bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noisy atomic magnetometry in real time
Authors: Amorós-Binefa Júlia , Kołodyński Jan 
Published: November 2021

Abstract
Continuously monitored atomic spin-ensembles allow, in principle, for real-time sensing of external magnetic fields beyond classical limits. Within the linear-Gaussian regime, thanks to the phenomenon of measurement-induced spin-squeezing, they attain a quantum-enhanced scaling of sensitivity both as a function of time, t, and the number of atoms involved, N. In our work, we rigorously study how such conclusions based on Kalman filtering methods change when inevitable imperfections are taken into account: in the form of collective noise, as well as stochastic fluctuations of the field in time. We prove that even an infinitesimal amount of noise disallows the error to be arbitrarily diminished by simply increasing N, and forces it to eventually follow a classical-like behaviour in t. However, we also demonstrate that, ‘thanks’ to the presence of noise, in most regimes the model based on a homodyne-like continuous measurement actually achieves the ultimate sensitivity allowed by the decoherence, yielding then the optimal quantum-enhancement. We are able to do so by constructing a noise-induced lower bound on the error that stems from a general method of classically simulating a noisy quantum evolution, during which the stochastic parameter to be estimated—here, the magnetic field—is encoded. The method naturally extends to schemes beyond the linear-Gaussian regime, in particular, also to ones involving feedback or active control.
Who’s Silenced? Who’s Not?
Authors: Allen Chadwick 
Published: November 2021

Abstract
This essay juxtaposes two stories of Indigenous-settler “first contact” in the twenty-first century. One describes an event of community-based research in coastal Maine in summer 2000; the other describes an event of community-based confrontation at the Serpent Mound earthworks site in Ohio on the winter solstice 2020. The stories overlap and intersect in surprising ways, and they prompt unresolved questions about the function of “American” literary criticism at the present time: What actually happens when Indigenous voices enter the structures of the settler academy? Who benefits, and whose interests are ultimately served? Within current conventions, is it possible to center Indigenous knowledges and research agendas, to address the pressing concerns of Indigenous communities? And what does it mean to pursue scholarship ostensibly focused on aspects of Indigenous cultures within social and political contexts that continue to allow or even to promote the settler erasure of Indigenous claims—not only to distant or recent histories but to ongoing presence? Is it enough for academic institutions to assume a neutral stance on such issues? Or are “Americanist” scholars obligated to pursue more rigorous forms of disrupting settler business as usual?
Corticofugal modulation of temporal and rate representations in the inferior colliculus of the awake marmoset
Authors: Wang Xiaohui , Zhang Yuanqing , Bai Siyi , Qi Runze , Sun Hao , Li Rui , Zhu Lin , Cao Xinyuan , Jia Guoqiang , Li Xinjian , Gao Lixia 
Published: November 2021

AbstractTemporal processing is crucial for auditory perception and cognition, especially for communication sounds. Previous studies have shown that the auditory cortex and the thalamus use temporal and rate representations to encode slowly and rapidly changing time-varying sounds. However, how the primate inferior colliculus (IC) encodes time-varying sounds at the millisecond scale remains unclear. In this study, we investigated the temporal processing by IC neurons in awake marmosets to Gaussian click trains with varying interclick intervals (2–100 ms). Strikingly, we found that 28% of IC neurons exhibited rate representation with nonsynchronized responses, which is in sharp contrast to the current view that the IC only uses a temporal representation to encode time-varying signals. Moreover, IC neurons with rate representation exhibited response properties distinct from those with temporal representation. We further demonstrated that reversible inactivation of the primary auditory cortex modulated 17% of the stimulus-synchronized responses and 21% of the nonsynchronized responses of IC neurons, revealing that cortico-colliculus projections play a role, but not a crucial one, in temporal processing in the IC. This study has significantly advanced our understanding of temporal processing in the IC of awake animals and provides new insights into temporal processing from the midbrain to the cortex.
Randomized Trial of Metformin With Anti-Tuberculosis Drugs for Early Sputum Conversion in Adults With Pulmonary Tuberculosis
Authors: Padmapriydarsini Chandrasekaran , Mamulwar Megha , Mohan Anant , Shanmugam Prema , Gomathy N S , Mane Aarti , Singh Urvashi B , Pavankumar Nathella , Kadam Abhijeet , Kumar Hemanth , Suresh Chandra , Reddy Devaraju , Devi Poornaganga , Ramesh P M , Sekar Lakshmanan , Jawahar Shaheed , Shandil R K , Singh Manjula , Menon Jaykumar , Guleria Randeep 
Published: November 2021

Abstract

Background
Metformin, by reducing intracellular Mycobacterium tuberculosis growth, can be considered an adjunctive therapy to anti-tuberculosis treatment (ATT). We determined whether metformin with standard ATT reduces time to sputum culture conversion and tissue inflammation in adults with pulmonary tuberculosis (PTB).

Methods
In a randomized, 8-week, clinical trial, newly diagnosed, culture-positive PTB patients were randomized to standard ATT (HREZ = control arm) or standard ATT plus daily 1000 mg metformin (MET-HREZ = Metformin with Rifampicin [METRIF] arm) for 8 weeks during 2018–2020 at 5 sites in India. The primary end point was time to sputum culture conversion by liquid culture during 8 weeks of ATT. Plasma inflammatory markers were estimated in a subset. A Cox proportional hazard model was used to estimate time and predictors of culture conversion.

Results
Of the 322 patients randomized, 239 (74%) were male, and 212 (66%) had bilateral disease on chest radiograph with 54 (18%) showing cavitation. The median time to sputum culture conversion by liquid culture was 42 days in the METRIF arm and 41 days in the control arm (hazard ratio, 0.8; 95% confidence interval [CI], .624–1.019). After 8 weeks of ATT, cavitary lesions on X-ray (7, 5.3% vs 18, 12.9%; relative risk, 0.42; 95% CI, .18–.96; P = .041) and inflammatory markers were significantly lower in the METRIF arm. Higher body mass index and lower sputum smear grading were associated with faster sputum culture conversion.

Conclusions
The addition of metformin to standard ATT did not hasten sputum culture conversion but diminished excess inflammation, thus reducing lung tissue damage as seen by faster clearance on X-ray and reduced inflammatory markers.

Clinical Trials Registration
Clinical Trial Registry of India (CTRI/2018/01/011176)
Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Virus in Symptomatic Coronavirus Disease 2019 (COVID-19) Outpatients: Host, Disease, and Viral Correlates
Authors: Mollan Katie R , Eron Joseph J , Krajewski Taylor J , Painter Wendy , Duke Elizabeth R , Morse Caryn G , Goecker Erin A , Premkumar Lakshmanane , Wolfe Cameron R , Szewczyk Laura J , Alabanza Paul L , Loftis Amy James , Degli-Angeli Emily J , Brown Ariane J , Dragavon Joan A , Won John J , Keys Jessica , Hudgens Michael G , Fang Lei , Wohl David A , Cohen Myron S , Baric Ralph S , Coombs Robert W , Sheahan Timothy P , Fischer William A 
Published: November 2021

Abstract

Background
Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectious virus isolation in outpatients with coronavirus disease 2019 (COVID-19) has been associated with viral RNA levels and symptom duration, little is known about the host, disease, and viral determinants of infectious virus detection.

Methods
COVID-19 adult outpatients were enrolled within 7 days of symptom onset. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay.

Results
Among 204 participants with mild-to-moderate symptomatic COVID-19, the median nasopharyngeal viral RNA was 6.5 (interquartile range [IQR] 4.7–7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies (immunoglobulin (Ig)A, IgM, IgG, and/or total Ig) at baseline. Infectious virus was recovered in 7% of participants with SARS-CoV-2 antibodies compared to 58% of participants without antibodies (prevalence ratio [PR] = 0.12, 95% confidence interval [CI]: .04, .36; P = .00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; P &lt; .0001) and fewer days since symptom onset (PR = 0.79, 95% CI: .71, .88 per day; P &lt; .0001).

Conclusions
The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus. Seropositivity and viral RNA levels are likely more reliable markers of infectious virus clearance than subjective measure of COVID-19 symptom duration. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion.

Clinical Trials Registration
NCT04405570.
Standardized Definitions of In Utero Human Immunodeficiency Virus and Antiretroviral Drug Exposure Among Children
Authors: Slogrove Amy L , Burmen Barbara , Davies Mary Ann , Edmonds Andrew , Abrams Elaine J , Chadwick Ellen G , Goetghebuer Tessa , Mofenson Lynne M , Paul Mary E , Thorne Claire , Williams Paige L , Vicari Marissa , Powis Kathleen M 
Published: November 2021

Abstract
In countries with high human immunodeficiency virus (HIV) prevalence, up to 30% of pregnant women are living with HIV, with fetal exposure to both HIV and antiretroviral therapy during pregnancy. In addition, pregnant women without HIV but at high risk of HIV acquisition are increasingly receiving HIV preexposure antiretroviral prophylaxis (PrEP). Investments are being made to establish and follow cohorts of children to evaluate the long-term effects of in utero HIV and antiretroviral exposure. Agreement on a key set of definitions for relevant exposures and outcomes is important both for interpreting individual study results and for comparisons across cohorts. Harmonized definitions of in utero HIV and antiretroviral drug (maternal treatment or PrEP) exposure will also facilitate improved classification of these exposures in future observational studies and clinical trials. The proposed definitions offer a uniform approach to facilitate the consistent description and estimation of effects of HIV and antiretroviral exposures on key child health outcomes.
Blood microbiome is associated with changes in portal hypertension after successful direct-acting antiviral therapy in patients with HCV-related cirrhosis
Authors: Virseda-Berdices Ana , Brochado-Kith Oscar , Díez Cristina , Hontañon Victor , Berenguer Juan , González-García Juan , Rojo David , Fernández-Rodríguez Amanda , Ibañez-Samaniego Luis , Llop-Herrera Elba , Olveira Antonio , Perez-Latorre Leire , Barbas Coral , Rava Marta , Resino Salvador , Jiménez-Sousa María Angeles 
Published: November 2021

AbstractBackgroundPatients with a significant decrease in hepatic venous pressure gradient (HVPG) have a considerable reduction of liver complications and higher survival after HCV eradication.ObjectivesTo evaluate the association between the baseline blood microbiome and the changes in HVPG after successful direct-acting antiviral (DAA) therapy in patients with HCV-related cirrhosis.MethodsWe performed a prospective study in 32 cirrhotic patients (21 HIV positive) with clinically significant portal hypertension (HVPG ≥10 mmHg). Patients were assessed at baseline and 48 weeks after HCV treatment completion. The clinical endpoint was a decrease in HVPG of ≥20% or HVPG &lt;12 mmHg at the end of follow-up. Bacterial 16S ribosomal DNA was sequenced using MiSeq Illumina technology, inflammatory plasma biomarkers were investigated using ProcartaPlex immunoassays and the metabolome was investigated using GC-MS.ResultsDuring the follow-up, 47% of patients reached the clinical endpoint. At baseline, those patients had a higher relative abundance of Corynebacteriales and Diplorickettsiales order, Diplorickettsiaceae family, Corynebacterium and Aquicella genus and Undibacterium parvum species organisms and a lower relative abundance of Oceanospirillales and Rhodospirillales order, Halomonadaceae family and Massilia genus organisms compared with those who did not achieve the clinical endpoint according to the LEfSe algorithm. Corynebacteriales and Massilia were consistently found within the 10 bacterial taxa with the highest differential abundance between groups. Additionally, the relative abundance of the Corynebacteriales order was inversely correlated with IFN-γ, IL-17A and TNF-α levels and the Massilia genus with glycerol and lauric acid.ConclusionsBaseline-specific bacterial taxa are related to an HVPG decrease in patients with HCV-related cirrhosis after successful DAA therapy.
Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)
Authors: Huang Yi , Escalona Merly , Morrison Glen , Marimuthu Mohan P A , Nguyen Oanh , Toffelmier Erin , Shaffer H Bradley , Litt Amy 
Published: November 2021

AbstractArctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.
NLR1 is a strong candidate for the Rm3 dominant green peach aphid (Myzus persicae) resistance trait in peach
Authors: Pan Lei , Lu Zhenhua , Yan Lele , Zeng Wenfang , Shen Zhijun , Yu Mingliang , Bu Lulu , Cui Guochao , Niu Liang , Wang Zhiqiang 
Published: November 2021

Abstract
The green peach aphid (GPA), Myzus persicae, is a polyphagous, sap-sucking aphid and a vector of many plant viruses. In peach, Prunus persica, three individual dominant GPA resistance loci have been genetically defined (Rm1–3), but knowledge of the underlying genes is limited. In this study, we focused on the Rm3 locus. Bulk segregant analysis (BSA) mapping in segregating progeny populations delimited Rm3 to an interval spanning 160 kb containing 21 genes on chromosome 1. RNA-seq data provided no evidence of candidate genes, but chromosomal structural variations were predicted around a nucleotide-binding site–leucine-rich repeat (NLR) gene (ppa000596m) within the Rm3 fine-mapping interval. Following bacterial artificial chromosome (BAC) library construction for a GPA-resistant peach cultivar and the sequencing of three target BAC clones, a chromosomal structural variation encompassing two novel TIR–NLR-class disease resistance (R) protein-coding genes was identified, and the expressed NLR gene (NLR1) was identified as a candidate for M. persicae resistance. Consistent with its proposed role in controlling GPA resistance, NLR1 was only expressed in the leaves of resistant peach phenotypes. A molecular marker that was designed based on the NLR1 sequence co-segregated with the GPA-resistant phenotype in four segregating populations, 162 peach cultivars, and 14 wild relatives, demonstrating the dominant inheritance of the Rm3 locus. Our findings can be exploited to facilitate future breeding for GPA-resistance in peach.
Author verification of Nahj Al-Balagha
Authors: Sarwar Raheem , Mohamed Emad 
Published: November 2021

Abstract
The primary purpose of this article is author verification of the Nahj Al-Balagha, a book attributed to Imam Ali and over which Sunni and Shi’i Muslims are proposing different theories. Given the morphologically complex nature of Arabic, we test whether morphological segmentation, applied to the book and works by the two authors suspected by Sunnis to have authored the texts, can be used for author verification of the Nahj Al-Balagha. Our findings indicate that morphological segmentation may lead to slightly better results than whole words and that regardless of the feature sets, the three sub-corpora cluster into three distinct groups using principal component analysis, hierarchical clustering, multi-dimensional scaling, and bootstrap consensus trees. Supervised classification methods such as Naive Bayes, Support Vector Machines, k Nearest Neighbours, Random Forests, AdaBoost, Bagging, and Decision Trees confirm the same results, which is a clear indication that (1) the book is internally consistent and can thus be attributed to a single person and (2) it was not authored by either of the suspected authors.
SDSS J1451 + 2709 a normal blue quasar but mis-classified as a H ii galaxy in the BPT diagram by flux ratios of narrow emission lines
Authors: Zhang X G 
Published: November 2021

ABSTRACT
In the manuscript, we discuss properties of SDSS J1451 + 2709, a normal blue quasar but mis-classified as a H ii galaxy in the BPT diagram (called as a mis-classified quasar). The emission lines around H α and around H β are well measured by different model functions with broad Balmer lines described by Gaussian or Lorentz functions, in the SDSS spectrum in 2007 and in the KPNO spectrum in 1990. After considering variations of broad emission lines, different model functions lead to different determined fluxes of narrow emission lines, but the different narrow emission line flux ratios lead the SDSS J1451 + 2709 as a H ii galaxy in the BPT diagram. In order to explain the unique properties of the mis-classified quasar SDSS J1451+2709 in the BPT diagram, two methods are proposed, the starforming contributions and compressed NLRs with high electron densities near to critical densities of forbidden emission lines. Unfortunately, the two methods cannot be preferred in the SDSS J1451+2709, further efforts are necessary to find the physical origin of the unique properties of the mis-classified quasar SDSS J1451+2709 in the BPT diagram. Meanwhile, there are not quite different long-term variabilities of SDSS J1451+2709 from the normal quasars. The mis-classified quasar SDSS J1451 + 2709, an extremely unique case or a special case among the normal quasars, could provide further clues on the applications of BPT diagrams to the normal broad line AGN and to narrow emission line objects, indicating part of narrow emission line H ii galaxies actually harbouring central AGN activities.
The dynamical state of massive clumps
Authors: Lu Zu-Jia , Pelkonen Veli-Matti , Juvela Mika , Padoan Paolo , Haugbølle Troels , Nordlund Åke 
Published: November 2021

ABSTRACT
The dynamical state of massive clumps is key to our understanding of the formation of massive stars. In this work, we study the kinematic properties of massive clumps using synthetic observations. We have previously compiled a very large catalogue of synthetic dust-continuum compact sources from our 250 pc, SN-driven, star formation simulation. Here, we compute synthetic $\rm N_{2}H^{+}$ line profiles for a subsample of those sources and compare their properties with the observations and with those of the corresponding three-dimensional (3D) clumps in the simulation. We find that the velocity dispersion of the sources estimated from the $\rm N_{2}H^{+}$ line is a good estimate of that of the 3D clumps, although its correlation with the source size is weaker than the velocity–size correlation of the 3D clumps. The relation between the mass of the 3D clumps, Mmain, and that of the corresponding synthetic sources, MSED, has a large scatter and a slope of 0.5, $M_{\rm main} \propto M_{\rm SED}^{0.5}$, due to uncertainties arising from the observational band-merging procedure and from projection effects along the line of sight. As a result, the virial parameters of the 3D clumps are not correlated with the clump masses, even if a negative correlation is found for the compact sources, and the virial parameter of the most massive sources may significantly underestimate that of the associated clumps.
The Bardeen–Petterson effect in accreting supermassive black hole binaries: disc breaking and critical obliquity
Authors: Nealon Rebecca , Ragusa Enrico , Gerosa Davide , Rosotti Giovanni , Barbieri Riccardo 
Published: November 2021

ABSTRACT
The inspiral of supermassive black hole (BH) binaries in a gas-rich environment is driven by the presence of an accretion disc and viscous interactions tend to align the spin of the BHs with the orbital angular momentum of the disc. Recent work introduced a new iterative approach to describe the alignment process and the resulting non-linear evolution of the surrounding warped accretion disc. Their model predicted that BH spins reach either full alignment or a ‘critical obliquity’ where solutions to the warp equations cease to exist. In this paper, we show that this critical region corresponds to the disc breaking phenomenon, where the disc is disrupted into two or more discrete sections. We use 3D hydrodynamical simulations to (i) recover the predictions of the semi-analytic model and (ii) unveil a richer phenomenology where the disc exhibits either unsuccessful, single and multiple breaks. We additionally identify hydrodynamic effects such as spiral arms that are able to stabilize the disc against breaking beyond criticality. Our results show that when disc breaking occurs, the ability of BHs and disc to align is compromised and in some cases even prevented as the binary inspirals.
Dynamics and habitability of the TESS circumbinary systems TOI-1338 and TIC-172900988
Authors: Georgakarakos Nikolaos 
Published: November 2021

ABSTRACT
Two circumbinary planets have been recently discovered by TESS. The main aim of this work is to explore whether it is possible, besides the discovered circumbinary planet, to have an Earth-like planet within the habitable zone of the system. We carry out numerical simulations over the whole range of the two habitable zones in order to see whether an Earth mass planet can exist there. We find that both systems seem to be able to host an additional planet in their habitable zone. We construct dynamically informed habitable zones and we find that a large percentage of the habitable zone can be suitable for a planet to retain liquid water on its surface no matter what its orbital evolution will be. Moreover, we investigate the possibility to detect an Earth-like planet in the habitable zone of the two systems. We find that for both systems, if such a planet existed, the radial velocity and astrometry signals would be rather small to be detected by our current instruments. Some discussion is also made for the dynamical evolution of the existing planet.