bluuebunny/crossref_metadata_2025_split huggingface dataset:
Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution
Authors: Larue Graham E , Roy Scott W 
Published: October 2023

AbstractSpliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second ‘minor’ spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes’ greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing’s persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.
Fusang: a framework for phylogenetic tree inference via deep learning
Authors: Wang Zhicheng , Sun Jinnan , Gao Yuan , Xue Yongwei , Zhang Yubo , Li Kuan , Zhang Wei , Zhang Chi , Zu Jian , Zhang Li 
Published: October 2023

Abstract
Phylogenetic tree inference is a classic fundamental task in evolutionary biology that entails inferring the evolutionary relationship of targets based on multiple sequence alignment (MSA). Maximum likelihood (ML) and Bayesian inference (BI) methods have dominated phylogenetic tree inference for many years, but BI is too slow to handle a large number of sequences. Recently, deep learning (DL) has been successfully applied to quartet phylogenetic tree inference and tentatively extended into more sequences with the quartet puzzling algorithm. However, no DL-based tools are immediately available for practical real-world applications. In this paper, we propose Fusang (http://fusang.cibr.ac.cn), a DL-based framework that achieves comparable performance to that of ML-based tools with both simulated and real datasets. More importantly, with continuous optimization, e.g. through the use of customized training datasets for real-world scenarios, Fusang has great potential to outperform ML-based tools.
PMhub 1.0: a comprehensive plant metabolome database
Authors: Tian Zhitao , Hu Xin , Xu Yingying , Liu Mengmeng , Liu Hongbo , Li Dongqin , Hu Lisong , Wei Guozhu , Chen Wei 
Published: October 2023

Abstract
The Plant Metabolome Hub (PMhub), available at https://pmhub.org.cn, is a valuable resource designed to provide scientists with comprehensive information on plant metabolites. It offers extensive details about their reference spectra, genetic foundations, chemical reactions, metabolic pathways and biological functions. The PMhub contains chemical data for 188 837 plant metabolites gathered from various sources, with 1 467 041 standard/in-silico high-resolution tandem mass-spectrometry (HRMS/MS) spectra corresponding to these metabolites. Beyond its extensive literature-derived data, PMhub also boasts a sizable collection of experimental metabolites; it contains 144 366 detected features in 10 typical plant species, with 16 423 successfully annotated by using standard/in-silico HRMS/MS data, this collection is further supplemented with thousands of features gathered from reference metabolites. For each metabolite, the PMhub enables the reconstructed of a simulated network based on structural similarities and existing metabolic pathways. Unlike previous plant-specific metabolome databases, PMhub not only contains a vast amount of metabolic data but also assembles the corresponding genomic and/or transcriptomic information, incorporating multiple methods for the comprehensive genetic analysis of metabolites. To validate the practicality, we verified a synthetic pathway for N-p-coumaroyltyramine by in vitro enzymatic activity experiments. In summary, the robust functionality provided by the PMhub will make it an indispensable tool for studying plant metabolomics.
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics
Authors: Martin Robert M , de Almeida Madalena R , Gameiro Eduardo , de Almeida Sérgio F 
Published: October 2023

AbstractWe have developed RHINO, a genetically encoded sensor that selectively binds RNA:DNA hybrids enabling live-cell imaging of cellular R-loops. RHINO comprises a tandem array of three copies of the RNA:DNA hybrid binding domain of human RNase H1 connected by optimized linker segments and fused to a fluorescent protein. This tool allows the measurement of R-loop abundance and dynamics in live cells with high specificity and sensitivity. Using RHINO, we provide a kinetic framework for R-loops at nucleoli, telomeres and protein-coding genes. Our findings demonstrate that R-loop dynamics vary significantly across these regions, potentially reflecting the distinct roles R-loops play in different chromosomal contexts. RHINO is a powerful tool for investigating the role of R-loops in cellular processes and their contribution to disease development and progression.
VARIDT 3.0: the phenotypic and regulatory variability of drug transporter
Authors: Yin Jiayi , Chen Zhen , You Nanxin , Li Fengcheng , Zhang Hanyu , Xue Jia , Ma Hui , Zhao Qingwei , Yu Lushan , Zeng Su , Zhu Feng 
Published: October 2023

Abstract
The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.
LncRNADisease v3.0: an updated database of long non-coding RNA-associated diseases
Authors: Lin Xiao , Lu Yingyu , Zhang Chenhao , Cui Qinghua , Tang Yi-Da , Ji Xiangwen , Cui Chunmei 
Published: October 2023

Abstract
Systematic integration of lncRNA-disease associations is of great importance for further understanding their underlying molecular mechanisms and exploring lncRNA-based biomarkers and therapeutics. The database of long non-coding RNA-associated diseases (LncRNADisease) is designed for the above purpose. Here, an updated version (LncRNADisease v3.0) has curated comprehensive lncRNA (including circRNA) and disease associations from the burgeoning literatures. LncRNADisease v3.0 exhibits an over 2-fold increase in experimentally supported associations, with a total of 25440 entries, compared to the last version. Besides, each lncRNA-disease pair is assigned a confidence score based on experimental evidence. Moreover, all associations between lncRNAs/circRNAs and diseases are classified into general associations and causal associations, representing whether lncRNAs or circRNAs can directly lead to the development or progression of corresponding diseases, with 15721 and 9719 entries, respectively. In a case study, we used the data of LncRNADisease v3.0 to calculate the phenotypic similarity between human and mouse lncRNAs. This database will continue to serve as a valuable resource for potential clinical applications related to lncRNAs and circRNAs. LncRNADisease v3.0 is freely available at http://www.rnanut.net/lncrnadisease.
SingPro: a knowledge base providing single-cell proteomic data
Authors: Lian Xichen , Zhang Yintao , Zhou Ying , Sun Xiuna , Huang Shijie , Dai Haibin , Han Lianyi , Zhu Feng 
Published: October 2023

Abstract
Single-cell proteomics (SCP) has emerged as a powerful tool for detecting cellular heterogeneity, offering unprecedented insights into biological mechanisms that are masked in bulk cell populations. With the rapid advancements in AI-based time trajectory analysis and cell subpopulation identification, there exists a pressing need for a database that not only provides SCP raw data but also explicitly describes experimental details and protein expression profiles. However, no such database has been available yet. In this study, a database, entitled ‘SingPro’, specializing in single-cell proteomics was thus developed. It was unique in (a) systematically providing the SCP raw data for both mass spectrometry-based and flow cytometry-based studies and (b) explicitly describing experimental detail for SCP study and expression profile of any studied protein. Anticipating a robust interest from the research community, this database is poised to become an invaluable repository for OMICs-based biomedical studies. Access to SingPro is unrestricted and does not mandate a login at: http://idrblab.org/singpro/.
Tobacco Imagery in the 50 Most Popular Malaysian Movies Released During 2015–2019
Authors: Billy Tay Jeanloong , Sreeramareddy Chandrashekhar T , Oo Phyu Synn , Aye Saint Nwe 
Published: October 2023

Abstract

Introduction
Exposure to tobacco imagery creates a positive impression about smoking and is associated with youth smoking uptake.

Methods
From the list of movies released during 2015–2019, we selected the top 10 movies per year rated by the Malaysian Film Development Corporation. Two researchers coded tobacco imagery in each movie considering 5-minute time intervals as a unit. The 5-minute interval coding was adopted from previous research for comparability. Frequencies and the average occurrence of tobacco imagery were compared by movie language, genre, and age categorization.

Results
In 50 movies analyzed, there were a total of 1037 five-minute intervals of which 26 (52%) movies and 277 (26.7%) of intervals tobacco imagery were present. Brand appearances were absent and health warnings about tobacco use were present in just one movie. The proportions of intervals containing actual use, paraphernalia, and implied use were 63.5%, 22.0%, and 14.5%. Tobacco imagery of actual use, paraphernalia, and implied use was present in 25, 20, and 10 movies, respectively. In those movies with tobacco imagery, the average number of occurrences of actual use, paraphernalia, and implied use was 3 (interquartile range [IQR] 2–11.5), 2.5 (IQR 1.3–4.0), and 1 (IQR 1–4), respectively. Movies classified as “p13” (median 6, IQR 6–13) and “18” (median 5, IQR 0–15) had higher average occurrences of tobacco imagery than “U” movies (median 0, IQR 0–2; p = .028).

Conclusions
The lack of health warnings despite the presence of tobacco imagery in Malaysian movies calls for measures to regulate tobacco-related content and reclassify such movies as “for adults-only.”

Implications
Tobacco imagery was prevalent in Malaysian movies that are allowed viewing by individuals aged 13 years and above. A review of the age categorization of Malaysian movies and the placement of health warnings in movies is needed. A comprehensive implementation of the ban on tobacco advertisements, promotion, and sponsorship should also include a ban on tobacco imagery in movies.
Perceived Effectiveness of Cigar Warnings in Discouraging Blunt Use
Authors: Kowitt Sarah D , Goldstein Adam O , Cornacchione Ross Jennifer , Clark Sonia A , Jarman Kristen L , Sheeran Paschal , Thrasher James F , Ranney Leah M 
Published: October 2023

Abstract

Introduction
Many people remove the tobacco leaf from cigars and replace it with cannabis (ie, blunts), but few studies have examined whether messages about the risks of cigars, like warnings on cigar packages, can affect blunt use.

Methods
Participants were 438 U.S. adults who reported past 30-day cigar use and ever blunt use, recruited from a probability-based national panel to take an online survey. In a 2 × 2 experiment with a between-subjects design, we manipulated two cigar warning characteristics: (1) warning type: text-only versus pictorial (ie, text + image) and (2) warning size: 30% (smaller) versus 50% (larger) of the product package. Participants then viewed six different warnings on a fictious cigarillo package, within their randomly assigned condition. After evaluating all stimuli, participants were asked the extent to which the warnings discouraged them from wanting to use cigars to smoke cannabis (ie, blunt perceived warning effectiveness). Response options ranged from “not at all” (1) to “a great deal” (5).

Results
We observed no main effects of warning type or size on blunt perceived warning effectiveness. However, a significant interaction existed between the two experimental manipulations (p = .009). Whereas adding images made no difference to blunt perceived warning effectiveness when warnings were smaller (simple effect: −0.22, p = .28), images mattered for larger warnings. Specifically, adding images increased blunt perceived warning effectiveness when warnings were 50% of the product package (simple effect: 0.52, p = .008).

Conclusions
This experiment provides preliminary evidence that larger pictorial cigar warnings may discourage blunt use relative to larger but text-only warnings.

Implications
Blunts, which are hollowed out cigars with tobacco leaf wrappers that are filled with cannabis leaf, are one of the most common ways in which tobacco and cannabis are used simultaneously, yet few studies have examined whether messages about the risks of cigars can affect blunt use. We conducted an online experiment concerning the perceived effectiveness of cigar warnings among people who use blunts recruited from a probability-based panel. Results provide novel, preliminary evidence that larger pictorial cigar warnings may discourage blunt use, relative to larger but text-only warnings. More research evaluating cigar warnings on blunt use is needed.
Historical racial redlining and contemporary patterns of income inequality negatively affect birds, their habitat, and people in Los Angeles, California
Authors: Wood Eric M , Esaian Sevan , Benitez Christian , Ethington Philip J , Longcore Travis , Pomara Lars Y 
Published: October 2023

Abstract
The Home Owners’ Loan Corporation (HOLC) was a U.S. government-sponsored program initiated in the 1930s to evaluate mortgage lending risk. The program resulted in hand-drawn “security risk” maps intended to grade sections of cities where investment should be focused (greenlined areas) or limited (redlined zones). The security maps have since been widely criticized as being inherently racist and have been associated with high levels of segregation and lower levels of green amenities in cities across the country. Our goal was to explore the potential legacy effects of the HOLC grading practice on birds, their habitat, and the people who may experience them throughout a metropolis where the security risk maps were widely applied, Greater Los Angeles, California (L.A.). We used ground-collected, remotely sensed, and census data and descriptive and predictive modeling approaches to address our goal. Patterns of bird habitat and avian communities strongly aligned with the luxury-effect phenomenon, where green amenities were more robust, and bird communities were more diverse and abundant in the wealthiest parts of L.A. Our analysis also revealed potential legacy effects from the HOLC grading practice. Associations between bird habitat features and avian communities in redlined and greenlined zones were generally stronger than in areas of L.A. that did not experience the HOLC grading, in part because redlined zones, which included some of the poorest locations of L.A., had the highest levels of dense urban conditions (e.g., impervious surface cover), whereas greenlined zones, which included some of the wealthiest areas of the city, had the highest levels of green amenities (e.g., tree canopy cover). The White population of L.A., which constitutes the highest percentage of a racial or ethnic group in greenlined areas, was aligned with a considerably greater abundance of birds affiliated with natural habitat features (e.g., trees and shrubs). Conversely, the Hispanic or Latino population, which is dominant in redlined zones, was positively related to a significantly greater abundance of synanthropic birds, which are species associated with dense urban conditions. Our results suggest that historical redlining and contemporary patterns of income inequality are associated with distinct avifaunal communities and their habitat, which potentially influence the human experience of these components of biodiversity throughout L.A. Redlined zones and low-income residential areas that were not graded by the HOLC can particularly benefit from deliberate urban greening and habitat enhancement projects, which would likely carry over to benefit birds and humans.
Serum cortisol level to screen for significant hypothalamic–pituitary–adrenal axis suppression in patients receiving multiple steroid injections
Authors: Lee Debbie , Carrera Eduardo J , Hagens Ryan , Yeung Gerald , Garvan Cynthia W , Rothman Micol S , Akuthota Venu 
Published: October 2023

Abstract

Background
Morning serum cortisol level (mSCL) is a practical screening tool for hypothalamic–pituitary–adrenal (HPA) axis suppression and has been used to assess for duration of cortisol deficiency after epidural and peripheral glucocorticoid injections. More evidence is needed to establish the utility of mSCL in patients undergoing repeat injections with increasing cumulative glucocorticoid equivalent dose (CGED) that could place them at higher risk of HPA axis suppression.

Objectives
To estimate the prevalence of spine injection candidates with significant HPA axis suppression (sigAS), to understand the correlation between 12 months of CGED and the presence of sigAS based on the timing of mSCL collection after the most recent glucocorticoid injection (within 6 weeks or between 6 weeks and 12 months), and to investigate demographic and clinical factors relating to sigAS.

Methods
Retrospective chart review of patients scheduled for spine injection who had an associated mSCL and documented histories of prior glucocorticoid injections. The steroid name, dose, type, and procedure location were recorded for each injection that occurred within 12 months before mSCL. CGED was calculated from standard glucocorticoid equivalent conversion factors.

Results
SigAS was present in 7.8% to 22% of the analysis cohorts. There was no association found between CGED and sigAS regardless of timing of mSCL. There was a trend toward lower mSCL and sigAS with increasing CGED. There were no significant relationships found between sigAS and overall demographic or clinical factors.

Conclusions
A 3-fold reduction in the rate of sigAS was noted 6 weeks after the most recent steroid injection. Using mSCL provides a template to investigate the impact of CGED and the best timing for mSCL collection in order to define a more practical guideline to identify patients at higher risk of sigAS earlier and plan for future spine injections.
The α-arrestin SUP-13/ARRD-15 promotes isoform turnover of actin-interacting protein 1 in Caenorhabditis elegans striated muscle
Authors: Lewis Mario , Ono Kanako , Qin Zhaozhao , Johnsen Robert C , Baillie David L , Ono Shoichiro 
Published: October 2023

Abstract
Precise arrangement of actin, myosin, and other regulatory components in a sarcomeric pattern is critical for producing contractile forces in striated muscles. Actin-interacting protein 1 (AIP1), also known as WD-repeat protein 1 (WDR1), is one of essential factors that regulate sarcomeric assembly of actin filaments. In the nematode Caenorhabditis elegans, mutation in unc-78, encoding one of the two AIP1 isoforms, causes severe disorganization of sarcomeric actin filaments and near paralysis, but mutation in sup-13 suppresses the unc-78-mutant phenotypes to restore nearly normal sarcomeric actin organization and worm motility. Here, we identified that sup-13 is a nonsense allele of arrd-15 encoding an α-arrestin. The sup-13/arrd-15 mutation suppressed the phenotypes of unc-78 null mutant but required aipl-1 that encodes a second AIP1 isoform. aipl-1 was normally expressed highly in embryos and downregulated in mature muscle. However, in the sup-13/arrd-15 mutant, the AIPL-1 protein was maintained at high levels in adult muscle to compensate for the absence of the UNC-78 protein. The sup-13/arrd-15 mutation caused accumulation of ubiquitinated AIPL-1 protein, suggesting that a normal function of sup-13/arrd-15 is to enhance degradation of ubiquitinated AIPL-1, thereby promoting transition of AIP1 isoforms from AIPL-1 to UNC-78 in developing muscle. These results suggest that α-arrestin is a novel factor to promote isoform turnover by enhancing protein degradation.
The Impact of Public School Choice: Evidence from Los Angeles’s Zones of Choice
Authors: Campos Christopher , Kearns Caitlin 
Published: October 2023

Abstract
Does a school district that expands school choice provide better outcomes for students than a neighborhood-based assignment system? This article studies the Zones of Choice (ZOC) program, a school choice initiative of the Los Angeles Unified School District (LAUSD) that created small high school markets in some neighborhoods but left attendance zone boundaries in place throughout the rest of the district. We study market-level effects of choice on student achievement and college enrollment using a difference-in-differences design. Student outcomes in ZOC markets increased markedly, narrowing achievement and college enrollment gaps between ZOC neighborhoods and the rest of the district. The effects of ZOC are larger for schools exposed to more competition, supporting the notion that competition is a key channel. Demand estimates suggest families place substantial weight on schools’ academic quality, providing schools with competition-induced incentives to improve their effectiveness. The evidence demonstrates that public school choice programs have the potential to improve school quality and reduce neighborhood-based disparities in educational opportunity.