bluuebunny/crossref_metadata_2025_split huggingface dataset:
Foreground modelling via Gaussian process regression: an application to HERA data
Authors: Ghosh Abhik , Mertens Florent , Bernardi Gianni , Santos Mário G , Kern Nicholas S , Carilli Christopher L , Grobler Trienko L , Koopmans Léon V E , Jacobs Daniel C , Liu Adrian , Parsons Aaron R , Morales Miguel F , Aguirre James E , Dillon Joshua S , Hazelton Bryna J , Smirnov Oleg M , Gehlot Bharat K , Matika Siyanda , Alexander Paul , Ali Zaki S , Beardsley Adam P , Benefo Roshan K , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Cheng Carina , Chichura Paul M , DeBoer David R , Acedo Eloy de Lera , Ewall-Wice Aaron , Fadana Gcobisa , Fagnoni Nicolas , Fortino Austin F , Fritz Randall , Furlanetto Steve R , Gallardo Samavarti , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Hickish Jack , Josaitis Alec , Julius Austin , Igarashi Amy S , Kariseb MacCalvin , Kohn Saul A , Kolopanis Matthew , Lekalake Telalo , Loots Anita , MacMahon David , Malan Lourence , Malgas Cresshim , Maree Matthys , Martinot Zachary E , Mathison Nathan , Matsetela Eunice , Mesinger Andrei , Neben Abraham R , Nikolic Bojan , Nunhokee Chuneeta D , Patra Nipanjana , Pieterse Samantha , Razavi-Ghods Nima , Ringuette Jon , Robnett James , Rosie Kathryn , Sell Raddwine , Smith Craig , Syce Angelo , Tegmark Max , Thyagarajan Nithyanandan , Williams Peter K G , Zheng Haoxuan 
Published: May 2020

ABSTRACT
The key challenge in the observation of the redshifted 21-cm signal from cosmic reionization is its separation from the much brighter foreground emission. Such separation relies on the different spectral properties of the two components, although, in real life, the foreground intrinsic spectrum is often corrupted by the instrumental response, inducing systematic effects that can further jeopardize the measurement of the 21-cm signal. In this paper, we use Gaussian Process Regression to model both foreground emission and instrumental systematics in ∼2 h of data from the Hydrogen Epoch of Reionization Array. We find that a simple co-variance model with three components matches the data well, giving a residual power spectrum with white noise properties. These consist of an ‘intrinsic’ and instrumentally corrupted component with a coherence scale of 20 and 2.4 MHz, respectively (dominating the line-of-sight power spectrum over scales k∥ ≤ 0.2 h cMpc−1) and a baseline-dependent periodic signal with a period of ∼1 MHz (dominating over k∥ ∼ 0.4–0.8 h cMpc−1), which should be distinguishable from the 21-cm Epoch of Reionization signal whose typical coherence scale is ∼0.8 MHz.
Mode identification in three pulsating hot subdwarfs observed with TESS satellite
Authors: Sahoo S K , Baran A S , Heber U , Ostrowski J , Sanjayan S , Silvotti R , Irrgang A , Uzundag M , Reed M D , Shoaf K A , Raddi R , Vuckovic M , Ghasemi H , Zong W , Bell K J 
Published: May 2020

ABSTRACT
We report on the detection of pulsations of three pulsating subdwarf B stars observed by the Transiting Exoplanet Survey Satellite (TESS) satellite and our results of mode identification in these stars based on an asymptotic period relation. SB 459 (TIC 067584818), SB 815 (TIC 169285097), and PG 0342 + 026 (TIC 457168745) have been monitored during single sectors resulting in 27 d coverage. These data sets allowed for detecting, in each star, a few tens of frequencies that we interpreted as stellar oscillations. We found no multiplets, though we partially constrained mode geometry by means of period spacing, which recently became a key tool in analyses of pulsating subdwarf B stars. Standard routine that we have used allowed us to select candidates for trapped modes that surely bear signatures of non-uniform chemical profile inside the stars. We have also done statistical analysis using collected spectroscopic and asteroseismic data of previously known subdwarf B stars along with our three stars. Making use of high precision trigonometric parallaxes from the Gaia mission and spectral energy distributions we converted atmospheric parameters to stellar ones. Radii, masses, and luminosities are close to their canonical values for extreme horizontal branch stars. In particular, the stellar masses are close to the canonical one of 0.47 M⊙ for all three stars but uncertainties on the mass are large. The results of the analyses presented here will provide important constrains for asteroseismic modelling.
An ALMA survey of the brightest sub-millimetre sources in the SCUBA-2–COSMOS field
Authors: Simpson J M , Smail Ian , Dudzevičiūtė U , Matsuda Y , Hsieh B-C , Wang W-H , Swinbank A M , Stach S M , An Fang Xia , Birkin J E , Ao Y , Bunker A J , Chapman S C , Chen Chian-Chou , Coppin K E K , Ikarashi S , Ivison R J , Mitsuhashi I , Saito T , Umehata H , Wang R , Zhao Y 
Published: May 2020

ABSTRACT
We present an ALMA study of the ∼180 brightest sources in the SCUBA-2 850-μm map of the COSMOS field from the S2COSMOS survey, as a pilot study for AS2COSMOS – a full survey of the ∼1000 sources in this field. In this pilot study, we have obtained 870-μm continuum maps of an essentially complete sample of the brightest 182 sub-millimetre sources ($S_{850\, \mu \rm m}\gt $ 6.2 mJy) in COSMOS. Our ALMA maps detect 260 sub-millimetre galaxies (SMGs) spanning a range in flux density of $S_{870\, \mu \rm m}$ = 0.7–19.2 mJy. We detect more than one SMG counterpart in 34 ± 2 per cent of sub-millimetre sources, increasing to 53 ± 8 per cent for SCUBA-2 sources brighter than $S_{850\, \mu \rm m}\gt $ 12 mJy. We estimate that approximately one-third of these SMG–SMG pairs are physically associated (with a higher rate for the brighter secondary SMGs, $S_{870\, \mu \rm m}\gtrsim$ 3 mJy), and illustrate this with the serendipitous detection of bright [C ii] 157.74-μm line emission in two SMGs, AS2COS 0001.1 and 0001.2 at z = 4.63, associated with the highest significance single-dish source. Using our source catalogue, we construct the interferometric 870-μm number counts at $S_{870\, \mu \rm m}\gt $ 6.2 mJy. We use the extensive archival data of this field to construct the multiwavelength spectral energy distribution of each AS2COSMOS SMG, and subsequently model this emission with magphys to estimate their photometric redshifts. We find a median photometric redshift for the $S_{870\, \mu \rm m}\gt $ 6.2 mJy AS2COSMOS sample of z = 2.87 ± 0.08, and clear evidence for an increase in the median redshift with 870-μm flux density suggesting strong evolution in the bright end of the 870-μm luminosity function.
MUSEQuBES: calibrating the redshifts of Ly α emitters using stacked circumgalactic medium absorption profiles
Authors: Muzahid Sowgat , Schaye Joop , Marino Raffaella Anna , Cantalupo Sebastiano , Brinchmann Jarle , Contini Thierry , Wendt Martin , Wisotzki Lutz , Zabl Johannes , Bouché Nicolas , Akhlaghi Mohammad , Chen Hsiao-Wen , Claeyssens Adélaîde , Johnson Sean , Leclercq Floriane , Maseda Michael , Matthee Jorryt , Richard Johan , Urrutia Tanya , Verhamme Anne 
Published: May 2020

ABSTRACT
Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ${\approx}10^{-17}~\rm erg~cm^{-2}~s^{-1}$ (${\approx}10^{42}~\rm erg~s^{-1}$) and a median star formation rate (SFR) of ≈1.3 $\rm M_{\odot }~yr^{-1}$ (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, $V_{\rm offset}\propto \rm SFR^{0.16\pm 0.03}$. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs.
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles
Authors: Guernsey Michael W , van Kruistum Henri , Reznick David N , Pollux Bart J A , Baker Julie C 
Published: May 2020

AbstractPlacentation evolved many times independently in vertebrates. Although the core functions of all placentas are similar, we know less about how this similarity extends to the molecular level. Here, we study Poeciliopsis, a unique genus of live-bearing fish that have independently evolved complex placental structures at least three times. The maternal follicle is a key component of these structures. It envelops yolk-rich eggs and is morphologically simple in lecithotrophic species but has elaborate villous structures in matrotrophic species. Through sequencing, the follicle transcriptome of a matrotrophic, Poeciliopsis retropinna, and lecithotrophic, P. turrubarensis, species we found genes known to be critical for placenta function expressed in both species despite their difference in complexity. Additionally, when we compare the transcriptome of different river populations of P. retropinna, known to vary in maternal provisioning, we find differential expression of secretory genes expressed specifically in the top layer of villi cells in the maternal follicle. This provides some of the first evidence that the placental structures of Poeciliopsis function using a secretory mechanism rather than direct contact with maternal circulation. Finally, when we look at the expression of placenta proteins at the maternal–fetal interface of a larger sampling of Poeciliopsis species, we find expression of key maternal and fetal placenta proteins in their cognate tissue types of all species, but follicle expression of prolactin is restricted to only matrotrophic species. Taken together, we suggest that all Poeciliopsis follicles are poised for placenta function but require expression of key genes to form secretory villi.
Physical Constraints on Epistasis
Authors: Husain Kabir , Murugan Arvind 
Published: May 2020

Abstract
Living systems evolve one mutation at a time, but a single mutation can alter the effect of subsequent mutations. The underlying mechanistic determinants of such epistasis are unclear. Here, we demonstrate that the physical dynamics of a biological system can generically constrain epistasis. We analyze models and experimental data on proteins and regulatory networks. In each, we find that if the long-time physical dynamics is dominated by a slow, collective mode, then the dimensionality of mutational effects is reduced. Consequently, epistatic coefficients for different combinations of mutations are no longer independent, even if individually strong. Such epistasis can be summarized as resulting from a global nonlinearity applied to an underlying linear trait, that is, as global epistasis. This constraint, in turn, reduces the ruggedness of the sequence-to-function map. By providing a generic mechanistic origin for experimentally observed global epistasis, our work suggests that slow collective physical modes can make biological systems evolvable.
Calixa Lavallée and the Construction of a National Anthem
Authors: Duffin Ross W 
Published: May 2020

Abstract
Calixa Lavallée's O Canada, composed in 1880, is beloved there as the national anthem, and admired around the world. Little known today, even in his home country, Lavallée enjoyed an international career as a performer and educator, and spent many years as a “popular” musician in the United States before turning exclusively to “classical” music. This article attempts to demonstrate that, contrary to the received view of the anthem as essentially Canadian, Lavallée used his broad experience of European and American music to assemble his “chant national” from a handful of pre-existing works.
Social network analysis for social neuroscientists
Authors: Baek Elisa C , Porter Mason A , Parkinson Carolyn 
Published: May 2020

AbstractAlthough social neuroscience is concerned with understanding how the brain interacts with its social environment, prevailing research in the field has primarily considered the human brain in isolation, deprived of its rich social context. Emerging work in social neuroscience that leverages tools from network analysis has begun to advance knowledge of how the human brain influences and is influenced by the structures of its social environment. In this paper, we provide an overview of key theory and methods in network analysis (especially for social systems) as an introduction for social neuroscientists who are interested in relating individual cognition to the structures of an individual’s social environments. We also highlight some exciting new work as examples of how to productively use these tools to investigate questions of relevance to social neuroscientists. We include tutorials to help with practical implementations of the concepts that we discuss. We conclude by highlighting a broad range of exciting research opportunities for social neuroscientists who are interested in using network analysis to study social systems.
Treatment outcomes among multidrug-resistant TB patients in Bahawal Victoria Hospital, Bahawalpur, Pakistan: a retrospective record review
Authors: Atif Muhammad , Ahmad Wajiha , Ahmad Nafees , Malik Iram , Sarwar Sajjad 
Published: May 2020

Abstract

Background
This study aims to evaluate the treatment outcomes and factors associated with unsuccessful treatment outcomes among multidrug-resistant TB (MDR-TB) patients.

Method
This was a retrospective observational study conducted at the Bahawal Victoria Hospital, Bahawalpur, Pakistan. The sociodemographic, clinical and treatment-related data of MDR-TB patients registered at the study site between June 2014 and December 2016 were retrospectively collected. Patients’ treatment outcomes were categorized on the basis of WHO-recommended criteria. Multivariate binary logistic regression analysis was used to find the independent factors associated with unsuccessful treatment outcomes.

Results
Out of 179 MDR-TB patients, 106 (59.2%) completed their treatment successfully. The remaining 73 patients (40.8%) had unsuccessful treatment outcomes, among whom 45 (25.1%) died, while 18 (10.1%) were lost to follow-up. Factors associated with unsuccessful treatment outcomes included age ≥40 y (AOR 4.310; p = 0.006), unsuccessful interim treatment outcomes (AOR 5.810; p = 0.032), occurrence of adverse events (AOR 0.290; p = 0.029) and ofloxacin resistance (AOR 2.952; p = 0.042).

Conclusion
The treatment success rate among the selected cohort of MDR-TB patients was less than the target of ≥75% set by the WHO in the End TB Strategy. The lower treatment success rate at the study site requires urgent attention from clinicians and program managers.
Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?
Authors: Cuypers Laura N , Baird Stuart J E , Hánová Alexandra , Locus Tatjana , Katakweba Abdul S , Gryseels Sophie , Bryja Josef , Leirs Herwig , Goüy de Bellocq Joëlle 
Published: May 2020

AbstractMastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
MIGRANTS IN TRANSIT AND ASYLUM SEEKERS IN MEXICO: AN EPIDEMIOLOGICAL ANALYSIS OF THE COVID-19 PANDEMIC
Authors: Bojorquez Ietza , Infante César , Vieitez Isabel , Larrea Silvana , Santoro Chiara 
Published: May 2020

ABSTRACTBACKGROUNDMigrants could be disproportionately affected by the COVID-19 pandemic, yet little is known so far of the epidemiology of the disease among them, especially in low- and middle-income countries.OBJECTIVETo describe the epidemiology of suspect cases of COVID-19 in migrants in transit and asylum seekers in Mexico, and to compare their characteristics with those of non-migrants.METHODSThis was a secondary analysis of information from the surveillance system of Mexico from January 1 to May 3 2020, identifying persons from the main sending countries of mixed migrant flows in Mexico (Central America, the Caribbean, Venezuela and African countries), in northern and southern Mexican border states. We compared the demographic and clinical characteristics, risk conditions, and epidemic curves for migrants and non-migrants. Also, we estimated the cumulative incidence for non-migrants, and for migrants in two scenarios defined by different estimations of their population size.RESULTSMigrants were on average younger, had less accompanying risk conditions, and a lower percentage of suspect cases tested positive for COVID-19. The odds of hospitalization were lower among migrants, but the difference disappeared after adjusting by age, gender and underlying risk conditions. The cumulative incidence ratios comparing migrants with non-migrants were 6.12 (CI95% 4.75,7.77) for the first scenario, and 1.49 (CI95% 1.15,1.89) for the second scenario.CONCLUSIONMigrants and asylum seekers in Mexico are at increased risk for infectious respiratory diseases, and could be disproportionately affected by COVID-19. It is important to continue monitoring the situation, with more detailed information about migration status, living conditions and other determinants of migrants health.
Demonstration of a Longitudinal Action Medical Mission (LAMM) Model to Teach Point-of-Care Ultrasound in Resource-Limited Settings
Authors: Yao Michael , Uhr Lauren , Daghlian George , Amrute Junedh M. , Deshpande Ramya , Mathews Benji , Patel Sanjay A. , Henri Ricardo , Liu Gigi , Reierson Kreegan , Johnson Gordon 
Published: May 2020

AbstractBACKGROUNDShort-term medical missions prevail as the most common form of international medical volunteerism, but they are ill-suited for medical education and training local providers in resource-limited settings.OBJECTIVEThe purpose of this study is to evaluate the effectiveness of a longitudinal educational program in training clinicians how to perform point-of-care ultrasound (POCUS) in resource-limited clinics.DESIGNA retrospective study of such a four-month POCUS training program was conducted with clinicians from a rural hospital in Haiti. The model included one-on-one, in-person POCUS teaching sessions by volunteer instructors from the United States and Europe. The Haitian trainees were assessed at the start of the program and at its conclusion by a direct objective structured clinical examination (OSCE), administered by the visiting instructors, with similar pre- and post-program ultrasound competency assessments.RESULTSPost-intervention, a significant improvement was observed (p < 0.0001), and each trainee showed significant overall improvement in POCUS competency independent of the initial competency pre-training (p < 0.005). There was a statistically significant improvement in POCUS application for five of the six medically relevant assessment categories tested.CONCLUSIONOur results provide a proof-of-concept for the longitudinal education-centered healthcare delivery framework in a resource-limited setting. Our longitudinal model provides local healthcare providers the skills to detect and diagnose significant pathologies, thereby reducing avoidable morbidity and mortality at little or no addition cost or risk to the patient. Furthermore, training local physicians obviates the need for frequent volunteering trips, saving costs in healthcare training and delivery.
Forecasting Transmission Dynamics of COVID-19 Epidemic in India Under Various Containment Measures- A Time-Dependent State-Space SIR Approach
Authors: Deo Vishal , Chetiya Anuradha R. , Deka Barnali , Grover Gurprit 
Published: May 2020

AbstractObjectivesOur primary objective is to predict the dynamics of COVID-19 epidemic in India while adjusting for the effects of various progressively implemented containment measures. Apart from forecasting the major turning points and parameters associated with the epidemic, we intend to provide an epidemiological assessment of the impact of these containment measures in India.MethodsWe propose a method based on time-series SIR model to estimate time-dependent modifiers for transmission rate of the infection. These modifiers are used in state-space SIR model to estimate reproduction numberR0, expected total incidence, and to forecast the daily prevalence till the end of the epidemic. We consider four different scenarios, two based on current developments and two based on hypothetical situations for the purpose of comparison.ResultsAssuming gradual relaxation in lockdown post 17 May 2020, we expect the prevalence of infecteds to cross 9 million, with at least 1 million severe cases, around the end of October 2020. For the same case, estimates ofR0for the phases no-intervention, partial-lockdown and lockdown are 4.46 (7.1), 1.47 (2.33), and 0.817 (1.29) respectively, assuming 14-day (24-day) infectious period.ConclusionsEstimated modifiers give consistent estimates of unadjustedR0across different scenarios, demonstrating precision. Results corroborate the effectiveness of lockdown measures in substantially reducingR0. Also, predictions are highly sensitive towards estimate of infectious period.