be imposed once per time step, reducing the simulation cost to nearly that of a completely deterministic simulation. By performing a series of simulations, we show that the DC with fluctuating FCM is an effective and versatile approach as it reproduces both the equilibrium distribution and the evolution of particulate suspensions in periodic as well as bounded domains. In addition, we demonstrate that fluctuating FCM coupled with the DC provides an efficient and accurate method for large-scale dynamic simulation of colloidal dispersions and the study of processes such as colloidal gelation.
Leveraging audio-visual speech effectively via deep learning
Creators: name: Schonburg Carrillo De Mira, Rodrigo
Publisher: name: Imperial College London
Year: 2023

description: The rising popularity of neural networks, combined with the recent proliferation of online audio-visual media, has led to a revolution in the way machines encode, recognize, and generate acoustic and visual speech. Despite the ubiquity of naturally paired audio-visual data, only a limited number of works have applied recent advances in deep learning to leverage the duality between audio and video within this domain. This thesis considers the use of neural networks to learn from large unlabelled datasets of audio-visual speech to enable new practical applications. We begin by training a visual speech encoder that predicts latent features extracted from the corresponding audio on a large unlabelled audio-visual corpus. We apply the trained visual encoder to improve performance on lip reading in real-world scenarios. Following this, we extend the idea of video learning from audio by training a model to synthesize raw speech directly from raw video, without the need for text transcriptions. Remarkably, we find that this framework is capable of reconstructing intelligible audio from videos of new, previously unseen speakers. We also experiment with a separate speech reconstruction framework, which leverages recent advances in sequence modeling and spectrogram inversion to improve the realism of the generated speech. We then apply our research in video-to-speech synthesis to advance the state-of-the-art in audio-visual speech enhancement, by proposing a new vocoder-based model that performs particularly well under extremely noisy scenarios. Lastly, we aim to fully realize the potential of paired audio-visual data by proposing two novel frameworks that leverage acoustic and visual speech to train two encoders that learn from each other simultaneously. We leverage these pre-trained encoders for deepfake detection, speech recognition, and lip reading, and find that they consistently yield improvements over training from scratch.
Language and Worldview in the Processing of Lies
Creators: Fiawornu, Vera Y.
Publisher: name: University of Alberta Library
Year: 2022

This thesis examined if the credibility of a speaker affects the hearer's processing of false (lies) vs true statements. Within the context of this thesis, credibility was established using a preliminary ratings task which asked participants to respond to the following statements: ‘I believe what this person says’, ‘This person has integrity’ and ‘This person is honest’. From this, we categorized our list of characters into trustworthy and untrustworthy. Lying is a complex cognitive process which is more mentally taxing than truth telling (e.g., induces less hand and arm movements, reduced blinking and more pauses during speech, Debey et al., 2012; Duñabeitia & Costa, 2015; Lelieveld et al., 2016). At the same time, lying is a socially relevant skill, and in some social contexts, white lies can be easier to process than blunt truths (Moreno et al., 2016). Also, habit and empathy have been found to lower the cognitive cost associated with producing lies (Verschuere et al., 2011; Yin et al., 2017). Subsequently, in a series of two experiments; a ratings task and self-paced reading experiment, we asked; 1) if participants personally agreed with and found true vs untrue statements acceptable and if those outcomes were influenced by the speaker; 2) if there was a processing cost for true vs untrue statements and if so, was this cost influenced by the speaker; and 3) the extent to which the comprehender’s individual political ideology and personal beliefs influenced the processing and outcomes (social acceptability and personal opinions) of these statements? Among proficient speakers of English who are resident in Canada, the findings from both experiments suggest that the identity of the person who gives truthful information affects the processing of those statements more than the speaker of false information. In addition, we found that perspective taking and personal distress and political views (right-wing) influence the processing of lies vs. truths. Higher scores perspective taking and lower scores personal distress led to faster reading times for true statements spoken by an untrustworthy speaker. Higher scores on the right-wing scale led to faster reading times in general. In addition, there was an interaction suggesting that this effect was stronger for false statements and less pronounced for true statements spoken by untrustworthy speakers; and vice versa for trustworthy speakers.
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Creators: name: O’Connell, Robert J.
name: Michael, Nelson L.
name: Oropeza, Celina
name: Arthos, James
name: Bose, Meera
name: Nitayaphan, Sorachai
name: Slike, Bonnie
name: Thomas, Rasmi
name: Chenine, Agnes-Laurence
name: Tovanabutra, Sodsai
name: Marovich, Mary A.
name: O’Sullivan, Anne Marie
name: Rolland, Morgane
name: Maganga, Lucas
name: Merbah, Melanie
name: Warren, Joanna A.
name: Shaw, George M.
name: Billings, Erik
name: Goonetilleke, Nilu
name: Cicala, Claudia
name: Eller, Michael A.
name: Poltavee, Kultida
name: Kibuuka, Hannah
name: Pham, Phuc
name: Kim, Jerome H.
name: Sanders-Buell, Eric
name: Korber, Bette T.
name: Fischer, Will
name: Li, Hui
name: Peachman, Kristina K.
name: Leviyang, Sivan
name: Sinei, Samuel
name: Harbolick, Elizabeth A.
name: Eller, Leigh A.
name: Krebs, Shelly J.
name: Gao, Feng
name: Costanzo, Margaret C.
name: Rao, Mangala
name: Robb, Merlin L.
name: Kijak, Gustavo H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.
Thermal history of recrystallized carbonate rocks using clumped isotopes
Creators: name: Adlan, Qi
Publisher: name: Imperial College London
Year: 2023

description: Developed in the last two decades, carbonate clumped isotope approach (Δ47) is suitable for temperature reconstruction of the (re)crystallization (TΔ47) of all carbonate phases (Ghosh et al., 2006; Eiler, 2007). Unlike traditional oxygen isotope (δ18O) thermometers, clumped isotopes do not depend on the δ18O of the fluid from which the carbonate minerals developed (Eiler, 2007). This has significant implications for diagenesis and thermal history reconstruction of carbonate rocks in sedimentary basins. In this study, geological samples were used as a natural laboratory which provides a testing ground to understand the behaviour of clumped isotope-exchange reactions through burial–exhumation complexity. The objectives are to investigate the robustness of clumped isotope thermometers to archive thermal history in recrystallized carbonates and to add more constraints on processes associated with the thermal history of a formation using several carbonate species (calcite and dolomite). First, a new approach was developed to safely cleans samples contaminated by organic matter and hydrocarbons. Using subsurface carbonate samples, the recrystallization and clumped isotope-thermal resetting of different limestone components work were then assessed. Finally, investigation of the kinetic differences between minerals in recrystallized limestone and dolostone at various stages of the burial process were conducted across a regional orogeny in Oman. The results of this thesis indicate that different carbonate fabrics recrystallize at different water/rock ratios and with different susceptibility to thermal resetting with respect to clumped isotopes. Fine-grained matrix continues to recrystallize even at a low water/rock ratio during the deep stage of burial and records a wide range of temperatures, suggesting continuous and probably partial recrystallization. Here the evidence of cessation of dissolution and re-precipitation reactions during burial are stopped by oil emplacement was found, extending the application of clumped isotope analyses to petroleum migration studies. This thesis also confirms for the first time in a natural environment that calcite and early dolomite record a different clumped isotope history when subjected to the same thermal history. Finally, this thesis demonstrates that more geological phenomena can be discovered using calcite and early dolomite at the same sampling point, which offers additional constraints on the burial model.
Graph2Vid: Flow graph to Video Grounding for Weakly-supervised Multi-Step Localization
Creators: name: Dvornik, Nikita
name: Hadji, Isma
name: Pham, Hai
name: Bhatt, Dhaivat
name: Martinez, Brais
name: Fazly, Afsaneh
name: Jepson, Allan D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: In this work, we consider the problem of weakly-supervised multi-step localization in instructional videos. An established approach to this problem is to rely on a given list of steps. However, in reality, there is often more than one way to execute a procedure successfully, by following the set of steps in slightly varying orders. Thus, for successful localization in a given video, recent works require the actual order of procedure steps in the video, to be provided by human annotators at both training and test times. Instead, here, we only rely on generic procedural text that is not tied to a specific video. We represent the various ways to complete the procedure by transforming the list of instructions into a procedure flow graph which captures the partial order of steps. Using the flow graphs reduces both training and test time annotation requirements. To this end, we introduce the new problem of flow graph to video grounding. In this setup, we seek the optimal step ordering consistent with the procedure flow graph and a given video. To solve this problem, we propose a new algorithm - Graph2Vid - that infers the actual ordering of steps in the video and simultaneously localizes them. To show the advantage of our proposed formulation, we extend the CrossTask dataset with procedure flow graph information. Our experiments show that Graph2Vid is both more efficient than the baselines and yields strong step localization results, without the need for step order annotation.
description: ECCV'22, oral
Modeling surface roughness scattering in metallic nanowires
Creators: name: Moors, Kristof
name: Sorée, Bart
name: Magnus, Wim
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Ando's model provides a rigorous quantum-mechanical framework for electron-surface roughness scattering, based on the detailed roughness structure. We apply this method to metallic nanowires and improve the model introducing surface roughness distribution functions on a finite domain with analytical expressions for the average surface roughness matrix elements. This approach is valid for any roughness size and extends beyond the commonly used Prange-Nee approximation. The resistivity scaling is obtained from the self-consistent relaxation time solution of the Boltzmann transport equation and is compared to Prange-Nee's approach and other known methods. The results show that a substantial drop in resistivity can be obtained for certain diameters by achieving a large momentum gap between Fermi level states with positive and negative momentum in the transport direction.
description: 25 pages, 11 figures
Sp100 colocalizes with HPV replication foci and restricts the productive stage of the infectious cycle
Creators: name: Warburton, Alix
name: Stamos, James D.
name: McBride, Alison A.
name: Khurana, Simran
name: Stepp, Wesley H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: We have shown previously that Sp100 (a component of the ND10 nuclear body) represses transcription, replication and establishment of incoming human papillomavirus (HPV) DNA in the early stages of infection. In this follow up study, we show that Sp100 does not substantially regulate viral infection in the maintenance phase, however at late stages of infection Sp100 interacts with amplifying viral genomes to repress viral processes. We find that Sp100 localizes to HPV16 replication foci generated in primary keratinocytes, to HPV31 replication foci that form in differentiated cells, and to HPV16 replication foci in CIN 1 cervical biopsies. To analyze this further, Sp100 was down regulated by siRNA treatment of differentiating HPV31 containing cells and levels of viral transcription and replication were assessed. This revealed that Sp100 represses viral transcription and replication in differentiated cells. Analysis of Sp100 binding to viral chromatin showed that Sp100 bound across the viral genome, and that binding increased at late stages of infection. Therefore, Sp100 represses the HPV life cycle at both early and late stages of infection.
The Gaia spectrophotometric standard stars survey -II. Instrumental effects of six ground-based observing campaigns
Creators: name: Altavilla, G.
name: Marinoni, S.
name: Pancino, E.
name: Galleti, S.
name: Ragaini, S.
name: Bellazzini, M.
name: Cocozza, G.
name: Bragaglia, A.
name: Carrasco, J. M.
name: Castro, A.
name: Di Fabrizio, L.
name: Federici, L.
name: Figueras, F.
name: Gebran, M.
name: Jordi, C.
name: Masana, E.
name: Schuster, W.
name: Valentini, G.
name: Voss, H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The Gaia SpectroPhotometric Standard Stars (SPSS) survey started in 2006, it was awarded almost 450 observing nights, and accumulated almost 100,000 raw data frames, with both photometric and spectroscopic observations. Such large observational effort requires careful, homogeneous, and automated data reduction and quality control procedures. In this paper, we quantitatively evaluate instrumental effects that might have a significant (i.e.,$\geq$1%) impact on the Gaia SPSS flux calibration. The measurements involve six different instruments, monitored over the eight years of observations dedicated to the Gaia flux standards campaigns: DOLORES@TNG in La Palma, EFOSC2@NTT and ROSS@REM in La Silla, CAFOS@2.2m in Calar Alto, BFOSC@Cassini in Loiano, and LaRuca@1.5m in San Pedro Martir. We examine and quantitatively evaluate the following effects: CCD linearity and shutter times, calibration frames stability, lamp flexures, second order contamination, light polarization, and fringing. We present methods to correct for the relevant effects, which can be applied to a wide range of observational projects at similar instruments.
description: 16 pages, 13 figures, accepted for publication in Astron. Nachr
T-cell responses targeting HIV Nef uniquely correlate with infected cell frequencies after long-term antiretroviral therapy
Creators: name: Thomas, Allison S.
name: Bosque, Alberto
name: Gandhi, Rajesh T.
name: Jones, Kimberley L.
name: Cyktor, Joshua C.
name: Kovacs, Colin
name: Jones, R. Brad
name: Bosch, Ronald J.
name: Benko, Erika
name: Truong, Ronald
name: Eron, Joseph J.
name: Simmens, Samuel
name: Walker, Bruce D.
name: Macedo, Amanda B.
name: Mellors, John W.
name: McMahon, Deborah K.
name: Chan, Dora
name: Huang, Szu-Han
name: Lalama, Christina M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: HIV-specific CD8+ T-cell responses limit viral replication in untreated infection. After the initiation of antiretroviral therapy (ART), these responses decay and the infected cell population that remains is commonly considered to be invisible to T-cells. We hypothesized that HIV antigen recognition may persist in ART-treated individuals due to low-level or episodic protein expression. We posited that if persistent recognition were occurring it would be preferentially directed against the early HIV gene products Nef, Tat, and Rev as compared to late gene products, such as Gag, Pol, and Env, which have higher barriers to expression. Using a primary cell model of latency, we observed that a Nef-specific CD8+ T-cell clone exhibited low-level recognition of infected cells prior to reactivation and robust recognition shortly thereafter. A Gag-specific CD8+ T-cell clone failed to recognized infected cells under these conditions, corresponding with a lack of detectable Gag expression. We measured HIV-specific T-cell responses in 96 individuals who had been suppressed on ART for a median of 7 years, and observed a significant, direct correlation between cell-associated HIV DNA levels and magnitudes of IFN-γ-producing Nef/Tat/Rev-specific T-cell responses. This correlation was confirmed in an independent cohort (n = 18). Correlations were not detected between measures of HIV persistence and T-cell responses to other HIV antigens. The correlation with Nef/Tat/Rev-specific T-cells was attributable to Nef-specific responses, the breadth of which also correlated with HIV DNA levels. These results suggest that ongoing Nef expression in ART-treated individuals drives preferential maintenance and/or expansion of T-cells reactive to this protein, implying sensing of infected cells by the immune system. The direct correlation, however, suggests that recognition does not result in efficient elimination of infected cells. These results raise the possibility that enhancing the cytolytic activity of Nef-specific T-cells may lead to reductions in infected cell frequencies, even in the absence of therapeutic latency reversal.
Dennstaedtia globulifera Hieron., Bot. Jahrb. Syst.
Creators: name: Schwartsburd, Pedro B.
name: Navarrete, Hugo
name: Smith, Alan R.
name: Kessler, Michael
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Dennstaedtiaceae
Dennstaedtia
Dennstaedtia globulifera

description: Dennstaedtia globulifera (Poir.) Hieron., Bot. Jahrb. Syst. 34: 455. 1904.
 Range:— Greater Antilles; southern U.S.A. (Texas) to Argentina (Yañez et al. 2014) and Uruguay. In Bolivia, known from CH, CO, LP, SC, and TA.
 Ecology:— Common; terrestrial in open areas, as well as inside forests in shady places; 600–2750 m.
 Notes:— The perpendicular wings bordering the continuous grooves of the axes of the blades resemble those of Dennstaedtia bipinnata, which also lacks petiolar buds and has similar rhizome pubescence. However, the rhizomes in D. globulifera tend to be thicker and more robust and with shorter internodes than in D. bipinnata. Additionally, Yañez et al. (2104) reported D. glauca as having pubescent rhizomes but the features of the blades clearly separate these species.
description: Published as part of Schwartsburd, Pedro B., Navarrete, Hugo, Smith, Alan R. & Kessler, Michael, 2017, Prodromus of a fern flora for Bolivia. XXVI. Dennstaedtiaceae, pp. 251-268 in Phytotaxa 332 (3) on page 254, DOI: 10.11646/phytotaxa.332.3.2, http://zenodo.org/record/13723580
Batch Reverse Osmosis: Improvements and New Applications
Creators: name: Das, Abhimanyu
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: classificationCode: 401702
subject: Dynamics, vibration and vibration control

description: Reverse osmosis (RO) is emerging as the world’s leading desalination technology due to its superior energy efficiency and the shift towards renewable electrification. However, RO systems need to further improve efficiency, increase operating flux, reach higher salinities (>7.5% w.t.), and minimize component complexity. Treating RO as a dynamical system, this dissertation invents new processes for high-efficiency desalination that achieve milestones for low downtime and high final salinity. It also introduces modeling methods that include more detail (e.g. salt retention, time-varying salinity, concentration polarization, salt transport, temporal multi-staging, etc.) and the first use of certain optimization methods in RO.Batch RO is an unsteady, pressure driven process that efficiently desalinates a saline feed volume over time by continuously recirculating the brine through the membrane module. A tank houses the concentrating feed and mediates the streams entering and leaving the membrane module. Most studies so far have concentrated on the high-pressure tank design that requires finite downtime at the end of each stroke. A scalable pressure exchanger batch RO (PX-BRO) configuration using atmospheric tanks that practically has zero downtime and produces permeate even while flushing is first described in this dissertation.To achieve high recovery at nominal RO pressures, osmotically assisted RO processes have both sides of the membrane saline and the streams usually in counterflow. The first unsteady osmotically assisted process based on the high-pressure piston tank design, batch counterflow RO (BCFRO) is introduced which dramatically reduces the energy needs. To address the issue of high component count in spatial multi-staging, the first “temporally multi-staged” BCFRO process is also introduced. The new process uses the pressure ex- changer and atmospheric pressure tank design for scalability and operational flexibility.For membranes with low salt rejection, it becomes imperative to integrate the salt trans- port dynamics for deciding operating and initial conditions. Trajectory optimization is used to match salinity and volume between stages of temporally multi-staged BCFRO. Treating the process as an optimal control problem, a framework for obtaining time varying flux pro- files that minimize the specific energy consumption is also developed. Both reduced order and discretized models are developed to analyze these new batch RO configurations.
Robust Candidate Generation for Entity Linking on Short Social Media Texts
Creators: name: Hebert, Liam
name: Makki, Raheleh
name: Mishra, Shubhanshu
name: Saghir, Hamidreza
name: Kamath, Anusha
name: Merhav, Yuval
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: Information Retrieval (cs.IR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: I.2.7
subject: 68T50, 68T07

description: Entity Linking (EL) is the gateway into Knowledge Bases. Recent advances in EL utilize dense retrieval approaches for Candidate Generation, which addresses some of the shortcomings of the Lookup based approach of matching NER mentions against pre-computed dictionaries. In this work, we show that in the domain of Tweets, such methods suffer as users often include informal spelling, limited context, and lack of specificity, among other issues. We investigate these challenges on a large and recent Tweets benchmark for EL, empirically evaluate lookup and dense retrieval approaches, and demonstrate a hybrid solution using long contextual representation from Wikipedia is necessary to achieve considerable gains over previous work, achieving 0.93 recall.
description: 7 pages, 2 figures. Accepted to Proceedings of the Eighth Workshop on Noisy User-generated Text (W-NUT 2022). URL: https://aclanthology.org/2022.wnut-1.8
How to discretize a quantum bath for real-time evolution
Creators: name: de Vega, Ines
name: Schollwöck, Ulrich
name: Wolf, F. Alexander
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Many numerical techniques for the description of quantum systems that are coupled to a continuous bath require the discretization of the latter. To this end, a wealth of methods has been developed in the literature, which we classify as (i) direct discretization, (ii) orthogonal polynomial, and (iii) numerical optimization strategies. We recapitulate strategies (i) and (ii) to clarify their relation. For quadratic Hamiltonians, we show that (ii) is the best strategy in the sense that it gives the numerically exact time evolution up to a maximum time $t_\text{max}$, for which we give a simple expression. For non-quadratic Hamiltonians, we show that no such best strategy exists. We present numerical examples relevant to open quantum systems and strongly correlated systems, as treated by dynamical mean-field theory (DMFT).
Efficient metallic spintronic emitters of ultrabroadband terahertz radiation
Creators: name: Seifert, T.
name: Jaiswal, S.
name: Martens, U.
name: Hannegan, J.
name: Braun, L.
name: Maldonado, P.
name: Freimuth, F.
name: Kronenberg, A.
name: Henrizi, J.
name: Radu, I.
name: Beaurepaire, E.
name: Mokrousov, Y.
name: Oppeneer, P. M.
name: Jourdan, M.
name: Jakob, G.
name: Turchinovich, D.
name: Hayden, L. M.
name: Wolf, M.
name: Münzenberg, M.
name: Kläui, M.
name: Kampfrath, T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Terahertz electromagnetic radiation is extremely useful for numerous applications such as imaging and spectroscopy. Therefore, it is highly desirable to have an efficient table-top emitter covering the 1-to-30-THz window whilst being driven by a low-cost, low-power femtosecond laser oscillator. So far, all solid-state emitters solely exploit physics related to the electron charge and deliver emission spectra with substantial gaps. Here, we take advantage of the electron spin to realize a conceptually new terahertz source which relies on tailored fundamental spintronic and photonic phenomena in magnetic metal multilayers: ultrafast photo-induced spin currents, the inverse spin-Hall effect and a broadband Fabry-Pérot resonance. Guided by an analytical model, such spintronic route offers unique possibilities for systematic optimization. We find that a 5.8-nm-thick W/CoFeB/Pt trilayer generates ultrashort pulses fully covering the 1-to-30-THz range. Our novel source outperforms laser-oscillator-driven emitters such as ZnTe(110) crystals in terms of bandwidth, terahertz-field amplitude, flexibility, scalability and cost.
description: 18 pages, 10 figures
The LOFAR Tied-Array All-Sky Survey: Timing of 35 radio pulsars and an overview of the properties of the LOFAR pulsar discoveries
Creators: name: van der Wateren, E.
name: Bassa, C. G.
name: Cooper, S.
name: Grießmeier, J. -M.
name: Stappers, B. W.
name: Hessels, J. W. T.
name: Kondratiev, V. I.
name: Michilli, D.
name: Tan, C. M.
name: Tiburzi, C.
name: Weltevrede, P.
name: Nielsen, A. -S. Bak
name: Carozzi, T. D.
name: Ciardi, B.
name: Cognard, I.
name: Dettmar, R. -J.
name: Karastergiou, A.
name: Kramer, M.
name: Künsemöller, J.
name: Osłowski, S.
name: Serylak, M.
name: Vocks, C.
name: Wucknitz, O.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The LOFAR Tied-Array All-Sky Survey (LOTAAS) is the most sensitive untargeted radio pulsar survey performed at low radio frequencies (119--151\,MHz) to date and has discovered 76 new radio pulsars, among which the 23.5-s pulsar J0250+5854, up until recently the slowest-spinning radio pulsar known. Here, we report on the timing solutions of 35 pulsars discovered by LOTAAS, which include a nulling pulsar and a mildly recycled pulsar, and thereby complete the full timing analysis of the LOTAAS pulsar discoveries. We give an overview of the findings from the full LOTAAS sample of 76 pulsars, discussing their pulse profiles, radio spectra and timing parameters. We found that the pulse profiles of some of the pulsars show profile variations in time or frequency and while some pulsars show signs of scattering, a large majority display no pulse broadening. The LOTAAS discoveries have on average steeper radio spectra and have longer spin periods ($1.4\times$) as well as lower spin-down rates ($3.1\times$) compared to the known pulsar population. We discuss the cause of these differences, and attribute them to a combination of selection effects of the LOTAAS survey as well as previous pulsar surveys, though can not rule out that older pulsars tend to have steeper radio spectra.
description: Accepted to Astronomy & Astrophysics
A Journey of a Lifetime! Privileged to be Part of the Benue State SPI Rating Project-A Student Report
Creators: name: Onah, Oplekwu Benson
name: Onah, Oplekwu Benson
Publisher: name: Unknown
Year: 2021
Subjects: subject: Teaching/Communication/Extension/Profession
subject: Nigeria
subject: soil testing
subject: extension
subject: training

description: First person account of a student's experience during the Benue State SPI Rating Project. Over 800 student and technical staff were in attendance during the one day training on soil testing.
Kinetically stabilized inflation
Creators: name: Li, Changhong
name: Gong, Hao
name: Cheung, Yeuk-kwan Edna
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this work, we propose a string-inspired two fields inflation model to address the fine-tuning problem that the standard inflation model suffers. The fast-rolling tachyon $\mathcal{T}$ originated from the D-brane and anti-D-brane pair annihilation locks the inflaton $φ$ slowly rolling on a Higgs-like potential $V(φ)=-m_φ^2φ^2+λφ^4$ and drives a kinetically stabilized (KS) inflation. Our numerical simulation confirms such a solution is a dynamic attractor. In particular, for $λ< 0.8\times 10^{-3}$, the e-folding number contributed by the KS inflation phase can be larger than $62$ to solve the horizon and flatness problems of Big Bang theory. Notably, this KS inflation generates a nearly scale-invariant primordial curvature perturbations spectrum consistent with current cosmic microwave background (CMB) observations. It predicts a low tensor-to-scalar ratio, which the current primordial gravitational wave background (the B-modes in CMB) searches favor.
description: 16 pages, 4 figures
An augmented phase plane approach for discrete planar maps: Introducing next-iterate operators
Creators: name: Streipert, Sabrina H.
name: Wolkowicz, Gail S. K.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: The next-iterate operators and corresponding next-iterate root-sets and root-curves associated with the nullclines of a planar discrete map are introduced. How to augment standard phase portraits that include the nullclines and the direction field, by including the signs of the root-operators associated with their nullclines, thus producing an augmented phase portrait, is described. The sign of a next-iterate operator associated with a nullcline determines whether a point is mapped above or below the corresponding nullcline and can, for example, identify positively invariant regions. Using a Lotka-Volterra type competition model, we demonstrate how to construct the augmented phase portrait. We show that the augmented phase portrait provides an elementary, alternative approach for determining the complete global dynamics of this model. We further explore the limitations and potential of the augmented phase portrait by considering a Ricker competition model, a model involving mutualism, and a predator-prey model.
description: Code to create augmented phase portrait available at: https://github.com/sabrinaheike/AugmentedPhasePortrait/tree/main
Outage Analysis of Full-Duplex Architectures in Cellular Networks
Creators: name: Psomas, Constantinos
name: Krikidis, Ioannis
Publisher: name: arXiv
Year: 2015
Subjects: subject: Information Theory (cs.IT)
subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: The implementation of full-duplex (FD) radio in wireless communications is a potential approach for achieving higher spectral efficiency. A possible application is its employment in the next generation of cellular networks. However, the performance of large-scale FD multiuser networks is an area mostly unexplored. Most of the related work focuses on the performance analysis of small-scale networks or on loop interference cancellation schemes. In this paper, we derive the outage probability performance of large-scale FD cellular networks in the context of two architectures: two-node and three-node. We show how the performance is affected with respect to the model's parameters and provide a comparison between the two architectures.
description: to appear in Proc. IEEE VTC 2015 Spring, Glasgow
Stability conditions for a large anharmonic bipolaron
Creators: name: Houtput, Matthew
name: Tempere, Jacques
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A large polaron is a quasiparticle that consists of a nearly free electron interacting with the phonons of a material, whose lattice parameters are much smaller than the polaron scale. The electron-phonon interaction also leads to an attractive interaction between electrons, which can allow two polarons to pair up and form a bipolaron. It has been shown that large bipolarons can form in theory due to strong 1-electron-1-phonon coupling, but they have not been seen in real materials because the critical value of the required electron-phonon interaction is too large. Here, we investigate the effect of 1-electron-2-phonon coupling on the large bipolaron problem. Starting from a generalization of the Fröhlich Hamiltonian that includes both the standard 1-electron-1-phonon interaction as well as an anharmonic 1-electron-2-phonon interaction, we use the path integral method to find a semi-analytical upper bound for the bipolaron energy that is valid at all values of the Fröhlich coupling strength $α$. We find the bipolaron phase diagram and conditions for the bipolaron stability by comparing the bipolaron energy to the energy of two free polarons. The critical value of the Fröhlich coupling strength $α_{\text{crit}}$ is calculated as a function of the strength of the 1-electron-2-phonon interaction. The results suggest that large bipolaron formation is more likely in materials with significant 1-electron-2-phonon interaction as well as strong 1-electron-1-phonon interaction, such as strontium titanate.
Intramolecular hydrogen transfer reactions catalyzed by pentamethylcyclopentadienyl rhodium and cobalt olefin complexes: Mechanistic studies
Creators: name: Lyons, Thomas W.
name: Bolig, Andrew D.
name: Brookhart, Maurice
name: DiSalvo, Darren T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The mechanism of intramolecular transfer dehydrogenation catalyzed by [Cp * M(VTMS) 2 ] ( 1 , M=Rh, 2 , M=Co, Cp* = C 5 Me 5 , VTMS = vinyltrimethylsilane) complexes has been studied using vinyl silane protected alcohols as substrates. Deuterium-labeled substrates have been synthesized and the regioselectivity of H/D transfers investigated using 1 H and 2 H NMR spectroscopy. The labeling studies establish a regioselective pathway consisting of alkene directed α C-H activation, 2,1 alkene insertion, and finally β-hydride elimination to give silyl enol ether products.