cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Testing Lorentz symmetry with space-based gravitational-wave detectors
Creators: name: Qin, Cheng-Gang
name: Ke, Jun
name: Li, Qin
name: Chen, Ya-Fen
name: Luo, Jie
name: Tan, Yu-Jie
name: Shao, Cheng-Gang
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Lorentz symmetry (LS), one of the most fundamental physical symmetries, has been extensively studied in the context of quantum gravity and unification theories. Many of these theories predict a LS violation, which could arise from the discreteness of spacetime, or extra dimensions. Standard-model extension (SME) is an effective field theory to describe Lorentz violation whose effects can be explored using precision instruments such as atomic clocks and gravitational-wave (GW) detectors. Considering the pure-gravity sector and matter-gravity coupling sector in the SME, we studied the leading Lorentz-violating modifications to the time delay of light and the relativistic frequency shift of the clock in the space-based GW detectors. We found that the six data streams from the GW mission can construct various combinations of measurement signals, such as single-arm round-trip path, interference path, triangular round-trip path, etc. These measurements are sensitive to the different combinations of SME coefficients and provide novel linear combinations of SME coefficients different from previous studies. Based on the orbits of TianQin, LISA, and Taiji missions, we calculated the response of Lorentz-violating effects on the combinations of the measurement signal data streams. Our results allow us to estimate the sensitivities for SME coefficients: $10^{-6}$ for the gravity sector coefficient $\bar{s}^{TT}$, $10^{-6}$ for matter-gravity coupling coefficients $(\bar{a}^{(e+p)}_{\text{eff}})_{T}$ and $\bar{c}^{(e+p)}_{TT}$, and $10^{-5}$ for $(\bar{a}^{n}_{\text{eff}})_{T}$ and $\bar{c}^{n}_{TT}$.
description: 17 pages, 10 figures
The He I $λ$10830 $Å$ line as a probe of winds and accretion in young stars in Lupus and Upper Scorpius
Creators: name: Erkal, J.
name: Manara, C. F.
name: Schneider, P. C.
name: Vincenzi, M.
name: Nisini, B.
name: Coffey, D.
name: Alcalá, J. M.
name: Fedele, D.
name: Antoniucci, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The He I 1 micron line is a high excitation line which allows us to probe the innermost regions of protostellar disks, and to trace both accreting and outflowing material. We use X-Shooter observations of a sample of 107 young stars in the Lupus (1-3 Myr) and Upper Scorpius (5-10 Myr) star-forming regions to search for correlations between the line properties, as well as the disk inclination and accretion luminosity. We identified eight distinct profile types in the sample. We fitted Gaussian curves to the line features to measure the maximum velocities traced in absorption, the full-width half-maximum (FWHM) of the line features, and the Gaussian area of the features. We compare the proportion of each profile type in our sample to previous studies in Taurus. We find significant variations between Taurus and Lupus in the proportion of P Cygni and inverse P Cygni profiles, and between Lupus and Upper Scorpius in the number of emission-only and combination profile types. We find that the blue-shifted absorption features appear less blue-shifted at disk inclinations close to edge-on, but no such trend with inclination is observed in sources with only red-shifted features. Higher accretion rates were observed in sources with strong blue-shifted features which, along with the changes in the proportions of each profile type observed in the two regions, indicates that younger sources may drive stronger jets or winds. Overall, we observe variations in the proportion of each profile type and in the line properties which indicates and evolution of accretion and ejection signatures over time, and with source properties. These results confirm past works and models of the He I line, but for a larger sample and for multiple star-forming regions. The work highlights the power of the He I line as a probe of the gas in the innermost regions of the disk.
description: 24 pages, 21 figures, 4 tables - accepted by A&A on 01/08/2022
Unveiling the warm dense ISM in $z>6$ quasar host galaxies via water vapor emission
Creators: name: Pensabene, A.
name: van der Werf, P.
name: Decarli, R.
name: Bañados, E.
name: Meyer, R. A.
name: Riechers, D.
name: Venemans, B.
name: Walter, F.
name: Weiß, A.
name: Brusa, M.
name: Fan, X.
name: Wang, F.
name: Yang, J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Water vapor (H$_{2}$O) is one of the brightest molecular emitters after carbon monoxide (CO) in galaxies with high infrared (IR) luminosity, and allows us to investigate the warm dense phase of the interstellar medium (ISM) where star formation occurs. However, due to the complexity of its radiative spectrum, H$_{2}$O is not frequently exploited as an ISM tracer in distant galaxies. Therefore, H$_{2}$O studies of the warm and dense gas at high-$z$ remains largely unexplored. In this work we present observations conducted with the Northern Extended Millimeter Array (NOEMA) toward three $z>6$ IR-bright quasars J2310+1855, J1148+5251, and J0439+1634 targeted in their multiple para-/ortho-H$_{2}$O transitions ($3_{12}-3_{03}$, $1_{11}-0_{00}$, $2_{20}-2_{11}$, and $4_{22}-4_{13}$), as well as their far-IR (FIR) dust continuum. By combining our data with previous measurements from the literature we estimate dust masses and temperatures, continuum optical depths, IR luminosities, and the star-formation rates from the FIR continuum. We model the H$_{2}$O lines using the MOLPOP-CEP radiative transfer code and find that water vapor lines in our quasar host galaxies are primarily excited in warm dense (gas kinetic temperature and density of $T_{\rm kin} = 50\,{\rm K}$, $n_{\rm H_{2}}\sim 10^{4.5}-10^{5}\,{\rm cm^{-3}}$) molecular medium with water vapor column density of $N_{\rm H_{2}O}\sim 2\times10^{17}-3\times10^{18}\,{\rm cm^{-3}}$. High-$J$ H$_{2}$O lines are mainly radiatively pumped by the intense optically-thin far-IR radiation field associated with a warm dust component with temperatures of $T_{\rm dust}\sim 80-190\,{\rm K}$ that account for $<5-10\%$ of the total dust mass. Our results are in agreement with expectations based on the H$_{2}$O spectral line energy distribution of local and high-$z$ ultra-luminous IR galaxies and AGN. [abridged]
description: Accepted for publication in A&A: 18 pages, 9 figures
Progressive reconfiguration of resting-state brain networks as psychosis develops: Preliminary results from the North American Prodrome Longitudinal Study (NAPLS) consortium
Creators: name: van Erp, T.G.M.
name: Belger, A.
name: Addington, J.
name: Hamann, S.
name: Chung, Y.
name: Cadenhead, K.S.
name: Tsuang, M.T.
name: Walker, E.F.
name: Mirzakhanian, H.
name: Goodyear, B.
name: Carrión, R.
name: Cao, H.
name: Perkins, D.O.
name: Bearden, C.E.
name: Anticevic, A.
name: Cannon, T.D.
name: Woods, S.W.
name: Mathalon, D.H.
name: Cornblatt, B.A.
name: McGlashan, T.H.
name: Thermenos, H.
name: McEwen, S.C.
name: Seidman, L.J.
Publisher: name: Elsevier B.V.
Year: 2020

description: Mounting evidence has shown disrupted brain network architecture across the psychosis spectrum. However, whether these changes relate to the development of psychosis is unclear. Here, we used graph theoretical analysis to investigate longitudinal changes in resting-state brain networks in samples of 72 subjects at clinical high risk (including 8 cases who converted to full psychosis) and 48 healthy controls drawn from the North American Prodrome Longitudinal Study (NAPLS) consortium. We observed progressive reduction in global efficiency (P = 0.006) and increase in network diversity (P = 0.001) in converters compared with non-converters and controls. More refined analysis separating nodes into nine key brain networks demonstrated that these alterations were primarily driven by progressively diminished local efficiency in the default-mode network (P = 0.004) and progressively enhanced node diversity across all networks (P < 0.05). The change rates of network efficiency and network diversity were significantly correlated (P = 0.003), suggesting these changes may reflect shared neural mechanisms. In addition, change rates of global efficiency and node diversity were significantly correlated with change rate of cortical thinning in the prefrontal cortex in converters (P < 0.03) and could be predicted by visuospatial memory scores at baseline (P < 0.04). These results provide preliminary evidence for longitudinal reconfiguration of resting-state brain networks during psychosis development and suggest that decreased network efficiency, reflecting an increase in path length between nodes, and increased network diversity, reflecting a decrease in the consistency of functional network organization, may be implicated in the progression to full psychosis.
Predictive validity of conversion from the clinical high risk syndrome to frank psychosis
Creators: name: Woodberry, K.A.
name: Powers, A.R., III
name: Cahill, J.D.
name: Seidman, L.J.
name: McGlashan, T.H.
name: Ponce, A.N.
name: Walker, E.F.
name: Cornblatt, B.A.
name: Cadenhead, K.S.
name: Mathalon, D.H.
name: Woods, S.W.
name: Tsuang, M.T.
name: Ferrara, M.
name: Srihari, V.H.
name: Cannon, T.D.
name: Addington, J.
name: Sykes, L.A.Y.
name: Perkins, D.O.
name: Pollard, J.M.
name: Bearden, C.E.
Publisher: name: Elsevier B.V.
Year: 2020

description: Although the clinical high risk for psychosis (CHR) paradigm has become well-established over the past two decades, one key component has received surprisingly little investigative attention: the predictive validity of the criteria for conversion or transition to frank psychosis. The current study evaluates the predictive validity of the transition to psychosis as measured by the Structured Interview for Psychosis-Risk Syndromes (SIPS) in CHR individuals. Participants included 33 SIPS converters and 399 CHR non-converters both from the North American Prodromal Longitudinal Study (NAPLS-2), as well as a sample of 67 separately ascertained first-episode psychosis (FEP) patients from the STEP program. Comparisons were made at baseline and one-year follow-up on demographic, diagnostic stability (SCID), and available measurement domains relating to severity of illness (psychotropic medication, psychosocial treatment, and resource utilization). Principal findings are: 1) a large majority of cases in both SIPS converters (n = 27/33, 81.8%) and FEP (n = 57/67, 85.1%) samples met criteria for continued psychosis at one-year follow-up; 2) follow-up prescription rates for current antipsychotic medication were higher in SIPS converters (n = 17/32, 53.1%) compared to SIPS non-converters (n = 81/397, 20.4%), and similar as compared to FEP cases (n = 39/65, 60%); and 3) at follow-up, SIPS converters had higher rates of resource utilization (psychiatric hospitalizations, day hospital admissions, and ER visits) than SIPS non-converters and were similar to FEP in most categories. The results suggest that the SIPS definition of psychosis onset carries substantial predictive validity. Limitations and future directions are discussed.
D-JRP-PARADISE-WP3.2: Report on the identification of markers for multi-locus sequence typing of Cryptosporidium parvum and Giardia duodenalis
Creators: name: SIMONE MARIO CACCIO'
name: Troell, Karin
name: Klotz, Christian
name: Betson, Martha
Publisher: name: Zenodo
Year: 2022
Subjects: Cryptosporidium parvum
Giardia duodenalis
Multi Locus Sequence Typing

description: This is a report of the OHEJP project: PARADISE, which details the procedures undertaken for in silico detection of variable regions suitable for subsequent selection of markers for C. parvum and G. duodenalis.
On the Fidelity Robustness of CHSH--Bell Inequality via Filtered Random States
Creators: name: Mandarino, Antonio
name: Scala, Giovanni
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The theorem developed by John Bell constituted the starting point of a revolution that translated a philosophical question about the nature of reality into the broad and intense field of research of the quantum information technologies. We focus on a system of two qubits prepared in a random, mixed state, and we study the typical behavior of their nonlocality via the CHSH--Bell inequality. Afterward, motivated by the necessity of accounting for inefficiency in the state preparation, we address to what extent states close enough to one with a high degree of nonclassicality can violate local realism with a previously chosen experimental setup.
Ultrabright and narrowband intra-fiber biphoton source at ultralow pump power
Creators: name: Bruns, Alexander
name: Hsu, Chia-Yu
name: Stryzhenko, Sergiy
name: Giese, Enno
name: Yatsenko, Leonid P.
name: Yu, Ite A.
name: Halfmann, Thomas
name: Peters, Thorsten
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Nonclassical photon sources of high brightness are key components of quantum communication technologies. We here demonstrate the generation of narrowband, nonclassical photon pairs by employing spontaneous four-wave mixing in an optically-dense ensemble of cold atoms within a hollow-core fiber. The brightness of our source approaches the limit of achievable generated spectral brightness at which successive photon pairs start to overlap in time. For a generated spectral brightness per pump power of up to $2\times 10^{9} \ \textrm{pairs/(s MHz mW)}$ we observe nonclassical correlations at pump powers below $100 \textrm{nW}$ and a narrow bandwidth of $2π\times 6.5 \ \textrm{MHz}$. In this regime we demonstrate that our source can be used as a heralded single-photon source. By further increasing the brightness we enter the regime where successive photon pairs start to overlap in time and the cross-correlation approaches a limit corresponding to thermal statistics. Our approach of combining the advantages of atomic ensembles and waveguide environments is an important step towards photonic quantum networks of ensemble based elements.
Duration of the psychosis prodrome
Creators: name: Mathalon, D.H.
name: Perkins, D.O.
name: Cornblatt, B.A.
name: Bearden, C.E.
name: Seidman, L.J.
name: Walker, E.F.
name: Powers, A.R.
name: Addington, J.
name: Cannon, T.D.
name: McGlashan, T.H.
name: Woods, S.W.
name: Tsuang, M.T.
name: Cadenhead, K.S.
Publisher: name: Elsevier B.V.
Year: 2020

description: The recognition of a prodromal period preceding the onset of frank psychosis dates back to its first descriptions. Despite insights gained from a prospective approach to the study of the Clinical High Risk syndrome for psychosis (CHR-P), a prospectively-based understanding of the duration of the psychosis prodrome and the factors that may influence is not well-established. Here we analyze data from the second North American Prodrome Longitudinal Study (NAPLS-2) to characterize prodrome duration in those who converted to psychosis. Of the 764 participants identified as being at CHR-P, 94 converted to psychosis and 92 of these had recorded estimates of prodrome onset. Estimates of prodrome duration were derived from CHR-P syndrome onset and conversion dates from the Structured Interview for Psychosis-risk Syndromes. Results identified a mean prodrome duration of 21.6 months. Neither CHR-P sub-syndrome nor medication exposure was found to significantly influence prodrome duration in this sample. These results provide the most precise estimate of prodrome duration to date, although results are limited to prodromes identified by ascertainment as being at CHR-P. Our findings also suggest a rule of thirds with regard to prodrome duration in those followed for two years: one third of CHR-P patients who convert will do so by 1 year after CHR-P syndrome onset, another third 1–2 years after onset, and the final third more than 2 years after onset.
Evaluating Machine Perception of Indigeneity: An Analysis of ChatGPT's Perceptions of Indigenous Roles in Diverse Scenarios
Creators: name: Solorzano, Cecilia Delgado
name: Hernandez, Carlos Toxtli
Publisher: name: arXiv
Year: 2023
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Large Language Models (LLMs), like ChatGPT, are fundamentally tools trained on vast data, reflecting diverse societal impressions. This paper aims to investigate LLMs' self-perceived bias concerning indigeneity when simulating scenarios of indigenous people performing various roles. Through generating and analyzing multiple scenarios, this work offers a unique perspective on how technology perceives and potentially amplifies societal biases related to indigeneity in social computing. The findings offer insights into the broader implications of indigeneity in critical computing.
description: 5 pages, 3 figures
North American Prodrome Longitudinal Study (NAPLS 3): Methods and baseline description
Creators: name: Seidman, L.J.
name: Liu, L.
name: Keshavan, M.
name: Bearden, C.E.
name: Cannon, T.D.
name: Perkins, D.O.
name: Walker, E.F.
name: Brummitt, K.
name: Mathalon, D.H.
name: Woods, S.W.
name: Cadenhead, K.S.
name: McGlashan, T.H.
name: Stone, W.
name: Addington, J.
name: Cornblatt, B.A.
name: Tsuang, M.T.
Publisher: name: Elsevier B.V.
Year: 2020

description: The North American Prodrome Longitudinal Study (NAPLS) is a consortium of nine programs focusing on youth at clinical high risk (CHR) for psychosis. Funded by the National Institute of Mental Health (NIMH), the sites are located at Emory University, Harvard University, University of Calgary, University of California at Los Angeles, at San Diego, and at San Francisco, University of North Carolina Chapel Hill, Yale University, and Zucker Hillside Hospital. There have been two previous endeavors completed by this consortium, known as NAPLS-1 and NAPLS-2. This paper first offers an overview of the methodology of the third phase of the NAPLS consortium, the second five-year prospective study NAPLS-3, which aims to determine mechanisms of the development of psychosis. In addition, we report on the ascertainment and demographics of the 710 CHR participants in NAPLS-3.
Dual-domain analysis of gun violence incidents in the United States
Creators: name: James, Nick
name: Menzies, Max
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Applications (stat.AP)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: This paper applies new and recently introduced approaches to study trends in gun violence in the United States. We use techniques in both the time and frequency domain to provide a more complete understanding of gun violence dynamics. We analyze gun violence incidents on a state-by-state basis as recorded by the Gun Violence Archive. We have numerous specific phenomena of focus, including periodicity of incidents, locations in time where behavioral changes occur, and shifts in gun violence patterns since April 2020. First, we implement a recently introduced method of spectral density estimation for nonstationary time series to investigate periodicity on a state-by-state basis, including revealing where periodic behaviors change with time. We can also classify different patterns of behavioral changes among the states. We then aim to understand the most significant shifts in gun violence since numerous key events in 2020, including the COVID-19 pandemic, lockdowns, and periods of civil unrest. Our dual-domain analysis provides a more thorough understanding and challenges numerous widely held conceptions regarding the prevalence of gun violence incidents.
description: Accepted manuscript. Minor edits since v1. Equal contribution
The Best Biosecurity practices in European slaughterhouses in regards to Salmonella and hepatitis E virus
Creators: name: Niine, Tarmo
name: Viltrop, Arvo
name: Nurmoja, Imbi
name: Smith, Richard
name: Burow, Elke
Publisher: name: Zenodo
Year: 2022
Subjects: salmonella
slaughterhouse
pigs
hepatitis E virus
Biosecurity

description: OHEJP Project: BIOPIGEE Poster for ONE – Health, Environment, Society – Conference 2022
Unconventional optical selection rules in ZrTe5 under an in-plane magnetic field
Creators: name: Wang, Yi-Xiang
name: Li, Fuxiang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The optical selection rules of an electron system under a magnetic field play key roles in determining its optical properties, from which the band structures and underlying symmetries can be derived. In this Letter, based on a three-dimensional strong topological insulator model describing ZrTe5,we study the Landau levels (LLs) and magneto-optical conductivity under an in-plane magnetic field. We reveal that in the transverse conductivity Re(σ_{zz}), the unconventional optical selection rules n\righatarrow n\pm 2 dominate, with n being the LL index. We attribute the unconventional selection rules to the peculiar distribution of parity carried by the LLs, resulting from the chiral symmetry of the sub-Hamiltonians. Moreover, we predict that, if the strong anisotropic system is tuned to be nearly isotropic, the LLs would redistribute and the conventional selection rules n\rightarrow n\pm 1 can be recovered.
description: 6 pages, 4 figures
Persistent nuclear burning in Nova Sgr 2016 N.4 (= V5856 Sgr = ASASSN-16ma) six years past its outburst
Creators: name: Munari, U.
name: Masetti, N.
name: Walter, F. M.
name: Williams, R. E.
name: Hambsch, F. -J.
name: Frigo, A.
name: Valisa, P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report on the fast Nova Sgr 2016 N.4 being surprisingly trapped in a long-lasting and bright plateau (Delta I >= 10 mag above quiescence) six years past the nova eruption. Very few other novae experience a similar occurrence. We carried out an intensive observing campaign collecting daily BVRI photometry and monthly high-resolution optical spectroscopy, and observed the nova in ultraviolet and X-rays with Swift satellite at five distinct epochs. The bolometric luminosity radiated during the plateau is ~4200 Lsun (scaled to the distance of the Galactic Bulge), corresponding to stable nuclear burning on a 0.6 Msun white dwarf. A stable wind is blown off at FWZI~1600 km/s, with episodic reinforcement of a faster FWZI~3400 km/s mass loss, probably oriented along the polar directions. The collision of these winds could power the emission detected in X-rays. The burning shell has an outer radius of ~25 Rsun at which the effective temperature is ~7600 K, values similar to those of a F0 II/Ib bright giant. The Delta m < 1 mag variability displayed during the plateau is best described as chaotic, with the irregular appearance of quasi-periodic oscillations with a periodicity of 15-17 days. A limited amount of dust (~3x10^(-11) Msun) continuously condenses at T(dust)~1200 K in the outflowing wind, radiating L(dust)~52 Lsun.
description: Accepted for publication in A&A
Stability of mismatch negativity event-related potentials in a multisite study
Creators: name: Tsuang, M.
name: Woods, S.W.
name: Seidman, L.
name: McGlashan, T.H.
name: Belger, A.
name: Cannon, T.D.
name: Walker, E.F.
name: Perkins, D.O.
name: Bearden, C.E.
name: Roach, B.J.
name: Addington, J.
name: Johannesen, J.
name: Bachman, P.
name: Light, G.
name: Hamilton, H.K.
name: Mathalon, D.H.
name: Kenney, J.G.
name: Niznikiewicz, M.
name: Cadenhead, K.S.
name: Cornblatt, B.A.
name: Owens, E.M.
name: Duncan, E.
name: Carrión, R.E.
Publisher: name: John Wiley and Sons Ltd
Year: 2020

description: Objectives: Mismatch negativity (MMN), an auditory event-related potential sensitive to deviance detection, is smaller in schizophrenia and psychosis risk. In a multisite study, a regression approach to account for effects of site and age (12–35 years) was evaluated alongside the one-year stability of MMN. Methods: Stability of frequency, duration, and frequency + duration (double) deviant MMN was assessed in 167 healthy subjects, tested on two occasions, separated by 52 weeks, at one of eight sites. Linear regression models predicting MMN with age and site were validated and used to derive standardized MMN z-scores. Variance components estimated for MMN amplitude and latency measures were used to calculate Generalizability (G) coefficients within each site to assess MMN stability. Trait-like aspects of MMN were captured by averaging across occasions and correlated with subject traits. Results: Age and site accounted for less than 7% of MMN variance. G-coefficients calculated at electrode Fz were stable (G = 0.63) across deviants and sites for amplitude measured in a fixed window, but not for latency (G = 0.37). Frequency deviant MMN z-scores averaged across tests negatively correlated with averaged global assessment of functioning. Conclusion: MMN amplitude is stable and can be standardized to facilitate longitudinal multisite studies of patients and clinical features.
Observational and numerical characterization of a recurrent arc-shaped front propagating along a coronal fan
Creators: name: Sieyra, M. V.
name: Prasad, S. Krishna
name: Stenborg, G.
name: Khomenko, E.
name: Van Doorsselaere, T.
name: Costa, A.
name: Esquivel, A.
name: Riedl, J. M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Recurrent, arc-shaped intensity disturbances were detected by EUV channels in an active region. The fronts were observed to propagate along a coronal loop bundle rooted in a small area within a sunspot umbra. Previous works have linked these intensity disturbances to slow magnetoacoustic waves that propagate from the lower atmosphere to the corona along the magnetic field. The slow magnetoacoustic waves propagate at the local cusp speed. However, the measured propagation speeds from the intensity images are usually smaller as they are subject to projection effects due to the inclination of the magnetic field with respect to the line-of-sight. Here, we aim to understand the effect of projection by comparing observed speeds with those from a numerical model. Using multi-wavelength data we determine the periods present in the observations at different heights of the solar atmosphere through Fourier analysis. We calculate the plane-of-sky speeds along one of the loops from the cross-correlation time lags obtained as a function of distance along the loop. We perform a 2D ideal MHD simulation of an active region embedded in a stratified atmosphere. We drive slow waves from the photosphere with a 3 minutes periodicity. Synthetic time-distance maps are generated from the forward-modelled intensities in coronal wavelengths and the projected propagation speeds are calculated. The intensity disturbances show a dominant period between [2-3] minutes at different heights of the atmosphere. The apparent propagation speeds calculated for coronal channels exhibit an accelerated pattern with values increasing from 40 to 120 km/s as the distance along the loop rises. The propagation speeds obtained from the synthetic time-distance maps also exhibit accelerated profiles within a similar range of speeds. We conclude that the accelerated propagation in our observations is due to the projection effect.
description: 12 pages, 12 figures
OHEJP BIOPIGEE deliverable: D-JRP21-WP3.19 "Information on the effect of different disinfectants on Salmonella in biofilm"
Creators: name: Osland, Ane Mohr
name: Vestby, Lene Karine
name: Oastler, Claire
name: Brooks, Emma
name: Gosling, Becky
name: Mardjan Arvand
name: Konrat, Katharina
name: Richter, Anja
Publisher: name: Zenodo
Year: 2022
Subjects: Salmonella
biofilm
disinfectant
disinfection

description: This is the deliverable D-JRP21-WP3.19 "Information on the effect of different disinfectants on Salmonella in biofilm" of the OHEJP BIOPIGEE project produced in WP3 T2.
Hints of a universal width-energy relation for classified fast radio bursts
Creators: name: Xiao, Di
name: Dai, Zi-Gao
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The total available sample of fast radio bursts (FRBs) has been growing steadily in recent years, facilitating the study of FRBs from a statistical point of view. At the same time, the classification of FRBs is currently an imperative issue. We propose that the brightness temperature of bursts can serve as an ideal criterion for classification. In this work, we gather the available data for all localized FRBs and we find a positive relation between the intrinsic pulse width and burst energy, $T_{\rm i}\propto E_ν^{0.25}$, for three repeating FRBs that is similar to that of our previous work using FRB 20121102A data alone. The critical line $T_{\rm B,cri}$ is found to vary for different FRBs, which may reflect the differences in source properties. This relation can put strong constraints on mainstream radiation mechanisms. It is evident that neither the coherent curvature radiation or synchrotron maser radiation have the capability to reach the high brightness temperature required to reproduce this relation.
description: 6 pages, 5 figures
Revisiting stellar properties of star-forming galaxies with stellar and nebular spectral modelling
Creators: name: Cardoso, Leandro S. M.
name: Gomes, Jean Michel
name: Papaderos, Polychronis
name: Pappalardo, Ciro
name: Miranda, Henrique
name: Paulino-Afonso, Ana
name: Afonso, José
name: Lagos, Patricio
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Spectral synthesis is a powerful tool for interpreting the physical properties of galaxies by decomposing their spectral energy distributions into the main luminosity contributors (e.g. stellar populations or ionised gas). However, the impact nebular emission has on the inferred properties of star-forming (SF) galaxies has been largely overlooked over the years. The objective of this work is to estimate the relations between stellar properties of SF galaxies from SDSS DR7 by simultaneously fitting the stellar and nebular continua with FADO and comparing them to the results derived using STARLIGHT, a representative of purely stellar population synthesis codes. Differences between codes regarding average mass, mean age and mean metallicity values can go as high as $\sim$0.06 dex for the overall population of galaxies and $\sim$0.12 dex for SF galaxies (galaxies with EW(H$α$)>3 Å), with the most prominent difference between both codes in the light-weighted mean stellar age. A closer look into the average light- and mass-weighted star formation histories of intensively SF galaxies (EW(H$α$)>75 Å) suggests that STARLIGHT is underestimating the average light-weighted age of intensively SF galaxies by up to $\sim$0.17 dex and overestimating the light-weighted metallicity by up to $\sim$0.13 dex compared to FADO (or vice versa). The comparison between the average stellar properties of passive, SF and intensively SF galaxy samples also reveals that differences between codes increase with increasing EW(H$α$) and decreasing total stellar mass. This work finds indirect evidence that a purely stellar population synthesis approach negatively impacts the inferred stellar properties of galaxies with relatively high star formation rates. In turn, this can bias interpretations of fundamental relations such as the mass-age or mass-metallicity.
description: 27 pages, 25 figures. Accepted for publication in Astronomy & Astrophysics
Sparse multi-view matrix factorisation: a multivariate approach to multiple tissue comparisons
Creators: name: Wang, Zi
name: Yuan, Wei
name: Montana, Giovanni
Publisher: name: arXiv
Year: 2015
Subjects: subject: Machine Learning (stat.ML)
subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Gene expression levels in a population vary extensively across tissues. Such heterogeneity is caused by genetic variability and environmental factors, and is expected to be linked to disease development. The abundance of experimental data now enables the identification of features of gene expression profiles that are shared across tissues, and those that are tissue-specific. While most current research is concerned with characterising differential expression by comparing mean expression profiles across tissues, it is also believed that a significant difference in a gene expression's variance across tissues may also be associated to molecular mechanisms that are important for tissue development and function. We propose a sparse multi-view matrix factorisation (sMVMF) algorithm to jointly analyse gene expression measurements in multiple tissues, where each tissue provides a different "view" of the underlying organism. The proposed methodology can be interpreted as an extension of principal component analysis in that it provides the means to decompose the total sample variance in each tissue into the sum of two components: one capturing the variance that is shared across tissues, and one isolating the tissue-specific variances. sMVMF has been used to jointly model mRNA expression profiles in three tissues - adipose, skin and LCL - which are available for a large and well-phenotyped twins cohort, TwinsUK. Using sMVMF, we are able to prioritise genes based on whether their variation patterns are specific to each tissue. Furthermore, using DNA methylation profiles available, we provide supporting evidence that adipose-specific gene expression patterns may be driven by epigenetic effects.
description: in Bioinformatics 2015
Automatic model-based telluric correction for the ESPRESSO data reduction software. Model description and application to radial velocity computation
Creators: name: Allart, R.
name: Lovis, C.
name: Faria, J.
name: Dumusque, X.
name: Sosnowska, D.
name: Figueira, P.
name: Silva, A. M.
name: Mehner, A.
name: Pepe, F.
name: Cristiani, S.
name: Rebolo, R.
name: Santos, N. C.
name: Adibekyan, V.
name: Cupani, G.
name: Di Marcantonio, P.
name: D'Odorico, V.
name: Hernández, J. I. González
name: Martins, C. J. A. P.
name: Milaković, D.
name: Nunes, N. J.
name: Sozzetti, A.
name: Mascareño, A. Suárez
name: Tabernero, H.
name: Osorio, M. R. Zapatero
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Ground-based high-resolution spectrographs are key instruments for several astrophysical domains. Unfortunately, the observed spectra are contaminated by the Earth's atmosphere. While different techniques exist to correct for telluric lines in exoplanet atmospheric studies, in radial velocity (RV) studies, telluric lines with an absorption depth of >2% are generally masked, which poses a problem for faint targets and M dwarfs as most of their RV content is present where telluric contamination is important. We propose a simple telluric model to be embedded in the ESPRESSO DRS. The goal is to provide telluric-free spectra and enable RV measurements, including spectral ranges where telluric lines fall. The model is a line-by-line radiative transfer code that assumes a single atmospheric layer. We use the sky conditions and the physical properties of the lines from HITRAN to create the telluric spectrum. A subset of selected telluric lines is used to robustly fit the spectrum through a Levenberg-Marquardt minimization algorithm. When applied to stellar spectra from A0- to M5-type stars, the residuals of the strongest H2O lines are below 2% for all spectral types, with the exception of M dwarfs, which are within the pseudo-continuum. We then determined the RVs from the telluric-corrected ESPRESSO spectra of Tau Ceti and Proxima. We created telluric-free masks and compared the obtained RVs with the DRS RVs. In the case of Tau Ceti, we identified that micro-telluric lines introduce systematics up to an amplitude of 58 cm/s and with a period of one year. For Proxima, the gain in spectral content at redder wavelengths is equivalent to a gain of 25% in photon noise. This leads to better constraints on the semi-amplitude and eccentricity of Proxima d. We showcase that our model can be applied to other molecules, and thus to other wavelength regions observed by other spectrographs, such as NIRPS.
description: 18 pages, 18 figures, accepted to A&A
Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry
Creators: name: Macedo, A.
name: Evgrafov, O.V.
name: McCarroll, S.A.
name: Marder, S.R.
name: Vawter, M.P.
name: Bromet, E.J.
name: Sullivan, P.F.
name: Purcell, S.M.
name: Azevedo, M.H.
name: Kotov, R.
name: Rakofsky, J.J.
name: Nicolini, H.
name: Moran, J.L.
name: Pato, M.T.
name: Genovese, G.
name: Dumont, A.L.
name: Fochtmann, L.J.
name: Braff, D.L.
name: Smoller, J.W.
name: Peterson, R.E.
name: Bigdeli, T.B
name: Chapman, S.B.
name: Rapaport, M.H.
name: Belliveau, R.A.
name: Kennedy, J.L.
name: Achtyes, E.D.
name: O'Dushlaine, C.
name: Nemesh, J.
name: Sklar, B.M.
name: Medeiros, H.
name: Perkins, D.O.
name: Sklar, P.
name: Iyegbe, C.O.
name: Escamilla, M.A.
name: Bevilacqua, E.
name: Knowles, J.A.
name: Scolnick, E.M.
name: Morley, C.P.
name: Carvalho, C.B.
name: Sobell, J.L.
name: Genomic Psychiatry Cohort (GPC) Consortium
name: Malaspina, D.
name: Lehrer, D.S.
name: Gage, D.
name: DeLisi, L.E.
name: Macciardi, F.
name: Dewan, M.J.
name: Meyers, J.L.
name: Consortium on the Genetics of Schizophrenia (COGS) Investigators
name: Abbott, C.
name: Kinkead, B.
name: Georgakopoulos, P.
name: Gur, R.E.
name: Stahl, E.A.
name: Gur, R.C.
name: Valderrama, J.
name: Buckley, P.F.
name: Byerley, W.
name: Pato, C.N.
Publisher: name: Springer Nature
Year: 2020

description: Schizophrenia is a common, chronic and debilitating neuropsychiatric syndrome affecting tens of millions of individuals worldwide. While rare genetic variants play a role in the etiology of schizophrenia, most of the currently explained liability is within common variation, suggesting that variation predating the human diaspora out of Africa harbors a large fraction of the common variant attributable heritability. However, common variant association studies in schizophrenia have concentrated mainly on cohorts of European descent. We describe genome-wide association studies of 6152 cases and 3918 controls of admixed African ancestry, and of 1234 cases and 3090 controls of Latino ancestry, representing the largest such study in these populations to date. Combining results from the samples with African ancestry with summary statistics from the Psychiatric Genomics Consortium (PGC) study of schizophrenia yielded seven newly genome-wide significant loci, and we identified an additional eight loci by incorporating the results from samples with Latino ancestry. Leveraging population differences in patterns of linkage disequilibrium, we achieve improved fine-mapping resolution at 22 previously reported and 4 newly significant loci. Polygenic risk score profiling revealed improved prediction based on trans-ancestry meta-analysis results for admixed African (Nagelkerke’s R2 = 0.032; liability R2 = 0.017; P < 10−52), Latino (Nagelkerke’s R2 = 0.089; liability R2 = 0.021; P < 10−58), and European individuals (Nagelkerke’s R2 = 0.089; liability R2 = 0.037; P < 10−113), further highlighting the advantages of incorporating data from diverse human populations.
Reliability of mismatch negativity event-related potentials in a multisite, traveling subjects study
Creators: name: Cornblatt, B.A.
name: Mathalon, D.H.
name: Bachman, P.
name: Seidman, L.
name: Light, G.A.
name: Perkins, D.O.
name: Cadenhead, K.S.
name: Niznikiewicz, M.
name: Cannon, T.D.
name: McGlashan, T.H.
name: Belger, A.
name: Woods, S.W.
name: Addington, J.
name: Walker, E.F.
name: Tsuang, M.
name: Roach, B.J.
name: Hamilton, H.K.
name: Carrión, R.E.
name: Bearden, C.E.
name: Johannesen, J.
name: Duncan, E.
Publisher: name: Elsevier Ireland Ltd
Year: 2020

description: Objective: To determine the optimal methods for measuring mismatch negativity (MMN), an auditory event-related potential (ERP), and quantify sources of MMN variance in a multisite setting. Methods: Reliability of frequency, duration, and double (frequency + duration) MMN was determined from eight traveling subjects, tested on two occasions at eight laboratory sites. Deviant-specific variance components were estimated for MMN peak amplitude and latency measures using different ERP processing methods. Generalizability (G) coefficients were calculated using two-facet (site and occasion), fully-crossed models and single-facet (occasion) models within each laboratory to assess MMN reliability. Results: G-coefficients calculated from two-facet models indicated fair (0.4 < G<=0.6) duration MMN reliability at electrode Fz, but poor (G < 0.4) double and frequency MMN reliability. Single-facet G-coefficients averaged across laboratory resulted in improved reliability (G > 0.5). MMN amplitude reliability was greater than latency reliability, and reliability with mastoid referencing significantly outperformed nose-referencing. Conclusions: EEG preprocessing methods have an impact on the reliability of MMN amplitude. Within site MMN reliability can be excellent, consistent with prior single site studies. Significance: With standardized data collection and ERP processing, MMN can be reliably obtained in multisite studies, providing larger samples sizeswithin rare patient groups.
Impact of stellar flares on the chemical composition and transmission spectra of gaseous exoplanets orbiting M dwarfs
Creators: name: Konings, Thomas
name: Baeyens, Robin
name: Decin, Leen
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Stellar flares of active M dwarfs can affect the atmospheric composition of close-orbiting gas giants, and can result in time-dependent transmission spectra. We aim to examine the impact of a variety of flares, differing in energy, duration, and occurrence frequency, on the composition and spectra of close-orbiting, tidally locked gaseous planets with climates dominated by equatorial superrotation. We used a series of pseudo-2D photo- and thermochemical kinetics models, which take advection by the equatorial jet stream into account, to simulate the neutral molecular composition of a gaseous planet (effective temperature 800 K) that orbits a flaring M dwarf. We then computed transmission spectra for the evening and morning limb. We find that the upper regions of the dayside and evening limb are heavily depleted in CH4 and NH3 up to several days after a flare with a total radiative energy of $ 2 \times 10^{33} $ erg. Molar fractions of C2H2 and HCN are enhanced up to a factor three on the nightside and morning limb after day-to-nightside advection of photodissociated species. CH4 depletion reduces transit depths by 100-300 parts per million (ppm) on the evening limb and C2H2 production increases the 14 micron feature up to 350 ppm on the morning limb. We find that repeated flaring drives the atmosphere to a composition that differs from its pre-flare distribution and that this translates to a permanent modification of the transmission spectrum. We show that single high-energy flares can affect the atmospheres of close-orbiting gas giants up to several days after the flare event, during which their transmission spectra are altered by several hundred ppm. Repeated flaring has important implications for future retrieval analyses of exoplanets around active stars, as the atmospheric composition and resulting spectral signatures substantially differ from models that do not include flaring.
description: 27 pages, 21 figures, accepted for publication in A&A
Avgust: Automating Usage-Based Test Generation from Videos of App Executions
Creators: name: Zhao, Yixue
name: Talebipour, Saghar
name: Baral, Kesina
name: Park, Hyojae
name: Yee, Leon
name: Khan, Safwat Ali
name: Brun, Yuriy
name: Medvidovic, Nenad
name: Moran, Kevin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Software Engineering (cs.SE)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Writing and maintaining UI tests for mobile apps is a time-consuming and tedious task. While decades of research have produced automated approaches for UI test generation, these approaches typically focus on testing for crashes or maximizing code coverage. By contrast, recent research has shown that developers prefer usage-based tests, which center around specific uses of app features, to help support activities such as regression testing. Very few existing techniques support the generation of such tests, as doing so requires automating the difficult task of understanding the semantics of UI screens and user inputs. In this paper, we introduce Avgust, which automates key steps of generating usage-based tests. Avgust uses neural models for image understanding to process video recordings of app uses to synthesize an app-agnostic state-machine encoding of those uses. Then, Avgust uses this encoding to synthesize test cases for a new target app. We evaluate Avgust on 374 videos of common uses of 18 popular apps and show that 69% of the tests Avgust generates successfully execute the desired usage, and that Avgust's classifiers outperform the state of the art.
Eccentric mergers of black holes with spinning neutron stars
Creators: name: East, William E.
name: Paschalidis, Vasileios
name: Pretorius, Frans
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study dynamical capture binary black hole-neutron star (BH-NS) mergers focusing on the effects of the neutron star spin. These events may arise in dense stellar regions, such as globular clusters, where the majority of neutron stars are expected to be rapidly rotating. We initialize the BH-NS systems with positions and velocities corresponding to marginally unbound Newtonian orbits, and evolve them using general-relativistic hydrodynamical simulations. We find that even moderate spins can significantly increase the amount of mass in unbound material. In some of the more extreme cases, there can be up to a third of a solar mass in unbound matter. Similarly, large amounts of tidally stripped material can remain bound and eventually accrete onto the BH---as much as a tenth of a solar mass in some cases. These simulations demonstrate that it is important to treat neutron star spin in order to make reliable predictions of the gravitational wave and electromagnetic transient signals accompanying these sources.
description: 7 pages, 4 figures; revised to match published version