bluuebunny/crossref_metadata_2025_split huggingface dataset:
Straightening the crooked: intraspecific divergence of stem posture control and associated trade-offs in a model conifer
Authors: Sierra-de-Grado Rosario , Pando Valentin , Voltas Jordi , Zas Rafael , Majada Juan , Climent Jose 
Published: December 2021

Abstract
Although the straightening capacity of the stem is key for light capture and mechanical stability in forest trees, little is known about its adaptive implications. Assuming that stem straightening is costly, trade-offs are expected with competing processes such as growth, maintenance, and defence. We established a manipulative experiment in a common garden of Pinus pinaster including provenances typically showing either straight-stemmed or crooked-stemmed phenotypes. We imposed a bending up to 35º on plants aged 9 years of both provenance groups and followed the straightening kinetics and shoot elongation after releasing. Eight months later, we destructively assessed biomass partitioning, reaction wood, wood microdensity, xylem reserve carbohydrates, and phloem secondary metabolites. The experimental bending and release caused significant, complex changes with a marked difference between straight- and crooked-type plants. The straight-type recovered verticality faster and to a higher degree and developed more compression wood, while displaying a transitory delay in shoot elongation, reducing resource allocation to defence and maintaining the levels of non-structural carbohydrates compared with the crooked type. This combination of responses indicates the existence of intraspecific divergence in the reaction to mechanical stresses that may be related to different adaptive phenotypic plasticity.
Braided Challah
Authors: Ron Zvi 
Published: December 2021

Abstract
Braided bread for Shabbat, commonly referred to as challah (plural: challot), is the familiar and traditional form known to Ashkenazic Jews. While the challah itself takes on various shapes, and the number of strands varies, the braided appearance remains an essential and distinctive component of this bread. This defining characteristic of challah was adopted from the baking styles of the communities among which Ashkenazic Jews lived. This article will explore the origins of this particular custom.
On the Courant–Friedrichs–Lewy condition for numerical solvers of the coagulation equation
Authors: Laibe Guillaume , Lombart Maxime 
Published: December 2021

ABSTRACTEvolving the size distribution of solid aggregates challenges simulations of young stellar objects. Among other difficulties, generic formulae for stability conditions of explicit solvers provide severe constraints when integrating the coagulation equation for astrophysical objects. Recent numerical experiments have reported that these generic conditions may be much too stringent. By analysing the coagulation equation in the Laplace space, we explain why this is indeed the case and provide a novel stability condition that avoids time oversampling.
The AGN fuelling/feedback cycle in nearby radio galaxies – IV. Molecular gas conditions and jet–ISM interaction in NGC 3100
Authors: Ruffa Ilaria , Prandoni Isabella , Davis Timothy A , Laing Robert A , Paladino Rosita , Casasola Viviana , Parma Paola , Bureau Martin 
Published: December 2021

ABSTRACT
This is the fourth paper of a series investigating the AGN fuelling/feedback processes in a sample of 11 nearby low-excitation radio galaxies (LERGs). In this paper, we present follow-up Atacama Large Millimeter/submillimeter Array (ALMA) observations of one source, NGC 3100, targeting the 12CO(1-0), 12CO(3-2), HCO+(4-3), SiO(3-2), and HNCO(6-5) molecular transitions. 12CO(1-0) and 12CO(3-2) lines are nicely detected and complement our previous 12CO(2-1) data. By comparing the relative strength of these three CO transitions, we find extreme gas excitation conditions (i.e. Tex ≳ 50 K) in regions that are spatially correlated with the radio lobes, supporting the case for a jet–ISM interaction. An accurate study of the CO kinematics demonstrates that although the bulk of the gas is regularly rotating, two distinct non-rotational kinematic components can be identified in the inner gas regions: one can be associated to inflow/outflow streaming motions induced by a two-armed spiral perturbation; the second one is consistent with a jet-induced outflow with vmax ≈ 200 km s−1 and $\dot{M}\lesssim 0.12$ M⊙ yr−1. These values indicate that the jet-CO coupling ongoing in NGC 3100 is only mildly affecting the gas kinematics, as opposed to what expected from existing simulations and other observational studies of (sub-)kpc scale jet–cold gas interactions. HCO+(4-3) emission is tentatively detected in a small area adjacent to the base of the northern radio lobe, possibly tracing a region of jet-induced gas compression. The SiO(3-2) and HNCO(6-5) shock tracers are undetected: this – along with the tentative HCO+(4-3) detection – may be consistent with a deficiency of very dense (i.e. ncrit &gt; 106 cm−3) cold gas in the central regions of NGC 3100.
Radio continuum properties of OH megamaser galaxies
Authors: Sotnikova Yu V , Wu Zhongzu , Mufakharov T V , Mikhailov A G , Mingaliev M G , Erkenov A K , Semenova T A , Bursov N N , Udovitskiy R Y , Stolyarov V A , Tsybulev P G , Chen Y J , Zhang J S , Shen Z , Jiang D R 
Published: December 2021

ABSTRACT
We present a study of the radio continuum properties of two luminous/ultraluminous infrared galaxy samples: the OH megamaser (OHM) sample (74 objects) and the control sample (128 objects) without detected maser emission. We carried out pilot observations for 140 objects with the radio telescope RATAN-600 at 1.2, 2.3, 4.7, 8.2, 11.2, and 22.3 GHz in 2019–2021. The OHM sample has two times more flat-spectrum sources (32 per cent) than the control sample. Steep radio spectra prevail in both samples. The median spectral index at 4.7 GHz α4.7 = −0.59 for the OHM sample, and α4.7 = −0.71 for the non-OHM galaxies. We confirm a tight correlation of the far-infrared (FIR) and radio luminosities for the OHM sample. We found correlations between isotropic OH line luminosity LOH and the spectral index α4.7 (ρ = 0.26, p-val. = 0.04) and between LOH and radio luminosity P1.4 (ρ = 0.35, p-val. = 0.005). Reviewing subsamples of masers powered by active galactic nuclei (AGNs) and star formation revealed insignificant differences for their FIR and radio properties. None the less, AGN-powered galaxies exhibit larger scatter in a range of parameters and their standard deviations. The similarities in the radio and FIR properties in the two samples are presumably caused by the presence of a significant amount of AGN sources in both samples (47 and 30 per cent in the OHM and control samples) and/or possibly by the presence of undetected OH emission sources in the control sample.
High accuracy wide-field imaging method in radio interferometry
Authors: Ye Haoyang , Gull Stephen F , Tan Sze M , Nikolic Bojan 
Published: December 2021

ABSTRACT
With the development of modern radio interferometers, wide-field continuum surveys have been planned and undertaken, for which accurate wide-field imaging methods are essential. Based on the widely used W-stacking method, we propose a new wide-field imaging algorithm that can synthesize visibility data from a model of the sky brightness via degridding, able to construct dirty maps from measured visibility data via gridding. Results carry the smallest approximation error yet achieve relative to the exact calculation involving the direct Fourier transform. In contrast to the original W-stacking method, the new algorithm performs least-misfit optimal gridding (and degridding) in all three directions, and is capable of achieving much higher accuracy than is feasible with the original algorithm. In particular, accuracy at the level of single precision arithmetic is readily achieved by choosing a least-misfit convolution function of width W = 7 and an image cropping parameter of x0 = 0.25. If the accuracy required is only that attained by the original W-stacking method, the computational cost for both the gridding and Fast Fourier Transform steps can be substantially reduced using the proposed method by making an appropriate choice of the width and image cropping parameters.
G17.8 + 16.7: A new supernova remnant
Authors: Araya M , Hurley-Walker N , Quirós-Araya S 
Published: December 2021

ABSTRACT
Non-thermal radio emission is detected in the region of the gamma-ray source FHES J1723.5 − 0501. The emission has an approximately circular shape 0.8° in diameter. The observations confirm its nature as a new supernova remnant, G 17.8 + 16.7. We derive constraints on the source parameters using the radio data and gamma-ray observations of the region. The distance to the object is possibly in the range 1.4–3.5 kpc. An SNR age of the order of 10 kyr is compatible with the radio and GeV features, but an older or younger SNR cannot be ruled out. A simple one-zone leptonic model naturally explains the multi-wavelength non-thermal fluxes of the source at its location outside the Galactic plane.
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells
Authors: Späth Gerald F , Bussotti Giovanni 
Published: December 2021

AbstractGenome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.
RNA self-splicing by engineered hairpin ribozyme variants
Authors: Hieronymus Robert , Zhu Jikang , Müller Sabine 
Published: December 2021

Abstract
Small RNAs capable of self-cleavage and ligation might have been the precursors for the much more complex self-splicing group I and II introns in an early RNA world. Here, we demonstrate the activity of engineered hairpin ribozyme variants, which as self-splicing introns are removed from their parent RNA. In the process, two cleavage reactions are supported at the two intron-exon junctions, followed by ligation of the two generated exon fragments. As a result, the hairpin ribozyme, here acting as the self-splicing intron, is cut out. Two self-splicing hairpin ribozyme variants were investigated, one designed by hand, the other by a computer-aided approach. Both variants perform self-splicing, generating a cut-out intron and ligated exons.
CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates
Authors: Lee Ryanggeun , Kang Moo-Koo , Kim Yong-Jin , Yang Bobae , Shim Hwanyong , Kim Sugyung , Kim Kyungwoo , Yang Chul Min , Min Byeong-gyu , Jung Woong-Jae , Lee Eun-Chong , Joo Jung-Sik , Park Gunhee , Cho Won-Ki , Kim Hyoung-Pyo 
Published: December 2021

Abstract
CTCF is crucial to the organization of mammalian genomes into loop structures. According to recent studies, the transcription apparatus is compartmentalized and concentrated at super-enhancers to form phase-separated condensates and drive the expression of cell-identity genes. However, it remains unclear whether and how transcriptional condensates are coupled to higher-order chromatin organization. Here, we show that CTCF is essential for RNA polymerase II (Pol II)-mediated chromatin interactions, which occur as hyperconnected spatial clusters at super-enhancers. We also demonstrate that CTCF clustering, unlike Pol II clustering, is independent of liquid-liquid phase-separation and resistant to perturbation of transcription. Interestingly, clusters of Pol II, BRD4, and MED1 were found to dissolve upon CTCF depletion, but were reinstated upon restoration of CTCF, suggesting a potent instructive function for CTCF in the formation of transcriptional condensates. Overall, we provide evidence suggesting that CTCF-mediated chromatin looping acts as an architectural prerequisite for the assembly of phase-separated transcriptional condensates.
PAGEANT: personal access to genome and analysis of natural traits
Authors: Huang Jie , Liang Zhi-Sheng , Pallotti Stefano , Ranson Janice M , Llewellyn David J , Zheng Zhi-Jie , King Daniel A , Zhou Qiang , Zheng Houfeng , Napolioni Valerio 
Published: December 2021

Abstract
GWASs have identified numerous genetic variants associated with a wide variety of diseases, yet despite the wide availability of genetic testing the insights that would enhance the interpretability of these results are not widely available to members of the public. As a proof of concept and demonstration of technological feasibility, we developed PAGEANT (Personal Access to Genome & Analysis of Natural Traits), usable through Graphical User Interface or command line-based version, aiming to serve as a protocol and prototype that guides the overarching design of genetic reporting tools. PAGEANT is structured across five core modules, summarized by five Qs: (i) quality assurance of the genetic data; (ii) qualitative assessment of genetic characteristics; (iii) quantitative assessment of health risk susceptibility based on polygenic risk scores and population reference; (iv) query of third-party variant databases (e.g. ClinVAR and PharmGKB) and (v) quick Response code of genetic variants of interest. Literature review was conducted to compare PAGEANT with academic and industry tools. For 2504 genomes made publicly available through the 1000 Genomes Project, we derived their genomic characteristics for a suite of qualitative and quantitative traits. One exemplary trait is susceptibility to COVID-19, based on the most up-to-date scientific findings reported.
Beyond Gutka: Evidence of Illegal Smokeless Tobacco in Rural and Semi-urban Areas in India
Authors: Welding Kevin , Saraf Sejal , Iacobelli Michael , Smith Katherine Clegg , Puntambekar Namrata , Gupta Prakash C , Cohen Joanna E 
Published: December 2021

Abstract

Introduction
Gutka, a popular smokeless tobacco (SLT) product combining chewing tobacco, areca nut, and spices, was banned by states in India beginning in 2012. Gutka can be recreated by the user mixing twin packets of tobacco and spice mixtures. We examine the availability of premixed gutka, the sale of twin packets (chewing tobacco and spice mixture sold together but in separate packets) and whether SLT was sold without legally mandated health warning labels (HWLs), without the printed maximum retail price (MRP), and above the MRP.

Aims and Methods
In October/November of 2017, unique SLT packets were purchased using a systematic protocol in 25 localities with populations under 50 000 across five Indian states. Purchase information (location, twin packets, price paid) and packaging information (SLT type, printed MRP, type of HWL) were used to assess legality.

Results
Of the 240 purchases of unique SLT packets, three were premade gutka. Twin packets were half of the sample, sold in every state, and illegally sold in Maharashtra where they were banned. Over half (62%) of single packets and 27% of twin packets did not feature a legal HWL. While only 5% of packets did not have a printed MRP, 29% of single packets, and 38% of twin packets were sold illegally for more than the MRP.

Conclusions
SLT without the proper HWL or sold above the MRP were common. Twin packets were widely available. India should consider a country-wide restriction to ban single serving tobacco packets that would decrease affordability.

Implications
This study is the earliest and that first outside of Mumbai that we are aware of to present evidence of tobacco products being sold above the MRP in India. While finding little evidence of premade gutka being sold, we found twin packets (chewing tobacco and spice mixture packets sold together) are widely available even in Maharashtra, which has a policy in place to ban twin packets. This study also finds evidence of SLT products sold without the correct HWL and without a MRP listed which shows that implementation and enforcement of regulations are as important as passing regulations.
Preliminary Evaluation of Short-Term Abstinence Effects Among Never-Smoking Experienced Users of Modern Electronic Cigarettes
Authors: Felicione Nicholas J , Douglas Ashley E , McClernon F Joseph , Blank Melissa D 
Published: December 2021

Abstract

Introduction
ECIG use has increased among non-smokers, with the potential negative consequence of developing nicotine dependence. ECIG users report withdrawal symptoms upon abstinence, though the significance of these symptoms has been questioned. This preliminary study aimed to characterize the early timecourse of ECIG withdrawal under forced abstinence.

Methods
Fifteen never-smoking ECIG users completed two conditions whereby participants either abstained from ECIG use (abstinence) or used their own ECIG (ad lib) for 3 h. Puff topography in this latter condition was measured via video observation. Outcome measures included heart rate, subjective ratings of withdrawal, cognitive performance, and choice behavior.

Results
Heart rate was lower during abstinence compared to ad lib use (F = 12.60, p &lt; .01, ƞp2 = 0.47). Higher levels of craving (F = 4.98, p &lt; .05, ƞp2 = 0.26) and lower levels of nicotine effects (e.g., dizzy, F = 4.62, p &lt; .05, ƞp2 = 0.36) were reported during abstinence compared to ad lib use. Interaction effects were observed for both factors of the Questionnaire of Smoking Urges: Brief (Fs &gt; 3.56, ps &lt; .05, ƞp2s = 0.21–0.27), with factor scores increasing from baseline to 90 min in the abstinent condition only. Inhibitory control was impaired at 120 min in the abstinent condition only (F = 7.51, p &lt; .05, ƞp2 = 0.50).

Conclusions
Never-smoking ECIG users experienced aversive withdrawal symptoms within 2–3 h of abstinence. Future work should include other control conditions, such as placebo ECIGs or nicotine replacement therapy, and biomarkers of nicotine exposure, as well as examine withdrawal as a function of device type.

Implications
Never-smoking ECIG users experience some aversive nicotine withdrawal symptoms within two to three hours of abstinence. Relative to ad lib ECIG use, abstinence decreased heart rate and inhibitory control, as well as increased subjective ratings of withdrawal such as craving and intention to vape. Those same symptoms might be suppressed by self-administration of ECIGs. Experiencing withdrawal upon abstinence may indicate that ECIGs can cause dependence without a history of other tobacco use.
Adherence to the Mediterranean diet and the risk of lung cancer: a systematic review and dose-response meta-analysis of observational studies
Authors: Bahrami Alireza , Khalesi Saman , Makiabadi Elham , Alibeyk Sepide , Hajigholam-Saryazdi Maryam , Hejazi Ehsan 
Published: December 2021

AbstractContextThe literature supports the protective role of the Mediterranean diet (MD) in the prevention of some types of cancer, such as colorectal and liver cancer. The link between the MD and lung cancer, however, is still unclear.ObjectiveThe aim of this systematic review and meta-analysis was to investigate the association between the MD and risk of lung cancer.Data SourcesElectronic databases (PubMed, Scopus, Embase, and Web of Science) were searched up to May 2021.Study SelectionCase-control and cohort studies reporting the association between intake of the MD and risk of lung cancer and with accessible full texts published in English were included. Review articles, laboratory and animal studies, abstracts, letters to the editor, and studies lacking sufficient data were excluded.Data ExtractionThe risk ratio (RR) was extracted from eligible studies, and meta-analysis was performed to calculate the pooled RR of the included studies.ResultsNine studies (8 cohort, 1 case-control) were included in the meta-analysis. High adherence to the MD was associated with a lower likelihood of lung cancer compared with low adherence (RR = 0.84; 95%CI, 0.77–0.91; I2 = 52%, heterogeneity P = 0.03). Dose-response analysis showed that a 2-score increment in MD adherence was associated with a 6% lower risk of lung cancer (RR = 0.94; 95%CI, 0.91–0.96; nonlinearity P = 0.97). Subgroup analyses showed a protective association between MD adherence and risk of lung cancer among former smokers (n = 3 studies) (RR = 0.81; 95%CI, 0.74–0.89), but no significant association was observed for never smokers (n = 3 studies) (RR = 0.78; 95%CI, 0.29–2.07) or current smokers (n = 3 studies) (RR = 0.82; 95%CI, 0.58–1.16). In addition, an inverse association between the MD and lung cancer was observed in both males (RR = 0.84; 95%CI, 0.74–0.96) and females (RR = 0.87; 95%CI, 0.77–0.98).ConclusionsHigh adherence to the MD is associated with a lower risk of lung cancer, especially in former smokers.Systematic Review RegistrationPROSPERO registration no. CRD42019146460.
Opposing views: associations of political polarization, political party affiliation, and social trust with COVID-19 vaccination intent and receipt
Authors: Dolman Andrew J , Fraser Timothy , Panagopoulos Costas , Aldrich Daniel P , Kim Daniel 
Published: December 2021

AbstractIntroductionPolitical polarization has increased in the USA within recent years. Studies have shown Republicans are less likely to accept COVID-19 vaccinations than Democrats; however, little is known regarding the association between COVID-19 vaccination acceptance and political polarization.MethodsWe used data from a nationally-representative survey of 1427 participants conducted between 9 February 2021 and 17 February 2021. We estimated multivariate-adjusted odds ratios for COVID-19 vaccination intent and receipt according to perceived political polarization (measured as the perceived size of the ideological gap between Democrats and Republicans), political party affiliation, and social trust, controlling for demographic and socioeconomic factors.ResultsAmong participants perceiving high levels of polarization, Republicans (versus Democrats) reported a 90% lower odds of vaccination intent (OR = 0.10 [0.05, 0.19], P &lt; 0.001). Participants with high (versus low) social trust and low perceived polarization had a 2-folder higher vaccination intent (OR = 2.39 [1.34, 4.21], P = 0.003); this association was substantially weaker in the high perceived polarization group.ConclusionsHigh perceived levels of political polarization appear to magnify the decrease in the odds of receiving the COVID-19 vaccine and the intent to get vaccinated among Republicans versus Democrats. Political polarization may further attenuate the protective associations of high social capital with vaccination.