bluuebunny/crossref_metadata_2025_split huggingface dataset:
Umbral flashes and their association with running penumbral waves: a study using MAST Ca ii 8542 Å narrow-band observations
Authors: Dubey Sandeep K , Mathew Shibu K , Bayanna A Raja 
Published: October 2024

ABSTRACT
Umbral flashes (UFs) are one of the most dynamic phenomena observed in the sunspot umbra at the chromospheric heights. In this paper, we present spectroscopic observations of UFs in the Ca ii 8542 Å line recorded by a narrow-band imager working with the Multi-Application Solar Telescope (MAST). The deduced data are analysed to obtain various properties of the UFs occuring at different locations inside the umbral boundary. An intensity enhancement of up to 30% or more was observed at the location of UFs, with a periodicity $\approx$3 min. The line-of-sight (LOS) velocity of UFs was estimated using bisector application to the emission profile resulting from the removal of mean umbral and the mean quiet Sun (QS) line profiles. The emission profiles resulting from removing the mean umbral profile were observed to better represent the emission component of the UF line profile. Both up-flows and down-flows of the order $\approx$5 km s$^{-1}$ were associated with the UFs with an average up-flow of $\approx$1 km s$^{-1}$. Out of all UFs analysed, 31% were observed to be associated with down-flows in case of removal of the mean umbral profile from the UF line profile. We observed multiple radially propagating LOS velocity disturbances ($\approx$20–40 km s$^{-1}$) in the penumbra, which might be associated with the UFs, even though we could not establish a one-to-one correspondence. The horizontally propagating LOS velocity disturbances could produce the visual effect of running penumbral waves, which produce intensity fluctuations in intensity images when observed at the line-centre wavelength. The simultaneous photospheric HMI observations showed no distinct intensity or velocity signatures corresponding to the UFs observed in the chromospheric Ca ii 8542 Å line.
Genomic and Acoustic Biogeography of the Iconic Sulphur-crested Cockatoo Clarifies Species Limits and Patterns of Intraspecific Diversity
Authors: Sands Arthur F , Andersson Astrid A L , Reid Kerry , Hains Taylor , Joseph Leo , Drew Alex , Mason Ian J , Rheindt Frank E , Dingle Caroline , Merilä Juha 
Published: October 2024

Abstract
Many highly recognizable species lack genetic data important for conservation due to neglect over their hyperabundance. This likely applies to the Sulfur-crested Cockatoo (Cacatua galerita), one of the world's most iconic parrots. The species is native to Australia, New Guinea, and some surrounding Melanesian islands of the latter. Four subspecies are currently recognised based on morphology. Australian subspecies and populations are abundant, but several factors threaten those in New Guinea and Melanesia. Genetic data from natural populations are scarce—information that is vital to identifying evolutionarily significant units (ESUs) important for modern conservation planning. We used whole-genome resequencing to investigate patterns of differentiation, evolutionary affinities, and demographic history across C. galerita's distribution range to assess whether currently recognised subspecies represent ESUs. We complement this with an assessment of bioacoustic variation across the species' distribution landscape. Our results point to C. galerita sensu lato (s.l.) comprising two species. We restrict C. galerita sensu stricto (s.s.) to populations in Australia and the Trans-Fly ecodomain of southern New Guinea. The second species, recognised here as Cacatua triton, likely occurs over much of the rest of New Guinea. Restricting further discussion of intraspecific diversity in C. triton, we show that within C. galerita s.s. two ESUs exist, which align to Cacatua galerita galerita in eastern Australia and southern New Guinea and Cacatua galerita fitzroyi in northern and north-western Australia. We suggest that the evolution of these species and ESUs are linked to Middle and Late Pleistocene glacial cycles and their effects on sea level and preferential habitats. We argue that conservation assessments need updating, protection of preferential forest and woodland habitats are important and reintroductions require careful management to avoid possible negative hybridization effects of non-complementary lineages.
Nitrogen fertilizers activate siderophore production by the common scab causative agent Streptomyces scabiei
Authors: Stulanovic Nudzejma , Kerdel Yasmine , Belde Loïc , Rezende Lucas , Deflandre Benoit , Burguet Pierre , Denoel Romane , Tellatin Déborah , Rigolet Augustin , Hanikenne Marc , Quinton Loïc , Ongena Marc , Rigali Sébastien 
Published: October 2024

Abstract
Streptomyces scabiei is the causative agent of common scab on root and tuber crops. Life in the soil imposes intense competition between soil-dwelling microorganisms, and we evaluated here the antimicrobial properties of S. scabiei. Under laboratory culture conditions, increasing peptone levels correlated with increased growth inhibitory properties of S. scabiei. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in growth inhibition. Mass spectrometry imaging further confirmed that the zones of secreted siderophores and growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to increased microbial growth. Replacement of peptone by natural nitrogen sources regularly used as fertilizers such as ammonium nitrate, ammonium sulfate, sodium nitrate, and urea also triggered siderophore production in S. scabiei. The observed effect is not mediated by alkalinization of the medium as increasing the pH without providing additional nitrogen sources did not induce siderophore production. The nitrogen-induced siderophore production also inhibited the growth of important plant pathogens. Overall, our work suggests that not only the iron availability but also the nitrogen fertilizer sources could significantly impact the competition for iron between crop-colonizing microorganisms.
RNase W, a conserved ribonuclease family with a novel active site
Authors: Vayssières Marlène , Jüttner Michael , Haas Karina , Ancelin Aurélie , Marchfelder Anita , Leulliot Nicolas , Ferreira-Cerca Sébastien , Blaud Magali 
Published: October 2024

Abstract
Ribosome biogenesis is a complex process requiring multiple precursor ribosomal RNA (rRNA) cleavage steps. In archaea, the full set of ribonucleases (RNases) involved in rRNA processing remains to be discovered. A previous study suggested that FAU-1, a conserved protein containing an RNase G/E-like protein domain fused to a domain of unknown function (DUF402), acts as an RNase in archaea. However, the molecular basis of this activity remained so far elusive. Here, we report two X-ray crystallographic structures of RNase G/E-like–DUF402 hybrid proteins from Pyrococcus furiosus and Sulfolobus acidocaldarius, at 2.1 and 2.0 Å, respectively. The structures highlight a structural homology with the 5′ RNA recognition domain of Escherichia coli RNase E but no homology with other known catalytic nuclease domains. Surprisingly, we demonstrate that the C-terminal domain of this hybrid protein, annotated as a putative diphosphatase domain, harbors the RNase activity. Our functional analysis also supports a model by which the RNase G/E-like domain acts as a regulatory subunit of the RNase activity. Finally, in vivo experiments in Haloferax volcanii suggest that this RNase participates in the maturation of pre-16S rRNA. Together, our study defines a new RNase family, which we termed the RNase W family, as the first archaea-specific contributor to archaeal ribosome biogenesis.
Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression
Authors: Fan Baochao , Li Yupeng , Wang Yi , Yang Shanshan , Peng Qi , Qian Jiali , Wang Chuanhong , Zhang Xue , Xu Hong , Liu Shiyu , He Wenlong , Zhang Gege , Zhu Xuejiao , Li Yunchuan , Zhao Yongxiang , Hu Mi , Wang Wei , Zhou Jinzhu , Guo Rongli , He Kongwang , Li Bin 
Published: October 2024

Abstract
The precise role of the highly variable coronavirus S protein in modulating innate immune responses remains unclear. In this study, we demonstrated that the mutant strain of swine coronavirus porcine enteric diarrhea virus induced significantly lower levels of double-stranded RNA (dsRNA) accumulation, inhibited protein kinase R (PKR) activation and suppressed stress granule (SG) formation compared with the classical strain. The 29th amino acid at N-terminus of S was identified as the key functional site for regulation of SG formation, and found that mutant S inhibited PKR phosphorylation and SG formation by upregulating adenosine deaminase acting on RNA 1 (ADAR1)-p150. Notably, the Zα domain of ADAR1-p150 was essential for inhibiting SG formation. Upregulation of ADAR1-p150 also reduced accumulation of dsRNA depending on its RNA editing function. Virus rescue confirmed that the mutant carrying a substitution at amino acid 29 failed to induce ADAR1-p150, leading to dsRNA accumulation, PKR activation and SG formation. Interestingly, the latest severe acute respiratory syndrome coronavirus-2 strains exhibit a novel 25PPA27 deletion at N-terminus of S that was also shown to lead to altered ADAR1-p150 expression and SG inhibition. The transcription factor TCF7L2 was identified as a player in S-mediated transcriptional enhancement of ADAR1-p150. This study is the first to clarify the crucial role of N-terminus of S in immune regulation of coronaviruses.
Intronic RNA secondary structural information captured for the human MYC pre-mRNA
Authors: Eich Taylor O , O’Leary Collin A , Moss Walter N 
Published: October 2024

Abstract
To address the lack of intronic reads in secondary structure probing data for the human MYC pre-mRNA, we developed a method that combines spliceosomal inhibition with RNA probing and sequencing. Here, the SIRP-seq method was applied to study the secondary structure of human MYC RNAs by chemically probing HeLa cells with dimethyl sulfate in the presence of the small molecule spliceosome inhibitor pladienolide B. Pladienolide B binds to the SF3B complex of the spliceosome to inhibit intron removal during splicing, resulting in retained intronic sequences. This method was used to increase the read coverage over intronic regions of MYC. The purpose for increasing coverage across introns was to generate complete reactivity profiles for intronic sequences via the DMS-MaPseq approach. Notably, depth was sufficient for analysis by the program DRACO, which was able to deduce distinct reactivity profiles and predict multiple secondary structural conformations as well as their suggested stoichiometric abundances. The results presented here provide a new method for intronic RNA secondary structural analyses, as well as specific structural insights relevant to MYC RNA splicing regulation and therapeutic targeting.
Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota
Authors: Liu Lan , Lian Zheng-Han , Lv Ai-Ping , Salam Nimaichand , Zhang Jian-Chao , Li Meng-Meng , Sun Wei-Min , Tan Sha , Luo Zhen-Hao , Gao Lei , Yuan Yang , Ming Yu-Zhen , OuYang Yu-Ting , Li Yu-Xian , Liu Ze-Tao , Hu Chao-Jian , Chen Ying , Hua Zheng-Shuang , Shu Wen-Sheng , Hedlund Brian P , Li Wen-Jun , Jiao Jian-Yu 
Published: October 2024

ABSTRACT
Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood–Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.
Unraveling the Effects of Economic Growth and Unemployment on Tobacco Use: A Panel Data Approach
Authors: Savaş Yunus , Erat Veysel , Alma Savaş Dilek 
Published: October 2024

Abstract

Introduction
The economic situation is recognized as a significant factor influencing tobacco consumption. Accordingly, this research aims to investigate the relationship between economic growth, unemployment, and tobacco use.

Methods
This investigation employs data from 1985 to 2019 to elucidate the relationship between economic growth, unemployment, and tobacco consumption in a select group of Organization for Economic Co-operation and Development countries. Employing Pedroni and Johansen–Fisher panel co-integration tests, we assess the co-integrating relationships. Furthermore, FMOLS and DOLS techniques are applied, complemented by the Dumitrescu–Hurlin panel causality test.

Results
FMOLS and DOLS results suggest that a 1% increase in gross domestic product (GDP) leads to a 6.46% and 7.29% rise in tobacco consumption, respectively, while GDP squared results in a 0.39% and 0.43% decrease. However, both tests failed to establish a significant relationship between tobacco consumption and unemployment. Co-integration was confirmed by Johansen–Fisher and Pedroni tests. Dumitrescu–Hurlin causality tests revealed the direction of Granger causality from economic growth to tobacco consumption, but not with unemployment.

Conclusion
Tobacco consumption declined across all countries studied. Economic growth shows a positive association, while GDP squared has a negative association, indicating an inverted U-shaped relationship. No significant relationship was found with unemployment in the employed tests.

Implications
In addition to the measures implemented by countries to reduce tobacco consumption, economic factors also exert a significant relation with smoking behavior. The available results suggest that economic growth is initially associated with an increase in tobacco consumption but the reduction in later stages indicating a long-term inverse relationship between economic growth and tobacco use.
Comparison of Waning Antibody Responses After Natural Monkeypox Virus Infection and Mpox Vaccination Beyond 6 Months in South Korea
Authors: Lim So Yun , Kim Hyang Su , Yim Hong Soon , Kim Hyesu , Han In Ae , Yoon Doran , Kim Min-Kyung , Kim Yeonjae , Um Jihye , Kim Gayeon , Chin BumSik , Park Jun-Sun , Bang Jihwan 
Published: October 2024

Abstract
Natural Monkeypox virus infection induced significantly higher neutralizing antibody titers than Jynneos vaccination, with similar antibody decay rates beyond 6 months. Jynneos recipients with prior smallpox vaccination showed antibody levels comparable to mpox convalescents.
Quantifying and Adjusting for Confounding From Health-Seeking Behavior and Health Care Access in Observational Research
Authors: Graham Sophie , Walker Jemma L , Andrews Nick , Hulme William J , Nitsch Dorothea , Parker Edward P K , McDonald Helen I 
Published: October 2024

Abstract

Background
Health-seeking behavior and health care access (HSB/HCA) are recognized confounders in many observational studies but are not directly measurable in electronic health records. We used proxy markers of HSB/HCA to quantify and adjust for confounding in observational studies of influenza and COVID-19 vaccine effectiveness (VE).

Methods
This cohort study used primary care data prelinked to secondary care and death data in England. We included individuals aged ≥66 years on 1 September 2019 and assessed influenza VE in the 2019–2020 season and early COVID-19 VE (December 2020–March 2021). VE was estimated with sequential adjustment for demographics, comorbidities, and 14 markers of HSB/HCA. Influenza vaccination in the 2019–2020 season was also considered a negative control exposure against COVID-19 before COVID-19 vaccine rollout.

Results
We included 1 991 284, 1 796 667, and 1 946 943 individuals in the influenza, COVID-19, and negative control exposure populations, respectively. Markers of HSB/HCA were positively correlated with influenza and COVID-19 vaccine uptake. For influenza, adjusting for HSB/HCA markers in addition to demographics and comorbidities increased VE against influenza-like illness from −1.5% (95% CI, −3.2% to .1%) to 7.1% (95% CI, 5.4%–8.7%) with a less apparent trend for more severe outcomes. For COVID-19, adjusting for HSB/HCA markers did not change VE estimates against infection or severe disease (eg, 2 doses of BNT162b2 against infection: 82.8% [95% CI, 78.4%–86.3%] to 83.1% [95% CI, 78.7%–86.5%]). Adjusting for HSB/HCA markers removed bias in the negative control exposure analysis (−7.5% [95% CI, −10.6% to −4.5%] vs −2.1% [95% CI, −6.0% to 1.7%] before vs after adjusting for HSB/HCA markers).

Conclusions
Markers of HSB/HCA can be used to quantify and account for confounding in observational vaccine studies.
Warm winters lead to increased reproductive effort, but lower reproductive success: Hidden costs of climate warming in a threatened bird
Authors: Barve Sahas , Bakley Tori D , Tringali Angela , Fitzpatrick John W , Bowman Reed 
Published: October 2024

ABSTRACT
Climate warming is affecting the phenology and life history of animals around the world. In birds, although warm winters have been shown to advance breeding dates and affect reproductive success in a diverse range of taxa, few studies document whether changes in breeding phenology are associated with variability in reproductive effort by breeders. We leveraged a 37-year dataset on the demography of Aphelocoma coerulescens (Florida Scrub-Jay) to investigate not only whether winter weather affects scrub-jay phenology and reproductive success, but also whether winter weather affects overall reproductive effort. Scrub-jays bred early but fledged fewer offspring in springs following warm winters. Surprisingly, this reduced reproductive success came at the expense of increased reproductive effort (number of nests built, number of eggs laid, and length of the breeding period across all attempts) by the breeders. Given the well-known trade-off between reproductive effort and survival, we highlight an important but typically unrecognized cost of climate warming on birds, as revealed by a long-term study of a large, well-protected population.
Salvaging a Teenage Wasteland
Authors: Finch Andrew J. 
Published: October 2024

Abstract
Recovery high schools have become a key setting supporting the adolescent recovery process over the last fifty years. This book provides the first major historical account of the recovery high school movement from its beginnings in the alternative schools of the 1970s that overlapped with the first adolescent substance use treatment programs. Our understanding of recovery high schools has evolved along with our understanding of addiction and recovery. This work explores the development of the earliest programs in South Carolina, Texas, Maryland, and Minnesota, which served as roots for later growth. The author interviewed dozens of pioneers, including early administrators, teachers, and students, and reviewed hundreds of historical artifacts to trace the creation and expansion of recovery high schools. The story that emerged was closely connected to some of the major events of the times, from the counterculture movement of the 1960s to the Drug War and advent of adolescent treatment in the 1970s to the anti-drug campaigns of the 1980s, such as Just Say No. Cultural touchstones such as Woodstock, school desegregation, high school drug raids, and fear of cults and teenage drug use figured prominently in the creation of recovery high schools, all in an effort to create sober school spaces for teenagers. The programs that evolved are now one of the major components of addressing adolescent mental health and substance use issues.
Carrying the Message
Authors: Finch Andrew J. 
Published: October 2024

Abstract
This chapter provides background of the counterculture movement and its association with youth drug use and explains the evolution of alcohol/drug services in Charleston, South Carolina. Sid Jordan completed a postdoctoral fellowship in San Francisco, encountering the youth drug culture. He worked with diverse clientele as part of a community mental health program and was later hired to develop mental health services in Charleston, where he met D. Ceth Mason, a native South Carolinian and a person in long-term recovery. The text explores how Mason had built an infrastructure for treating both White and Black citizens in a segregated state. Shirley Beckett, a librarian in a Black school, was one of the first people Jordan hired to get trained in substance use counseling. Jordan, Mason, Beckett, and other key stakeholders assured youth substance use programs would be included in a new public family health center, which paved the way for a recovery high school.
Spontaneous Generation
Authors: Finch Andrew J. 
Published: October 2024

Abstract
The first alternative peer group (APG) started in the Palmer Episcopal Church when the rector, Father Charles Wyatt-Brown, asked Bob Meehan to begin meeting with teenagers there. Meehan was trying to get sober, and Father Charlie believed Meehan’s struggles might help young people decide to avoid drug use themselves. The group became known as the Palmer Drug Abuse Program (PDAP), and a local schoolteacher, John Cates, had begun attending gatherings there. Cates started a GED school in his apartment in 1976, and he marketed it to PDAP members, making it the first independent recovery school program. After a few months, PDAP took over the GED school. Other GED schools would open at PDAP satellite programs, but they had closed by 1980, after Cates and Meehan resigned in the wake of negative publicity from the media.
A Lighthouse District
Authors: Finch Andrew J. 
Published: October 2024

Abstract
The main people involved in starting the first recovery high school run by a school district included the Montgomery County, Maryland, police chief, Robert di Grazia; the superintendent, Charles Bernardo; the director of alternative programs, Richard Towers; and a teacher, Brian Berthiaume. The background for each person is described, focusing on salient experiences. All four had moved from the northeastern United States, and their careers intertwined in 1978 when drug use in local schools prompted the police to start arresting students at school. Each brought progressive ideas into their jobs, leading Towers to call Montgomery a “Lighthouse District.” This was evidenced by Berthiaume, who had run an alternative program called the Other Way. Inspired by Meher Baba, the same spiritual master who had influenced rock star Pete Townshend, Berthiaume wanted to create a drug-free school environment, and the police raids would give him that opportunity.
Crackdown
Authors: Finch Andrew J. 
Published: October 2024

Abstract
Teenage drug use had rapidly increased across the nation during the 1970s, and this was evident in Montgomery County, Maryland, a suburb of Washington, DC. In the fall of 1978, the county police raided local high schools over the course of the fall semester, arresting over three hundred students for possession or use of drugs. This chapter provides the background and daily account of those raids, including a brief history of the county and its schools. By the end of November, the crackdown had drawn the attention of national media. The raids created protests from the students, and eventually parents demanded a program from the school board that would address the district’s drug problem.