bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of black holes in the pair-instability mass gap: hydrodynamical simulations of a head-on massive star collision
Authors: Ballone Alessandro , Costa Guglielmo , Mapelli Michela , MacLeod Morgan , Torniamenti Stefano , Pacheco-Arias Juan Manuel 
Published: December 2022

ABSTRACT
The detection of the binary black hole merger GW190521, with primary black hole mass $85^{+21}_{-14} {\rm M}_{\odot }$, proved the existence of black holes in the theoretically predicted pair-instability gap ($\sim 60-120 \, {\rm M}_{\odot }$) of their mass spectrum. Some recent studies suggest that such massive black holes could be produced by the collision of an evolved star with a carbon–oxygen core and a main sequence star. Such a post-coalescence star could end its life avoiding the pair-instability regime and with a direct collapse of its very massive envelope. It is still not clear, however, how the collision shapes the structure of the newly produced star and how much mass is actually lost in the impact. We investigated this issue by means of hydrodynamical simulations with the smoothed particle hydrodynamics code StarSmasher, finding that a head-on collision can remove up to 12 per cent of the initial mass of the colliding stars. This is a non-negligible percentage of the initial mass and could affect the further evolution of the stellar remnant, particularly in terms of the final mass of a possibly forming black hole. We also found that the main sequence star can plunge down to the outer boundary of the core of the primary, changing the inner chemical composition of the remnant. The collision expels the outer layers of the primary, leaving a remnant with an helium-enriched envelope (reaching He fractions of about 0.4 at the surface). These more complex abundance profiles can be directly used in stellar evolution simulations of the collision product.
CALSAGOS: Clustering algorithms applied to galaxies in overdense systems
Authors: Olave-Rojas D E , Cerulo P , Araya-Araya P , Olave-Rojas D A 
Published: December 2022

ABSTRACTIn this paper, we present CALSAGOS: Clustering ALgorithmS Applied to Galaxies in Overdense Systems which is a PYTHON package developed to select cluster members and to search, find, and identify substructures. CALSAGOS is based on clustering algorithms, and was developed to be used in spectroscopic and photometric samples. To test the performance of CALSAGOS, we use the S-PLUS’s mock catalogues, and we found an error of 1–6 per cent on member selection depending on the function that is used. Besides, CALSAGOS has a F1-score of 0.8, a precision of 85 per cent and a completeness of 100 per cent in the identification of substructures in the outer regions of galaxy clusters (r &gt; r200). The F1-score, precision, and completeness of CALSAGOS fall to 0.5, 75, and 40 per cent when we consider all substructure identifications (inner and outer) due to the function that searches, finds, and identifies the substructures works in 2D, and cannot resolve the substructures projected over others.
DNA–TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families
Authors: Zhang Yi , Xu Yong-ping , Nie Ju-kui , Chen Hong , Qin Genji , Wang Bo , Su Xiao-Dong 
Published: December 2022

Abstract
Plant-specific TCP transcription factors are key regulators of diverse plant functions. TCP transcription factors have long been annotated as basic helix–loop–helix (bHLH) transcription factors according to remote sequence homology without experimental validation, and their consensus DNA-binding sequences and protein–DNA recognition mechanisms have remained elusive. Here, we report the crystal structures of the class I TCP domain from AtTCP15 and the class II TCP domain from AtTCP10 in complex with different double-stranded DNA (dsDNA). The complex structures reveal that the TCP domain is a distinct DNA-binding motif and the homodimeric TCP domains adopt a unique three-site recognition mode, binding to dsDNA mainly through a central pair of β-strands formed by the dimer interface and two basic flexible loops from each monomer. The consensus DNA-binding sequence for class I TCPs is a perfectly palindromic 11 bp (GTGGGNCCCAC), whereas that for class II TCPs is a near-palindromic 11 bp (GTGGTCCCCAC). The unique DNA binding mode allows the TCP domains to display broad specificity for a range of DNA sequences even shorter than 11 bp, adding further complexity to the regulatory network of plant TCP transcription factors.
Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
Authors: Kohl Maximilian P , Kompatscher Maria , Clementi Nina , Holl Lena , Erlacher Matthias D 
Published: December 2022

Abstract
During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria.
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies
Authors: Morova Tunc , Ding Yi , Huang Chia-Chi F , Sar Funda , Schwarz Tommer , Giambartolomei Claudia , Baca Sylvan C , Grishin Dennis , Hach Faraz , Gusev Alexander , Freedman Matthew L , Pasaniuc Bogdan , Lack Nathan A 
Published: December 2022

AbstractThe vast majority of disease-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and the number of variants tested per loci. Using this strategy, we interrogated known prostate cancer (PCa) risk-associated loci and demonstrated that 35% of them harbor SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
CK2 promotes jasmonic acid signaling response by phosphorylating MYC2 in Arabidopsis
Authors: Zhu Jiang , Wang Wen-Shu , Yan Da-Wei , Hong Li-Wei , Li Ting-Ting , Gao Xiang , Yang Yun-Huang , Ren Feng , Lu Ying-Tang , Yuan Ting-Ting 
Published: December 2022

Abstract
Jasmonic acid (JA) signaling plays a pivotal role in plant development and defense. MYC2 is a master transcription factor in JA signaling, and was found to be phosphorylated and negatively regulated by MAP kinase and receptor-like kinase. However, the kinases that positively regulate MYC2 through phosphorylation and promote MYC2-mediated activation of JA response have not been identified. Here, we identified CK2 as a kinase that phosphorylates MYC2 and thus regulates the JA signaling. CK2 holoenzyme can interact with MYC2 using its regulatory subunits and phosphorylate MYC2 at multiple sites with its catalytic subunits. Inhibition of CK2 activity in a dominant-negative plant line, CK2mut, repressed JA response. On the other hand, increasing CK2 activity by overexpression of CKB4, a regulatory subunit gene of CK2, enhanced JA response in a MYC2-dependent manner. Substitution of the Ser and Thr residues at phosphorylation sites of MYC2 by CK2 with Ala impaired MYC2 function in activating JA response. Further investigations evidenced that CK2 facilitated the JA-induced increase of MYC2 binding to the promoters of JA-responsive genes in vivo. Our study demonstrated that CK2 plays a positive role in JA signaling, and reveals a previously undiscovered mechanism that regulates MYC2 function.
The effects of fatty acid–based dietary interventions on circulating bioactive lipid levels as intermediate biomarkers of health, cardiovascular disease, and cardiovascular disease risk factors: a systematic review and meta-analysis of randomized clinical trials
Authors: Calderón-Pérez Lorena , Companys Judit , Solà Rosa , Pedret Anna , Valls Rosa M 
Published: December 2022

Abstract

Context
Dietary fatty acids (FAs), primarily n-3 polyunsaturated FAs, have been associated with enrichment of the circulating bioactive lipidome and changes in the enzymatic precursor lipoprotein-associated phospholipase A2 (Lp-PLA2) mass; however, the magnitude of this effect remains unclear.

Objective
The aim of this systematic review and meta-analysis was to evaluate the effect of different dietary FAs on the bioactive lipid profile of healthy participants and those with cardiovascular disease (CVD) and CVD risk factors.

Data sources
PubMed, SCOPUS and the Cochrane Library databases were searched for relevant articles published between October 2010 and May 2022.

Data extraction
Data were screened for relevance and then retrieved in full and evaluated for eligibility by 2 reviewers independently.

Data analysis
The net difference in the bioactive lipid mean values between the endpoint and the baseline, and the corresponding SDs or SEs, were used for the qualitative synthesis. For the meta-analysis, a fixed-effects model was used.

Results
Twenty-seven randomized clinical trials (representing &gt;2560 participants) were included. Over 78% of the enrolled participants had ≥1 associated CVD risk factor, whereas &lt;22% were healthy. In the meta-analysis, marine n-3 supplements (dose range, 0.37–1.9 g/d) significantly increased pro-inflammatory lysophosphatidylcholines (lyso-PCs; for lyso-PC(16:0): mean, +0.52 [95% confidence interval (CI), 0.02–1.01] µM; for lyso-PC(18:0): mean, +0.58 [95%CI, 0.09–1.08] µM) in obese participants. Additionally, n-3 supplementation (1–5.56 g/d) decreased plasma Lp-PLA2 mass, a well-known inflammation marker, in healthy (–0.35 [95%CI, –0.59 to –0.10] ng/mL), dyslipidemic (–0.36 [95%CI, –0.47 to –0.25] ng/mL), and stable coronary artery disease participants (–0.52 [95%CI, –0.91 to –0.12] ng/mL).

Conclusions
Daily n-3 provided as EPA+DHA supplements and consumed from 1 to 6 months reduced plasma Lp-PLA2 mass in healthy participants and those with CVD and CVD risk factors, suggesting an anti-inflammatory effect. However, the saturated lyso-PC response to n-3 was impaired in obese participants.

Systematic Review Registration
PROSPERO registration no. CRD42021218335
The Sustainabilitarian Approach
Authors: Roemer John E. 
Published: December 2022

Abstract
This chapter discusses foundational issues of intergenerational ethics in a model with only two generations and endogenous growth. We argue that many important questions can be studied in this simple model, rather than the usual model with an infinite or unknown number of generations. We begin by criticizing (undiscounted) utilitarianism as giving rise to a ‘utility monster’ when there is endogenous growth, and then propose that economists have dealt with this problem by discounting utilities of future generations. We argue that the usual choice of discount factor is far too small (that is, utilities of future generations are discounted too much). There is a ‘discount-factor fallacy’ which holds that the discount factor applied in intergenerational analysis should be the same as the one individuals apply to maximizing their utility over a lifetime. We present in contrast a definition of sustainability and of growth sustainability. The latter’s objective is to maximize the utility of the first generation subject to guaranteeing a rate utility growth of g per generation. We finally discuss how to discount the sustainabilitarian objective, which can be done if there is a positive probability π that each generation might be the last one.
Key words: discounted utilitarianism, discount factor size, endogenous growth, sustainability, growth sustainability
Jane Mansbridge, Beyond Adversary Democracy
Authors: Beerbohm Eric 
Published: December 2022

Abstract
Rules of order can perform two kinds of work in a democratic setting: they can be regulative, taking conflicts among groups for granted, or they can be constitutive, making possible the formation of new ways of relating to each other as equals. Jane Mansbridge’s now classic Beyond Adversary Democracy is a vivid possibility proof for the latter kind of democratic theory. Its mix of participant observation and case studies showed how the rules of order can make a group that is marked by its equal standing. In doing so, Mansbridge’s work anticipated two core literatures in political theory. It pointed to the deliberative turn in democratic theory and the relational turn in debates about distributive equality. At the same time, it modeled a way of doing political theory that integrates analytic and ethnographic approaches.
Factors associated with change in health-related quality of life in people with gout: a 3-year prospective cohort study in primary care
Authors: Watson Lorraine , Belcher John , Nicholls Elaine , Chandratre Priyanka , Blagojevic-Bucknall Milica , Hider Samantha , Lawton Sarah A , Mallen Christian D , Muller Sara , Rome Keith , Roddy Edward 
Published: December 2022

Abstract

Objective
To describe factors associated with change in health-related quality of life (HRQOL) in people living with gout in primary care.

Methods
In a UK prospective cohort study, adults with a diagnosis of gout registered with 20 general practices completed the Gout Impact Scale (GIS; scale 0–100), 36-item Short Form Physical Function subscale (PF-10; 0–100) and HAQ Disability Index (HAQ-DI; 0–3) via postal questionnaires at baseline and 6, 12, 24 and 36 months. Linear mixed modelling was used to investigate factors associated with changes in HRQOL over 3 years.

Results
A total of 1184 participants responded at baseline (adjusted response 65.6%); 990 (83.6%) were male, with a mean age of 65.6 years (s.d. 12.5). A total of 818, 721, 696 and 605 responded at 6, 12, 24 and 36 months, respectively. Factors associated with worse disease-specific and generic HRQOL over 3 years were flare frequency (five or more flares; GIS subscales, PF-10), oligo/polyarticular flares (GIS subscales, PF-10, HAQ-DI), worse pain (GIS subscales, PF-10, HAQ-DI), body pain (GIS subscales, PF-10, HAQ-DI) and more severe depression (GIS subscales, PF-10, HAQ-DI) (P ≤ 0.05). More severe anxiety was associated with worse disease-specific HRQOL only (GIS subscales). Older age (PF-10), being female (PF-10, HAQ-DI) and BMI (HAQ-DI) were associated with worse generic HRQOL (P ≤ 0.05).

Conclusion
Gout-specific, comorbid and sociodemographic factors were associated with change in HRQOL over a 3-year period, highlighting people at risk of worse outcomes who could be targeted for interventions.
Immune complex-mediated neutrophil activation in patients with polymyalgia rheumatica
Authors: Michailidou Despina , Johansson Linda , Kuley Runa , Wang Ting , Hermanson Payton , Rantapää-Dahlqvist Solbritt , Lood Christian 
Published: December 2022

Abstract

Objective
Neutrophils are important in host defence. However, neutrophils are also linked to inflammation and organ damage. The purpose of this study was to assess whether markers of neutrophil activation are increased in PMR.

Methods
Levels of immune complexes (IC), calprotectin and neutrophil extracellular traps (NETs) were measured in plasma of healthy individuals (n = 30) and patients with PMR (n = 60), at flare and upon treatment with glucocorticoids using ELISA. Plasma-mediated neutrophil activation was assessed in presence of an FcγRIIA inhibitory antibody (IV.3).

Results
Plasma levels of calprotectin and NETs were elevated in PMR (P &lt; 0.001). Mechanistically, neutrophil activation was driven by ICs, present in plasma, able to up-regulate neutrophil activation markers CD66b and CD11b (P &lt; 0.0001) in an FcγRIIA-dependent manner (P &lt; 0.01). Of note, circulating levels of IC correlated with plasma induced CD66b and CD11b (r = 0.51, P = 0.004, and r = 0.46, P = 0.01, respectively) and decreased after glucocorticoid therapy. In contrast to NETs, calprotectin significantly decreased after glucocorticoid therapy (P &lt; 0.001) and was higher in PMR without overlapping GCA compared with patients with overlapping disease (P = 0.014). Interestingly, musculoskeletal involvement was associated with elevated levels of calprotectin before initiation of glucocorticoid therapy (P = 0.036).

Conclusions
Neutrophil activation, including NET formation, is increased in PMR, through IC-mediated engagement of FcγRIIA. Clinically, neutrophil activation is associated with musculoskeletal involvement, with calprotectin, but not NETs, being a biomarker of treatment response in PMR patients. In all, IC-mediated neutrophil activation is a central process in PMR pathogenesis identifying potential novel therapeutic targets (FcγRIIA), as well as soluble markers for disease monitoring (calprotectin).
‘Amate ma non generate’: Sexual Pleasure and Marital Hygiene in Paolo Mantegazza’s Sexual Science
Authors: Campani Francesca 
Published: December 2022

Summary
By exploring the links between popular marital medicine and Paolo Mantegazza’s sexual science, this article will shed light on the positive discourses on sexual pleasure that circulated during the second half of the nineteenth century in Italy. By doing so, it aims to draw attention to popular medicine’s contribution to the emergence of modern ideas on sexuality. First, the article will show how nineteenth-century marital sexual guides were influenced by eighteenth-century embryology, which considered mutual sexual pleasure as necessary for procreation. Second, it will demonstrate how, in Mantegazza’s sexual science, pleasure acquired importance in itself, as demonstrated by his committed advocacy of methods of contraception that safeguarded pleasure for both partners. Finally, the article will argue that the sexualisation of marriage in the 1920s can be understood as part of a long-standing positive discourse on pleasure embedded in the genre of marital sexual guides.
Contribution of post-trauma insomnia to depression and posttraumatic stress disorder in women service members: findings from the Millennium Cohort Study
Authors: Carlson Gwendolyn C , Sharifian Neika , Jacobson Isabel G , LeardMann Cynthia A , Rull Rudolph P , Martin Jennifer L ,   Millennium Cohort Study Team, Belding Jenn , Boparai Satbir , Carey Felicia R , Castañeda Sheila F , Villalobos Javier , Geronimo-Hara Toni Rose , Kolaja Claire , Magallon Sandra , Rivera Anna , Roesch Scott , Seay Julia , Sheppard Beverly , Daniel Trone , Jennifer Walstrom , Wooten Nikki , Zhu Katie 
Published: December 2022

AbstractStudy ObjectivesWe examined whether women service members and veterans who reported recent combat and/or sexual trauma experiences had a greater risk of insomnia compared with women who did not report these recent experiences, and whether insomnia would be associated with a greater risk of mental health outcomes.MethodsWe analyzed two waves of survey data (2011–2013, Time 1 [T1] and 2014–2016, Time 2 [T2]) from 26 443 current and former women service members from the Millennium Cohort Study. We assessed recent traumas in the past 3 years, and probable insomnia at T1 and probable post-traumatic stress disorder (PTSD) and depression at T2. A longitudinal mediation model was used to quantify separate indirect effects of recent traumas on mental health outcomes through probable insomnia.ResultsWomen who had experienced recent sexual assault (odds ratio [OR] = 1.68; 95% CI = 1.24–2.10), sexual harassment (OR = 1.22; 95% CI = 1.05–1.41), and combat (OR = 1.34; 95% CI = 1.20–1.49) at T1 had a greater risk of probable insomnia at T1 compared with women who had not recently experienced these events. Probable insomnia at T1, in turn, was associated with probable depression (OR = 2.66; 95% CI = 2.31–3.06) and PTSD (OR = 2.57; 95% CI = 2.27–2.90) at T2. Recent combat experience did not moderate the associations of recent sexual trauma with insomnia or mental health outcomes.ConclusionsInsomnia contributes to the risk of subsequent mental health conditions following trauma. The diagnosis and treatment of post-trauma insomnia should be prioritized to mitigate the development of posttraumatic mental health conditions.
A randomized-controlled trial of a digital, small incentive-based intervention for working adults with short sleep
Authors: Ong Ju Lynn , Massar Stijn A A , Lau TeYang , Ng Ben K L , Chan Lit Fai , Koek Daphne , Cheong Karen , Chee Michael W L 
Published: December 2022

Abstract

Study Objectives
We evaluated the efficacy of a digitally delivered, small and scalable incentive-based intervention program on sleep and wellbeing in short-sleeping, working adults.

Methods
A 22-week, parallel-group, randomized-controlled trial was conducted on 21–40 y participants gifted with FitbitTM devices to measure sleep for ≥2 years, as part of a broader healthy lifestyle study. About 225 short sleepers (141 males; average time-in-bed, TIB &lt; 7h) were randomly assigned in a 2:1 ratio to Goal-Setting or Control groups. The Goal-Setting group received health vouchers (~USD 0.24) for meeting each sleep goal (i.e. increasing weeknight TIB by 30 min/sleeping before midnight).The study spanned three phases: (1) 2-week Baseline, (2) 10-week Intervention, and (3) 10-week Follow-Up. Wellbeing questionnaires were administered on Weeks 1–2, 11–12, and 21–22.

Results
Baseline weeknight TIB (mean ± SD) was 387 ± 43 min (Goal-Setting) and 399 ± 44 min (Control), while bedtime was 00:53 ± 01:13 (Goal-Setting), and 00:38 ± 00:56 (Control). No difference in sleep outcomes was observed at study endpoints, but exploratory week-by-week analysis showed that on Weeks 3–5, TIB in the Goal-Setting group increased (9–18 min; ps &lt; 0.05) while on Week 5, bedtimes shifted earlier (15 min; p &lt; 0.01) compared to Baseline. Morning sleepiness was reduced in the Goal-Setting group (mean[SEM] = −3.17(1.53); p = 0.04) compared to Baseline, although between-group differences were not significant (p = 0.62). Main barriers to sleeping longer were work hours (35%), followed by leisure activities (23%) and family commitments (22%).

Conclusion
Our program resulted in encouraging subjective sleep improvements and short-term sleep extension, but sustained transformation of sleep will probably require structural measures to overcome significant obstacles to sleep.

Trial Registration
ClinicalTrials.gov Identifier: NCT04878380 (hiSG Sleep Health Study (hiSG-SHS); https://clinicaltrials.gov/ct2/show/NCT04878380)