bluuebunny/crossref_metadata_2025_split huggingface dataset:
An enquiry on the origins of N-rich stars in the inner Galaxy based on APOGEE chemical compositions
Authors: Kisku Shobhit , Schiavon Ricardo P , Horta Danny , Mason Andrew , Mackereth J Ted , Hasselquist Sten , García-Hernández D A , Bizyaev Dmitry , Brownstein Joel R , Lane Richard R , Minniti Dante , Pan Kaike , Roman-Lopes Alexandre 
Published: February 2021

ABSTRACT
Recent evidence based on APOGEE data for stars within a few kpc of the Galactic Centre suggests that dissolved globular clusters (GCs) contribute significantly to the stellar mass budget of the inner halo. In this paper, we enquire into the origins of tracers of GC dissolution, N-rich stars, that are located in the inner 4 kpc of the Milky Way. From an analysis of the chemical compositions of these stars, we establish that about 30 per cent of the N-rich stars previously identified in the inner Galaxy may have an accreted origin. This result is confirmed by an analysis of the kinematic properties of our sample. The specific frequency of N-rich stars is quite large in the accreted population, exceeding that of its in situ counterparts by near an order of magnitude, in disagreement with predictions from numerical simulations. We hope that our numbers provide a useful test to models of GC formation and destruction.
Cosmology with the Roman Space Telescope: synergies with the Rubin Observatory Legacy Survey of Space and Time
Authors: Eifler Tim , Simet Melanie , Krause Elisabeth , Hirata Christopher , Huang Hung-Jin , Fang Xiao , Miranda Vivian , Mandelbaum Rachel , Doux Cyrille , Heinrich Chen , Huff Eric , Miyatake Hironao , Hemmati Shoubaneh , Xu Jiachuan , Rogozenski Paul , Capak Peter , Choi Ami , Doré Olivier , Jain Bhuvnesh , Jarvis Mike , Kruk Jeffrey , MacCrann Niall , Masters Dan , Rozo Eduardo , Spergel David N , Troxel Michael , von der Linden Anja , Wang Yun , Weinberg David H , Wenzl Lukas , Wu Hao-Yi 
Published: February 2021

ABSTRACT
We explore synergies between the Nancy Grace Roman Space Telescope and the Vera Rubin Observatory’s Legacy Survey of Space and Time (LSST). Specifically, we consider scenarios where the currently envisioned survey strategy for the Roman Space Telescope’s High Latitude Survey (HLS reference), i.e. 2000 deg2 in four narrow photometric bands is altered in favour of a strategy of rapid coverage of the LSST area (to full LSST depth) in one band. We find that in only five months, a survey in the W-band can cover the full LSST survey area providing high-resolution imaging for &gt;95 per cent of the LSST Year 10 gold galaxy sample. We explore a second, more ambitious scenario where the Roman Space Telescope spends 1.5 yr covering the LSST area. For this second scenario, we quantify the constraining power on dark energy equation-of-state parameters from a joint weak lensing and galaxy clustering analysis. Our survey simulations are based on the Roman Space Telescope exposure-time calculator and redshift distributions from the CANDELS catalogue. Our statistical uncertainties account for higher order correlations of the density field, and we include a wide range of systematic effects, such as uncertainties in shape and redshift measurements, and modelling uncertainties of astrophysical systematics, such as galaxy bias, intrinsic galaxy alignment, and baryonic physics. We find a significant increase in constraining power for the joint LSST + HLS wide survey compared to LSST Y10 (FoMHLSwide = 2.4 FoMLSST) and compared to LSST + HLS (FoMHLSwide = 5.5 FoMHLSref).
Mock halo catalogues: assigning unresolved halo properties using correlations with local halo environment
Authors: Ramakrishnan Sujatha , Paranjape Aseem , Sheth Ravi K 
Published: February 2021

ABSTRACT
Large-scale sky surveys require companion large volume simulated mock catalogues. To ensure precision cosmology studies are unbiased, the correlations in these mocks between galaxy properties and their large-scale environments must be realistic. Since galaxies are embedded in dark matter haloes, an important first step is to include such correlations – sometimes called assembly bias – for dark matter haloes. However, galaxy properties correlate with smaller scale physics in haloes which large simulations struggle to resolve. We describe an algorithm that addresses and largely mitigates this problem. Our algorithm exploits the fact that halo assembly bias is unchanged as long as correlations between halo property c and the intermediate-scale tidal environment α are preserved. Therefore, knowledge of α is sufficient to assign small-scale, otherwise unresolved properties to a halo in a way that preserves its large-scale assembly bias accurately. We demonstrate this explicitly for halo internal properties like formation history (concentration c200b), shape c/a, dynamics cv/av, velocity anisotropy β, and angular momentum (spin λ). Our algorithm increases a simulation’s reach in halo mass and number density by an order of magnitude, with improvements in the bias signal as large as 45 per cent for 30-particle haloes, thus significantly reducing the cost of mocks for future weak lensing and redshift space distortion studies.
A fully kinetic model for orphan gamma-ray flares in blazars
Authors: Sobacchi Emanuele , Nättilä Joonas , Sironi Lorenzo 
Published: February 2021

ABSTRACT
Blazars emit a highly variable non-thermal spectrum. It is usually assumed that the same non-thermal electrons are responsible for the IR-optical-UV emission (via synchrotron) and the gamma-ray emission (via inverse Compton). Hence, the light curves in the two bands should be correlated. Orphan gamma-ray flares (i.e. lacking a luminous low-frequency counterpart) challenge our theoretical understanding of blazars. By means of large-scale two-dimensional radiative particle-in-cell simulations, we show that orphan gamma-ray flares may be a self-consistent by-product of particle energization in turbulent magnetically dominated pair plasmas. The energized particles produce the gamma-ray flare by inverse Compton scattering an external radiation field, while the synchrotron luminosity is heavily suppressed since the particles are accelerated nearly along the direction of the local magnetic field. The ratio of inverse Compton to synchrotron luminosity is sensitive to the initial strength of turbulent fluctuations (a larger degree of turbulent fluctuations weakens the anisotropy of the energized particles, thus increasing the synchrotron luminosity). Our results show that the anisotropy of the non-thermal particle population is key to modelling the blazar emission.
F-Seq2: improving the feature density based peak caller with dynamic statistics
Authors: Zhao Nanxiang , Boyle Alan P 
Published: February 2021

AbstractGenomic and epigenomic features are captured at a genome-wide level by using high-throughput sequencing (HTS) technologies. Peak calling delineates features identified in HTS experiments, such as open chromatin regions and transcription factor binding sites, by comparing the observed read distributions to a random expectation. Since its introduction, F-Seq has been widely used and shown to be the most sensitive and accurate peak caller for DNase I hypersensitive site (DNase-seq) data. However, the first release (F-Seq1) has two key limitations: lack of support for user-input control datasets, and poor test statistic reporting. These constrain its ability to capture systematic and experimental biases inherent to the background distributions in peak prediction, and to subsequently rank predicted peaks by confidence. To address these limitations, we present F-Seq2, which combines kernel density estimation and a dynamic ‘continuous’ Poisson test to account for local biases and accurately rank candidate peaks. The output of F-Seq2 is suitable for irreproducible discovery rate analysis as test statistics are calculated for individual candidate summits, allowing direct comparison of predictions across replicates. These improvements significantly boost the performance of F-Seq2 for ATAC-seq and ChIP-seq datasets, outperforming competing peak callers used by the ENCODE Consortium in terms of precision and recall.
Adherence to the vegetarian diet may increase the risk of depression: a systematic review and meta-analysis of observational studies
Authors: Fazelian Siavash , Sadeghi Erfan , Firouzi Somayyeh , Haghighatdoost Fahimeh 
Published: February 2021

Abstract

Context
Several epidemiological studies have investigated the association between a vegetarian diet and risk of depression, but because of inconsistency between studies, the exact association remains unclear.

Objective
In this systematic review and meta-analysis, the relationship between vegetarian diets and risk of depression in observational studies was evaluated.

Data sources
The Medline, Embase, Scopus, ISI Web of Science, and Cochrane Library databases were searched from inception through September 1, 2020.

Study selection
Observational studies were included that examined mean levels of depression and risk for depression in vegetarians compared with nonvegetarians.

Data extraction
Pooled effect sizes were estimated using the random-effects model and were reported as standardized mean differences or odds ratios (ORs) with their corresponding 95%CIs. Heterogeneity was tested using the I2 statistic.

Results
Combining 9 effect sizes in this meta-analysis illustrated that adherence to a vegetarian diet was associated with a 53% greater risk of depression compared with that of omnivores (95%CI, 1.14–2.07; I2 = 69.1%). Subgroup analysis of depression risk suggested that results depended on the type of vegetarian diet and country where the study was conducted. For studies that assessed a semivegetarian diet (OR, 1.86; 95%CI, 1.42–2.44; I2 = 35.7%) and those conducted in Europe and the United States (OR, 1.45; 95%CI, 1.06–1.98; I2 = 73.2%), there was a positive association between a vegetarian diet and depression, but in lacto-ovo vegetarians and Asian countries, a null association was found. Comparing mean depression scores showed no evidence of difference between vegetarians and nonvegetarians (n = 16; standardized mean difference, 0.10; 95%CI, –0.01 to 0.21; I2 = 79.1%).

Conclusion
Vegetarian diet significantly increased depression risk; however, the findings were not robust, and more studies are required to investigate the vegetarian diet and depression association.
Comparative Analysis of the Extradiol Ring-Cleavage Dioxygenase LigB from Arabidopsis and 3,4-Dihydroxyphenylalanine Dioxygenase from Betalain-Producing Plants
Authors: Kasei Akane , Watanabe Hanako , Ishiduka Natsumi , Noda Kyoko , Murata Masatsune , Sakuta Masaaki 
Published: February 2021

Abstract
Diverse arrays of naturally occurring compounds in plants are synthesized by specialized metabolic enzymes, many of which are distributed taxonomically. Although anthocyanin pigments are widely distributed and ubiquitous, betalains have replaced anthocyanins in most families in Caryophyllales. Anthocyanins and betalains never occur together in the same plant. The formation of betalamic acid, catalyzed by 3,4-dihydroxyphenylalanine (DOPA) 4,5-extradiol dioxygenase (DOD), is a key step in betalain biosynthesis. DODs in betalain-producing plants are coded by LigB genes, homologs of which have been identified in a wide range of higher plant orders, as well as in certain fungi and bacteria. Two classes of LigB homologs have been reported: those found in anthocyanin-producing species and those found in betalain-producing species, which contain DOD. To gain insight into the evolution of specialized metabolic enzymes involved in betalain biosynthesis, we performed a comparative biochemical analysis of Arabidopsis LigB, an extradiol ring-cleavage dioxygenase in anthocyanin-producing Arabidopsis and Phytolacca DOD1 of betalain-producing Phytolacca americana. We show that Arabidopsis LigB catalyzes 2,3-extradiol cleavage of DOPA to synthesize muscaflavin, whereas Phytolacca DOD1 converts DOPA to betalamic acid via 4,5-extradiol cleavage. Arabidopsis LigB also converts caffeic acid, a ubiquitous phenolic compound in higher plants, to iso-arabidopic acid in vitro via 2,3-extradiol cleavage of the aromatic ring. Amino-acid substitution in Arabidopsis LigB and Phytolacca DOD1 led to variable extradiol ring-cleavage function, supporting the suggestion that catalytic promiscuity serves as a starting point for the divergence of new enzymatic activities.
Incidence and prevalence of systemic sclerosis globally: a comprehensive systematic review and meta-analysis
Authors: Bairkdar Majd , Rossides Marios , Westerlind Helga , Hesselstrand Roger , Arkema Elizabeth V , Holmqvist Marie 
Published: February 2021

Abstract

Objectives
We aimed to conduct a systematic review and meta-analysis on the incidence and prevalence of SSc covering the entire literature.

Methods
This study followed the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement of 2009. We conducted a systematic search in MEDLINE, Web of Science and Embase to identify articles reporting incidence and/or prevalence of SSc. Two authors conducted the search, reviewed articles for inclusion and extracted relevant data. We used random-effects models to estimate the pooled prevalence and incidence of SSc and performed subgroup analyses by sex, case definition and region to investigate heterogeneity. We explored the association between calendar period and reported estimates using meta-regression.

Results
Among 6983 unique records identified, we included 61 studies of prevalence and 39 studies of incidence in the systematic review. The overall pooled prevalence of SSc was 17.6 (95% CI 15.1, 20.5) per 100 000 and the overall pooled incidence rate of SSc was 1.4 (95% CI 1.1, 1.9) per 100 000 person-years. We observed significant regional variations in reported estimates; studies conducted in North America reported considerably higher estimates than other regions. The pooled incidence and prevalence in women were five times higher than in men. More recent studies reported higher estimates than older ones.

Conclusion
In this comprehensive review of the incidence and prevalence of SSc across the world, there was large heterogeneity among estimates, which should be taken into consideration when interpreting the results.
Quantitative Macromolecular Proton Fraction Mapping Reveals Altered Cortical Myelin Profile in Schizophrenia Spectrum Disorders
Authors: Sui Yu Veronica , Bertisch Hilary , Lee Hong-Hsi , Storey Pippa , Babb James S , Goff Donald C , Samsonov Alexey , Lazar Mariana 
Published: February 2021

Abstract
Myelin abnormalities have been reported in schizophrenia spectrum disorders (SSD) in white matter. However, in vivo examinations of cortical myeloarchitecture in SSD, especially those using quantitative measures, are limited. Here, we employed macromolecular proton fraction (MPF) obtained from quantitative magnetization transfer imaging to characterize intracortical myelin organization in 30 SSD patients versus 34 healthy control (HC) participants. We constructed cortical myelin profiles by extracting MPF values at various cortical depths and quantified their shape using a nonlinearity index (NLI). To delineate the association of illness duration with myelin changes, SSD patients were further divided into 3 duration groups. Between-group comparisons revealed reduced NLI in the SSD group with the longest illness duration (&gt;5.5 years) compared with HC predominantly in bilateral prefrontal areas. Within the SSD group, cortical NLI decreased with disease duration and was positively associated with a measure of spatial working memory capacity as well as with cortical thickness (CT). Layer-specific analyses suggested that NLI decreases in the long-duration SSD group may arise in part from significantly increased MPF values in the midcortical layers. The current study reveals cortical myelin profile changes in SSD with illness progression, which may reflect an abnormal compensatory mechanism of the disorder.
The Coutinho index as a simple tool for screening patients with advanced forms of Schistosomiasis mansoni: a validation study
Authors: Barreto Ana V M S , Domingues Ana L C , Diniz George T N , Cavalcanti Ana M S , Lopes Edmundo P , Montenegro Silvia M L , Morais Clarice N L 
Published: February 2021

Abstract

Background
Periportal fibrosis (PPF) is the major pathological consequence of Schistosoma mansoni infection. The Coutinho index—the alkaline phosphatase (ALP) to platelet ratio ([ALP/upper limit of normality {ULN}]/platelet count [106/L] x 100)—was validated. Validation consisted of modest laboratory tests to predict advanced PPF.

Methods
A total of 378 individuals from an endemic area of Brazil with a previous history of the disease and/or a positive parasitological examination were evaluated. We used ultrasound examination as the gold standard for classification of the PPF pattern and measured the biological markers of the index.

Results
Forty-one individuals (10.8%) without PPF, 291 (77%) with moderate PPF and 46 (12.2%) with advanced PPF, were identified. ALP and platelet count were used for the index. The cut-off point ≥0.228 predicted the presence of fibrosis with an area under the receiver operating characteristic curve (AUROC) of 0.56, sensitivity of 68.6% and specificity of 46.3%. There was an absence of PPF in 46.3% of individuals without fibrosis and the presence of PPF in 68.5% of cases with moderate and advanced ultrasound fibrosis. The identification of advanced fibrosis with a cut-off point ≥0.316 revealed an AUROC curve of 0.70, sensitivity of 67.4% and specificity of 68.3%, thus confirming the advanced phase in 65.2% of cases compared with ultrasound.

Conclusion
The Coutinho index was able to predict advanced PPF in most individuals. It is valid as a new tool, uses routine laboratory tests and therefore is more accessible for screening patients with a severe form of the disease in endemic areas.
Hydration Mediated G‐Protein‐Coupled Receptor Activation
Authors: Weerasinghe Nipuna , Fried Steven D.E. , Perera Suchithrang M.D.C. , Chawla Udeep , Brown Michael F. 
Published: February 2021

G‐protein–coupled receptors (GPCRs) are the largest family of cell membrane‐bound receptors in humans. They are involved with sensing molecules outside the cell and the subsequent transduction of this signal to activate intracellular signaling pathways. Rhodopsin is a canonical GPCR, which upon photoactivation undergoes a series of conformational changes leading to a chemical equilibrium between closed inactive Metarhodopsin I (Meta‐I ) and open active Metarhodopsin II (Meta‐II ) states. According to molecular dynamics simulation work carried out by Nicholas Leioatts et al [1] activation of rhodopsin leads to an increase in hydrated protein volume in the active Meta‐II state. Using UV‐visible spectroscopy, we tested this hypothesis by evaluating how the Meta‐I/Meta‐II equilibrium is influenced by changing the osmotic pressure of aqueous environment of the protein in native lipid membrane. We discovered that osmolytes of varying molar mass affect rhodopsin activation differently by altering the Meta‐I/Meta‐II equilibrium. Large osmolytes shift the equilibrium to the inactive Meta‐I state, in conjunction with the efflux of water. By contrast, small osmolytes shift the equilibrium toward Meta‐II state. We attribute the shift caused by large osmolytes to the ability of these osmolytes to remove large quantities of water from the protein interior. Since these osmolytes are large, they are entropically hindered from penetrating into the protein core, and thus withdraw water to collapse the protein into the inactive Meta‐I state. Small osmolytes are able to enter into the protein core, minimizing the effect of withdrawing water from the protein as seen with larger osmolytes, although the reversal effect is still not fully understood. Further work will seek to determine whether this effect is robust with respect to type of osmolyte (e.g. Polyvinyl Pyrrolidone, dextran), and how the effect is altered when the lipid environment of the protein is changed.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Preventing Clinician Suicide: A Call to Action During the COVID-19 Pandemic and Beyond
Authors: Moutier Christine Yu , Myers Michael F. , Feist Jennifer Breen , Feist J. Corey , Zisook Sidney 
Published: February 2021

In this commentary, the authors offer a call to action in the long-standing fight to prevent clinicians from dying by suicide. In April 2020, the nation was shocked by the suicide of New York City emergency physician Dr. Lorna Breen, who died while recovering from COVID-19. She joins an unknown number of clinicians who have taken their lives over the past year. The authors introduce Dr. Breen, a highly talented physician working on the frontlines of the COVID-19 pandemic, and examine how pervasive distress and suicide are in clinicians. Then, they explain the lived experience movement and highlight how clinicians speaking openly about their mental illness and treatment are making it easier for their colleagues to seek lifesaving help, despite the stigma still surrounding mental illness and treatment in medicine.
The authors sort through the science of clinician distress; critique how the COVID-19 pandemic is affecting the lives of clinicians; and describe existing national initiatives to address clinician stress, burnout, and suicide. Finally, they recommend evidence-based actions to prevent clinician suicide that multiple stakeholder groups can take, including regulatory agencies, licensing boards, and hospital privileging boards; specialty boards, professional associations, and continuing education organizations; medical educators; and individual clinicians. Suicide is a complex but generally preventable cause of death. Those in medicine must forge ahead with collective momentum. Dr. Breen, so many other clinicians, and those they have left behind deserve nothing less.