bluuebunny/crossref_metadata_2025_split huggingface dataset:
The warm-hot circumgalactic medium around EAGLE-simulation galaxies and its detection prospects with X-ray-line emission
Authors: Wijers Nastasha A , Schaye Joop 
Published: June 2022

ABSTRACT
We estimate the detectability of X-ray metal-line emission from the circumgalactic medium (CGM) of galaxies over a large halo mass range ($\, {M}_{{\rm 200c}}=10^{11.5}$–$10^{14.5}\, {\rm M}_{\odot }$), using the EAGLE simulations. With the XRISM Resolve instrument, a few bright (K α or Fe L-shell) lines from $\, {M}_{{\rm 200c}}\gtrsim 10^{13} \, {\rm M}_{\odot }$ haloes should be detectable. Using the Athena X-IFU or the Lynx Main Array, emission lines (especially from O viii and O vii) from the inner CGM of $\, {M}_{{\rm 200c}}\gtrsim 10^{12.5}\, {\rm M}_{\odot }$ haloes become detectable, and intragroup and intracluster gas will be detectable out to the virial radius. With the Lynx Ultra-high Resolution Array, the inner CGM of haloes hosting $\, {L}_{*}$ galaxies is accessible. These estimates do assume long exposure times (∼1 Ms) and large spatial bins (∼1–$10\, \mathrm{arcmin}^{2}$). This emission is dominated by collisionally ionized (CI) gas, and tends to come from halo centres. The emission is biased towards temperatures close to the maximum emissivity temperature for CI gas (Tpeak), and high densities and metallicities. However, for the K α lines, emission can come from hotter gas in haloes where the virialized, volume-filling gas is hotter than Tpeak. Trends of emission with halo mass can largely be explained by differences in virial temperature. Differences in the mass trends of K α, He α-like, and Fe L-shell lines mirror differences in their emissivities as a function of temperature. We conclude that upcoming X-ray missions will open up a new window on to the hot CGM.
Ergomagnetosphere, ejection disc, magnetopause in M87 – I. Global flow of mass, angular momentum, energy, and current
Authors: Blandford Roger , Globus Noémie 
Published: June 2022

ABSTRACT
We interpret the 1.3 mm VLBI observations made by the Event Horizon Telescope of the black hole in M87. It is proposed that, instead of being a torus of accreting gas, the observed annular ring is a rotating, magnetically dominated ergomagnetosphere that can transmit electromagnetic angular momentum and energy outward to the disc through a combination of large scale magnetic torque and small scale instabilities. It is further proposed that energy may be extracted by magnetic flux threading the ergosphere through the efficient emission of long wavelength electromagnetic disturbances on to negative energy orbits, after the invariant B2 − E2 approaches zero on small scales. In this way, the spinning black hole and its ergosphere not only power the jets but also the ejection disc so as to drive away most of the gas supplied near the Bondi radius. This outflow takes the form of an MHD wind, extending over many decades of radius, with a unidirectional magnetic field, that is collimated by the infalling gas across a magnetopause. This wind, in turn, collimates the relativistic jets and the emission observed from the jet sheath may be associated with a return current. A model for the global flow of mass, angular momentum, energy, and current, on scales from the horizon to the Bondi radius, is outlined and discussed.
A gap in the double white dwarf separation distribution caused by the common-envelope evolution: astrometric evidence from Gaia
Authors: Korol Valeriya , Belokurov Vasily , Toonen Silvia 
Published: June 2022

ABSTRACT
The trajectory of the center of light of an unresolved binary is different from that of its center of mass. Binary-induced stellar centroid wobbling can therefore be detected as an excess in the goodness-of-fit of the single-star astrometric model. We use reduced χ2 of the astrometric fit in the Gaia Early Data Release 3 to detect the likely unresolved double white dwarfs (DWDs). Using parallax-based distances we convert the excess of reduced χ2 into the amplitude of the centroid wobble δa, which is proportional to the binary separation a. The measured δa distribution drops towards larger wobble amplitudes and shows a break around log10δa ≈ −0.7 where it steepens. The integral of the distribution yields DWD fraction of 6.5 ± 3.7 per cent in the range $0.01 \lt a\, (\text{au}) \lt 2$. Using synthetic models of the Galactic DWDs we demonstrate that the break in the δa distribution corresponds to one side of a deep gap in the DWD separation distribution at around a ≈ 1 au. Model DWDs with separations less than several au shrink dramatically due to (at least one) common envelope phase, reshaping the original separation distribution, clearing a gap and creating a pile-up of systems with a ≈ 0.01 au and log10δa &lt; −2. Our models reproduce the overall shape of the observed δa distribution and its normalization, however the predicted drop in the numbers of DWDs beyond the break is steeper than in the data.
A Monte Carlo study of early gas expulsion and evolution of star clusters: new simulations with the MOCCA code in the amuse framework
Authors: Leveque A , Giersz M , Banerjee S , Vesperini E , Hong J , Portegies Zwart S 
Published: June 2022

ABSTRACT
We introduce a new prescription for the evolution of globular clusters (GCs) during the initial embedded gas phase into a Monte Carlo method. With a simplified version of the Monte Carlo MOCCA code embedded in the amuse framework, we study the survival of GCs after the removal of primordial gas. We first test our code and show that our results for the evolution of mass and Lagrangian radii are in good agreement with those obtained with N-body simulations. The Monte Carlo code enables a more rapid exploration of the evolution of systems with a larger number of stars than N-body simulations. We have carried out a new survey of simulations to explore the evolution of globular clusters with up to N = 500 000 stars for a range of different star formation efficiencies and half-mass radii. Our study shows the range of initial conditions leading to the clusters’ dissolution and those for which the clusters can survive this early evolutionary phase.
Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo
Authors: Derakhshan Maria , Kessler Noah J , Ishida Miho , Demetriou Charalambos , Brucato Nicolas , Moore Gudrun E , Fall Caroline H D , Chandak Giriraj R , Ricaut Francois-Xavier , Prentice Andrew M , Hellenthal Garrett , Silver Matt J 
Published: June 2022

AbstractWe analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs (‘hvCpGs’) with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
Decoding phage resistance by mpr and its role in survivability of Mycobacterium smegmatis
Authors: Seniya Surya Pratap , Jain Vikas 
Published: June 2022

Abstract
Bacteria and bacteriophages co-evolve in a constant arms race, wherein one tries and finds newer ways to overcome the other. Phage resistance poses a great threat to the development of phage therapy. Hence, it is both essential and important to understand the mechanism of phage resistance in bacteria. First identified in Mycobacterium smegmatis, the gene mpr, upon overexpression, confers resistance against D29 mycobacteriophage. Presently, the mechanism behind phage resistance by mpr is poorly understood. Here we show that Mpr is a membrane-bound DNA exonuclease, which digests DNA in a non-specific manner independent of the sequence, and shares no sequence or structural similarity with any known nuclease. Exonuclease activity of mpr provides resistance against phage infection, but the role of mpr may very well go beyond just phage resistance. Our experiments show that mpr plays a crucial role in the appearance of mutant colonies (phage resistant strains). However, the molecular mechanism behind the emergence of these mutant/resistant colonies is yet to be understood. Nevertheless, it appears that mpr is involved in the survival and evolution of M. smegmatis against phage. A similar mechanism may be present in other organisms, which requires further exploration.
Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules
Authors: Guo Li-Tao , Olson Sara , Patel Shivali , Graveley Brenton R , Pyle Anna Marie 
Published: June 2022

Abstract
Although reverse-transcriptase (RT) enzymes are critical reagents for research and biotechnology, their mechanical properties are not well understood. In particular, we know little about their relative speed and response to structural obstacles in the template. Commercial retroviral RTs stop at many positions along mixed sequence templates, resulting in truncated cDNA products that complicate downstream analysis. By contrast, group II intron-encoded RTs appear to copy long RNAs with high processivity and minimal stops. However, their speed, consistency and pausing behavior have not been explored. Here, we analyze RT velocity as the enzyme moves through heterogeneous sequences and structures that are embedded within a long noncoding RNA transcript. We observe that heterogeneities in the template are highly disruptive to primer extension by retroviral RTs. However, sequence composition and template structure have negligible effects on behavior of group II intron RTs, such as MarathonRT (MRT). Indeed, MRT copies long RNAs in a single pass, and displays synchronized primer extension at a constant speed of 25 nt/sec. In addition, it passes through stable RNA structural motifs without perturbation of velocity. Taken together, the results demonstrate that consistent, robust translocative behavior is a hallmark of group II intron-encoded RTs, some of which operate at high velocity.
Association of Hyponatremia on Mortality in Cryptococcal Meningitis: A Prospective Cohort
Authors: Tugume Lillian , Fieberg Ann , Ssebambulidde Kenneth , Nuwagira Edwin , Williams Darlisha A , Mpoza Edward , Rutakingirwa Morris K , Kagimu Enoch , Kasibante John , Nsangi Laura , Jjunju Samuel , Musubire Abdu K , Muzoora Conrad , Lawrence David S , Rhein Joshua , Meya David B , Hullsiek Kathy Huppler , Boulware David R , Abassi Mahsa ,   Adjunctive Sertraline for HIV-Associated Cryptococcal Meningitis (ASTRO-CM) Team, Rhein Joshua , Kiggundu Reuben , Akampurira Andrew , Kirumira Paul , Francis Ndyetukira Jane , Ahimbisibwe Cynthia , Kugonza Florence , Namuju Carolyne , Sadiq Alisat , Kiiza Kandole Tadeo , Luggya Tony , Kaboggoza Julian , Laker Eva , Namudde Alice , Lofgren Sarah , Kwizera Richard , Rwomushana Irene , Ssemusu Mike , Rukundo Joan , Mwesigye James , Nielsen Kirsten , Stadelman Anna , Bangdiwala Ananta S. , Lawrence David , Youssouf Nabila 
Published: June 2022

Abstract

Background
Sodium abnormalities are frequent in central nervous system infections and may be caused by cerebral salt wasting, syndrome of inappropriate antidiuretic hormone secretion, or medication adverse events. In cryptococcal meningitis (CM), the prevalence of baseline hyponatremia and whether hyponatremia adversely impacts survival is unknown.

Methods
We conducted a secondary analysis of data from 2 randomized trials of human immunodeficiency virus–infected adult Ugandans with CM. We grouped serum sodium into 3 categories: &lt;125, 125–129, and 130–145 mmol/L. We assessed whether baseline sodium abnormalities were associated with clinical characteristics and survival.

Results
Of 816 participants with CM, 741 (91%) had a baseline sodium measurement available: 121 (16%) had grade 3–4 hyponatremia (&lt;125 mmol/L), 194 (26%) had grade 2 hyponatremia (125–129 mmol/L), and 426 (57%) had a baseline sodium of 130–145 mmol/L. Hyponatremia (&lt;125 mmol/L) was associated with higher initial cerebrospinal fluid (CSF) quantitative culture burden (P &lt; .001), higher initial CSF opening pressure (P &lt; .01), lower baseline Glasgow Coma Scale score (P &lt; .01), and a higher percentage of baseline seizures (P = .03). Serum sodium &lt;125 mmol/L was associated with increased 2-week mortality in unadjusted and adjusted survival analyses (adjusted hazard ratio, 1.87 [95% confidence interval, 1.26–2.79]; P &lt; .01) compared to those with sodium 130–145 mmol/L.

Conclusions
Hyponatremia is common in CM and is associated with excess mortality. A standardized management approach to correctly diagnose and correct hyponatremia in CM needs to be developed and tested.
Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize
Authors: Singh Zeenu , Singh Harshita , Garg Tushar , Mushahary Khrang Khrang Khunggur , Yadav Shri Ram 
Published: June 2022

Abstract
The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.
Abnormal antibodies to self-carbohydrates in SARS-CoV-2-infected patients
Authors: Butler Dorothy L , Imberti Luisa , Quaresima Virginia , Fiorini Chiara ,   NIAID COVID-19 Consortium, Barnett Jason , Chauvin Samuel , Cheng Xi , Danielson Jeffrey , Dobbs Kerry , Garabedian Elizabeth , Kuram Vasu , Lau William , Li Zhiwen , Magliocco Mary , Matthews Helen , Nambiar Marshall , Samuel Smilee , Shaw Elana , Stack Michael , Weber Sarah , Xirasagar Sandhya , Zhang Yu , Gildersleeve Jeffrey C 
Published: June 2022

AbstractOur immune system is critical for preventing and treating SARS-CoV-2 infections, but aberrant immune responses can have deleterious effects. While antibodies to glycans could recognize the virus and influence the clinical outcome, little is known about their roles. Using a carbohydrate antigen microarray, we profiled serum antibodies in healthy control subjects and COVID-19 patients from two separate cohorts. COVID-19 patients had numerous autoantibodies to self-glycans, including antiganglioside antibodies that can cause neurological disorders. Additionally, nearly all antiglycan IgM signals were lower in COVID-19 patients, indicating a global dysregulation of this class of antibodies. Autoantibodies to certain N-linked glycans correlated with more severe disease, as did low levels of antibodies to the Forssman antigen and ovalbumin. Collectively, this study indicates that expanded testing for antiglycan antibodies could be beneficial for clinical analysis of COVID-19 patients and illustrates the importance of including host and viral carbohydrate antigens when studying immune responses to viruses.
An intranasally administrated SARS-CoV-2 beta variant subunit booster vaccine prevents beta variant replication in rhesus macaques
Authors: Sui Yongjun , Li Jianping , Andersen Hanne , Zhang Roushu , Prabhu Sunaina K , Hoang Tanya , Venzon David , Cook Anthony , Brown Renita , Teow Elyse , Velasco Jason , Pessaint Laurent , Moore Ian N , Lagenaur Laurel , Talton Jim , Breed Matthew W , Kramer Josh , Bock Kevin W , Minai Mahnaz , Nagata Bianca M , Choo-Wosoba Hyoyoung , Lewis Mark G , Wang Lai-Xi , Berzofsky Jay A 
Published: June 2022

Abstract
Emergence of SARS-CoV-2 variants and waning of vaccine/infection-induced immunity pose threats to curbing the COVID-19 pandemic. Effective, safe, and convenient booster vaccines are in need. We hypothesized that a variant-modified mucosal booster vaccine might induce local immunity to prevent SARS-CoV-2 infection at the port of entry. The beta-variant is one of the hardest to cross-neutralize. Herein, we assessed the protective efficacy of an intranasal booster composed of beta variant-spike protein S1 with IL-15 and TLR agonists in previously immunized macaques. The macaques were first vaccinated with Wuhan strain S1 with the same adjuvant. A total of 1 year later, negligibly detectable SARS-CoV-2-specific antibody remained. Nevertheless, the booster induced vigorous humoral immunity including serum- and bronchoalveolar lavage (BAL)-IgG, secretory nasal- and BAL-IgA, and neutralizing antibody against the original strain and/or beta variant. Beta-variant S1-specific CD4+ and CD8+ T cell responses were also elicited in PBMC and BAL. Following SARS-CoV-2 beta variant challenge, the vaccinated group demonstrated significant protection against viral replication in the upper and lower respiratory tracts, with almost full protection in the nasal cavity. The fact that one intranasal beta-variant booster administrated 1 year after the first vaccination provoked protective immunity against beta variant infections may inform future SARS-CoV-2 booster design and administration timing.
Districts for a New Decade—Partisan Outcomes and Racial Representation in the 2021–22 Redistricting Cycle
Authors: Warshaw Christopher , McGhee Eric , Migurski Michal 
Published: June 2022

AbstractThis article provides an overview of the new congressional and state legislative districts that were drawn around the country during the 2021–2022 redistricting cycle. We provide background on the redistricting landscape, most notably the changing federal role in both partisan and minority representation. We also discuss the process used to draw the new districts in each state. We then provide an empirical look at partisan fairness, competitiveness, and minority representation in the new plans. We find that both parties have enacted increasingly extreme partisan gerrymanders when they control the redistricting process. The combination of Republicans’ control of the redistricting process in far more states than Democrats and the inefficient concentration of Democrats in cities has enabled Republicans to largely maintain an advantage in the translation of votes to seats in both Congress and many state legislatures. As a result, the policymaking process in many states will continue to be skewed in a conservative direction. At the same time, nonpartisan commissions appear to offer a consistent means to produce less biased and more competitive maps than when parties drawn the lines. Finally, while Black and Latino representation has improved in some places, both groups of voters remain underrepresented. We conclude by discussing lessons for both scholars and advocates.
Use of primary health care and radiological imaging preceding a diagnosis of rheumatoid arthritis: a nationwide cohort study in Denmark
Authors: de Thurah Annette , Jensen Henry , Maribo Thomas , Jensen Martin B , Sandbæk Annelli , Hauge Ellen-Margrethe , Rasmussen Linda Aa 
Published: June 2022

Abstract

Objective
To explore health-care use in the 12 months preceding a diagnosis of RA in Denmark.

Methods
We conducted a population-based cohort study using data from national registries. Every patient diagnosed with RA in 2014–18 was matched to 10 reference individuals without RA from the Danish background population. Health-care use was defined as contacts to general practitioners, contacts to private practicing physiotherapists, and X-rays of hands and/or feet performed in primary or secondary care. We estimated the monthly contact rates for patients and references in the 12 months preceding the diagnosis, and we compared incidence rates for health-care use in each month between the two groups while adjusting for sociodemographic characteristics and comorbidity.

Results
We included 7427 patients with RA and 74 270 references. Patients with RA had increasing contact rates with general practitioners and physiotherapists from 6 to 8 months before the diagnosis. Compared with references, women with RA had statistically significantly more contacts to general practitioners and physiotherapists during all 12 months. A similar contact pattern was seen in men, albeit less distinct. The number of X-rays increased slightly from 8 months before the diagnosis, with a steep increase in the last 3 months.

Conclusion
Increased contacts to general practitioners and physiotherapists were seen in all 12 months preceding the RA diagnosis, intensifying in the last 6 to 8 months. Imaging increased from 3 months before the diagnosis. This indicates an opportunity to expedite referral to specialist care and ensure earlier diagnosis of RA.
Pretreatment attrition and treatment initiation delay among rifampicin-resistant tuberculosis patients in Lagos, Nigeria: a retrospective cohort study
Authors: Adejumo Olusola A , Daniel Olusoji , Adepoju Victor A , Onoh Moses O , Sokoya Olusola D , Abdur-Razzaq Hussein , Moronfolu Olanike , Oyadotun Omolara M , Olusola-Faleye Bolanle 
Published: June 2022

Abstract

Background
Assessing associated factors of pretreatment attrition and treatment delays among rifampicin-resistant tuberculosis (RR-TB) patients could serve as a valuable tool to control and prevent its community spread. We assessed the factors associated with pretreatment attrition and treatment initiation delays among RR-TB patients in Lagos, Nigeria.

Methods
A retrospective cohort study was conducted involving secondary program data of RR-TB patients diagnosed using the Xpert MTB/RIF assay and initiated on treatment between 1 January 2015 and 31 December 2017 in Lagos. Factors associated with pretreatment attrition and treatment initiation delay were determined using logistic regression.

Results
Of the 606 RR-TB patients diagnosed during the review period, 135 (22.3%) had pretreatment attrition. Previously treated TB patients had a 2.4-fold greater chance of having pretreatment attrition than new RR-TB patients (adjusted odds ratio 2.4 [95% confidence interval 1.2–5.0]). The median time to treatment initiation was 29 d (interquartile range [IQR] 18–49). It was longer for new RR-TB patients (49 d [IQR 36–59]) than previously treated TB patients (28 d [IQR 17–44]). A total of 47% had long treatment delays. Being newly diagnosed with RR-TB was associated with long treatment delays.

Conclusions
The pretreatment attrition rate and proportion of RR-TB patients with treatment delays were high. Pragmatic approaches to address the high pretreatment attrition and treatment delays in Lagos, Nigeria, are urgently needed.