bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs
Authors: Morales Ariadna E , Burbrink Frank T , Segall Marion , Meza Maria , Munegowda Chetan , Webala Paul W , Patterson Bruce D , Thong Vu Dinh , Ruedi Manuel , Hiller Michael , Simmons Nancy B 
Published: August 2024

Abstract
Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies—gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features—have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.
Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq
Authors: Morgan Ian L , McKie Shannon J , Kim Rachel , Seol Yeonee , Xu Jing , Harami Gabor M , Maxwell Anthony , Neuman Keir C 
Published: August 2024

Abstract
Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability and a number of clinically important anticancer and antibacterial drugs, e.g. quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20–50-fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e. negative versus positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
H3T11 phosphorylation by CKII is required for heterochromatin formation in Neurospora
Authors: Tian Yuan , Zhang Chengcheng , Tian Xiang , Zhang Lu , Yin Tong , Dang Yunkun , Liu Yi , Lou Huiqiang , He Qun 
Published: August 2024

Abstract
Heterochromatin is a key feature of eukaryotic genomes and is crucial for maintaining genomic stability. In fission yeast, heterochromatin nucleation is mainly mediated by DNA-binding proteins or the RNA interference (RNAi) pathway. In the filamentous fungus Neurospora crassa, however, the mechanism that causes the initiation of heterochromatin at the relics of repeat-induced point mutation is unknown and independent of the classical RNAi pathway. Here, we show that casein kinase II (CKII) and its kinase activity are required for heterochromatin formation at the well-defined 5-kb heterochromatin of the 5H-cat-3 region and transcriptional repression of its adjacent cat-3 gene. Similarly, mutation of the histone H3 phosphorylation site T11 also impairs heterochromatin formation at the same locus. The catalytic subunit CKA colocalizes with H3T11 phosphorylation (H3pT11) within the 5H-cat-3 domain and the deletion of cka results in a significant decrease in H3T11 phosphorylation. Furthermore, the loss of kinase activity of CKII results in a significant reduction of H3pT11, H3K9me3 (histone H3 lysine 9 trimethylation) and DNA methylation levels, suggesting that CKII regulates heterochromatin formation by promoting H3T11 phosphorylation. Together, our results establish that histone H3 phosphorylation by CKII is a critical event required for heterochromatin formation.
The characteristics of CTCF binding sequences contribute to enhancer blocking activity
Authors: Tsang Felice H , Stolper Rosa J , Hanifi Muhammad , Cornell Lucy J , Francis Helena S , Davies Benjamin , Higgs Douglas R , Kassouf Mira T 
Published: August 2024

Abstract
While the elements encoding enhancers and promoters have been relatively well studied, the full spectrum of insulator elements which bind the CCCTC binding factor (CTCF), is relatively poorly characterized. This is partly due to the genomic context of CTCF sites greatly influencing their roles and activity. Here we have developed an experimental system to determine the ability of minimal, consistently sized, individual CTCF elements to interpose between enhancers and promoters and thereby reduce gene expression during differentiation. Importantly, each element is tested in the identical location thereby minimising the effect of genomic context. We found no correlation between the ability of CTCF elements to block enhancer–promoter activity with the degree of evolutionary conservation; their resemblance to the consensus core sequences; or the number of CTCF core motifs harboured in the element. Nevertheless, we have shown that the strongest enhancer–promoter blockers include a previously described bound element lying upstream of the CTCF core motif. In addition, we found other uncharacterised DNaseI footprints located close to the core motif that may affect function. We have developed an assay of CTCF sequences which will enable researchers to sub-classify individual CTCF elements in a uniform and unbiased way.
Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ
Authors: Riccio Amanda A , Bouvette Jonathan , Pedersen Lars C , Somai Shruti , Dutcher Robert C , Borgnia Mario J , Copeland William C 
Published: August 2024

Abstract
The mitochondrial single-stranded DNA (ssDNA) binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.
Effects of Very Low Nicotine Content Cigarettes and Nicotine Vaping Device Characteristics on Choices to Smoke, Vape, or Abstain in Early Young Adults
Authors: Cassidy Rachel N , Tidey Jennifer W , Bello Mariel S , Denlinger-Apte Rachel , Goodwin Christine , Godin Julissa , Cioe Patricia A , Swift Robert , Demorest Connor , Koopmeiners Joseph S , Donny Eric , Hatsukami Dorothy , Colby Suzanne M 
Published: August 2024

Abstract

Introduction
A national nicotine reduction policy could reduce the public health toll of smoking. However, reducing nicotine in cigarettes may lead to changes in the use of other tobacco products such as nicotine vaping devices, particularly among young people. Product use outcomes may depend on the characteristics of available nicotine vaping devices. We aimed to determine the impact of cigarette nicotine content, vaping device nicotine concentration, and vaping device flavors on choices to smoke, vape, or abstain.

Aims and Methods
Early young adults (ages 18–20 inclusive, N = 80) who reported smoking daily and vaping nicotine at least twice in their lifetime participated in a laboratory study. Participants received either very low nicotine content (VLNC; 0.4 mg nicotine/g of tobacco) or normal nicotine content (NNC; 15.8 mg/g) cigarettes. First, participants chose between their assigned cigarette or abstaining. Subsequently, participants chose between 2 cigarette puffs, 2 vape puffs, or abstaining. Vaping device nicotine concentration (3 mg vs. 18 mg/mL) and flavor (tobacco vs. non-tobacco) were manipulated within subjects.

Results
When only cigarettes were available, there were no differences between the VLNC and NNC groups on cigarette choices. When the nicotine vaping device was concurrently available, the VLNC group made fewer choices to smoke than the NNC group. Non-tobacco flavors and lower vaping device nicotine concentration were associated with fewer choices to smoke.

Conclusions
Nicotine vaping device availability reduced choices to smoke VLNC cigarettes, and vaping devices with lower nicotine and non-tobacco flavors led to the fewest choices to smoke. Regulators should consider that the availability and characteristics of alternative tobacco products can moderate the product standard’s impact.

Implications
The U.S. Food and Drug Administration may enact a reduced nicotine product standard that would affect all commercially available cigarettes. One important population affected by this policy would be early young adults who smoke. We aimed to determine the impact of cigarette nicotine content, vaping device nicotine concentration, and vaping device flavors on choices to smoke, vape, or abstain. Lower nicotine in cigarettes, along with non-tobacco flavors and lower nicotine concentration in the vaping device, were associated with the fewest choices to smoke. Regulators should consider that the availability and characteristics of alternative tobacco products can moderate the product standard’s impact.
An unstable Union? The Conservative Party, the British Political Tradition, and devolution in Scotland and Wales 2010–23
Authors: Anderson Paul , Brown Swan Coree 
Published: August 2024

Abstract
While devolution in Scotland and Wales is often established as the settled will, it has been built on unsettled ground, lacking a robust system of intergovernmental relations, and sitting increasingly at odds with the central principle of parliamentary sovereignty. Examining successive UK Conservative-led governments, we evaluate devolution in Scotland and Wales through the lens of the Asymmetric Power Model and the British Political Tradition, documenting changes in the position of successive Conservative governments, from the more plurinationally sensitive respect agenda of David Cameron to the more assertive and intrusive Unionism advanced under those in post after 2016, notably Theresa May and Boris Johnson.
Electoral Violence in England and Wales, 1832–1914
Authors: Blaxill Luke , Cohen Gidon , Hutchison Gary , Kuhn Patrick M , Vivyan Nick 
Published: August 2024

Abstract
This article analyses over 19,000 articles from newspapers and parliamentary commission reports to reveal endemic electoral violence in England and Wales between 1832 and 1914. It offers a new understanding of the phenomenon in three main ways. First, the extent of election violence, which regularly featured major riots requiring police and military intervention, disturbances of the peace, and deaths, questions conventional understandings of Britain's comparatively peaceful political development through a century of gradual suffrage expansion, rising literacy and economic development. Second, the trajectory of the electoral violence, which peaked in the period after the Second Reform Act of 1867 rather than after the Great Reform Act of 1832, challenges the linearity of these accounts. Third, despite the recent historiographical emphasis on explaining electoral violence as a ritual expression of discontent, much violence resulted from elites strategizing to win elections. Electoral violence occurred disproportionately when and where it was most useful to candidates and parties, and often involved the previously overlooked figure of the ‘hired rough’: men employed to disrupt elections by force. We thus advance a political, rather than cultural, explanation for electoral violence.
Wheat Cybrid Plants, OryzaWheat, Regenerated from Wheat–Rice Hybrid Zygotes via in Vitro Fertilization System Possess Wheat–Rice Hybrid Mitochondria
Authors: Maryenti Tety , Koshimizu Shizuka , Onda Nonoka , Ishii Takayoshi , Yano Kentaro , Okamoto Takashi 
Published: August 2024

Abstract
Hybridization generates biodiversity, and wide hybridization plays a pivotal role in enhancing and broadening the useful attributes of crops. The hybridization barrier between wheat and rice, the two most important cereals, was recently overcome by in vitro production of allopolyploid wheat–rice hybrid zygotes, which can develop and grow into mature plants. In the study, genomic sequences and compositions of the possible hybrid plants were investigated through short- and long-read sequencing analyses and fluorescence in situ hybridization (FISH)-based visualization. The possible hybrid possessed whole wheat nuclear and cytoplasmic DNAs and rice mitochondrial (mt) DNA, along with variable retention rates of rice mtDNA ranging from 11% to 47%. The rice mtDNA retained in the wheat cybrid, termed Oryzawheat, can be transmitted across generations. In addition to mitochondrial hybridization, translocation of rice chromosome 1 into wheat chromosome 6A was detected in a F1 hybrid individual. OryzaWheat can provide a new horizon for utilizing inter-subfamily genetic resources among wheat and rice belonging to different subfamilies, Pooideae and Ehrhartoideae, respectively.
Behavioral nudges in social media ads show limited ability to encourage COVID-19 vaccination across countries
Authors: Çat Olgahan , Chang Jiseon , Hlatky Roman , Li Huimin , Nielson Daniel L 
Published: August 2024

Abstract
Behavioral nudges in Facebook ads reached nearly 15 million people across six diverse countries and, consequently, many thousands took the step of navigating to governments’ vaccine signup sites. However, none of the treatment ads caused significantly more vaccine signup intent than placebo uniformly across all countries. Critically, reporting the descriptive norm that 87% of people worldwide had either been vaccinated or planned vaccination—social proof—did not meaningfully increase vaccine signup intent in any country and significantly backfired in Taiwan. This result contradicts prominent prior findings. A charge to “protect lives in your family” significantly outperformed placebo in Taiwan and Turkey but saw null effects elsewhere. A message noting that vaccination significantly reduces hospitalization risk decreased signup intent in Brazil and had no significant effects in any other country. Such heterogeneity was the hallmark of the study: some messages saw significant treatment effects in some countries but failed in others. No nudge outperformed the placebo in Russia, a location of high vaccine skepticism. In all, widely touted behavioral nudges often failed to promote vaccine signup intent and appear to be moderated by cultural context.
SPOT-RASTR—A cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface
Authors: Esfahani Behrouz G , Randolph Peter S , Peng Ruizhi , Grant Timothy , Stroupe M Elizabeth , Stagg Scott M 
Published: August 2024

Abstract
In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method's ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR holds promise for overcoming air–water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.
Clustering of negative topological charges precedes plastic failure in 3D glasses
Authors: Bera Arabinda , Baggioli Matteo , Petersen Timothy C , Sirk Timothy W , Liu Amelia C Y , Zaccone Alessio 
Published: August 2024

Abstract
The deformation mechanism in amorphous solids subjected to external shear remains poorly understood because of the absence of well-defined topological defects mediating the plastic deformation. The notion of soft spots has emerged as a useful tool to characterize the onset of irreversible rearrangements and plastic flow, but these entities are not clearly defined in terms of geometry and topology. In this study, we unveil the phenomenology of recently discovered, precisely defined topological defects governing the microscopic mechanical and yielding behavior of a model 3D glass under shear deformation. We identify the existence of vortex-like and antivortex-like topological defects within the 3D nonaffine displacement field. The number density of these defects exhibits a significant anticorrelation with the plastic events, with defect proliferation–annihilation cycles matching the alternation of elastic-like segments and catastrophic plastic drops, respectively. Furthermore, we observe collective annihilation of these point-like defects via plastic events, with large local topological charge fluctuations in the vicinity of regions that feature strong nonaffine displacements. We reveal that plastic yielding is driven by several large sized clusters of net negative topological charge, the massive annihilation of which triggers the onset of plastic flow. These findings suggest a geometric and topological characterization of soft spots and pave the way for the mechanistic understanding of topological defects as mediators of plastic deformation in glassy materials.
Deep learning-based amyloid PET harmonization to predict cognitive decline in non-demented elderly
Authors: Choi Yoon Seong , Ngam Pei Ing , Lee Jeong Ryong , Hwang Dosik , Tan Eng-King ,   for the Harvard Aging Brain Study,   for the Australian Imaging Biomarkers and Lifestyle Study of Aging,   for the Japanese Alzheimer’s Disease Neuroimaging Initiative,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2024

Abstract

Background
The robustness of conventional amyloid PET harmonization across tracers has been questioned.

Purpose
To evaluate deep learning-based harmonization of amyloid PET in predicting conversion from cognitively unimpaired (CU) to mild cognitive impairment (MCI) and MCI to Alzheimer’s disease (AD).

Materials and Methods
We developed an amyloid PET-based deep-learning model to classify participants with a clinical diagnosis of AD-dementia vs CU across different tracers from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Japanese ADNI, and Australian Imaging, Biomarker, and Lifestyle cohorts (n = 1050). The model output [deep learning-based probability of Alzheimer’s disease-dementia (DL-ADprob)], with other prognostic factors, was evaluated for predicting cognitive decline in ADNI-MCI (n = 451) and Harvard Aging Brain Study (HABS)-CU (n = 271) participants using Cox regression and area under time-dependent receiver operating characteristics curve (tdAUC) at 4-year follow-up. Subgroup analyses were performed in the ADNI-MCI group for conversion from amyloid-positive to AD and from amyloid negative to positive. Intraclass correlation coefficient (ICC) of DL-ADprob between tracers was calculated in the Global Alzheimer’s Association Interactive Network dataset (n = 155).

Results
DL-ADprob was independently prognostic in both ADNI-MCI (P &lt; .001) and HABS-CU (P = .048) sets. Adding DL-ADprob to other factors increased prognostic performances in both ADNI-MCI (tdAUC 0.758 [0.721-0.792] vs 0.782 [0.742-0.818], tdAUC difference 0.023 [0.007-0.038]) and HABS-CU (tdAUC 0.846 [0.755-0.925] vs 0.870 [0.773-0.943], tdAUC difference 0.022 [−0.004 to 0.053]). DL-ADprob was independently prognostic in amyloid-positive (P &lt; .001) and amyloid-negative subgroups (P = .007). DL-ADprob showed incremental prognostic value in amyloid-positive (tdAUC 0.666 [0.623-0.713] vs 0.706 [0.657-0.755], tdAUC difference 0.039 [0.016-0.064]), but not in amyloid-negative (tdAUC 0.818 [0.757-0.882] vs 0.816 [0.751-0.880], tdAUC difference −0.002 [−0.031 to 0.029]) subgroup. The pairwise ICCs of DL-ADprob between Pittsburgh compound B and florbetapir, florbetaben, and flutemetamol, respectively, ranged from 0.913 to 0.935.

Conclusion
Deep learning-based harmonization of amyloid PET improves cognitive decline prediction in non-demented elderly, suggesting it could complement conventional amyloid PET measures.