cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Synthesis and physical properties of LaNiO$_2$ crystals
Creators: name: Puphal, Pascal
name: Wehinger, Björn
name: Nuss, Jürgen
name: Küster, Kathrin
name: Starke, Ulrich
name: Garbarino, Gaston
name: Keimer, Bernhard
name: Isobe, Masahiko
name: Hepting, Matthias
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Infinite-layer (IL) nickelates are an emerging family of superconductors whose similarities and differences to cuprate superconductors are under intense debate. To date, the IL phase of nickelates can only be reached via topotactic oxygen reduction of the perovskite phase, using H$_2$ gas or reducing agents such as CaH$_2$. While the topotactic reduction method has been widely employed on thin film and polycrystalline powder samples, the reduction of La$_{1-x}$Ca$_x$NiO$_3$ single-crystals with lateral dimensions up to 150 $μ$m was achieved only recently, using an indirect contact method with CaH$_2$. Here we report the topotactic transformation of much larger LaNiO$_3$ crystals with lateral dimensions of more than one millimeter, via direct contact with CaH$_2$. We characterize the crystalline, magnetic, and electronic properties of the obtained IL LaNiO$_{2}$ crystals by powder and single-crystal x-ray diffraction (XRD), magnetometry, electrical transport, and x-ray photoelectron spectroscopy (XPS) measurements. The amount of incorporated topotactic hydrogen due to the reduction process is determined by a gas extraction method. In addition, we investigate the evolution of the lattice parameters under hydrostatic pressure up to 12 GPa, using high-resolution synchrotron XRD. Furthermore, we provide a direct comparison of several physical properties of the LaNiO$_{2}$ crystals to their powder and thin film counterparts.
Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF
Creators: name: Schulmeyer, Kayley H.
name: Diaz, Manisha R.
name: Laederach, Alain
name: Sanders, Wes
name: Wolfgang, Matthew C.
name: Bair, Thomas B.
name: Yahr, Timothy L.
name: Gode, Cindy J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT CsrA family RNA-binding proteins are widely distributed in bacteria and regulate gene expression at the posttranscriptional level. Pseudomonas aeruginosa has a canonical member of the CsrA family (RsmA) and a novel, structurally distinct variant (RsmF). To better understand RsmF binding properties, we performed parallel systematic evolution of ligands by exponential enrichment (SELEX) experiments for RsmA and RsmF. The initial target library consisted of 62-nucleotide (nt) RNA transcripts with central cores randomized at 15 sequential positions. Most targets selected by RsmA and RsmF were the expected size and shared a common consensus sequence (CANGGAYG) that was positioned in a hexaloop region of the stem-loop structure. RsmA and RsmF also selected for longer targets (≥96 nt) that were likely generated by rare PCR errors. Most of the long targets contained two consensus-binding sites. Representative short (single consensus site) and long (two consensus sites) targets were tested for RsmA and RsmF binding. Whereas RsmA bound the short targets with high affinity, RsmF was unable to bind the same targets. RsmA and RsmF both bound the long targets. Mutation of either consensus GGA site in the long targets reduced or eliminated RsmF binding, suggesting a requirement for two tandem binding sites. Conversely, RsmA bound long targets containing only a single GGA site with unaltered affinity. The RsmF requirement for two binding sites was confirmed with tssA1 , an in vivo regulatory target of RsmA and RsmF. Our findings suggest that RsmF binding requires two GGA-containing sites, while RsmA binding requirements are less stringent. IMPORTANCE The CsrA family of RNA-binding proteins is widely conserved in bacteria and plays important roles in the posttranscriptional regulation of protein synthesis. P. aeruginosa has two CsrA proteins, RsmA and RsmF. Although RsmA and RsmF share a few RNA targets, RsmF is unable to bind to other targets recognized by RsmA. The goal of the present study was to better understand the basis for differential binding by RsmF. Our data indicate that RsmF binding requires target RNAs with two consensus-binding sites, while RsmA recognizes targets with just a single binding site. This information should prove useful to future efforts to define the RsmF regulon and its contribution to P. aeruginosa physiology and virulence.
Statistical Properties of X-Ray Bursts from SGR J1935+2154 Detected by Insight-HXMT
Creators: name: Zhang, Wen-Long
name: Li, Xiu-Juan
name: Yang, Yu-Peng
name: Yi, Shuang-Xi
name: Li, Cheng-Kui
name: Tang, Qing-Wen
name: Qin, Ying
name: Wang, Fa-Yin
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: As one class of the most important objects in the universe, magnetars can produce a lot of different frequency bursts including X-ray bursts. In \cite{2022ApJS..260...24C}, 75 X-ray bursts produced by magnetar SGR J1935+2154 during an active period in 2020 are published, including the duration and net photon counts of each burst, and waiting time based on the trigger time difference. In this paper, we utilize the power-law model, $dN(x)/dx\propto (x+x_0)^{-α_x}$, to fit the cumulative distributions of these parameters. It can be found that all the cumulative distributions can be well fitted, which can be interpreted by a self-organizing criticality theory. Furthermore, we check whether this phenomenon still exist in different energy bands and find that there is no obvious evolution. These findings further confirm that the X-ray bursts from magnetars are likely to be generated by some self-organizing critical process, which can be explained by a possible magnetic reconnection scenario in magnetars.
description: 6 pages, 1 figure and 3 tables; published in Research in Astronomy and Astrophysics
Generalized Quantum PageRank Algorithm with Arbitrary Phase Rotations
Creators: name: Ortega, Sergio A.
name: Martin-Delgado, Miguel A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The quantization of the PageRank algorithm is a promising tool for a future quantum internet. Here we present a modification of the quantum PageRank introducing arbitrary phase rotations (APR) in the underlying Szegedy's quantum walk. We define three different APR schemes with only one phase as a degree of freedom. We have analyzed the behavior of these algorithms in a small generic graph, observing that a decrease of the phase reduces the standard deviation of the instantaneous PageRank, so the nodes of the network can be distinguished better. However, the algorithm takes more time to converge, so the phase can not be decreased arbitrarily. With these results we choose a concrete value for the phase to later apply the algorithm to complex scale-free graphs. In these networks, the original quantum PageRank is able to break the degeneracy of the residual nodes and detect secondary hubs that the classical algorithm suppresses. Nevertheless, not all of the detected secondary hubs are real according to the PageRank's definition. Some APR schemes can overcome this problem, restoring the degeneration of the residual nodes and highlighting the truly secondary hubs of the networks. Finally, we have studied the stability of the new algorithms. The original quantum algorithm was known to be more stable than the classical. We have found that one of our algorithms, whose PageRank distribution resembles the classical one, has a stability similar to the original quantum algorithm.
description: RevTex 4.2, 19 color figures, 4 tables
Dynamics of the Energy Relaxation in a Parabolic Quantum Well Laser
Creators: name: Trifonov, A. V.
name: Cherotchenko, E. D.
name: Carthy, J. L.
name: Ignatiev, I. V.
name: Tzimis, A.
name: Tsintzos, S.
name: Hatzopoulos, Z.
name: Savvidis, P. G.
name: Kavokin, A. V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We explore two parabolic quantum well (PQW) samples, with and without Bragg mirrors, in order to optimise the building blocks of a Bosonic Cascade Laser. The photoluminescence spectra of a PQW microcavity sample is compared against that of a conventional microcavity with embedded quantum wells (QWs) to demonstrate that the weak coupling lasing in a PQW sample can be achieved. The relaxation dynamics in a conventional QW microcavity and in the PQW microcavity was studied by a non-resonant pump-pump excitation method. Strong difference in the relaxation characteristics between the two samples was found. The semi-classical Boltzmann equations were adapted to reproduce the evolution of excitonic populations within the PQW as a function of the pump power and the output intensity evolution as a function of the pump-pump pulse delay. Fitting the PQW data confirms the anticipated cascade relaxation, paving the way for such a system to produce terahertz radiation.
description: 8 pages, 6 figures
Comparing the writing style of real and artificial papers
Creators: name: Amancio, Diego R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Recent years have witnessed the increase of competition in science. While promoting the quality of research in many cases, an intense competition among scientists can also trigger unethical scientific behaviors. To increase the total number of published papers, some authors even resort to software tools that are able to produce grammatical, but meaningless scientific manuscripts. Because automatically generated papers can be misunderstood as real papers, it becomes of paramount importance to develop means to identify these scientific frauds. In this paper, I devise a methodology to distinguish real manuscripts from those generated with SCIGen, an automatic paper generator. Upon modeling texts as complex networks (CN), it was possible to discriminate real from fake papers with at least 89\% of accuracy. A systematic analysis of features relevance revealed that the accessibility and betweenness were useful in particular cases, even though the relevance depended upon the dataset. The successful application of the methods described here show, as a proof of principle, that network features can be used to identify scientific gibberish papers. In addition, the CN-based approach can be combined in a straightforward fashion with traditional statistical language processing methods to improve the performance in identifying artificially generated papers.
description: To appear in Scientometrics (2015)
Curvature of the chiral pseudo-critical line in QCD: continuum extrapolated results
Creators: name: Bonati, Claudio
name: D'Elia, Massimo
name: Mariti, Marco
name: Mesiti, Michele
name: Negro, Francesco
name: Sanfilippo, Francesco
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We determine the curvature of the pseudo-critical line of strong interactions by means of numerical simulations at imaginary chemical potentials. We consider $N_f=2+1$ stout improved staggered fermions with physical quark masses and the tree level Symanzik gauge action, and explore four different sets of lattice spacings, corresponding to $N_t = 6,8,10,12$, in order to extrapolate results to the continuum limit. Our final estimate is $κ= 0.0135(20)$.
description: 11 pages, 10 figures, 4 tables. Version to appear in Physical Review D
Road Rutting Detection using Deep Learning on Images
Creators: name: Saha, Poonam Kumari
name: Arya, Deeksha
name: Kumar, Ashutosh
name: Maeda, Hiroya
name: Sekimoto, Yoshihide
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences
subject: E.0; J.0

description: Road rutting is a severe road distress that can cause premature failure of road incurring early and costly maintenance costs. Research on road damage detection using image processing techniques and deep learning are being actively conducted in the past few years. However, these researches are mostly focused on detection of cracks, potholes, and their variants. Very few research has been done on the detection of road rutting. This paper proposes a novel road rutting dataset comprising of 949 images and provides both object level and pixel level annotations. Object detection models and semantic segmentation models were deployed to detect road rutting on the proposed dataset, and quantitative and qualitative analysis of model predictions were done to evaluate model performance and identify challenges faced in the detection of road rutting using the proposed method. Object detection model YOLOX-s achieves mAP@IoU=0.5 of 61.6% and semantic segmentation model PSPNet (Resnet-50) achieves IoU of 54.69 and accuracy of 72.67, thus providing a benchmark accuracy for similar work in future. The proposed road rutting dataset and the results of our research study will help accelerate the research on detection of road rutting using deep learning.
description: 9 pages, 7 figures
Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci
Creators: name: Pollet, Rebecca M.
name: Eto, Karina Yui
name: Eakes, Thomas C.
name: Hymes, Jeff P.
name: Ingle, James D.
name: Ramsay, Joshua P.
name: Firth, Neville
name: Redinbo, Matthew R.
name: Kwong, Stephen M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT Antimicrobial resistance in Staphylococcus aureus presents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at the oriT region of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES protein in vitro . Second, pSK156 and pCA347 are nonconjugative Staphylococcus aureus plasmids that contain sequences similar to the oriT region of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate the oriT sequences of these nonconjugative plasmids in vitro . Although pSK41 could mobilize a coresident plasmid harboring its cognate oriT , it was unable to mobilize plasmids containing the pSK156 and pCA347 variant oriT mimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-like oriT . These data indicate that the conjugative relaxase in trans mechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids. IMPORTANCE Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variant oriT -like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase in trans mechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution.
Construction of the Radio Map with Defective GPS Position Information
Creators: name: Kang, Taewon
name: Rhee, Joon Hyo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The basic idea of RSS-based indoor positioning is to estimate the receiver location by matching the measured received signal strength indicator (RSSI) with preestablished RSSI collections with corresponding locations, known as the radio map. Hence, constructing an accurate radio map directly relates to accurate positioning performance in RSS-based indoor positioning. RSS-based indoor positioning can be easily conducted with a radio map that surveys every location, but a complete radio map cannot be constructed when the map area includes locations that are physically impossible to reach or denied access. In addition, measurement errors or device problems can occur during the survey, resulting in degradation of the radio map. We analyzed incidents that occurred in actual RSSI surveys that could disrupt the construction of the radio map and proposed methods to construct a more accurate radio map.
description: 5 pages
Curing spurious magneto-mechanical coupling in soft non-magnetic materials
Creators: name: Rambausek, Matthias
name: Schöberl, Joachim
Publisher: name: arXiv
Year: 2022
Subjects: subject: Numerical Analysis (math.NA)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 65N30

description: The present work is concerned with the issue of spurious coupling effects that are pervasive in fully coupled magneto-mechanical finite element simulations involving very soft non-magnetic or air-like media. We first address the characterization of the spurious magneto-mechanical effects and their intuitive interpretation based on energy considerations. Then, as main contribution, we propose two new ways to prune the undesired spurious magneto-mechanical coupling in non-magnetic media. The proposed methods are compared with established methods in the context of magnetic bodies embedded in (i) air or vacuum and (ii) very soft elastic non-magnetic media. The comparison shows that the proposed approaches are accurate and effective. They, furthermore, allow for a consistent linearization of the coupled boundary value problems, which is crucial for the simulation of compliant structures. For reproducibility and accessibility of the proposed methods, we provide our implementations with Netgen/NGSolve as well as all codes necessary for the reproduction of our results as supplementary material.
description: 31 pages, 17 figures, to be submitted to the International Journal of Numerical Methods in Engineering, supplementary material for this version hosted on zenodo with doi 10.5281/zenodo.7128677
Regulation of Type IV Pili Contributes to Surface Behaviors of Historical and Epidemic Strains of Clostridium difficile
Creators: name: Burrus, Vincent
name: Purcell, Erin B.
name: Bordeleau, Eric
name: Tamayo, Rita
name: McKee, Robert W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT The intestinal pathogen Clostridium difficile is an urgent public health threat that causes antibiotic-associated diarrhea and is a leading cause of fatal nosocomial infections in the United States. C. difficile rates of recurrence and mortality have increased in recent years due to the emergence of so-called “hypervirulent” epidemic strains. A great deal of the basic biology of C. difficile has not been characterized. Recent findings that flagellar motility, toxin synthesis, and type IV pilus (TFP) formation are regulated by cyclic diguanylate (c-di-GMP) reveal the importance of this second messenger for C. difficile gene regulation. However, the function(s) of TFP in C. difficile remains largely unknown. Here, we examine TFP-dependent phenotypes and the role of c-di-GMP in controlling TFP production in the historical 630 and epidemic R20291 strains of C. difficile . We demonstrate that TFP contribute to C. difficile biofilm formation in both strains, but with a more prominent role in R20291. Moreover, we report that R20291 is capable of TFP-dependent surface motility, which has not previously been described in C. difficile . The expression and regulation of the pilA1 pilin gene differs between R20291 and 630, which may underlie the observed differences in TFP-mediated phenotypes. The differences in pilA1 expression are attributable to greater promoter-driven transcription in R20291. In addition, R20291, but not 630, upregulates c-di-GMP levels during surface-associated growth, suggesting that the bacterium senses its substratum. The differential regulation of surface behaviors in historical and epidemic C. difficile strains may contribute to the different infection outcomes presented by these strains. IMPORTANCE How Clostridium difficile establishes and maintains colonization of the host bowel is poorly understood. Surface behaviors of C. difficile are likely relevant during infection, representing possible interactions between the bacterium and the intestinal environment. Pili mediate bacterial interactions with various surfaces and contribute to the virulence of many pathogens. We report that type IV pili (TFP) contribute to biofilm formation by C. difficile . TFP are also required for surface motility, which has not previously been demonstrated for C. difficile . Furthermore, an epidemic-associated C. difficile strain showed higher pilin gene expression and greater dependence on TFP for biofilm production and surface motility. Differences in TFP regulation and their effects on surface behaviors may contribute to increased virulence in recent epidemic strains.
Regulatory Requirements for Staphylococcus aureus Nitric Oxide Resistance
Creators: name: Weiss, Andy
name: Shaw, Lindsey N.
name: Grosser, Melinda R.
name: Richardson, Anthony R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT The ability of Staphylococcus aureus to resist host innate immunity augments the severity and pervasiveness of its pathogenesis. Nitric oxide (NO˙) is an innate immune radical that is critical for the efficient clearance of a wide range of microbial pathogens. Exposure of microbes to NO˙ typically results in growth inhibition and induction of stress regulons. S. aureus , however, induces a metabolic state in response to NO˙ that allows for continued replication and precludes stress regulon induction. The regulatory factors mediating this distinctive response remain largely undefined. Here, we employ a targeted transposon screen and transcriptomics to identify and characterize five regulons essential for NO˙ resistance in S. aureus : three virulence regulons not formerly associated with NO˙ resistance, SarA, CodY, and Rot, as well as two regulons with established roles, Fur and SrrAB. We provide new insights into the contributions of Fur and SrrAB during NO˙ stress and show that the S. aureus Δ sarA mutant, the most sensitive of the newly identified mutants, exhibits metabolic dysfunction and widespread transcriptional dysregulation following NO˙ exposure. Altogether, our results broadly characterize the regulatory requirements for NO˙ resistance in S. aureus and suggest an intriguing overlap between the regulation of NO˙ resistance and virulence in this well-adapted human pathogen. IMPORTANCE The prolific human pathogen Staphylococcus aureus is uniquely capable of resisting the antimicrobial radical nitric oxide (NO˙), a crucial component of the innate immune response. However, a complete understanding of how S. aureus regulates an effective response to NO˙ is lacking. Here, we implicate three central virulence regulators, SarA, CodY, and Rot, as major players in the S. aureus NO˙ response. Additionally, we elaborate on the contribution of two regulators, SrrAB and Fur, already known to play a crucial role in S. aureus NO˙ resistance. Our study sheds light on a unique facet of S. aureus pathogenicity and demonstrates that the transcriptional response of S. aureus to NO˙ is highly pleiotropic and intrinsically tied to metabolism and virulence regulation.
Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2
Creators: name: Braunstein, Miriam
name: Miller, Brittany K.
name: Rigel, Nathan W.
name: Swanson, Stephanie
name: Sacchettini, James C.
name: Ioerger, Thomas R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 ( Mtb SecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how Mtb SecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.
Exploring Users' Pointing Performance on Virtual and Physical Large Curved Displays
Creators: name: Ullah, A K M Amanat
name: Delamare, William
name: Hasan, Khalad
Publisher: name: arXiv
Year: 2023
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Large curved displays have emerged as a powerful platform for collaboration, data visualization, and entertainment. These displays provide highly immersive experiences, a wider field of view, and higher satisfaction levels. Yet, large curved displays are not commonly available due to their high costs. With the recent advancement of Head Mounted Displays (HMDs), large curved displays can be simulated in Virtual Reality (VR) with minimal cost and space requirements. However, to consider the virtual display as an alternative to the physical display, it is necessary to uncover user performance differences (e.g., pointing speed and accuracy) between these two platforms. In this paper, we explored users' pointing performance on both physical and virtual large curved displays. Specifically, with two studies, we investigate users' performance between the two platforms for standard pointing factors such as target width, target amplitude as well as users' position relative to the screen. Results from user studies reveal no significant difference in pointing performance between the two platforms when users are located at the same position relative to the screen. In addition, we observe users' pointing performance improves when they are located at the center of a semi-circular display compared to off-centered positions. We conclude by outlining design implications for pointing on large curved virtual displays. These findings show that large curved virtual displays are a viable alternative to physical displays for pointing tasks.
description: In 29th ACM Symposium on Virtual Reality Software and Technology (VRST 2023)
The YsrS Paralog DygS Has the Capacity To Activate Expression of the Yersinia enterocolitica Ysa Type III Secretion System
Creators: name: Griggs, Lauren A.
name: Bode, Addys
name: Walker, Kimberly A.
name: Patrick Summers,
name: Obrist, Markus
name: Miller, Virginia L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT The Yersinia enterocolitica Ysa type III secretion system (T3SS) is associated with intracellular survival, and, like other characterized T3SSs, it is tightly controlled. Expression of the ysa genes is only detected following growth at low temperatures (26°C) and in high concentrations of sodium chloride (290 mM) in the medium. The YsrSTR phosphorelay (PR) system is required for ysa expression and likely responds to NaCl. During our investigations into the Ysr PR system, we discovered that genes YE3578 and YE3579 are remarkably similar to ysrR and ysrS , respectively, and are probably a consequence of a gene duplication event. The amino acid differences between YE3578 and ysrR are primarily clustered into two short regions. The differences between YE3579 and ysrS are nearly all located in the periplasmic sensing domain; the cytoplasmic domains are 98% identical. We investigated whether these paralogs were capable of activating ysa gene expression. We found that the sensor paralog, named DygS, is capable of compensating for loss of ysrS , but the response regulator paralog, DygR, cannot complement a ysrR gene deletion. In addition, YsrR, but not DygR, interacts with the histidine phosphorelay protein YsrT. Thus, DygS likely activates ysa gene expression in response to a signal other than NaCl and provides an example of a phosphorelay system in which two sensor kinases feed into the same regulatory pathway. IMPORTANCE All organisms need mechanisms to promote survival in changing environments. Prokaryotic phosphorelay systems are minimally comprised of a histidine kinase (HK) that senses an extracellular stimulus and a response regulator (RR) but can contain three or more proteins. Through gene duplication, a unique hybrid HK was created. We show that, while the hybrid appears to retain all of the phosphorelay functions, it responds to a different signal than the original. Both HKs transmit the signal to the same RR, which activates a promoter that transcribes a set of genes encoding a type III secretion system (T3SS) whose function is not yet evident. The significance of this work lies in finding that two HKs regulate this T3SS, highlighting its importance.
Vfr Directly Activates exsA Transcription To Regulate Expression of the Pseudomonas aeruginosa Type III Secretion System
Creators: name: Simmons-Patterson, Ethan R.
name: Urbanowski, Mark L.
name: Yahr, Timothy L.
name: Marsden, Anne E.
name: Intile, Peter J.
name: Schulmeyer, Kayley H.
name: Wolfgang, Matthew C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT The Pseudomonas aeruginosa cyclic AMP (cAMP)-Vfr system (CVS) is a global regulator of virulence gene expression. Regulatory targets include type IV pili, secreted proteases, and the type III secretion system (T3SS). The mechanism by which CVS regulates T3SS gene expression remains undefined. Single-cell expression studies previously found that only a portion of the cells within a population express the T3SS under inducing conditions, a property known as bistability. We now report that bistability is altered in a vfr mutant, wherein a substantially smaller fraction of the cells express the T3SS relative to the parental strain. Since bistability usually involves positive-feedback loops, we tested the hypothesis that virulence factor regulator (Vfr) regulates the expression of exsA . ExsA is the central regulator of T3SS gene expression and autoregulates its own expression. Although exsA is the last gene of the exsCEBA polycistronic mRNA, we demonstrate that Vfr directly activates exsA transcription from a second promoter (P exsA ) located immediately upstream of exsA . P exsA promoter activity is entirely Vfr dependent. Direct binding of Vfr to a P exsA promoter probe was demonstrated by electrophoretic mobility shift assays, and DNase I footprinting revealed an area of protection that coincides with a putative Vfr consensus-binding site. Mutagenesis of that site disrupted Vfr binding and P exsA promoter activity. We conclude that Vfr contributes to T3SS gene expression through activation of the P exsA promoter, which is internal to the previously characterized exsCEBA operon. IMPORTANCE Vfr is a cAMP-dependent DNA-binding protein that functions as a global regulator of virulence gene expression in Pseudomonas aeruginosa . Regulation by Vfr allows for the coordinate production of related virulence functions, such as type IV pili and type III secretion, required for adherence to and intoxication of host cells, respectively. Although the molecular mechanism of Vfr regulation has been defined for many target genes, a direct link between Vfr and T3SS gene expression had not been established. In the present study, we report that Vfr directly controls exsA transcription, the master regulator of T3SS gene expression, from a newly identified promoter located immediately upstream of exsA .
The Sphaleron Rate from 4D Euclidean Lattices
Creators: name: Mancha, Marc Barroso
name: Moore, Guy D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We develop a new method to determine thermal activation rates, such as for bubble nucleation, topology change, \textsl{etc.}, using 4-dimensional Euclidean methods. This allows nonperturbative study on the lattice. We then investigate the strong sphaleron rate in pure-glue QCD at temperatures between 1.3 $\Tc$ and 1000 $T_\mathrm{c}$, making contact with previous results but extending them down close to the critical temperature. The extension to full QCD will be straightforward. Limitations of the proposal (the inability to compute a certain dynamical prefactor, puzzling large-volume behavior, and the inability to treat temperatures $T < 1.3 \, T_\mathrm{c}$) are also discussed.
description: 32 pages, 14 figures, 2 tables. Updated to JHEP version
Nonlinear multi-frequency phonon lasers with active levitated optomechanics
Creators: name: Kuang, Tengfang
name: Huang, Ran
name: Xiong, Wei
name: Zuo, Yunlan
name: Han, Xiang
name: Nori, Franco
name: Qiu, Cheng-Wei
name: Luo, Hui
name: Jing, Hui
name: Guangzong
name: Xiao
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Phonon lasers, exploiting coherent amplifications of phonons, have been a cornerstone for exploring nonlinear phononics, imaging nanomaterial structures, and operating phononic devices. Very recently, by levitating a nanosphere in an optical tweezer, a single-mode phonon laser governed by dispersive optomechanical coupling has been demonstrated, assisted by alternating mechanical nonlinear cooling and linear heating. Such levitated optomechanical (LOM) devices, with minimal noises in high vacuum, can allow flexible control of large-mass objects without any internal discrete energy levels. However, untill now, it is still elusive to realize phonon lasing with levitated microscale objects, due to much stronger optical scattering losses. Here, by employing a Yb3+-doped active system, we report the first experiment on nonlinear multi-frequency phonon lasers with a micro-size sphere governed instead by dissipative LOM coupling. In this work, active gain plays a key role since not only 3-order enhancement can be achieved for the amplitude of the fundamental-mode phonon lasing, compared with the passive device, but also nonlinear mechanical harmonics can emerge spontaneously above the lasing threshold. Furthermore, for the first time, coherent correlations of phonons are observed for both the fundamental mode and its harmonics. Our work drives the field of LOM technology into a new regime where it becomes promising to engineer collective motional properties of typical micro-size objects, such as atmospheric particulates and living cells, for a wide range of applications in e.g., acoustic sensing, gravimetry, and inertial navigation.
description: Accepted for Publication in Nature Physics
Anxiety sensitivity as a predictor of outcome in the treatment of obsessive-compulsive disorder
Creators: name: Blakey, Shannon M.
name: Abramowitz, Jonathan S.
name: Reuman, Lillian
name: Leonard, Rachel C.
name: Riemann, Bradley C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: BACKGROUND AND OBJECTIVES: To address the fact that not all individuals who receive cognitive-behavioral therapy (CBT) for obsessive-compulsive disorder (OCD) exhibit complete symptom reduction, research has examined factors that predict outcome; however, no studies have examined anxiety sensitivity (AS) as a predictor of outcome of CBT for OCD. AS refers to the fear of anxious arousal that results from mistaken beliefs about the dangerousness of anxiety-related body sensations. It is important to understand whether AS influences OCD treatment outcome, considering that (a) some obsessions directly relate to AS, and (b) OCD patients with high AS may be reluctant to engage in anxiety-provoking components of CBT for OCD.

METHODS: Patients (N = 187) with a primary diagnosis of OCD who received residential CBT for OCD participated in this study, which involved completing a self-report battery at pre- and post-treatment.

RESULTS: Results supported study hypotheses, in that (a) baseline AS positively correlated with baseline OCD severity, and (b) greater baseline AS prospectively predicted higher posttreatment OCD symptom severity even after controlling for pretreatment OCD and depression severity.

LIMITATIONS: The study was limited by its use of an older measure of AS, reliance on self-report measures, and nonstandardized treatment across participants.

CONCLUSIONS: Findings highlight the importance of AS in the nature and treatment of OCD. Clinical implications and future directions are discussed.
Helicity, chirality and spin of optical fields without vector potentials
Creators: name: Aiello, Andrea
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Helicity $H$, chirality $C$, and spin angular momentum $\mathbf{S}$ are three physical observables that play an important role in the study of optical fields. These quantities are closely related, but their connection is hidden by the use of four different vector fields for their representation, namely, the electric and magnetic fields $\mathbf{E}$ and $\mathbf{B}$, and the two transverse potential vectors $\mathbf{C}^\perp$ and $\mathbf{A}^\perp$. Helmholtz's decomposition theorem restricted to solenoidal vector fields, entails the introduction of a bona fide inverse curl operator, which permits one to express the above three quantities in terms of the observable electric and magnetic fields only. This yields clear expressions for $H, C$, and $\mathbf{S}$, which are automatically gauge-invariant and display electric-magnetic democracy.
description: 15 pages, 2 appendices, url = https://link.aps.org/doi/10.1103/PhysRevA.106.043519
Bayes risk CTC: Controllable CTC alignment in Sequence-to-Sequence tasks
Creators: name: Tian, Jinchuan
name: Yan, Brian
name: Yu, Jianwei
name: Weng, Chao
name: Yu, Dong
name: Watanabe, Shinji
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computation and Language (cs.CL)
subject: Sound (cs.SD)
subject: Audio and Speech Processing (eess.AS)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Sequence-to-Sequence (seq2seq) tasks transcribe the input sequence to a target sequence. The Connectionist Temporal Classification (CTC) criterion is widely used in multiple seq2seq tasks. Besides predicting the target sequence, a side product of CTC is to predict the alignment, which is the most probable input-long sequence that specifies a hard aligning relationship between the input and target units. As there are multiple potential aligning sequences (called paths) that are equally considered in CTC formulation, the choice of which path will be most probable and become the predicted alignment is always uncertain. In addition, it is usually observed that the alignment predicted by vanilla CTC will drift compared with its reference and rarely provides practical functionalities. Thus, the motivation of this work is to make the CTC alignment prediction controllable and thus equip CTC with extra functionalities. The Bayes risk CTC (BRCTC) criterion is then proposed in this work, in which a customizable Bayes risk function is adopted to enforce the desired characteristics of the predicted alignment. With the risk function, the BRCTC is a general framework to adopt some customizable preference over the paths in order to concentrate the posterior into a particular subset of the paths. In applications, we explore one particular preference which yields models with the down-sampling ability and reduced inference costs. By using BRCTC with another preference for early emissions, we obtain an improved performance-latency trade-off for online models. Experimentally, the proposed BRCTC reduces the inference cost of offline models by up to 47% without performance degradation and cuts down the overall latency of online systems to an unseen level.
The decoherence-free subalgebra of Gaussian Quantum Markov Semigroups
Creators: name: Agredo, Julián
name: Fagnola, Franco
name: Poletti, Damiano
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81S22 (Primary), 81R15 (Secondary)

description: We demonstrate a method for finding the decoherence-subalgebra $\mathcal{N}(\mathcal{T})$ of a Gaussian quantum Markov semigroup on the von Neumann algebra $\mathcal{B}(Γ(\mathbb{C}^d))$ of all bounded operator on the Fock space $Γ(\mathbb{C}^d)$ on $\mathbb{C}^d$. We show that $\mathcal{N}(\mathcal{T})$ is a type I von Neumann algebra $L^\infty(\mathbb{R}^{d_c};\mathbb{C})\bar{\otimes}\mathcal{B}(Γ(\mathbb{C}^{d_f}))$ determined, up to unitary equivalence, by two natural numbers $d_c,d_f\leq d$. This result is illustrated by some applications and examples.
Localization detection based on quantum dynamics
Creators: name: Kudo, Kazue
Publisher: name: arXiv
Year: 2022
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Detecting many-body localization (MBL) typically requires the calculation of high-energy eigenstates using numerical approaches. This study investigates methods that assume the use of a quantum device to detect disorder-induced localization. Numerical simulations for small systems demonstrate how the magnetization and twist overlap, which can be easily obtained from the measurement of qubits in a quantum device, change from the thermal phase to the localized phase. The twist overlap evaluated using the wave function at the end of the time evolution behaves similarly to the one evaluated with eigenstates in the middle of the energy spectrum under a specific condition. The twist overlap evaluated using the wave function after time evolution for many disorder realizations is a promising probe for detecting MBL in quantum computing approaches.
description: 9 pages, 4 figures
Bigravity from gradient expansion
Creators: name: Yamashita, Yasuho
name: Tanaka, Takahiro
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss how the ghost-free bigravity coupled with a single scalar field can be derived from a braneworld setup. We consider DGP two-brane model without radion stabilization. The bulk configuration is solved for given boundary metrics, and it is substituted back into the action to obtain the effective four-dimensional action. In order to obtain the ghost-free bigravity, we consider the gradient expansion in which the brane separation is supposed to be sufficiently small so that two boundary metrics are almost identical. The obtained effective theory is shown to be ghost free as expected, however, the interaction between two gravitons takes the Fierz-Pauli form at the leading order of the gradient expansion, even though we do not use the approximation of linear perturbation. We also find that the radion remains as a scalar field in the four-dimensional effective theory, but its coupling to the metrics is non-trivial.
description: 16 pages
Tetragonal-phase SnOFeSe: A possible parent compound of FeSe-based superconductor
Creators: name: Man, Xiao-Xiao
name: Sun, Pei-Han
name: Zhang, Jian-Feng
name: Lu, Zhong-Yi
name: Liu, Kai
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Recent experiments have reported that inserting metal atoms or small molecules in between the FeSe layers of $β$-FeSe can significantly enhance the superconducting transition temperature. Here, based on first-principles electronic structure calculations, we propose a stable compound SnOFeSe by alternatively stacking the SnO and $β$-FeSe layers. The predicted SnOFeSe has the same tetragonal structure as the well-known FeAs-based compound LaOFeAs, meanwhile their electronic structures in the nonmagnetic state are quite similar. The magnetic ground state of SnOFeSe is predicted to be the dimer antiferromagnetic (AFM) state, which is energetically only 2.77 (2.15) meV/Fe lower than the trimer (dimer-trimer-dimer-trimer) AFM state, indicating that strong magnetic fluctuations might be induced via slight modulation. Interestingly, SnOFeSe is at the verge of metal-insulator transition in these low-energy magnetic states, hence bridging the metallic parent compounds of iron-based superconductors and the insulating ones of cuprate superconductors. With the reduced dimensionality, monolayer SnOFeSe also shows great similarities in the electronic and magnetic properties to its bulk phase. Given that SnOFeSe is adjacent to magnetic frustration and resembles LaOFeAs in both crystal and electronic structures, we suggest that SnOFeSe is a possible superconductor parent compound, which may provide a promising platform to study the interplay between magnetism and unconventional superconductivity in FeSe-derived materials.
description: 8 pages, 7 figures, 2 tables