bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolved low-J12CO excitation at 190 parsec resolution across NGC 2903 and NGC 3627
Authors: den Brok J S , Leroy A K , Usero A , Schinnerer E , Rosolowsky E , Koch E W , Querejeta M , Liu D , Bigiel F , Barnes A T , Chevance M , Colombo D , Dale D A , Glover S C O , Jimenez-Donaire M J , Teng Y-H , Williams T G
Published: October 2023

The low-J rotational transitions of 12CO are commonly used to trace the distribution of molecular gas in galaxies. Their ratios are sensitive to excitation and physical conditions in the molecular gas. Spatially resolved studies of CO ratios are still sparse and affected by flux calibration uncertainties, especially since most do not have high angular resolution or do not have short-spacing information and hence miss any diffuse emission. We compare the low-J CO ratios across the disc of two massive, star-forming spiral galaxies NGC 2903 and NGC 3627 to investigate whether and how local environments drive excitation variations at GMC scales. We use Atacama Large Millimeter Array (ALMA) observations of the three lowest-J CO transitions at a common angular resolution of 4 arcsec (190 pc). We measure median line ratios of $R_{21}=0.67^{+0.13}_{-0.11}$, $R_{32}=0.33^{+0.09}_{-0.08}$, and $R_{31}=0.24^{+0.10}_{-0.09}$ across the full disc of NGC 3627. We see clear CO line ratio variation across the galaxy consistent with changes in temperature and density of the molecular gas. In particular, towards the centre, R21, R32, and R31 increase by 35  per cent, 50  per cent, and 66  per cent, respectively, compared to their average disc values. The overall line ratio trends suggest that CO(3–2) is more sensitive to changes in the excitation conditions than the two lower J transitions. Furthermore, we find a similar radial R32 trend in NGC 2903, albeit a larger disc-wide average of $\langle R_{32}\rangle =0.47^{+0.14}_{-0.08}$. We conclude that the CO low-J line ratios vary across environments in such a way that they can trace changes in the molecular gas conditions, with the main driver being changes in temperature.
Beyond the 3rd moment: a practical study of using lensing convergence CDFs for cosmology with DES Y3
Authors: Anbajagane D , Chang C , Banerjee A , Abel T , Gatti M , Ajani V , Alarcon A , Amon A , Baxter E J , Bechtol K , Becker M R , Bernstein G M , Campos A , Rosell A Carnero , Kind M Carrasco , Chen R , Choi A , Davis C , DeRose J , Diehl H T , Dodelson S , Doux C , Drlica-Wagner A , Eckert K , Elvin-Poole J , Everett S , Ferté A , Gruen D , Gruendl R A , Harrison I , Hartley W G , Huff E M , Jain B , Jarvis M , Jeffrey N , Kacprzak T , Kokron N , Kuropatkin N , Leget P-F , MacCrann N , McCullough J , Myles J , Navarro-Alsina A , Pandey S , Prat J , Raveri M , Rollins R P , Roodman A , Rykoff E S , Sánchez C , Secco L F , Sevilla-Noarbe I , Sheldon E , Shin T , Troxel M A , Tutusaus I , Whiteway L , Yanny B , Yin B , Zhang Y , Abbott T M C , Allam S , Aguena M , Alves O , Andrade-Oliveira F , Annis J , Bacon D , Blazek J , Brooks D , Cawthon R , da Costa L N , Pereira M E S , Davis T M , Desai S , Doel P , Ferrero I , Frieman J , Giannini G , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Lahav O , Marshall J L , Mena-Fernández J , Menanteau F , Miquel R , Palmese A , Pieres A , Malagón A A Plazas , Reil K , Sanchez E , Smith M , Swanson M E C , Tarle G , Wiseman P ,   (DES Collaboration)
Published: October 2023

Widefield surveys probe clustered scalar fields – such as galaxy counts, lensing potential, etc. – which are sensitive to different cosmological and astrophysical processes. Constraining such processes depends on the statistics that summarize the field. We explore the cumulative distribution function (CDF) as a summary of the galaxy lensing convergence field. Using a suite of N-body light-cone simulations, we show the CDFs’ constraining power is modestly better than the second and third moments, as CDFs approximately capture information from all moments. We study the practical aspects of applying CDFs to data, using the Dark Energy Survey (DES Y3) data as an example, and compute the impact of different systematics on the CDFs. The contributions from the point spread function and reduced shear approximation are $\lesssim 1~{{\ \rm per\ cent}}$ of the total signal. Source clustering effects and baryon imprints contribute 1–10 per cent. Enforcing scale cuts to limit systematics-driven biases in parameter constraints degrade these constraints a noticeable amount, and this degradation is similar for the CDFs and the moments. We detect correlations between the observed convergence field and the shape noise field at 13σ. The non-Gaussian correlations in the noise field must be modelled accurately to use the CDFs, or other statistics sensitive to all moments, as a rigorous cosmology tool.
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility
Authors: Kosek David M , Banijamali Elnaz , Becker Walter , Petzold Katja , Andersson Emma R
Published: October 2023

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression by binding to specific sites in mRNAs. Site recognition is primarily mediated by the seed region (nucleotides g2–g8 in the miRNA), but pairing beyond the seed (3′-pairing) is important for some miRNA:target interactions. Here, we use SHAPE, luciferase reporter assays and transcriptomics analyses to study the combined effect of 3′-pairing and secondary structures in mRNAs on repression efficiency. Using the interaction between miR-34a and its SIRT1 binding site as a model, we provide structural and functional evidence that 3′-pairing can compensate for low seed-binding site accessibility, enabling repression of sites that would otherwise be ineffective. We show that miRNA 3′-pairing regions can productively base-pair with nucleotides far upstream of the seed-binding site and that both hairpins and unstructured bulges within the target site are tolerated. We use SHAPE to show that sequences that overcome inaccessible seed-binding sites by strong 3′-pairing adopt the predicted structures and corroborate the model using luciferase assays and high-throughput modelling of 8177 3′-UTR targets for six miRNAs. Finally, we demonstrate that PHB2, a target of miR-141, is an inaccessible target rescued by efficient 3′-pairing. We propose that these results could refine predictions of effective target sites.
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

Spliceosomal 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

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

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

We 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

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

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

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

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

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

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

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

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

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.
Lethal Phenotype-Based Database Screening Identifies Ceramide as a Negative Regulator of Primitive Streak Formation
Authors: Pu Jing , Kofuji Satoshi , Okamoto-Uchida Yoshimi , Danzaki Keiko , Yu Ruoxing , Suzuki Akira , Kitajima Satoshi , Nishina Hiroshi
Published: October 2023

In early embryogenesis, the primitive streak (PrS) generates the mesendoderm and is essential for organogenesis. However, because the PrS is a minute and transient tissue, elucidating the mechanism of its formation has been challenging. We performed comprehensive screening of 2 knockout mouse databases based on the fact that failure of PrS formation is lethal. We identified 812 genes involved in various cellular functions and responses that might be linked to PrS formation, with the category of greatest abundance being “Metabolism.” In this study, we focused on genes of sphingolipid metabolism and investigated their roles in PrS formation using an in vitro mouse ES cell differentiation system. We show here that elevated intracellular ceramide negatively regulates gene expression essential for PrS formation and instead induces neurogenesis. In addition, sphingosine-1-phosphate (a ceramide derivative) positively regulates neural maturation. Our results indicate that ceramide regulates both PrS formation and the induction of neural differentiation.
Living together in dead coral rocks: macrosymbiotic communities associated with Bonellia echiuran worms (Annelida: Thalassematidae: Bonelliinae), involving new commensal bivalve and amphipod species
Authors: Goto Ryutaro , Hirabayashi Isao , Seike Koji , Yamashita Momo , Shimomura Michitaka
Published: October 2023

Dead coral rocks are prevalent hard substrates in shallow warm waters, providing habitat for various infaunal and boring invertebrates. Despite this, the nature of species interactions, especially symbiotic relationships, among them remains poorly understood. Bonellia (Annelida: Thalassematidae: Bonelliinae) is a group of greenish echiuran worms commonly inhabiting cavities inside dead coral rocks. Although echiuran burrows in marine sediments are known to harbour various host-specific macrosymbionts, it remains unclear whether such associations also occur in hard substrates. To address this, we investigated the diversity of macrosymbionts associated with the burrows of Bonellia sp. aff. minor in the warm-temperate coast of the Kii Peninsula, Japan, and the evolutionary origins of those symbionts. The host’s burrow morphology was also examined using micro-computed tomography (CT) scanning. Our field survey revealed that the burrows of Bo. sp. aff. minor hosted three commensal species including a polychaete, Oxydromus fauveli, and two new species, a bivalve (Basterotia bonelliphila sp. nov.) and an amphipod (Leucothoe bonelliae sp. nov.). Our molecular phylogenetic analyses showed that each symbiont species belongs to a clade comprising commensal species specific to echiurans or annelids. Overall, our findings contribute to a better understanding of symbiotic associations in marine hard substrates.
PA access to provider health programs
Authors: Roman Christopher , Neary Stephanie
Published: October 2023

Objective:

This study assessed the availability of provider health programs (PHPs) for physician associates/assistants (PAs), as well as the accessibility of information about these resources through state licensing boards and PA constituent organizations.

Methods:

Data were collected through audits of the websites of the PA licensing board and state/district constituent group for each state and the District of Columbia from October to November 2022.

Results:

Every state except Massachusetts has a PHP that serves PAs. Review of the 51 respective state licensing board websites revealed that 23 states (45.1%) list PHP information; only 9 states (17.6%) have PHP information listed on state PA constituent organization websites.

Conclusions:

The results of this study indicate that PHPs for PAs are widely available. Unfortunately, the broad availability of PHPs may be limited by the lack of accessible information about these programs in many states.
The Anatomic Position of the Sciatic Nerve During Percutaneous Retrograde Posterior Column Fixation is Determined by Hip Position
Authors: Murasko Marlon J. , Nourie Blake , Cooley Michael R. , Chisena Ernest N.
Published: October 2023

Objectives:

There are multiple established patient positions for placement of a percutaneous retrograde posterior column screw for fixation of acetabulum fractures. The sciatic nerve is at risk of injury during this procedure, as it lies adjacent to the start point at the ischial tuberosity. The purpose of this study is to define how the position of the sciatic nerve, relative to the ischial tuberosity, changes with respect to the patient’s hip position.

Methods:

In a cohort of 11 healthy volunteers, ultrasound was used to measure the absolute distance between the ischial tuberosity and the sciatic nerve. Measurements were made with the hip and knee flexed to 90 degrees to simulate supine and lateral positioning, and with the hip extended to simulate prone positioning. In both positions, the hip was kept in neutral abduction and neutral rotation.

Results:

The distance from the lateral border of the ischial tuberosity to the medial border of the sciatic nerve was greater in all subjects in the hip flexed position versus the extended position. The mean distance was 17 mm (range, 14-27 mm) in the hip extended position, and 39 mm (range, 26-56 mm) in the hip flexed position (P < .001).

Conclusion:

The sciatic nerve demonstrates marked excursion away from the ischial tuberosity when the hip is flexed compared with when it is extended. The safest patient position for percutaneous placement of a retrograde posterior column screw is lateral or supine with the hip flexed to 90 degrees.
Influence of Body Mass Index on Surgical and Patient Outcomes for Cervical Spine Surgery
Authors: Naik Anant , Moawad Christina , Harrop James S. , Dhawan Sanjay , Cramer Samuel W. , Arnold Paul M.
Published: October 2023

Study Design:

Secondary analysis of prospectively collected registry.

Objective:

We aim to investigate the effects of body mass index (BMI) on postsurgical cervical spine surgery outcomes and identify a potential substratification of obesity with worse outcomes.

Summary of Background Data:

The impact of BMI on cervical spine surgery is unknown, with controversial outcomes for patients high and low BMI.

Methods:

The cervical spine Quality Outcomes Database was queried for a total of 10,381 patients who underwent single-stage cervical spine surgery. Patients were substratified into 6 groups based on BMI. Surgical outcomes, complications, hospitalization outcomes, and patient-reported outcomes for each cohort, including modified Japanese Orthopedic Association Score, Numeric Rating Scale arm pain, Numeric Rating Scale neck pain, Neck Disability Index, and EuroQol Health Survey, were assessed. Univariate analysis was performed for 3- and 12-month follow-up after surgical intervention.

Results:

Obese patients (class I, II, and III) requiring spine surgery were statistically younger than nonobese patients and had higher rates of diabetes compared with normal BMI patients. The surgical length was found to be longer for overweight and all classes of obese patients (P < 0.01). Class III obese patients had higher odds of postoperative complications. Patients with class II and III obesity had lower odds of achieving optimal modified Japanese Orthopedic Association Score at 3 months [OR = 0.8 (0.67–0.94), P < 0.01, OR = 0.68 (0.56–0.82), P < 0.001, respectively] and 12 months [OR = 0.82 (0.68–0.98), P = 0.03, OR = 0.79 (0.64–0.98), P = 0.03, respectively].

Conclusions:

This study investigates the relationship between substratified BMI and postoperative outcomes of cervical spine surgery. Class II and III obese patients have substantially greater risk factors and poor outcomes postoperatively. In addition, low BMI also presents unique challenges for patients. Further research is needed for comprehensive analysis on outcomes of cervical spine surgery after correcting BMI.
Ulnar Nerve Injury during Treatment of Fourth and Fifth Metacarpal Fractures: A Case Report and Anatomical Review
Authors: Muneer Mohammed , Alborno Yahya
Published: October 2023

The deep branch of the ulnar nerve (DBUN) is a pure motor nerve. It passes through a hypothenar fibromuscular tunnel and courses radially on the interossei surface. The DBUN is not frequently considered during hand fracture surgery, despite the anatomical course of the nerve in close relation to the carpal and metacarpal bones, which makes it vulnerable to penetrating injury and being injured during hand surgery fixations. In this article, we describe a case of DBUN injury after percutaneous pinning of the fourth and fifth metacarpal bone fractures complicated by intrinsic muscle wasting of the hand that was treated with neuroma excision and sural nerve graft. We present the case of a 36-year-old man, who had a fracture of the base of the fourth and fifth metacarpal bones, which was treated with multiple K-wires. A few months later, the patient presented with weak abduction/adduction of the three ulnar fingers and prominent wasting in the intrinsic muscles of the hand. On hand exploration, a 2-cm neuroma was found along the course of the DBUN distal to the hypothenar fibromuscular tunnel, which was treated by neuroma excision and nerve grafting. Fractures of the fourth and fifth metacarpals and carpometacarpal dislocations are very common and are often treated surgically. To fix these fractures, awareness of the DBUN course in the hand and its proximity to the carpal and metacarpal bones is important. High caution should be taken during percutaneous pinning by inserting K-wires under radiological guidance, minimizing pining attempts and limiting pin tip protrusion to 1–2 mm.
Differentiate Clinical Characteristics Between Viral Pneumonia and Mycoplasma pneumoniae and Nomograms for Predicting Mycoplasma pneumoniae: A Retrospective Study in Primary Hospitals
Authors: Guo Huixian , Liang Jingyi , Lin Haowen , Zhou Xingyou , Zhang Zhou , Lai Laiqing , Zhang Tao , Wang Zhufeng , Zhou Junhou , Sun Jiaxi , Liao Jiayi , Jiang Mei , Yang Zifeng
Published: October 2023

Objective:

To identify the difference in clinical characteristics between viral pneumonia and Mycoplasma pneumoniae, providing cues on their differential diagnosis for primary hospitals with the insufficient pathogen detection capacity.

Methods:

We retrospectively reviewed the medical records of hospitalized children with acute respiratory tract infections, and pathogenic microbes test results were analyzed. Clinical characteristics, routine blood parameters and hospitalization duration and fee were compared between M. pneumoniae and viral pneumonia. We used in the multivariable logistic regression to predict the probability of children with M. pneumoniae and graphically represented by a dynamic nomogram. The discrimination and clinical utility of the model were confirmed by receiver operating characteristic and decision curve analysis curves.

Result:

A total of 375 children with community-acquired pneumonia were included. Mycoplasma infection accounted for the largest proportion (22.13%). The incidence of both hypothermia and vomiting was lower in M. pneumoniae compared to viral pneumonia (hypothermia: 10.50% vs. 0.00%; vomiting: 7.90% vs. 0.00%). The prevalence of hyperthermia was higher in M. pneumoniae (hyperthermia: 89.5% vs. 100%). Procalcitonin, peripheral blood white blood cell count and lymphocyte levels were higher in the viral pneumonia group, and eosinophil levels were conversely lower. As for the duration of illness, the mean length of stay was 5.20 ± 2.12 (viral pneumonia) and 6.27 ± 2.48 days (M. pneumoniae). Children with M. pneumoniae had higher overall hospital costs and required more medical treatment. The above were all statistically significant with a P < 0.05. The scoring system was established based on the above results. Receiver operating characteristic curves showed good model-discrimination ability with 0.844 of the area under the curve in the training set and 0.778 in the test set. Decision curve analysis curves demonstrated the discriminative superiority of this model. The web-based dynamic nomogram calculator is accessible at https://zhxylxy0160128.shinyapps.io/Nomogram/.

Conclusion:

Nomograms have satisfactory discrimination, and clinical utility may benefit in predicting the probability of developing M. pneumoniae in children. Children with M. pneumoniae have a higher burden than those with viral pneumonia and may require more intensive in-hospital monitoring.
Assessment of the Clinical Course of Human Rhinovirus/Enterovirus Infections in Pediatric Intensive Care
Authors: Kocoglu Barlas Ulkem , Akcay Nihal , Menentoglu Mehmet Emin , Sevketoglu Esra , Duyu Muhterem , Telhan Leyla , Kangin Murat , Tugrul Hazal Ceren , Erdogan Seher , Durak Cansu , Guney Sahin Ebru , Umur Ozge , Sik Sare Guntulu , Citak Agop , Yaman Ayhan
Published: October 2023

Background:

This study aims to evaluate the clinical course of human rhinovirus/enterovirus (HRV/EV) infections in the pediatric intensive care unit.

Methods:

The study was conducted as a multicenter, prospective observational study from September 2022 to December 2022. Cases with positive polymerase chain reaction testing for HRV/EV of nasopharyngeal swab samples within the first 24 hours of pediatric intensive care unit admission were recorded. There were 2 groups: 1–24 months and >24 months.

Results:

A total of 75 cases (39 male) were included in the study. The median age for all cases was 21 months. The highest polymerase chain reaction positivity rates were observed in October (37.33%). Among the cases, 32 (42.67%) presented with bronchopneumonia/pneumonia, 24 (32%) presented with acute bronchiolitis/bronchitis and 7 (9.33%) presented with sepsis/septic shock. The frequency of pediatric acute respiratory distress syndrome was found to be 6.67%. In the age group of 1–24 months, mean lymphocyte and liver enzyme levels were higher, while in the age group of >24 months, mean hemoglobin and mean kidney function test levels were higher (P ≤ 0.05). Continuous oxygen therapy was provided to 65.3% of the cases, noninvasive ventilation to 33.3%, high-flow nasal cannula-oxygen therapy to 32% and invasive mechanical ventilation to 16%.

Conclusions:

HRV/EV infections primarily affect the respiratory system and generally exhibit a clinical course with low mortality rates (1, 1.3%). In cases with underlying chronic diseases, more severe clinical conditions such as pediatric acute respiratory distress syndrome and septic shock may occur.
Pediatric Utilization of Methicillin-resistant Staphylococcus aureus Nasal Swabs for Antimicrobial Stewardship
Authors: Braga Shienna , Rajapakse Nipunie , Heyliger Jamie , Dierkhising Ross , Dinnes Laura
Published: October 2023

Background:

Methicillin-resistant Staphylococcus aureus (MRSA) can cause serious infections and empiric treatment regimens in children frequently include an anti-MRSA antibiotic. Studies in adults have demonstrated a high negative predictive value (NPV) of MRSA nasal swabs (MNS) in a variety of infectious syndromes. Negative MNS have been utilized as a tool to guide de-escalation of anti-MRSA antibiotics in adults, especially in those with lower respiratory tract infections, but data in children is minimal. The primary objective of this study was to determine the NPV and positive predictive value (PPV) of MNS in children hospitalized for treatment of an infection.

Methods:

This was a single-site, retrospective cohort study of pediatric patients admitted with a suspected infectious diagnosis who had an MNS performed during their hospitalization between June 1, 2018 and November 25, 2022.

Results:

This study identified 172 patients who met the inclusion criteria. Eleven (6.4%) nasal swabs were positive for MRSA and 10 (5.8%) microbiological cultures from suspected sources of infection were identified to be positive for MRSA. The MNS was found to have a sensitivity of 20%, specificity of 94%, PPV of 18% and NPV of 95% for all sites of infection.

Conclusion:

MNS has a high NPV and low PPV in children. MNS can be utilized as an antimicrobial stewardship tool to guide the safe de-escalation of anti-MRSA antibiotics in children.
Functional and anatomical analyses of active spinal circuits in a mouse model of chronic pain
Authors: Targowska-Duda Katarzyna M. , Peters Darian , Marcus Jason L. , Zribi Gilles , Toll Lawrence , Ozawa Akihiko
Published: October 2023

Decades of efforts in elucidating pain mechanisms, including pharmacological, neuroanatomical, and physiological studies have provided insights into how nociceptive information transmits from the periphery to the brain and the locations receiving nociceptive signals. However, little is known about which specific stimulus-dependent activated neurons, amongst heterogeneous neural environments, discriminatively evoke the cognate pain behavior. We here shed light on the population of neurons in the spinal cord activated by a painful stimulus to identify chronic pain-dependent activated neuronal subsets using Fos2A-iCreER (TRAP2) mice. We have found a large number of neurons activated by a normally nonpainful stimulus in the spinal cord of spinal nerve–ligated mice, compared with sham. Neuronal activation was observed in laminae I and II outer under heat hyperalgesia. A large number of neurons in laminae II inner were activated in both mechanical allodynia and heat hyperalgesia conditions, while mechanical allodynia tends to be the only stimulus that activates cells at lamina II inner dorsal region. Neuroanatomical analyses using spinal cell markers identified a large number of spinal inhibitory neurons that are recruited by both mechanical allodynia and heat hyperalgesia. Of interest, spinal neurons expressing calretinin, calbindin, and parvalbumin were activated differently with distinct pain modalities (ie, mechanical allodynia vs heat hyperalgesia). Chemogenetic inhibition of those activated neurons significantly and specifically reduced the response to the pain stimulus associated with the stimulus modality originally given to the animals. These findings support the idea that spinal neuronal ensembles underlying nociceptive transmission undergo dynamic changes to regulate selective pain responses.