bluuebunny/crossref_metadata_2025 huggingface dataset:
Smoking Quit Rates Among Menthol vs Nonmenthol Smokers: Implications Regarding a US Ban on the Sale of Menthol Cigarettes
Authors: Munro Heather M , Shrubsole Martha J , Zheng Wei , Wen Wanqing , Blot William J
Published: April 2022

Background

A ban on the sale of menthol cigarettes in the United States is currently under consideration. A justification is that menthol cigarettes are harder to quit, particularly for African American smokers who use menthols much more frequently than White smokers, but epidemiologic data are limited.

Methods

In a cohort of 16 425 mostly low-income African American and White current cigarette smokers enrolled during 2002-2009, we computed smoking quit and reuptake rates at 3 follow-ups conducted means of 4.6, 7.7, and 11 years after entry. Generalized estimation equations were used to compute odds ratios (ORs) and 95% confidence intervals (CIs) for quitting and resuming smoking for menthol vs nonmenthol smokers adjusted for race, age, education, income, and smoking pack-years.

Results

Crude annual quit rates among current smokers were 4.3% for menthol and 4.5% for nonmenthol smokers, with adjusted odds ratios of quitting for menthol vs nonmenthol smokers of 1.01 (95% CI = 0.91 to 1.11) overall, 0.99 (95% CI = 0.87 to 1.12) among African American smokers, and 1.02 (95% CI = 0.88 to 1.20) among White smokers. Crude annual smoking reuptake rates were somewhat higher among menthol smokers (8.4%) than nonmenthol smokers (7.1%), with an adjusted odds ratio of 1.19 (95% CI = 0.97 to 1.47), but net quit rates remained similar (OR = 1.01, 95% CI = 0.90 to 1.13 overall; OR = 1.00, 95% CI = 0.86 to 1.15 among African American participants; and OR = 1.04, 95% CI = 0.87 to 1.24 among White participants).

Conclusions

This large-scale prospective survey revealed similar quit rates among menthol and nonmenthol smokers. Results contribute to policy discussions, especially if, as a meta-analysis suggests, lung cancer risk is higher for nonmenthol smokers and a ban leads menthol smokers to switch to nonmenthol cigarettes.
Advancing Predictability via a Judicialized Investment Court? A Fresh Look Through the Lens of Constructivism
Authors: Yu Chen
Published: April 2022

It has long been debated whether a multilateral court with an appellate mechanism should be established to reinforce the doctrine of precedent and improve the predictability of international investment law. Predictability is widely considered a fundamental canon of law. This article, however, cautions that the pursuit of predictability must be examined against the broader institutional context of investment law. To this end, it canvasses the issue through the lens of International Relations constructivist theory that highlights shared understandings as an essential precondition for legitimate law-making. It further conducts case study of the evolution of international trade law, which serves not only as empirical support for the constructivist framework but also a benchmark for comparative study between the two regimes. It argues that, as currently the investment law regime lacks foundational shared understandings regarding investment protection obligations, entrusting a judicialized court to advance predictability may cause the problem of ‘over-institutionalization’.
Psychosocial Intervention Outcomes for Children with Congenital and Neonatal Conditions: Systematic Review
Authors: Lamond Bronwyn , Roberts Samantha D , Miller Steven P , Wade Shari L , Williams Tricia S
Published: April 2022

There has been a historic lack of psychosocially geared treatment studies for congenital and neonatal conditions that impact brain development, despite well-established knowledge that these conditions impact cognitive development, quality of life (QoL), mental health, and academic success.

Objective

The aim of the present study was to systematically investigate the research literature focusing on the effects of interventions in psychosocially geared programs for children with neonatal brain injury on school and psychological outcomes.

Methods

Psychosocially geared programs broadly refer to interventions to improve parenting and school functioning, or child behavior, as well as other interventions that have a psychological component but may be more physically oriented, such as goal-directed physiotherapy. A comprehensive search of PubMed, Medline, PsychINFO, and Embase was completed between June and July 2020. The methodological quality of included articles was assessed using the Cochrane Risk of Bias Tool for Randomized Trials (RoB-2).

Results and Conclusion

Twenty studies met the inclusion criteria and demonstrated adequate risk of bias (i.e., low risk of bias or some concerns). The studies included family (n = 2), parenting (n = 7), and child (n = 10) interventions. There is some evidence supporting the effectiveness of psychosocial interventions for children with neonatal brain injury and their families on academic outcomes, behavior, and QoL, indicated by positive intervention effects in 65% (n = 13) of studies.
Phytochemicals in traditional Chinese medicine can treat gout by regulating intestinal flora through inactivating NLRP3 and inhibiting XOD activity
Authors: Liu Zi-Qi , Sun Xue , Liu Zi-Bo , Zhang Ting , Zhang Li-Lin , Wu Chun-Jie
Published: April 2022

Objectives

Gout is a common disease caused by hyperglycemia. Traditional drugs for gout have both good therapeutic effects and serious side effects. Traditional Chinese medicine (TCM) is one of the potential sources of modern medicine, and is the development of new drugs for many diseases, including gout. TCM is an indispensable part of gout treatment. Compared with anti-gout medication commonly used in clinic (e.g. the xanthine oxidase inhibitors allopurinol and febuxostat), traditional Chinese medicine has fewer side effects in the treatment of gout and can safely control serum uric acid and the level of inflammation. However, there have been few studies on how traditional Chinese medicine controls uric acid and inflammation levels in patients with gout.

Key findings

Herbs are a valuable resource in the search for new drugs to treat many diseases, including gout. Phytochemicals in TCM treatment of gout mainly includes two aspects, anti-inflammatory and reducing uric acid content. The anti-inflammatory mechanism is mainly through the inactivation of NF-κB and NLRP3 inflammasome to reduce the inflammatory response induced by uric acid crystals. The mechanism of lowering uric acid is mainly through inhibiting the activity of xanthine oxidase and up-regulating the expression of URAT1 and GLUT9.In recent years, the intestinal flora has become a new field of understanding diseases. It has been observed that the occurrence of gout is closely related to changes in the intestinal flora. Herbaceous plants contain fiber, polyphenols, polysaccharides and other active components. When taken orally, Chinese herbs act like prebiotics. After traditional Chinese medicine treatment, the abundance levels of Bifidobacterium, Lactobacillus, Bacteroidetes and Prevotella were increased, while the abundance of Proteus and the Firmicutes/Bacteroidetes ratio were decreased. Changes in the intestinal flora led to further changes in its metabolites, including short-chain fatty acids (SCFAs) and lipopolysaccharide (LPS), which ultimately down-regulate the TLR4/NF-κB inflammatory signaling pathway, up-regulate GLUT9 and URAT1 gene expression and inhibition of xanthine oxidase activity. Destruction of the intestinal barrier is also an important factor in the occurrence of gout. Disruption of the intestinal barrier allows LPS to enter the bloodstream and activates the expression of various inflammatory factors, which causes gout.
Anti-histamine effects of dipotassium glycyrrhizinate on lung fibroblasts, implicating its therapeutic mechanism for pulmonary fibrosis
Authors: Huang Wenwen , Zhou Xiaoying
Published: April 2022

Objectives

To examine the possible anti-histamine effects of dipotassium glycyrrhizinate (DG), a dipotassium salt of glycyrrhizic acid, on histamine-mediated lung fibroblast activation, differentiation and proliferation; to investigate the potential and underlying mechanisms for pulmonary fibrosis (PF) treatment.

Methods

Rat primary lung fibroblasts were extracted to establish cell models; histamine, DG and loratadine (LTD, a histamine receptor antagonist) were applied. Cell proliferation, migration and cell cycle were explored; intracellular signal proteins were detected; mitochondrial membrane potential was examined.

Key findings

The anti-histamine effects of DG were found in a similar pattern of LTD on lung fibroblasts. DG inhibited histamine-induced cell activation, proliferation and migration; DG altered histamine-mediated mitochondrial membrane potentials. DG reduced the histamine-induced PAR-2 (a tryptase receptor) expression to impair mast cell tryptase co-working. Histamine-induced expressions of MMP-2, FAK, TNF-α, P38, iNOS were decreased by DG, while Bax and caspase-3, P53 were increased by DG against histamine effects. Histamine drove cells from G0/G1 to S phases, whereas DG rested cells by inhibiting G0/G1 and G2/M phases.

Conclusions

This study provided the evidences that DG can inhibit histamine-induced effects on lung fibroblasts and promote apoptosis of abnormally activated lung fibroblasts, implicating its potential therapeutic mechanisms against PF development, also for those histamine-related diseases.
(Re-)Construction of Identity and Belonging after Forced Migration: A Sociology of Knowledge Approach
Authors: Mijić Ana
Published: April 2022

This study uses a sociology of knowledge perspective to analyse how former Bosnian refugees in Austria have integrated the experiences of ethnicized war and forced migration into their lives over the past three decades. The objective hermeneutical analysis of narrative interviews with Bosnian-Austrians reveals significant differences between former child refugees and those who experienced war and migration as adolescents. From a sociology of knowledge perspective, these differences can be attributed to varying ‘stratifications of experience’: The central crisis in the adolescents’ lives was triggered by experiencing the destruction of their Yugoslavian life-world, which significantly eroded their trust in their social reality’s stability and in their belonging. The former child refugees, however, particularly struggle with their double marginalization. While the former typically manage this crisis through an exaggerated adherence to the ideal of personal performance, the latter draw on collective imaginations of ethnic/national affiliation and try to comply with them.
Instrumentation failure during microlaryngoscopy
Authors: van den Berg Nadia , Corbett Mel , Cleere Eoin , Keogh Ivan
Published: April 2022

Equipment failure can be a cause of morbidity during surgical procedures. We present two cases where a broken surgical instrument, a heart-shaped curved micro-grasper, colloquially termed ‘sweetheart’ micro-forceps, compromised patient safety during microlaryngoscopy. We discuss the importance of thorough safety protocols and communication between team members to mitigate this risk. Microinstruments used during microlaryngoscopy are at risk of failure or breakage due to their small size. Surgeons must be alert to the risk of equipment failure during surgery as a potential cause of patient morbidity. In our patient, loss of the broken instrument in the respiratory tract could have resulted in iatrogenic aspiration, respiratory infection and would have necessitated rigid bronchoscopy for removal. Instruments and equipment must checked and communicated by the surgical team before and after use to prevent potential patient morbidity.
Reverse total shoulder arthroplasty for treatment of ochronotic arthropathy
Authors: Butterfield Brian P , Garver Thomas H
Published: April 2022

Ochronotic arthropathy is a chronic manifestation of disease in patients with alkaptonuria. Connective tissue and large joint spaces accumulate discolored homogentisic acid aggregates, resulting in joint degeneration of the axial and appendicular skeleton. One case of right shoulder ochronotic osteoarthritis treated with joint replacement is presented. To our knowledge, this is the first reported surgical intervention of ochronotic arthropathy using the reverse total shoulder arthroplasty technique.
Chest pain in six Taiwanese teenagers at high altitudes
Authors: Lo Chih-Hung , Kao Wei-Fong , How Chorng-Kuang , Li Li-Hua , Chien Ding-Kuo , Chiu Yu-Hui
Published: April 2022

There is scant literature to date about the application of point-of-care devices for diagnosis of high-altitude pulmonary edema and clinical management in symptomatic teenagers. Hence, we characterized the early changes in point-of-care assessments to gain a deeper insight into the physiological responses in teenagers during a 3-day trek.
Molecular mechanisms of seed dormancy release by gas plasma-activated water technology
Authors: Grainge Giles , Nakabayashi Kazumi , Steinbrecher Tina , Kennedy Sue , Ren Junchen , Iza Felipe , Leubner-Metzger Gerhard
Published: April 2022

Developing innovative agri-technologies is essential for the sustainable intensification of global food production. Seed dormancy is an adaptive trait which defines the environmental conditions in which the seed is able to germinate. Dormancy release requires sensing and integration of multiple environmental signals, a complex process which may be mimicked by seed treatment technologies. Here, we reveal molecular mechanisms by which non-thermal (cold) atmospheric gas plasma-activated water (GPAW) releases the physiological seed dormancy of Arabidopsis thaliana. GPAW triggered dormancy release by synergistic interaction between plasma-generated reactive chemical species (NO3–, H2O2, ·NO, and ·OH) and multiple signalling pathways targeting gibberellin and abscisic acid (ABA) metabolism and the expression of downstream cell wall-remodelling genes. Direct chemical action of GPAW on cell walls resulted in premature biomechanical endosperm weakening. The germination responses of dormancy signalling (nlp8, prt6, and dog1) and ABA metabolism (cyp707a2) mutants varied with GPAW composition. GPAW removes seed dormancy blocks by triggering multiple molecular signalling pathways combined with direct chemical tissue weakening to permit seed germination. Gas plasma technologies therefore improve seed quality by mimicking permissive environments in which sensing and integration of multiple signals lead to dormancy release and germination.
Multiple caleosins have overlapping functions in oil accumulation and embryo development
Authors: Liu Xiangling , Yang Zheng , Wang Yun , Shen Yue , Jia Qingli , Zhao Cuizhu , Zhang Meng
Published: April 2022

Caleosins are lipid droplet- and endoplasmic reticulum-associated proteins. To investigate their functions in oil accumulation, expression levels of caleosins in developing seeds of Arabidopsis thaliana were examined and four seed-expressed caleosins (CLO1, CLO2, CLO4, and CLO6) were identified. The four single mutants showed similar minor changes of fatty acid composition in seeds. Two double mutants (clo1 clo2 and clo1×clo2) demonstrated distinct changes of fatty acid composition, a 16–23% decrease of oil content, and a 10–13% decrease of seed weight. Moreover, a 40% decrease of oil content, further fatty acid changes, and misshapen membranes of smaller lipid droplets were found in seeds of quadruple CLO RNAi lines. Notably, ~40% of quadruple CLO RNAi T1 seeds failed to germinate, and deformed embryos and seedlings were also observed. Complementation experiments showed that CLO1 rescued the phenotype of clo1 clo2. Overexpression of CLO1 in seedlings and BY2 cells increased triacylglycerol content up to 73.6%. Transcriptome analysis of clo1 clo2 developing seeds showed that expression levels of some genes related to lipid, embryo development, calcium signaling, and stress responses were affected. Together, these results suggest that the major seed-expressed caleosins have overlapping functions in oil accumulation and show pleiotropic effects on embryo development.
Phytomelatonin and gasotransmitters: a crucial combination for plant physiological functions
Authors: Wang Yueqiao , Cheng Pengfei , Zhao Gan , Li Longna , Shen Wenbiao
Published: April 2022

Melatonin, a molecule that was first identified in animal tissues, has been confirmed to be involved as a potential phytohormone in a variety of plant physiological responses. It is considered primarily as an antioxidant with important actions in controlling reactive oxygen and reactive nitrogen species. In addition to its role in regulating plant growth and development, phytomelatonin is involved in protection against abiotic and biotic stresses. The ‘gasotransmitter’—that is, a gaseous signaling molecule—is a new concept that has been advanced in the past two decades, with functions in animal and plant physiological regulation. Gasotransmitters including nitric oxide, carbon monoxide, hydrogen sulfide, methane, and, more recently identified, hydrogen gas are critical and indispensable in a wide range of biological processes. This review investigates the interrelationship between phytomelatonin and the above-mentioned gasotransmitters from the perspective of biosynthetic origin and functions. Moreover, the potential future research directions for phytomelatonin and gasotransmitters interactions are discussed.
Highly Sensitive Serum miRNA Panel for the Diagnosis of Hepatocellular Carcinoma in Egyptian Patients with HCV-Related HCC
Authors: Yosry Ayman , Zayed Naglaa , Dawood Reham M , Ibrahim Marwa K , Elsharkawy Marwa , Ekladious Sherif M , Khairy Ahmed , Elsharkawy Aisha , Khairy Marwa , Abdel Alem Shereen , Bader El Din Noha G , El Awady Mostafa K , Abdellatif Zeinab
Published: April 2022

Objective

This study aimed at exploring the potential role of a panel of serum micro-RNA (miRNA) markers in liver fibrosis and hepatocellular carcinoma (HCC) diagnosis in patients with chronic hepatitis C virus (HCV) infection.

Methods

The study included 157 chronic HCV patients and 62 HCC patients who presented to the Cairo University Center for Hepatic Fibrosis, Endemic Medicine Department, from 2015 to 2017. Relevant clinical and laboratory data were collected and sera were subjected to miRNA expression profiling. Eleven miRNA markers were studied and receiver operating characteristic curves were constructed to investigate the best cutoff values of the miRNAs that showed altered expression in HCC compared to HCV-associated advanced fibrosis.

Results

miRNA expression profiling revealed 5 miRNAs (miR-124, miR-141, miR-205, miR-208a, miR-499a) were significantly upregulated and 2 miRNAs were significantly downregulated (miR-103a, miR-15a) in HCC compared to advanced fibrosis patients. No significant difference was observed in miRNA expression between advanced fibrosis and early hepatic fibrosis apart from a significant downregulation of miR-155-5p in advanced fibrosis.

Conclusion

Serum miRNAs could serve as potential diagnostic tools for the diagnosis of HCC.
The Fear of Losing Control: The Crisis of Posen’s Orthodox Elite During the First Half of the 19th Century
Authors: Sariel Eliezer
Published: April 2022

The response of the Orthodox Elites in the Posen district of Poland to the acculturation process during the first half of the nineteenth century reveals both the increasing strength of this process and the depth of the crisis they perceived. The current academic discourse on the theory of Jacob Katz, who categorizes Orthodox society as a modern society because of its fear of change which led to increased resistance and stringency—as compared to the less stressed traditional society and the more lenient traditional Halacha—examines the modern characteristics of Orthodoxy. It may be claimed that the “historical laboratory” of the Posen Orthodox community offers fertile ground for future, in-depth research of the modern impact on the crystallization of Orthodoxy.
Songs Lost and Found: Katherine Philips’s ‘Pompey’s Ghost’
Authors: Cunningham John
Published: April 2022

First staged in Dublin in 1663, Katherine Philips’s Pompey, a translation of Corneille’s Pompée, was the first play by a woman to be performed on the British stage. It was also pathbreaking in its dramatic incorporation of entr’acte songs, which Philips newly added. This essay explores the complex afterlife of one song from the play, Pompey’s Ghost. It was her most widely disseminated text, though it largely circulated anonymously or attributed to other authors. Between 1663 and 1806 the song was set to music at least five times. One late seventeenth-century setting became popular in New England and was known there into the nineteenth century. By the late eighteenth century, through another setting, the song became identified as Scottish in origin. The tune to which Pompey’s Ghost was sung in Scotland had been thought lost but can now be identified, restoring more of the song’s complex reception history and significance.
The impact of the uncertainties in the 12C(α, γ)16O reaction rate on the evolution of low- to intermediate-mass stars
Authors: Pepper Ben T , Istrate A G , Romero A D , Kepler S O
Published: April 2022

One of the largest uncertainties in stellar evolutionary computations is the accuracy of the considered reaction rates. The 12C(α, γ)16O reaction is particularly important for the study of low- and intermediate-mass stars as it determines the final C/O ratio in the core which influences the white dwarf (WD) cooling evolution. Thus, there is a need for a study of how the computations of WDs and their progenitors that are made to date may be affected by the uncertainties of the 12C(α, γ)16O reaction rates. In this work, we compute fully evolutionary sequences using the mesa code with initial masses in the range of 0.90 ≤ Mi/M⊙ ≤ 3.05. We consider different adopted reaction rates, obtained from the literature, as well as the extreme limits within their uncertainties. As expected, we find that previous to the core helium burning (CHB) stage, there are no changes to the evolution of the stars. However, the subsequent stages are all affected by the uncertainties of the considered reaction rate. In particular, we find differences to the convective core mass during the CHB stage which may affect pulsation properties of subdwarfs, the number of thermal pulses during the asymptotic giant branch and trends between final oxygen abundance in the core and the progenitor masses of the remnant WDs.
Far-ultraviolet investigation into the galactic globular cluster M30 (NGC 7099) – II. Potential X-ray counterparts and variable sources
Authors: Mansfield Santana , Dieball Andrea , Kroupa Pavel , Knigge Christian , Zurek David R , Shara Michael , Long Knox S
Published: April 2022

We present a far-ultraviolet (FUV) study of the globular cluster M30 (NGC 7099). The images were obtained using the Advanced Camera for Surveys (ACS/SBC, F150LP, FUV) and the Wide Field Planetary Camera 2 (WFPC2; F300W, UV) on board the Hubble Space Telescope (HST). We compare the catalogue of FUV objects to 10 known X-ray sources and find six confident matches of two cataclysmic variables (CVs), one RS CVn, one red giant with strong FUV emission, and two sources only detected in the FUV. We also searched for variable sources in our data set and found a total of seven blue stragglers (BSs), four horizontal branch (HB) stars, five red giant branch stars, 28 main-sequence stars, and four gap objects that demonstrated variability. One BS star is a known W-UMa contact binary, one of the gap objects is a known CV identified in this work to be a dwarf nova, and the three other gap sources are weak variables. The periods and positions of two of the variable HB stars match them to two previously known RR Lyrae variables of types RRab and RRc.
A systematic search for galaxy protocluster cores at the transition epoch of their star formation activity
Authors: Ando Makoto , Shimasaku Kazuhiro , Momose Rieko , Ito Kei , Sawicki Marcin , Shimakawa Rhythm
Published: April 2022

The redshift of z ∼ 1.5 is the transition epoch of protoclusters (PCs) from the star-forming phase into the quenching phase, and hence an appropriate era to investigate the build up of the quenched population. We define a ‘core’ as the most massive halo in a given PC, where environmental effects are likely to work most effectively, and search for cores at 1 < z < 1.5. We use a photometric redshift catalogue of a wide (effective area of ${\sim}22.2\, \mathrm{deg}^{2}$) and deep ($i\sim 26.8\, \mathrm{mag}$) optical survey with Subaru Hyper-Suprime Cam. Regarding galaxies with log (M*/M⊙) > 11.3 as the central galaxies of PC cores, we estimate their average halo mass by clustering analysis and find it to be log (Mh/M⊙) ∼ 13.7. An expected mass growth by the IllustrisTNG simulation and the observed overdensities around them suggest that the PC cores we find are progenitors of present-day clusters. Classifying our galaxy sample into red and blue galaxies, we calculate the stellar mass function (SMF) and the red galaxy fraction. The SMFs in the PC cores are more-top heavy than field, implying early high-mass galaxy formation and disruption of low-mass galaxies. We also find that the red fraction increases with stellar mass, consistent with stellar mass dependent environmental quenching recently found at z > 1. Interestingly, although the cores with red and blue centrals have similar halo masses, only those with red centrals show a significant red fraction excess compared to the field, suggesting a conformity effect. Some observational features of PC cores may imply that the conformity is caused by assembly bias.
Observational constraints on the deceleration parameter in a tilted universe
Authors: Asvesta Kerkyra , Kazantzidis Lavrentios , Perivolaropoulos Leandros , Tsagas Christos G
Published: April 2022

We study a parametrization of the deceleration parameter in a tilted universe, namely a cosmological model equipped with two families of observers. The first family follows the smooth Hubble flow, while the second is the real observers residing in a typical galaxy inside a bulk flow and moving relative to the smooth Hubble expansion with finite peculiar velocity. We use the compilation of Type Ia supernovae (SNe Ia) data, as described in the Pantheon data set, to find the quality of fit to the data and study the redshift evolution of the deceleration parameter. In so doing, we consider two alternative scenarios, assuming that the bulk-flow observers live in the ΛCDM and in the Einstein-de Sitter universe. We show that a tilted Einstein-de Sitter model can reproduce the recent acceleration history of the universe, without the need of a cosmological constant or dark energy, by simply taking into account linear effects of peculiar motions. By means of a Markov chain Monte Carlo (MCMC) method, we also constrain the magnitude and the uncertainties of the parameters of the two models. From our statistical analysis, we find that the tilted Einstein-de Sitter model, equipped with one or two additional parameters that describe the assumed large-scale velocity flows, performs similar to the standard ΛCDM paradigm in the context of model selection criteria (Akaike information criterion and Bayesian information criterion).
Jets in common envelopes: a low-mass main-sequence star in a red giant
Authors: López-Cámara Diego , De Colle Fabio , Moreno Méndez Enrique , Shiber Sagiv , Iaconi Roberto
Published: April 2022

We present small-scale 3D hydrodynamical simulations of the evolution of a 0.3 M⊙ main-sequence (MS) star that launches two perpendicular jets within the envelope of a 0.88 M⊙ red giant (RG). Based on previous large-scale simulations, we study the dynamics of the jets either when the secondary star is grazing, when it has plunged-in, or when it is well within the envelope of the RG (in each stage for ∼11 d). The dynamics of the jets through the common envelope (CE) depend on the conditions of the environment as well as on their powering. In the grazing stage and the commencement of the plunge self-regulated jets need higher efficiencies to break out of the envelope of the RG. Deep inside the CE, on the time-scales simulated, jets are choked independently of whether they are self-regulated or constantly powered. Jets able to break out of the envelope of the RG in large-scale simulations, are choked in our small-scale simulations. The accreted angular momentum on to the secondary star is not large enough to form a disc. The mass accretion on to the MS star is 1–10 per cent of the Bondi–Hoyle–Littleton rate (∼10−3–10−1 M⊙ yr−1). High-luminosity emission, from X-rays to ultraviolet and optical, is expected if the jets break out of the CE. Our simulations illustrate the need for inclusion of more realistic accretion and jet models in the dynamical evolution of the CEs.
Probing computational methodologies in predicting mid-infrared spectra for large polycyclic aromatic hydrocarbons
Authors: Kerkeni B , García-Bernete I , Rigopoulou D , Tew D P , Roche P F , Clary D C
Published: April 2022

We extend the prediction of vibrational spectra to large sized polycyclic aromatic hydrocarbon (PAH) molecules comprising up to ∼1500 carbon atoms by evaluating the efficiency of several computational chemistry methodologies. We employ classical mechanics methods (Amber and Gaff) with improved atomic point charges, semi-empirical (PM3, and density functional tight binding), and density functional theory (B3LYP) and conduct global optimizations and frequency calculations in order to investigate the impact of PAH size on the vibrational band positions. We primarily focus on the following mid-infrared emission bands 3.3, 6.2, 7.7, 8.6, 11.3, 12.7, and 17.0 μm. We developed a general Frequency Scaling Function ($\mathcal {FSF}$) to shift the bands and to provide a systematic comparison versus the three methods for each PAH. We first validate this procedure on IR scaled spectra from the NASA Ames PAH Database, and extend it to new large PAHs. We show that when the $\mathcal {FSF}$ is applied to the Amber and Gaff IR spectra, an agreement between the normal mode peak positions with those inferred from the B3LYP/4-31G model chemistry is achieved. As calculations become time intensive for large sized molecules Nc > 450, this proposed methodology has advantages. The $\mathcal {FSF}$ has enabled extending the investigations to large PAHs where we clearly see the emergence of the 17.0 μm feature, and the weakening of the 3.3 μm one. We finally investigate the trends in the 3.3 μm/17.0 μm PAH band ratio as a function of PAH size and its response following the exposure to fields of varying radiation intensities.
Stellar and black hole assembly inz< 0.3 infrared-luminous mergers: intermittent starbursts versus super-Eddington accretion
Authors: Farrah Duncan , Efstathiou Andreas , Afonso Jose , Bernard-Salas Jeronimo , Cairns Joe , Clements David L , Croker Kevin , Hatziminaoglou Evanthia , Joyce Maya , Lacy Mark , Lebouteiller Vianney , Lieblich Alix , Lonsdale Carol , Oliver Seb , Pearson Chris , Petty Sara , Pitchford Lura K , Rigopoulou Dimitra , Rowan-Robinson Michael , Runburg Jack , Spoon Henrik , Verma Aprajita , Wang Lingyu
Published: April 2022

We study stellar and black hole mass assembly in a sample of 42 infrared-luminous galaxy mergers at z < 0.3 by combining results from radiative transfer modelling with archival measures of molecular gas and black hole mass. The ratios of stellar mass, molecular gas mass, and black hole mass to each other are consistent with those of massive gas-rich galaxies at z < 0.3. The advanced mergers may show increased black hole mass to stellar mass ratios, consistent with the transition from active galactic nucleus (AGN) to ellipticals and implying substantial black hole mass growth over the course of the merger. Star formation rates are enhanced relative to the local main sequence, by factors of ∼100 in the starburst and ∼1.8 in the host, respectively. The starburst star formation rates appear distinct to star formation in the main sequence at all redshifts up to at least z ∼ 5. Starbursts may prefer late-stage mergers, but are observed at any merger stage. We do not find evidence that the starbursts in these low-redshift systems substantially increase the total stellar mass, with a soft upper limit on the stellar mass increase from starburst activity of about a factor of two. In contrast, 12 objects show evidence for super-Eddington accretion, associated with late-stage mergers, suggesting that many AGN in infrared-luminous mergers go through a super-Eddington phase. The super-Eddington phase may increase black hole mass by up to an order of magnitude at an accretion efficiency of $42\pm 33{{\ \rm per\ cent}}$ over a period of 44 ± 22 Myr. Our results imply that super-Eddington accretion is an important black hole growth channel in infrared-luminous galaxies at all redshifts.
Species-dependent solar rotation effects on the Martian ionosphere
Authors: Wu S-Q , Wu X-S , Cui J , Yao Z-H , Cao Y-T , Lu H-Y , He F , Li L , Wei Y , Cao J-B
Published: April 2022

Atmospheric escape is a central issue in understanding how Mars lost the habitability and it is critically controlled by the link between the atmosphere and the interplanetary space, i.e. the ionosphere. The predominant driver of the Martian ionospheric variability is the solar extreme ultraviolet radiation. To date, how the ionospheric electrons respond to this radiation has been well investigated, but the responses of various ion species are to be understood. Based on a multi-instrument data set from the Mars Atmosphere and Volatile Evolution, we report direct observations of quasi-periodical variations of photoelectrons and ions, with a common period of ≈27.2 d and almost in exact phase with the solar rotation. These diverse variations present remarkably different amplitudes. The ion density variation has a much larger amplitude than the solar flux variation and the electron density variation has a smaller amplitude. For comparison, the amplitude of the photoelectron intensity variation is nearly identical to that of the solar flux variation. The species-dependent solar rotation effects provide a good diagnostic of the upper atmospheric and ionospheric chemistry, urging reconsiderations of the solar-driven composition and variability of any planetary ionosphere.
A standard siren cosmological measurement from the potential GW190521 electromagnetic counterpart ZTF19abanrhr
Authors: Chen Hsin-Yu , Haster Carl-Johan , Vitale Salvatore , Farr Will M , Isi Maximiliano
Published: April 2022

The identification of the electromagnetic (EM) counterpart candidate ZTF19abanrhr to the binary black hole merger GW190521 opens the possibility to infer cosmological parameters from this standard siren with a uniquely identified host galaxy. The distant merger allows for cosmological inference beyond the Hubble constant. Here, we show that the three-dimensional spatial location of ZTF19abanrhr calculated from the EM data remains consistent with the latest sky localization of GW190521 provided by the LIGO-Virgo Collaboration. If ZTF19abanrhr is associated with the GW190521 merger, and assuming a flat wCDM model, we find that $H_0=48^{+23}_{-10}\, \mathrm{km} \, \mathrm{s}^{-1}\, \mathrm{Mpc}^{-1}$, $\Omega _m=0.35^{+0.41}_{-0.26}$, and $w_0=-1.31^{+0.61}_{-0.48}$ (median and $68{{\ \rm per\ cent}}$ credible interval). If we use the Hubble constant value inferred from another gravitational-wave event, GW170817, as a prior for our analysis, together with assumption of a flat ΛCDM and the model-independent constraint on the physical matter density ωm from Planck, we find $H_0=68.9^{+8.7}_{-6.0}\, \mathrm{km} \, \mathrm{s}^{-1}\, \mathrm{Mpc}^{-1}$.
Early evolution of a newborn magnetar with strong precession motion in GRB 180620A
Authors: Zou Le , Liang En-Wei
Published: April 2022

The observed early X-ray plateau in the afterglow lightcurves of some gamma-ray bursts (GRBs) is attributed to the dipole radiations (DRs) of a newborn magnetar. A quasi-periodic oscillation (QPO) signal in the plateau would be strong evidence of the magnetar precession motion. By making a time-frequency domain analysis for the X-ray afterglow lightcurve of GRB 180620A, we find a QPO signal of ∼650 s in its early X-ray plateau. We fit the lightcurve with a magnetar precession model by adopting the Markov chain Monte Carlo algorithm. The observed lightcurve and the QPO signal are well represented with our model. The derived magnetic field strength of the magnetar is $B_{\rm p}= (1.02^{+0.59}_{-0.61})\times 10^{15}$ G. It rapidly spins down with angular velocity evolving as Ωs ∝ (1 + t/τsd)−0.96, where τsd = 9430 s. Its precession velocity evolution is even faster than Ωs, i.e. Ωp ∝ (1 + t/τp)−2.18 ± 0.11, where τp = 2239 ± 206 s. The inferred braking index is n = 2.04. We argue that the extra energy loss via the magnetospheric processes results in its rapid spin-down, low braking index, and strong precession motion of the magnetar.
Disentangling Signatures of Selection Before and After European Colonization in Latin Americans
Authors: Mendoza-Revilla Javier , Chacón-Duque J. Camilo , Fuentes-Guajardo Macarena , Ormond Louise , Wang Ke , Hurtado Malena , Villegas Valeria , Granja Vanessa , Acuña-Alonzo Victor , Jaramillo Claudia , Arias William , Barquera Rodrigo , Gómez-Valdés Jorge , Villamil-Ramírez Hugo , Silva de Cerqueira Caio C. , Badillo Rivera Keyla M. , Nieves-Colón Maria A. , Gignoux Christopher R. , Wojcik Genevieve L. , Moreno-Estrada Andrés , Hünemeier Tábita , Ramallo Virginia , Schuler-Faccini Lavinia , Gonzalez-José Rolando , Bortolini Maria-Cátira , Canizales-Quinteros Samuel , Gallo Carla , Poletti Giovanni , Bedoya Gabriel , Rothhammer Francisco , Balding David , Fumagalli Matteo , Adhikari Kaustubh , Ruiz-Linares Andrés , Hellenthal Garrett
Published: April 2022

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
Rates of Mutations and Transcript Errors in the Foodborne PathogenSalmonella entericasubsp.enterica
Authors: Pan Jiao , Li Weiyi , Ni Jiahao , Wu Kun , Konigsberg Iain , Rivera Caitlyn E. , Tincher Clayton , Gregory Colin , Zhou Xia , Doak Thomas G. , Lee Heewook , Wang Yan , Gao Xiang , Lynch Michael , Long Hongan
Published: April 2022

Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures
Authors: Hill Rowena , Buggs Richard J.A. , Vu Dang Toan , Gaya Ester
Published: April 2022

The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.
DNA damage in peripheral blood lymphocytes of severely ill COVID-19 patients in relation to inflammatory markers and parameters of hemostasis
Authors: Mihaljevic Olgica , Zivancevic-Simonovic Snezana , Cupurdija Vojislav , Marinkovic Milos , Tubic Vukajlovic Jovana , Markovic Aleksandra , Stanojevic-Pirkovic Marijana , Milosevic-Djordjevic Olivera
Published: April 2022

Bearing in the mind that a variety of agents can contribute to genome instability, including viral infections, the aim of this study was to analyze DNA damage in hospitalized COVID-19 patients and its relationship with certain laboratory parameters. The potential impact of applied therapy and chest X-rays on DNA damage was also estimated. The study population included 24 severely COVID-19 patients and 15 healthy control subjects. The level of DNA damage was measured as genetic damage index (GDI) by comet assay. The standard laboratory methods and certified enzymatic reagents for the appropriate autoanalyzers were performed for the determination of the biochemical and hematological parameters. COVID-19 patients had significantly higher level of DNA damage compared with control subjects. The absolute number of neutrophil leukocytes was statistically higher, while the absolute number of lymphocytes was statistically lower in COVID-19 patients than in healthy controls. The analysis of the relationship between DNA damage and laboratory parameters indicated that GDI was positively correlated with interleukin 6 (IL-6) concentration and negatively with platelet count in COVID-19 patients. The level of DNA damage was slightly higher in female patients, in whom it was demonstrated a positive correlation of GDI with C-reactive protein (CRP) and procalcitonin. Likewise, there was a negative relationship of GDI and platelet count, and positive relationship of GDI and activated partial thromboplastin time (aPTT) in female population. The applied therapy (antibiotics, corticosteroid, anticoagulant, and antiviral therapy) as well as chest X rays has been shown to have genotoxic potential. The level of DNA damage significantly corresponds to the inflammatory markers and parameters of hemostasis in COVID-19 patients. In conclusion, inflammation, smoking habit, applied therapy, and chest X rays contribute to a higher level of DNA damage in COVID-19 patients.
m6A and YTHDF proteins contribute to the localization of select neuronal mRNAs
Authors: Flamand Mathieu N , Meyer Kate D
Published: April 2022

The transport of mRNAs to distal subcellular compartments is an important component of spatial gene expression control in neurons. However, the mechanisms that control mRNA localization in neurons are not completely understood. Here, we identify the abundant base modification, m6A, as a novel regulator of this process. Transcriptome-wide analysis following genetic loss of m6A reveals hundreds of transcripts that exhibit altered subcellular localization in hippocampal neurons. Additionally, using a reporter system, we show that mutation of specific m6A sites in select neuronal transcripts diminishes their localization to neurites. Single molecule fluorescent in situ hybridization experiments further confirm our findings and identify the m6A reader proteins YTHDF2 and YTHDF3 as mediators of this effect. Our findings reveal a novel function for m6A in controlling mRNA localization in neurons and enable a better understanding of the mechanisms through which m6A influences gene expression in the brain.
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures
Authors: Schmitz Mirko , Schultze Anne , Vanags Raimonds , Voigt Karsten , Di Ventura Barbara , Öztürk Mehmet Ali
Published: April 2022

pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/).