bluuebunny/crossref_metadata_2025_split huggingface dataset:
The quantitative genetic basis of variation in sexual versus non-sexual butterfly wing colouration: autosomal, Z-linked, and maternal effects
Authors: Kemp Darrell J , Wedell Nina 
Published: April 2024

Abstract
Viability indicator traits are expected to be integrated extensively across the genome yet sex-limited to ensure that any benefits are sexually concordant. Understanding how such expectations are accommodated requires elucidating the quantitative genetic architecture of candidate traits in and across the sexes. Here we applied an animal modelling approach to partition the autosomal, allosomal, and direct maternal bases of variation in sexual versus non-sexual dorsal wing colouration in the butterfly Eurema hecabe. The sexual colour trait—coherently scattered ultraviolet that is under strong directional selection due to female choice—is brighter and more expansive in males, and overlays non-sexual pigmentary yellow markings that otherwise dominate both wing surfaces in each sex. Our modelling estimated high and sexually equivalent autosomal variances for ultraviolet reflectance (furnishing h2 ~ 0.58 overall and ~0.75 in males), accompanied by smaller but generally significant Z-linked and maternal components. By contrast, variation in non-sexual yellow was largely attributed to Z-linked sources. Intersexual genetic correlations based upon the major source of variation in each trait were high and not different from 1.0, implying regulation by a pool of genes common to each sex. An expansive autosomal basis for ultraviolet is consistent with its hypothesized role as a genome-wide viability indicator and ensures that both sons and daughters will inherit their father’s attractiveness.
Phylogeography, systematics, and conservation status of pocket mice (Chaetodipus) of the Sonoran–Sinaloan thorn forest
Authors: Hafner David J , Light Jessica E , Neiswenter Sean A , Hernandez Krymsen L , Riddle Brett R 
Published: April 2024

Abstract
Three species of pocket mice (Chaetodipus artus, C. goldmani, and C. pernix) characterize the Sinaloan subregion of the Sonoran regional desert. They occur primarily in Sinaloan thornscrub and monsoon (dry deciduous) forest biotic communities, both of which have suffered from agricultural conversion. Sinaloan thornscrub occurs along the coastal plains of southern Sonora and Sinaloa, México, and grades into monsoon forest in the foothills of the Sierra Madre Occidental. We describe the geographical and ecological distributions of the 3 species of Chaetodipus, evaluate evolutionary relationships within each species based on mitochondrial DNA sequence data, and compare these to previously described phenetic, allozymic, and chromosomal variation. We elevate the subspecies of C. pernix to full species, delineate evolutionary units within C. goldmani and C. artus that we formally recognize as subspecies, and evaluate the conservation status of all 3 species of Chaetodipus.
Spatial variations in leaf trichomes and their coordination with stomata in Quercus variabilis across Eastern Asia
Authors: Zhu Yanhua , Zheng Ji , Kang Hongzhang , Hui Nan , Yin Shan , Chen Zhicheng , Du Baoming , Liu Chunjiang 
Published: April 2024

Abstract
Leaf trichomes are derived from epidermal cells and serve an important function in regulating leaf heat balance and gas exchange. Variation in leaf functional traits is critical for predicting how plants will react to global climate change. In this study, we aimed to investigate how leaf trichome densities vary along large geographic gradients and how they interact with stomata in response to environmental change. We investigated the leaf trichome densities of 44 Quercus variabilis populations in Eastern Asia (24°–51.8° N, 99°–137° E) and their correlation with climatic factors and stomatal traits. In addition, 15 populations were grown in a common garden to study their adaptive variation and coordination with stomata. The mean value of trichome density in situ conditions was 459.78 trichome mm−2 with a range of 325.79–552.38 trichome mm−2. Trichome density increased with latitude and decreased with longitude. Both temperature and precipitation reduced the trichome density. Moreover, trichome density was positively correlated with stomatal density whether in situ or in the common garden, and both increased with drought. Our results suggested that leaf trichomes possess highly adaptive variation and are in close coordination with stomata in response to climate change. Our findings provide new insights toward elucidating the interactions between leaf traits and the adaptive strategies of plants under climate change.
The SAMI Galaxy Survey: galaxy spin is more strongly correlated with stellar population age than mass or environment
Authors: Croom Scott M , van de Sande Jesse , Vaughan Sam P , Rutherford Tomas H , Lagos Claudia del P , Barsanti Stefania , Bland-Hawthorn Joss , Brough Sarah , Bryant Julia J , Colless Matthew , Cortese Luca , D’Eugenio Francesco , Fraser-McKelvie Amelia , Goodwin Michael , Lorente Nuria P F , Richards Samuel N , Ristea Andrei , Sweet Sarah M , Yi Sukyoung K , Zafar Tayyaba 
Published: April 2024

ABSTRACT
We use the SAMI Galaxy Survey to examine the drivers of galaxy spin, $\lambda _{R_{\rm e}}$, in a multidimensional parameter space including stellar mass, stellar population age (or specific star formation rate), and various environmental metrics (local density, halo mass, satellite versus central). Using a partial correlation analysis, we consistently find that age or specific star formation rate is the primary parameter correlating with spin. Light-weighted age and specific star formation rate are more strongly correlated with spin than mass-weighted age. In fact, across our sample, once the relation between light-weighted age and spin is accounted for, there is no significant residual correlation between spin and mass, or spin and environment. This result is strongly suggestive that the present-day environment only indirectly influences spin, via the removal of gas and star formation quenching. That is, environment affects age, then age affects spin. Older galaxies then have lower spin, either due to stars being born dynamically hotter at high redshift, or due to secular heating. Our results appear to rule out environmentally dependent dynamical heating (e.g. galaxy–galaxy interactions) being important, at least within 1 Re where our kinematic measurements are made. The picture is more complex when we only consider high-mass galaxies (M* ≳ 1011 M⊙). While the age-spin relation is still strong for these high-mass galaxies, there is a residual environmental trend with central galaxies preferentially having lower spin, compared to satellites of the same age and mass. We argue that this trend is likely due to central galaxies being a preferred location for mergers.
BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL
Authors: Gothwal Santosh K , Refaat Ahmed M , Nakata Mikiyo , Stanlie Andre , Honjo Tasuku , Begum Nasim A 
Published: April 2024

Abstract
Efficient repair of DNA double-strand breaks in the Ig heavy chain gene locus is crucial for B-cell antibody class switch recombination (CSR). The regulatory dynamics of the repair pathway direct CSR preferentially through nonhomologous end joining (NHEJ) over alternative end joining (AEJ). Here, we demonstrate that the histone acetyl reader BRD2 suppresses AEJ and aberrant recombination as well as random genomic sequence capture at the CSR junctions. BRD2 deficiency impairs switch (S) region synapse, optimal DNA damage response (DDR), and increases DNA break end resection. Unlike BRD4, a similar bromodomain protein involved in NHEJ and CSR, BRD2 loss does not elevate RPA phosphorylation and R-loop formation in the S region. As BRD2 stabilizes the cohesion loader protein NIPBL in the S regions, the loss of BRD2 or NIPBL shows comparable deregulation of S-S synapsis, DDR, and DNA repair pathway choice during CSR. This finding extends beyond CSR, as NIPBL and BRD4 have been linked to Cornelia de Lange syndrome, a developmental disorder exhibiting defective NHEJ and Ig isotype switching. The interplay between these proteins sheds light on the intricate mechanisms governing DNA repair and immune system functionality.
Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes
Authors: De Silva Naiduwadura Ivon Upekala , Lehman Nathan , Fargason Talia , Paul Trenton , Zhang Zihan , Zhang Jun 
Published: April 2024

Abstract
SRSF1 governs splicing of over 1500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but not other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.
Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor
Authors: Wu Yaokang , Li Yang , Liu Yanfeng , Xiu Xiang , Liu Jiaheng , Zhang Linpei , Li Jianghua , Du Guocheng , Lv Xueqin , Chen Jian , Ledesma-Amaro Rodrigo , Liu Long 
Published: April 2024

Abstract
Mutagenesis driving genetic diversity is vital for understanding and engineering biological systems. However, the lack of effective methods to generate in-situ mutagenesis in multiple genomic loci combinatorially limits the study of complex biological functions. Here, we design and construct MultiduBE, a dCas12a-based multiplexed dual-function base editor, in an all-in-one plasmid for performing combinatorial in-situ mutagenesis. Two synthetic effectors, duBE-1a and duBE-2b, are created by amalgamating the functionalities of cytosine deaminase (from hAPOBEC3A or hAID*Δ ), adenine deaminase (from TadA9), and crRNA array processing (from dCas12a). Furthermore, introducing the synthetic separator Sp4 minimizes interference in the crRNA array, thereby facilitating multiplexed in-situ mutagenesis in both Escherichia coli and Bacillus subtilis. Guided by the corresponding crRNA arrays, MultiduBE is successfully employed for cell physiology reprogramming and metabolic regulation. A novel mutation conferring streptomycin resistance has been identified in B. subtilis and incorporated into the mutant strains with multiple antibiotic resistance. Moreover, surfactin and riboflavin titers of the combinatorially mutant strains improved by 42% and 15-fold, respectively, compared with the control strains with single gene mutation. Overall, MultiduBE provides a convenient and efficient way to perform multiplexed in-situ mutagenesis.
Nanoscale millefeuilles produce iridescent bill ornaments in birds
Authors: Nicolaï Michaël P J , Debruyn Gerben , Soenens Mieke , Shawkey Matthew D , D’Alba Liliana 
Published: April 2024

Abstract
Colors are well studied in bird plumage but not in other integumentary structures. In particular, iridescent colors from structures other than plumage are undescribed in birds. Here, we show that a multilayer of keratin and lipids is sufficient to produce the iridescent bill of Spermophaga haematina. Furthermore, that the male bill is presented to the female under different angles during display provides support for the hypothesis that iridescence evolved in response to sexual selection. This is the first report of an iridescent bill, and only the second instance of iridescence in birds in which melanosomes are not involved. Furthermore, an investigation of museum specimens of an additional 98 species, showed that this evolved once, possibly twice. These results are promising, as they suggest that birds utilize a wider array of physical phenomena to produce coloration and should further stimulate research on nonplumage integumentary colors.
Effects of Benzodiazepine Exposure on Real-World Clinical Outcomes in Individuals at Clinical High Risk for Psychosis
Authors: Livingston Nicholas R , De Micheli Andrea , McCutcheon Robert A , Butler Emma , Hamdan Marwa , Grace Anthony A , McGuire Philip , Egerton Alice , Fusar-Poli Paolo , Modinos Gemma 
Published: April 2024

Abstract

Background and Hypothesis
Animal models indicate GABAergic dysfunction in the development of psychosis, and that benzodiazepine (BDZ) exposure can prevent the emergence of psychosis-relevant phenotypes. However, whether BDZ exposure influences real-world clinical outcomes in individuals at clinical high risk for psychosis (CHR-P) is unknown.

Study Design
This observational cohort study used electronic health record data from CHR-P individuals to investigate whether BDZ exposure (including hypnotics, eg, zopiclone) reduces the risk of developing psychosis and adverse clinical outcomes. Cox proportional-hazards models were employed in both the whole-unmatched sample, and a propensity score matched (PSM) subsample.

Study Results
567 CHR-P individuals (306 male, mean[±SD] age = 22.3[±4.9] years) were included after data cleaning. The BDZ-exposed (n = 105) and BDZ-unexposed (n = 462) groups differed on several demographic and clinical characteristics, including psychotic symptom severity. In the whole-unmatched sample, BDZ exposure was associated with increased risk of transition to psychosis (HR = 1.61; 95% CI: 1.03–2.52; P = .037), psychiatric hospital admission (HR = 1.93; 95% CI: 1.13–3.29; P = .017), home visit (HR = 1.64; 95% CI: 1.18–2.28; P = .004), and Accident and Emergency department attendance (HR = 1.88; 95% CI: 1.31–2.72; P &lt; .001). However, after controlling for confounding-by-indication through PSM, BDZ exposure did not modulate the risk of any outcomes (all P &gt; .05). In an analysis restricted to antipsychotic-naïve individuals, BDZ exposure reduced the risk of transition to psychosis numerically, although this was not statistically significant (HR = 0.59; 95% CI: 0.32–1.08; P = .089).

Conclusions
BDZ exposure in CHR-P individuals was not associated with a reduction in the risk of psychosis transition or adverse clinical outcomes. Results in the whole-unmatched sample suggest BDZ prescription may be more likely in CHR-P individuals with higher symptom severity.
Sleep-Deep-Learner is taught sleep–wake scoring by the end-user to complete each record in their style
Authors: Katsuki Fumi , Spratt Tristan J , Brown Ritchie E , Basheer Radhika , Uygun David S 
Published: April 2024

Abstract
Sleep–wake scoring is a time-consuming, tedious but essential component of clinical and preclinical sleep research. Sleep scoring is even more laborious and challenging in rodents due to the smaller EEG amplitude differences between states and the rapid state transitions which necessitate scoring in shorter epochs. Although many automated rodent sleep scoring methods exist, they do not perform as well when scoring new datasets, especially those which involve changes in the EEG/EMG profile. Thus, manual scoring by expert scorers remains the gold standard. Here we take a different approach to this problem by using a neural network to accelerate the scoring of expert scorers. Sleep-Deep-Learner creates a bespoke deep convolution neural network model for individual electroencephalographic or local-field-potential (LFP) records via transfer learning of GoogLeNet, by learning from a small subset of manual scores of each EEG/LFP record as provided by the end-user. Sleep-Deep-Learner then automates scoring of the remainder of the EEG/LFP record. A novel REM sleep scoring correction procedure further enhanced accuracy. Sleep-Deep-Learner reliably scores EEG and LFP data and retains sleep–wake architecture in wild-type mice, in sleep induced by the hypnotic zolpidem, in a mouse model of Alzheimer’s disease and in a genetic knock-down study, when compared to manual scoring. Sleep-Deep-Learner reduced manual scoring time to 1/12. Since Sleep-Deep-Learner uses transfer learning on each independent recording, it is not biased by previously scored existing datasets. Thus, we find Sleep-Deep-Learner performs well when used on signals altered by a drug, disease model, or genetic modification.
Enhanced protein‐metabolite correlation analysis: To investigate the association between Staphylococcus aureus mastitis and metabolic immune pathways
Authors: Chen Kuo , Hu Binhong , Ren Jingyuan , Deng Xin , Li Qing , Zhang Rong , Zhang Yuanyuan , Shen Gengyu , Liu Songqing , Zhang Jiacheng , Lu Pengwei 
Published: April 2024

AbstractMastitis is a disease characterized by congestion, swelling, and inflammation of the mammary gland and usually caused by infection with pathogenic microorganisms. Furthermore, the development of mastitis is closely linked to the exogenous pathway of the gastrointestinal tract. However, the regulatory mechanisms governing the gut‐metabolism‐mammary axis remain incompletely understood. The present study revealed alterations in the gut microbiota of mastitis rats characterized by an increased abundance of the Proteobacteria phylum. Plasma analysis revealed significantly higher levels of L‐isoleucine and cholic acid along with 7‐ketodeoxycholic acid. Mammary tissue showed elevated levels of arachidonic acid metabolites and norlithocholic acid. Proteomic analysis showed increased levels of IFIH1, Tnfaip8l2, IRGM, and IRF5 in mastitis rats, which suggests that mastitis triggers an inflammatory response and immune stress. Follistatin (Fst) and progesterone receptor (Pgr) were significantly downregulated, raising the risk of breast cancer. Extracellular matrix (ECM) receptors and focal adhesion signaling pathways were downregulated, while blood–milk barrier integrity was disrupted. Analysis of protein‐metabolic network regulation revealed that necroptosis, protein digestion and absorption, and arachidonic acid metabolism were the principal regulatory pathways involved in the development of mastitis. In short, the onset of mastitis leads to changes in the microbiota and alterations in the metabolic profiles of various biological samples, including colonic contents, plasma, and mammary tissue. Key manifestations include disturbances in bile acid metabolism, amino acid metabolism, and arachidonic acid metabolism. At the same time, the integrity of the blood–milk barrier is compromised while inflammation is promoted, thereby reducing cell adhesion in the mammary glands. These findings contribute to a more comprehensive understanding of the metabolic status of mastitis and provide new insights into its impact on the immune system.
Biological treatments in childhood asthma
Authors: Nieto-García Antonio , Nieto-Cid María , Mazón-Ramos Ángel 
Published: April 2024

Purpose of review
The aim is to update the information currently available for the use of biologics in severe asthma in children, in order to facilitate their prescription as far as possible.

Recent findings
The appearance of biologics for the treatment of severe asthma has meant a revolutionary change in the therapeutic approach to this disease. Currently, five biologics have been approved for severe asthma in children and/or adolescents by the regulatory agencies: omalizumab, mepolizumab, benralizumab, dupilumab and tezepelumab. But despite their positive results in terms of efficacy, there are still relevant points of debate that should induce caution when selecting the most appropriate biologic in a child with severe asthma. Indeed, safety is essential and, for several of the existing treatments, the availability of medium-term to long-term data in this regard is scarce.

Summary
The use of biologics can facilitate the therapeutic paradigm shift from pleiotropic treatments to personalized medicine. However, the choice of the most appropriate biologics remains a pending issue. On the other hand, to the extent that several of the biologics have been available for a relatively short time, the most robust evidence in terms of efficacy and safety in children is that of omalizumab.
Pooled and global burdens and trends of five common cancers attributable to diet in 204 countries and territories from 1990 to 2019: an analysis of the Global Burden of Disease Study
Authors: Ding Qiang , Ma Xiaoli , Zhang Zerui , Lu Panpan , Liu Mei 
Published: April 2024

Objective
Increasing evidence has shown that dietary behaviors are closely correlated with the carcinogenesis and progression of many types of cancer. However, few studies have assessed the global diet-related burden of cancer. This study aimed to estimate the pooled burdens and trends of five types of cancers attributable to dietary behaviors.

Methods
Data regarding cancer attributable to dietary behaviors were extracted from the Global Burden of Disease study 2019, including the death cases and age-standardized death rates, and disability-adjusted life years (DALYs) estimated according to diseases, age, sex, the socio-demographic index (SDI) and location.

Results
According to the Global Burden of Disease study 2019, five types of cancer were affected by dietary behaviors: colon and rectum cancer; tracheal, bronchus and lung cancer; stomach cancer; esophageal cancer and breast cancer. Unhealthy dietary behaviors for cancer caused a total of 605.4 thousand deaths and 13951.3 thousand DALYs globally. The burden of cancer attributable to dietary risks was higher for men than for women. The highest age-standardized death rates in 2019 were observed in southern Latin America, and the lowest rates were observed in North Africa and the Middle East. The greatest increases in the age-standardized death rates, from 1990 to 2019, were found in Western Sub-Saharan Africa, with the greatest decreases in Central Asia. The highest attributable proportions of death or DALYs were colon and rectum cancer. The greatest diet-related cancer burden was observed in regions with a high-middle SDI.

Conclusion
Global age-standardized deaths and DALYs rates attributable to diet-related cancer are considerable and cause a substantial burden. Successful population-wide initiatives targeting unhealthy dietary behaviors would reduce this burden.