bluuebunny/crossref_metadata_2025_split huggingface dataset:
The peculiar galaxy HRG 705: A possible on-going merging?
Authors: Wenderoth E , Faúndez-Abans M , da Rocha-Poppe P C , de Oliveira-Abans M , Krabbe A C , Fernandes-Martin V A 
Published: June 2022

ABSTRACT
We report the results of the first spectroscopic study of the galaxy HRG 705, which belongs to the Solitaire class of peculiar (collisional) Ring Galaxies, which, in turn, are little studied. The nuclear emission-line spectrum resembles that of a star-forming galaxy (H ii galaxy), with $\boldsymbol z = 0.0305$ and heliocentric velocity of $v = 9\, 144\, \pm \, 36~ {\rm km\, s}^{-1}$. The nuclear region is dominated by intermediate and old stellar populations, in addition to a contribution of 8 per cent of young stars. Based on the complex velocity profile along the slit position angle of 59°, we suggest that the nuclear region is composed by two bodies in gravitational interaction (a possible on-going merging). Analysis of the surface brightness distribution confirmed the existence of the second body, a probable intruder, which lies inside a central pseudo-bulge/disc. HRG 705 does not appear to be oxygen-rich, but it is slightly more (O/H)-enriched than the galaxies of our nearby Universe.
Accurate Identification of Subclones in Tumor Genomes
Authors: Ahmadinejad Navid , Troftgruben Shayna , Wang Junwen , Chandrashekar Pramod B , Dinu Valentin , Maley Carlo , Liu Li 
Published: June 2022

AbstractUnderstanding intratumor heterogeneity is critical for studying tumorigenesis and designing personalized treatments. To decompose the mixed cell population in a tumor, subclones are inferred computationally based on variant allele frequency (VAF) from bulk sequencing data. In this study, we showed that sequencing depth, mean VAF, and variance of VAF of a subclone are confounded. Without considering this effect, current methods require deep-sequencing data (&gt;300× depth) to reliably infer subclones. Here, we present a novel algorithm that incorporates depth-variance and mean-variance dependencies in a clustering error model and successfully identifies subclones in tumors sequenced at depths of as low as 30×. We implemented the algorithm as a model-based adaptive grouping of subclones (MAGOS) method. Analyses of computer simulated data and empirical sequencing data showed that MAGOS outperformed existing methods on minimum sequencing depth, decomposition accuracy, and computation efficiency. The most prominent improvements were observed in analyzing tumors sequenced at depths between 30× and 200×, whereas the performance was comparable between MAGOS and existing methods on deeply sequenced tumors. MAGOS supports analysis of single-nucleotide variants and copy number variants from a single sample or multiple samples of a tumor. We applied MAGOS to whole-exome data of late-stage liver cancers and discovered that high subclone count in a tumor was a significant risk factor of poor prognosis. Lastly, our analysis suggested that sequencing multiple samples of the same tumor at standard depth is more cost-effective and robust for subclone characterization than deep sequencing a single sample. MAGOS is available at github (https://github.com/liliulab/magos).
Synthesis of the NarP response regulator of nitrate respiration in Escherichia coli is regulated at multiple levels by Hfq and small RNAs
Authors: Brosse Anaïs , Boudry Pierre , Walburger Anne , Magalon Axel , Guillier Maude 
Published: June 2022

Abstract
Two-component systems (TCS) and small RNAs (sRNA) are widespread regulators that participate in the response and the adaptation of bacteria to their environments. TCSs and sRNAs mostly act at the transcriptional and post-transcriptional levels, respectively, and can be found integrated in regulatory circuits, where TCSs control sRNAs transcription and/or sRNAs post-transcriptionally regulate TCSs synthesis. In response to nitrate and nitrite, the paralogous NarQ-NarP and NarX-NarL TCSs regulate the expression of genes involved in anaerobic respiration of these alternative electron acceptors to oxygen. In addition to the previously reported repression of NarP synthesis by the SdsN137 sRNA, we show here that RprA, another Hfq-dependent sRNA, also negatively controls narP. Interestingly, the repression of narP by RprA actually relies on two independent mechanisms of control. The first is via the direct pairing of the central region of RprA to the narP translation initiation region and presumably occurs at the translation initiation level. In contrast, the second requires only the very 5′ end of the narP mRNA, which is targeted, most likely indirectly, by the full-length or the shorter, processed, form of RprA. In addition, our results raise the possibility of a direct role of Hfq in narP control, further illustrating the diversity of post-transcriptional regulation mechanisms in the synthesis of TCSs.
Migrating bubble synthesis promotes mutagenesis through lesions in its template
Authors: Osia Beth , Twarowski Jerzy , Jackson Tyler , Lobachev Kirill , Liu Liping , Malkova Anna 
Published: June 2022

Abstract
Break-induced replication (BIR) proceeds via a migrating D-loop for hundreds of kilobases and is highly mutagenic. Previous studies identified long single-stranded (ss) nascent DNA that accumulates during leading strand synthesis to be a target for DNA damage and a primary source of BIR-induced mutagenesis. Here, we describe a new important source of mutagenic ssDNA formed during BIR: the ssDNA template for leading strand BIR synthesis formed during D-loop migration. Specifically, we demonstrate that this D-loop bottom template strand (D-BTS) is susceptible to APOBEC3A (A3A)-induced DNA lesions leading to mutations associated with BIR. Also, we demonstrate that BIR-associated ssDNA promotes an additional type of genetic instability: replication slippage between microhomologies stimulated by inverted DNA repeats. Based on our results we propose that these events are stimulated by both known sources of ssDNA formed during BIR, nascent DNA formed by leading strand synthesis, and the D-BTS that we describe here. Together we report a new source of mutagenesis during BIR that may also be shared by other homologous recombination pathways driven by D-loop repair synthesis.
Structural and dynamic studies of DNA recognition by NF-κB p50 RHR homodimer using methyl NMR spectroscopy
Authors: Singh Amrinder , Martinez-Yamout Maria A , Wright Peter E , Dyson H Jane 
Published: June 2022

Abstract
Protein dynamics involving higher-energy sparsely populated conformational substates are frequently critical for protein function. This study describes the dynamics of the homodimer (p50)2 of the p50 Rel homology region (RHR) of the transcription factor NF-κB, using 13C relaxation dispersion experiments with specifically (13C, 1H)-labeled methyl groups of Ile (δ), Leu and Val. Free (p50)2 is highly dynamic in solution, showing μs-ms relaxation dispersion consistent with exchange between the ground state and higher energy substates. These fluctuations propagate from the DNA-binding loops through the core of the domain. The motions are damped in the presence of κB DNA, but the NMR spectra of the DNA complexes reveal multiple local conformations of the p50 RHR homodimer bound to certain κB DNA sequences. Varying the length and sequence of κB DNA revealed two factors that promote a single bound conformation for the complex: the length of the κB site in the duplex and a symmetrical sequence of guanine nucleotides at both ends of the recognition motif. The dynamic nature of the DNA-binding loops, together with the multiple bound conformations of p50 RHR with certain κB sites, is consistent with variations in the transcriptional activity of the p50 homodimer with different κB sequences.
Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides
Authors: Sui Yang , Epstein Anastasiya , Dominska Margaret , Zheng Dao-Qiong , Petes Thomas D , Klein Hannah L 
Published: June 2022

Abstract
Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term ‘ribodysgenesis’. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.
Lithium-plasmon-based low-powered dynamic color display
Authors: Liang Jie , Jin Yan , Yu Huiling , Chen Xinjie , Zhou Lin , Huo Pengcheng , Zhang Ye , Ma Haiyang , Jiang Yi , Zhu Bin , Xu Ting , Liu Hui , Zhu Shining , Zhu Jia 
Published: June 2022

ABSTRACTDisplay and power supply have been two essential and independent cornerstones of modern electronics. Here, we report a lithium-plasmon-based low-powered dynamic color display with intrinsic dual functionality (plasmonic display and energy recycling unit) which is a result of the electric-field-driven transformation of nanostructured lithium metals. Dynamic color displays are enabled by plasmonic transformation through electrodeposition (electrostripping) of lithium metals during the charging (discharging) process, while the consumed energy for coloring can be retrieved in the inverse process respectively. Energy recycling of lithium metals brings energy consumption down to 0.390 mW cm−2 (0.105 mW cm−2) for the active (static) coloration state of a proof-of-concept display/battery device, which approaches nearly-zero-energy-consumption in the near-100%-energy-efficiency limit of commercial lithium batteries. Combining the subwavelength feature of plasmonics with effective energy recycling, the lithium-plasmon-based dynamic display offers a promising route towards next-generation integrated photonic devices, with the intriguing advantages of low energy consumption, a small footprint and high resolution.
Impact of the Tips From Former Smokers Anti-Smoking Media Campaign on Youth Smoking Behaviors and Anti-Tobacco Attitudes
Authors: Slocum Elizabeth , Xie Yanmei , Colston David C , Emery Sherry , Patrick Megan E , Thrasher James F , Elliott Michael R , Fleischer Nancy L 
Published: June 2022

AbstractIntroductionAnti-tobacco media campaigns can prevent youth smoking, but there is little research on how adult-targeted campaigns affect youth. We investigated the association between the Tips From Former Smokers (Tips) campaign and youth smoking behaviors and anti-tobacco attitudes, and variation by sex, race and/or ethnicity, or socioeconomic status.Aims and MethodsWe used data from the monitoring of the future study, a nationally representative survey on 8th, 10th, and 12th graders, from 2013–2015. Quartiles of Tips gross rating points (GRPs) were used to estimate exposure. Youth smoking behavior outcomes included smoking prevalence, initiation, and susceptibility. The anti-tobacco attitude outcomes included the extent that anti-tobacco ads made participants (1) less favorable towards smoking or (2) less likely to smoke cigarettes. Modified Poisson regression models estimated average marginal effects; separate additive interactions between Tips GRP exposure and sex, race and/or ethnicity, parents’ highest education, and college plans (12th graders only) were used to test for effect modification.ResultsTips GRPs were not associated with smoking behaviors within any grade. However, 12th graders in the highest quartile of Tips had a 7.0 percentage point higher probability (95% CI = 0.023–0.116) of responding that anti-tobacco ads made them less likely to smoke. Tips GRPs were associated with a lower probability of past 30-day smoking prevalence among 10th grade females, but not males (joint P-value = .002). No additional statistically significant interactions were found for any other outcomes for any grade.ConclusionsThis study revealed the potential for adult-targeted campaigns to increase youth’s anti-smoking attitudes, but campaign exposure was not associated with smoking behaviors.ImplicationsFew studies have examined the potential for anti-smoking media campaigns to influence audiences outside their targeted audience. In this study, we show the potential for adult-targeted campaigns to impact youth and suggest that Tips exposure may promote anti-smoking attitudes among youth.
Effect of Social Determinants of Health on Uncontrolled Human Immunodeficiency Virus (HIV) Infection Among Persons With HIV in San Francisco, California
Authors: Melo Jason S , Hessol Nancy A , Pipkin Sharon , Buchbinder Susan P , Hsu Ling C 
Published: June 2022

Abstract

Background
In 2010–2014, the San Francisco Department of Public Health (SFDPH) established programs to rapidly link people with human immunodeficiency virus (PWH) to care and offer antiretroviral therapy (ART) at human immunodeficiency virus (HIV) diagnosis. Such programs reduced the number of PWH out of care or with detectable HIV viral load (ie, uncontrolled HIV infection). We investigated the role of social determinants of health (SDH) on uncontrolled HIV.

Methods
Cross-sectional data from adult PWH diagnosed and reported to the SFDPH as of December 31, 2019, prescribed ART, and with confirmed San Francisco residency during 2017–2019 were analyzed in conjunction with SDH metrics derived from the American Community Survey 2015–2019. We focused on 5 census tract-level SDH metrics: percentage of residents below the federal poverty level, with less than a high school diploma, or uninsured; median household income; and Gini index. We compared uncontrolled HIV prevalence odds ratios (PORs) across quartiles of each metric independently using logistic regression models.

Results
The analysis included 7486 PWH (6889 controlled HIV; 597 uncontrolled HIV). Unadjusted PORs of uncontrolled HIV rose with increasingly marginalized quartiles, compared to the least marginalized quartile for each metric. Adjusting for demographics and transmission category, the POR for uncontrolled HIV for PWH in the most marginalized quartile remained significant across metrics for poverty (POR = 2.0; confidence interval [CI] = 1.5–2.6), education (POR = 2.4; CI = 1.8–3.2), insurance (POR = 1.8; CI = 1.3–2.5), income (POR = 1.8; CI = 1.4–2.3), and income inequality (POR = 1.5; CI = 1.1–2.0).

Conclusions
Beyond demographics, SDH differentially affected the ability of PWH to control HIV. Despite established care programs, PWH experiencing socioeconomic marginalization require additional support to achieve health outcome goals.
Gyrohydrodynamics: Relativistic spinful fluid with strong vorticity
Authors: Cao Zheng , Hattori Koichi , Hongo Masaru , Huang Xu-Guang , Taya Hidetoshi 
Published: June 2022

Abstract
We develop a relativistic (quasi-)hydrodynamic framework, dubbed gyrohydrodynamics, to describe the fluid dynamics of many-body systems with spin under strong vorticity based on entropy-current analysis. This framework generalizes the recently developed spin hydrodynamics to the regime where the spin density is at the leading order in derivatives but suppressed by another small parameter, the Planck constant ℏ, due to its quantum nature. Our analysis shows that the complete first-order constitutive relations of gyrohydrodynamics involve 17 transport coefficients and are highly anisotropic.
The Sleep Well Baby project: an automated real-time sleep–wake state prediction algorithm in preterm infants
Authors: Sentner Thom , Wang Xiaowan , de Groot Eline R , van Schaijk Lieke , Tataranno Maria Luisa , Vijlbrief Daniel C , Benders Manon J N L , Bartels Richard , Dudink Jeroen 
Published: June 2022

Abstract

Study Objectives
Sleep is an important driver of early brain development. However, sleep is often disturbed in preterm infants admitted to the neonatal intensive care unit (NICU). We aimed to develop an automated algorithm based on routinely measured vital parameters to classify sleep–wake states of preterm infants in real-time at the bedside.

Methods
In this study, sleep–wake state observations were obtained in 1-minute epochs using a behavioral scale developed in-house while vital signs were recorded simultaneously. Three types of vital parameter data, namely, heart rate, respiratory rate, and oxygen saturation, were collected at a low-frequency sampling rate of 0.4 Hz. A supervised machine learning workflow was used to train a classifier to predict sleep–wake states. Independent training (n = 37) and validation datasets were validation n = 9) datasets were used. Finally, a setup was designed for real-time implementation at the bedside.

Results
The macro-averaged area-under-the-receiver-operator-characteristic (AUROC) of the automated sleep staging algorithm ranged between 0.69 and 0.82 for the training data, and 0.61 and 0.78 for the validation data. The algorithm provided the most accurate prediction for wake states (AUROC = 0.80). These findings were well validated on an independent sample (AUROC = 0.77).

Conclusions
With this study, to the best of our knowledge, a reliable, nonobtrusive, and real-time sleep staging algorithm was developed for the first time for preterm infants. Deploying this algorithm in the NICU environment may assist and adapt bedside clinical work based on infants’ sleep–wake states, potentially promoting the early brain development and well-being of preterm infants.
Association of sleep quality, media use and book reading with behavioral problems in early childhood. The Ulm SPATZ Health Study
Authors: Ricci C , Poulain T , Keil J , Rothenbacher D , Genuneit J 
Published: June 2022

AbstractStudy ObjectivesThe objective of the study was to investigate the association of sleep quality, media use and book reading on internalizing, externalizing and prosocial behavior in early childhood.MethodsIn this cross-sectional study, we investigated a data set consisting of three consecutive yearly waves of the prospective Ulm SPATZ Health Study, conducted in southern Germany with 565, 496, and 421 children of 4–6 years of age, respectively.Standardized effects of the overall score and subscales of the Children’s Sleep Habits Questionnaire, parent-reported child media use and book reading as well as their interaction term on the total score of the Strengths and Difficulties Questionnaire along with its externalizing, internalizing and prosocial subscales were estimated by multivariate adjusted random intercept mixed models.ResultsOverall sleep quality was associated more with internalizing than externalizing behavior; parasomnias associated with both behaviors. Night waking and sleep anxiety associated only with internalizing behavior. High levels of media use were associated with less internalizing behavior. More book reading resulted in less externalizing and internalizing behavior but more prosocial behavior. Finally, book reading and media use do not interact to determine child’s behavior.ConclusionsThe current work supports a strategy of monitoring sleep quality, reducing media use and promoting book reading in order to avoid behavioral problems in early childhood.
A montane species treeline is defined by both temperature and drought effects on growth season length
Authors: Bar-On Peleg , Yaakobi Assaf , Moran Uri , Rozenstein Offer , Kopler Idan , Klein Tamir 
Published: June 2022

AbstractMontane treelines are defined by a threshold low temperature. However, what are the dynamics when the snow-free summer growth season coincides with a 6-month seasonal drought? We tested this fundamental question by measuring tree growth and leaf activity across elevations in Mt Hermon (2814 m; in Israel and Syria), where oak trees (Quercus look and Quercus boissieri) form an observed treeline at 1900 m.While in theory, individuals can be established at higher elevations (minimum daily temperature &gt;6.5 °C for &gt;4 months even at the summit), soil drying and vapor pressure deficit in summer enforces growth cessation in August, leaving only 2–3 months for tree growth. At lower elevations, Q. look Kotschy is replaced by Quercus cerris L. (1300 m) and Quercus calliprinos Webb (1000 m) in accompanying Q. boissieri Reut., and growth season length (GSL) is longer due to an earlier start in April. Leaf gas exchange continues during autumn, but assimilates are no longer utilized in growth. Interestingly, the growth and activity of Q. boissieri were equivalent to that of each of the other three species across the ~1 km elevation gradient. A planting experiment at 2100 m showed that seedlings of the four oak species survived the cold winter and showed budding of leaves in summer, but wilted in August. Our unique mountain site in the Eastern Mediterranean introduces a new factor to the formation of treelines, involving a drought limitation on GSL. This site presents the elevation edge for each species and the southern distribution edge for both the endemic Q. look and the broad-range Q. cerris. With ongoing warming, Q. look and Q. boissieri are slowly expanding to higher elevations, while Q. cerris is at risk of future extirpation.
Changes in Alcohol Consumption by Beverage Type Attributable to the COVID-19 Pandemic for 10 States, March 2020 to November 2020: An Ecological Simulation-based Analysis
Authors: Pytell Jarratt D. , Thakrar Ashish P. , Chander Geetanjali , Colantuoni Elizabeth 
Published: June 2022

Objectives
Consumption of high potency alcohol is associated with greater healthcare burden, yet little attention has been placed on the change in types of alcohol consumed during the COVID-19 pandemic. We estimate the change in alcohol consumption by beverage type attributable to the COVID-19 pandemic.

Methods
The National Institute on Alcohol Abuse and Alcoholism provided apparent alcohol consumption (“consumption”) by beverage type for 10 states for January 2017 through November 2020 based on sales and tax data. The 38-month period to February 2020 was used to train quasi-Poisson regression models. The models then predicted the monthly consumption based on the historical trends in the absence of the COVID-19 pandemic from March through November 2020. The difference between the observed and predicted is the change in consumption attributable to the COVID-19 pandemic.

Results
Beyond what was expected based on historical trends, spirits consumption increased significantly for 6 states (Colorado, Massachusetts, Missouri, North Dakota, Minnesota, and Tennessee) ranging from 4% (95% confidence interval [CI] 1%–6%) to 17% (95% CI 6%–28%) which is equivalent to 7 (95% CI 2–18) to 32 95% CI 12–48) excess standard spirits drinks per-capita; Alaska, Florida, Illinois, and Kentucky had no significant change. Wine consumption increased 10% (95% CI 3%–18%) in Colorado and 8% (95% CI 3%–12%) in Tennessee. Wine consumption in Alaska decreased 6% (95% CI, 3%–10%) and beer consumption decreased 8% (95% CI 4%–11%).

Conclusions
During the COVID-19 pandemic, spirits consumption increased relative to wine and beer. Increased consumption of higher potency alcohol beverages could lead to higher alcohol-related healthcare and societal burden.