bluuebunny/crossref_metadata_2025 huggingface dataset:
The Health of Children in U.S. Military Families: Evaluation of the 2020-21 National Survey of Children’s Health
Authors: Crouch Elizabeth , Bennett Kevin , Boswell Emma , Odahowski Cassie
Published: September 2024

Introduction

The health of children and adolescents, particularly children of military families, is instrumental for military departments; yet, there has not been an examination on the overall physical health status, or access to health care, among children of military families compared to children of civilian families.

Materials and Methods

This study used the 2020-2021 National Survey of Children’s Health, children aged 0–17 years, to examine the association between military status of the caregiver of the child and the child’s health status, financial stability, and health care access via health insurance coverage (n = 90,711 children). Bivariate analyses used Pearson’s chi-squared tests and were weighted to be nationally representative. Multivariable regression analyses were used to examine the association between military status and selected health outcomes.

Results

In unadjusted analyses, we found that children who had ever had a caregiver serve on active duty were overall more financially stable than children with a civilian caregiver, with children of military families less likely to reside below the federal poverty level and more likely to have continuous health insurance coverage. We also found that children with a caregiver who has ever been on active duty were more likely to have reported mental health needs and more likely to have special health care needs than their civilian counterparts. In adjusted analyses, children with a caregiver who has ever been on active duty were more likely to have special health care needs (adjusted odds ratio [aOR] 1.22; 95% confidence interval [CI] 1.10–1.36) and mental health needs (aOR 1.22; 95% CI 1.10–1.35).

Conclusions

This is the first study, to our knowledge, to do a national examination of overall physical and mental health, as well as specific health conditions and access to health care, among children of military families compared to their civilian counterparts. The findings from this study may be instructive for policymakers and stakeholders in evaluating special needs and mental health resources for military families and improve continuity of health care access through insurance coverage to improve the health of all U.S. children and adolescents.
Evaluation of an in-house pan-Malassezia quantitative PCR in human clinical samples
Authors: Euzen Victor , Ghelfenstein-Ferreira Théo , Benhadid-Brahmi Yasmine , Teboul Alexandra , Dellière Sarah , Benderdouche Mazouz , Charlier Véronique , Desnos-Ollivier Marie , Hamane Samia , Alanio Alexandre
Published: September 2024

Althought Malassezia spp. have been involved in various pathologies, they are an integral part of the cutaneous, gut, oral, ears, nose and throat (ENT) mycobiota. Since Malassezia are difficult to grow in culture, unexhaustive molecular biology methods have been developed to detect them. The aim of the study was to evaluate an in-house pan-Malassezia quantitative polymerase chain reaction (panM-qPCR) on various clinical human samples and determine Malassezia burden in various human mycobiota. The panM-qPCR was designed to target the repeated 28S rDNA gene from all Malassezia species. We used the assay to quantify the Malassezia burden on 361 samples from 161 subjects (80 skin swabs from 10 healthy volunteers (HV), 13 samples from 2 seborrheic dermatitis patients (SD), 90 skin samples from 19 burned patients, 119 stool samples from 89 immunocompromised patients, 59 ENT samples from 41 patients). For HV, the amount of Malassezia was different according to the swabbed areas. Quantification cycle (Cq) in SD is lower than in HV. In burned patients, Cq was significantly lower compared to HV. In stool samples, 6.7% were positive for Malassezia spp. with a high Cq. For the ENT area, a higher proportion of positive specimens were detected in ear samples than in nose samples. Our findings emphasized the importance of qPCR, confirming elevated Malassezia spp. levels on individuals' faces and scalps, increased burden in SD patients and in severely burnt patients than in HV. The pan-MqPCR appears to be a promising tool for studying Malassezia in various human mycobiota.
The effects of stellar and AGN feedback on the cosmic star formation history in the simba simulations
Authors: Scharré Lucie , Sorini Daniele , Davé Romeel
Published: September 2024

Using several variants of the cosmological simba simulations, we investigate the impact of different feedback prescriptions on the cosmic star formation history. Adopting a global-to-local approach, we link signatures seen in global observables, such as the star formation rate density (SFRD) and the galaxy stellar mass function (GSMF), to feedback effects in individual galaxies. We find a consistent picture: stellar feedback mainly suppresses star formation below halo masses of $M_{\rm H} = 10^{12} \rm \, {\rm M}_{\odot }$ and before $z = 2$, whereas AGN feedback quenches the more massive systems after $z = 2$. Among simba’s AGN feedback modes, AGN jets are the dominant quenching mechanism and set the shape of the SFRD and the GSMF at late times. AGN-powered winds only suppress the star formation rate in intermediate-mass galaxies ($M_{\rm \star } = 10^{9.5 - 10} \rm \, {\rm M}_{\odot }$), without affecting the overall stellar mass-assembly significantly. At late times, the AGN X-ray feedback mode mainly quenches residual star formation in massive galaxies. Our analysis reveals that this mode is also necessary to produce the first fully quenched galaxies before $z=2$, where the jets alone are inefficient. These initially highly star-forming galaxies contain relatively large black holes, likely strengthening the X-ray-powered heating and ejection of gas from the dense, central region of galaxies. Such extra heating source quenches the local star formation and produces a more variable accretion rate. More generally, this effect also causes the break down of correlations between the specific star formation rate, the accretion rate and the black hole mass.
Signatures of gas flows – II. Connecting the kinematics of the multiphase circumgalactic medium to galaxy rotation
Authors: Nateghi Hasti , Kacprzak Glenn G , Nielsen Nikole M , Sameer  , Murphy Michael T , Churchill Christopher W , Charlton Jane C
Published: September 2024

The multiphase circumgalactic medium (CGM) hosts critical processes that affect galaxy evolution such as accretion and outflows. We searched for evidence of these phenomena by using the EW co-rotation fraction ($f_{\rm EWcorot}$) to study the kinematic connection between the multiphase CGM and host galaxy rotation. We examined CGM absorption from Hubble Space Telescope /Cosmic Origins Spectrograph (including, but not limited to, Si ii, C ii, Si iii, C iii, and O vi) within $21\le D\le ~276$ kpc of 27 galaxies. We find the median $f_{\rm EWcorot}$ for all ions is consistent within errors and the $f_{\rm EWcorot}$ increases with increasing N$({{{\rm H} \rm{\small I}}})$. The $f_{\rm EWcorot}$ of lower ionization gas decreases with increasing $D/R_{\rm vir}$, while O vi and H i are consistent with being flat. The $f_{\rm EWcorot}$ varies minimally as a function of azimuthal angle and is similar for all ions at a fixed azimuthal angle. The larger number of O vi detections enabled us to investigate where the majority of co-rotating gas is found. Highly co-rotating O vi primarily resides along the galaxies’ major axis. Looking at the $f_{\rm EWcorot}$ as a function of ionization potential (${{\rm d}{({f_{\rm EWcorot}})}}/{{\rm d}{(\rm eV)}}$), we find a stronger co-rotation signature for lower ionization gas. There are suggestions of a connection between the CGM metallicity and major axis co-rotation where low-ionization gas with higher $f_{\rm EWcorot}$ exhibits lower metallicity and may trace large-scale filamentary inflows. Higher ionization gas with higher $f_{\rm EWcorot}$ exhibits higher metallicity and may instead trace co-planar recycled gas accretion. Our results stress the importance of comparing absorption originating from a range of ionization phases to differentiate between various gas flow scenarios.
McFine: python-based Monte Carlo multicomponent hyperfine structure fitting
Authors: Williams Thomas G , Watkins Elizabeth J
Published: September 2024

Modelling complex line emission in the interstellar medium (ISM) is a degenerate high-dimensional problem. Here, we present McFine, a tool for automated multicomponent fitting of emission lines with complex hyperfine structure, in a fully automated way. We use Markov chain Monte Carlo (MCMC) to efficiently explore the complex parameter space, allowing for characterizing model denegeracies. This tool allows for both local thermodynamic equilibrium (LTE) and radiative-transfer (RT) models. McFine can fit individual spectra and data cubes, and for cubes encourage spatial coherence between neighbouring pixels. It is also built to fit the minimum number of distinct components, to avoid overfitting. We have carried out tests on synthetic spectra, where in around 90 per cent of cases it fits the correct number of components, otherwise slightly fewer components. Typically, $T_{\rm ex}$ is overestimated and $\tau$ underestimated, but accurate within the estimated uncertainties. The velocity and line widths are recovered with extremely high accuracy, however. We verify McFine by applying to a large Atacama Large Millimeter/submillimeter Array (ALMA) N$_2$H$^+$ mosaic of an high-mass star forming region, G316.75−00.00. We find a similar quality of fit to our synthetic tests, aside from in the active regions forming O-stars, where the assumptions of Gaussian line profiles or LTE may break down. To show the general applicability of this code, we fit CO(J = 2-1) observations of NGC 3627, a nearby star-forming galaxy, again obtaining excellent fit quality. McFine provides a fully automated way to analyse rich data sets from interferometric observations, is open source, and pip-installable.
Using neural network models to estimate stellar ages from lithium equivalent widths: an eagles expansion
Authors: Weaver G , Jeffries R D , Jackson R J
Published: September 2024

We present an artificial neural network (ANN) model of photospheric lithium depletion in cool stars ($3000\lt T_{\rm eff}/{\rm K} \lt 6500$), producing estimates and probability distributions of age from $^7$Li 6708 Å equivalent width (LiEW) and effective temperature data inputs. The model is trained on the same sample of 6200 stars from 52 open clusters, observed in the Gaia-ESO spectroscopic survey, and used to calibrate the previously published analytical eagles model, with ages 2–6000 Myr and $-0.3 \lt $ [Fe/H] $\lt 0.2$. The additional flexibility of the ANN provides some improvements, including better modelling of the ‘lithium dip’ at ages $\lt 50$ Myr and $T_{\rm eff}\sim 3500$ K, and of the intrinsic dispersion in LiEW at all ages. Poor age discrimination is still an issue at ages >1 Gyr, confirming that additional modelling flexibility is not sufficient to fully represent the LiEW–age–T$_{\text{eff}}$ relationship, and suggesting the involvement of further astrophysical parameters. Expansion to include such parameters–rotation, accretion, and surface gravity–is discussed, and the use of an ANN means these can be more easily included in future iterations, alongside more flexible functional forms for the LiEW dispersion. Our methods and ANN model are provided in an updated version 2.0 of the eagles software.
The PIPER survey. II. The globular cluster systems of low surface brightness galaxies in the Perseus cluster
Authors: Janssens Steven R , Forbes Duncan A , Romanowsky Aaron J , Gannon Jonah , Pfeffer Joel , Couch Warrick J , Brodie Jean P , Harris William E , Durrell Patrick R , Bekki Kenji
Published: September 2024

We present Hubble Space Telescope ACS/WFC and WFC3/UVIS imaging for a sample of 50 low-surface brightness (LSB) galaxies in the $\sim 10^{15}$ M$_{\odot }$ Perseus cluster, which were originally identified in ground-based imaging. We measure the structural properties of these galaxies and estimate the total number of globular clusters (GCs) they host. Around half of our sample galaxies meet the strict definition of an ultra-diffuse galaxy (UDG), while the others are UDG-like but are either somewhat more compact or slightly brighter. A small number of galaxies reveal systems with many tens of GCs, rivalling some of the richest GC systems known around UDGs in the Coma cluster. We find the sizes of rich GC systems, in terms of their half-number radii, extending to $\sim$1.2 times the half-light radii of their host galaxy on average. The mean colours of the GC systems are the same, within the uncertainties, as those of their host galaxy stars. This suggests that GCs and galaxy field stars may have formed at the same epoch from the same enriched gas. It may also indicate a significant contribution from disrupted GCs to the stellar component of the host galaxy as might be expected in the ‘failed galaxy’ formation scenario for UDGs.
Prospect of precision cosmology and testing general relativity using binary black holes – galaxies cross-correlation
Authors: Afroz Samsuzzaman , Mukherjee Suvodip
Published: September 2024

Modified theories of gravity predict deviations from general relativity (GR) in the propagation of gravitational waves (GWs) across cosmological distances. A key prediction is that the GW luminosity distance will vary with redshift, differing from the electromagnetic (EM) luminosity distance due to varying effective Planck mass. We introduce a model-independent, data-driven approach to explore these deviations using multimessenger observations of dark standard sirens [binary black holes (BBH)]. By combining GW luminosity distance measurements from dark sirens with baryon acoustic oscillation measurements, BBH redshifts inferred from cross-correlation with spectroscopic or photometric galaxy surveys, and sound horizon measurements from the cosmic microwave background, we can make a data-driven test of GR (jointly with the Hubble constant) as a function of redshift. Using the multimessenger technique with the spectroscopic DESI galaxy survey, we achieve precise measurements of deviations in the effective Planck mass variation with redshift. For the Cosmic Explorer and Einstein Telescope (CEET), the best precision is approximately 3.6 per cent, and for LIGO–Virgo–KAGRA (LVK), it is 7.4 per cent at a redshift of $\rm {z = 0.425}$. Additionally, we can measure the Hubble constant with a precision of about 1.1 per cent from CEET and 7 per cent from LVK over 5 yr of observation with a 75 per cent duty cycle. We also explore the potential of cross-correlation with photometric galaxy surveys from the Rubin Observatory, extending measurements up to a redshift of $\rm {z \sim 2.5}$. This approach can reveal potential deviations from models affecting GW propagation using numerous dark standard sirens in synergy with DESI and the Rubin Observatory.
One-point statistics in various cosmic environments in the presence of massive neutrinos
Authors: Khoshtinat Mohadese , Hatamnia Hossein , Baghram Shant
Published: September 2024

Studying the structures (haloes and galaxies) within the cosmic environments (void, sheet, filament, and node) where they reside is an ongoing attempt in cosmological studies. The link between the properties of structures and the cosmic environments may help to unravel the nature of the dark sector of the Universe. In this paper, we study the cosmic web environments from the spatial pattern perspective in the context of Lambda cold dark matter ($\Lambda$CDM) and $\nu \Lambda$CDM as an example of an extension to the vanilla model. To do this, we use the T-web classification method and classify the cosmic environments for the catalogues from the gevolution N-body simulations for $\Lambda$CDM and $\nu \Lambda$CDM cosmology. Then, we compute the first nearest neighbour cumulative distribution function, spherical contact cumulative distribution function, and $J$-function for every cosmic environment. In the context of the standard model, the results indicate that these functions can differentiate the various cosmic environments. In association with distinguishing between extensions of the standard model of cosmologies, these functions within the cosmic environment seem beneficial as a complementary probe.
Vertical shear instability with partially reflecting boundary conditions
Authors: Wu Yuzi , Yu Cong , Cui Can
Published: September 2024

The vertical shear instability (VSI) is widely believed to be effective in driving turbulence in protoplanetary discs (PPDs). Prior studies on VSI exclusively exploit the reflecting boundary conditions (BCs) at the disc surfaces. VSI depends critically on the boundary behaviours of waves at the disc surfaces. We extend earlier studies by performing a comprehensive numerical analysis of VSI with partially reflecting BCs for both the axisymmetric and non-axisymmetric unstable VSI modes. We find that the growth rates of the unstable modes diminish when the outgoing component of the flow is greater than the incoming one for high-order body modes. When the outgoing wave component dominates, the growth of VSI is notably suppressed. We find that the non-axisymmetric modes are unstable and they grow at a rate that decreases with the azimuthal wavenumber. The different BCs at the lower and upper disc surfaces naturally lead to non-symmetric modes relative to the disc mid-plane. The potential implications of our studies for further understanding planetary formation and evolution in PPDs are also briefly discussed.
Why Naturalism? Translating Homo Natura Back into Nietzsche’s Text
Authors: Janaway Christopher
Published: September 2024

This article questions a common reading of Section 230 of Beyond Good and Evil as containing a canonical statement of Nietzsche’s naturalism. The section cannot be read simply as the programmatic statement of an investigative task, and is relatively vague as to its nature. Nietzsche’s aim is aporetic. He presents the naturalist task as involving mental self-cruelty and a struggle with unconscious vanity, suggesting that thinkers have found no way to justify why they choose this task, unless they invoke self-descriptions which are false and belong to a metaphysical conception of truth and inquiry that naturalism must resist. In the Genealogy, Nietzsche revisits this theme and announces his task as that of calling into question these justifications of naturalist inquiry.
Nietzsche’s Curse on Christianity
Authors: Tevenar Gudrun von
Published: September 2024

This paper explores background features in the development of Nietzsche’s criticism of Christianity by following him through what I have termed his conventional stage, his critical stage, and his stage of outrage. Next to examining some of his various criticisms during those stages, I also ask what the challenges were to which these criticisms responded and why Nietzsche eventually responded to these challenges with outrage. Outrage towards Christianity is unmistakably expressed in Nietzsche’s late work The Antichrist: A Curse on Christianity. To understand Nietzsche’s outrage better we need to explore the role of ‘Antichrist’ in the title of that work and the meaning of ‘curse’ in its subtitle.
Nanoscale elemental and morphological imaging of nitrogen-fixing cyanobacteria
Authors: Duersch Bobby G , Soini Steven A , Luo Yanqi , Liu Xiaoyang , Chen Si , Merk Vivian M
Published: September 2024

Nitrogen-fixing cyanobacteria bind atmospheric nitrogen and carbon dioxide using sunlight. This experimental study focused on a laboratory-based model system, Anabaena sp., in nitrogen-depleted culture. When combined nitrogen is scarce, the filamentous prokaryotes reconcile photosynthesis and nitrogen fixation by cellular differentiation into heterocysts. To better understand the influence of micronutrients on cellular function, 2D and 3D synchrotron X-ray fluorescence mappings were acquired from whole biological cells in their frozen-hydrated state at the Bionanoprobe, Advanced Photon Source. To study elemental homeostasis within these chain-like organisms, biologically relevant elements were mapped using X-ray fluorescence spectroscopy and energy-dispersive X-ray microanalysis. Higher levels of cytosolic K+, Ca2+, and Fe2+ were measured in the heterocyst than in adjacent vegetative cells, supporting the notion of elevated micronutrient demand. P-rich clusters, identified as polyphosphate bodies involved in nutrient storage, metal detoxification, and osmotic regulation, were consistently co-localized with K+ and occasionally sequestered Mg2+, Ca2+, Fe2+, and Mn2+ ions. Machine-learning-based k-mean clustering revealed that P/K clusters were associated with either Fe or Ca, with Fe and Ca clusters also occurring individually. In accordance with XRF nanotomography, distinct P/K-containing clusters close to the cellular envelope were surrounded by larger Ca-rich clusters. The transition metal Fe, which is a part of nitrogenase enzyme, was detected as irregularly shaped clusters. The elemental composition and cellular morphology of diazotrophic Anabaena sp. was visualized by multimodal imaging using atomic force microscopy, scanning electron microscopy, and fluorescence microscopy. This paper discusses the first experimental results obtained with a combined in-line optical and X-ray fluorescence microscope at the Bionanoprobe.
Using nucleolytic toxins as restriction enzymes enables new RNA applications
Authors: Rothweiler Ulli , Gundesø Sigurd Eidem , Mikalsen Emma Wu , Svenning Steingrim , Singh Mahavir , Combes Francis , Pettersson Frida J , Mangold Antonia , Piotrowski Yvonne , Schwab Felix , Lanes Olav , Striberny Bernd Ketelsen
Published: September 2024

Over the past five decades, DNA restriction enzymes have revolutionized biotechnology. While these enzymes are widely used in DNA research and DNA engineering, the emerging field of RNA and mRNA therapeutics requires sequence-specific RNA endoribonucleases. Here, we describe EcoToxN1, a member of the type III toxin-antitoxin family of sequence-specific RNA endoribonucleases, and its use in RNA and mRNA analysis. This enzyme recognizes a specific pentamer in a single-stranded RNA and cleaves the RNA within this sequence. The enzyme is neither dependent on annealing of guide RNA or DNA oligos to the template nor does it require magnesium. Furthermore, it performs over a wide range of temperatures. With its unique functions and characteristics, EcoToxN1 can be classified as an RNA restriction enzyme. EcoToxN1 enables new workflows in RNA analysis and biomanufacturing, meeting the demand for faster, cheaper, and more robust analysis methods.
Mei5–Sae3 stabilizes Dmc1 nucleating clusters for efficient Dmc1 assembly on RPA-coated single-stranded DNA
Authors: Wei Chin-Dian , Chang Hao-Yen , Lu Chia-Hua , Chang Chih-Chun , Furukohri Asako , Mwaniki Stephen , Shinohara Akira , Chi Peter , Li Hung-Wen
Published: September 2024

Interhomolog recombination in meiosis requires a meiosis-specific recombinase, Dmc1. In Saccharomyces cerevisiae, the Mei5–Sae3 complex facilitates the loading of Dmc1 onto the replication protein A (RPA)-coated single-stranded DNA (ssDNA) to form nucleoprotein filaments. In vivo, Dmc1 and Mei5–Sae3 are interdependent in their colocalization on the chromosomes. However, the mechanistic role of Mei5–Sae3 in mediating Dmc1 activity remains unclear. We used single-molecule fluorescence resonance energy transfer and colocalization single-molecule spectroscopy experiments to elucidate how Mei5–Sae3 stimulates Dmc1 assembly on ssDNA and RPA-coated ssDNA. We showed that Mei5–Sae3 stabilized Dmc1 nucleating clusters with two to three molecules on naked DNA by preferentially reducing Dmc1 dissociation rates. Mei5–Sae3 also stimulated Dmc1 assembly on RPA-coated DNA. Using green fluorescent protein-labeled RPA, we showed the coexistence of an intermediate with Dmc1 and RPA on ssDNA before RPA dissociation. Moreover, the displacement efficiency of RPA depended on Dmc1 concentration, and its dependence was positively correlated with the stability of Dmc1 clusters on short ssDNA. These findings suggest a molecular model that Mei5–Sae3 mediates Dmc1 binding on RPA-coated ssDNA by stabilizing Dmc1 nucleating clusters, thus altering RPA dynamics on DNA to promote RPA dissociation.
Reconstruction of a robust bacterial replication module
Authors: Wang Tao , He Fan , He Ting , Lin Chen , Guan Xin , Qin Zhongjun , Xue Xiaoli
Published: September 2024

Chromosomal DNA replication is a fundamental process of life, involving the assembly of complex machinery and dynamic regulation. In this study, we reconstructed a bacterial replication module (pRC) by artificially clustering 23 genes involved in DNA replication and sequentially deleting these genes from their naturally scattered loci on the chromosome of Escherichia coli. The integration of pRC into the chromosome, moving from positions farther away to close to the replication origin, leads to an enhanced efficiency in DNA synthesis, varying from lower to higher. Strains containing replication modules exhibited increased DNA replication by accelerating the replication fork movement and initiating chromosomal replication earlier in the replication cycle. The minimized module pRC16, containing only replisome and elongation encoding genes, exhibited chromosomal DNA replication efficiency comparable to that of pRC. The replication module demonstrated robust and rapid DNA replication, regardless of growth conditions. Moreover, the replication module is plug-and-play, and integrating it into Mb-sized extrachromosomal plasmids improves their genetic stability. Our findings indicate that DNA replication, being a fundamental life process, can be artificially reconstructed into replication functional modules. This suggests potential applications in DNA replication and the construction of synthetic modular genomes.
DrugMAP 2.0: molecular atlas and pharma-information of all drugs
Authors: Li Fengcheng , Mou Minjie , Li Xiaoyi , Xu Weize , Yin Jiayi , Zhang Yang , Zhu Feng
Published: September 2024

The escalating costs and high failure rates have decelerated the pace of drug development, which amplifies the research interests in developing combinatorial/repurposed drugs and understanding off-target adverse drug reaction (ADR). In other words, it is demanded to delineate the molecular atlas and pharma-information for the combinatorial/repurposed drugs and off-target interactions. However, such invaluable data were inadequately covered by existing databases. In this study, a major update was thus conducted to the DrugMAP, which accumulated (a) 20831 combinatorial drugs and their interacting atlas involving 1583 pharmacologically important molecules; (b) 842 repurposed drugs and their interacting atlas with 795 molecules; (c) 3260 off-targets relevant to the ADRs of 2731 drugs and (d) various types of pharmaceutical information, including diverse ADMET properties, versatile diseases, and various ADRs/off-targets. With the growing demands for discovering combinatorial/repurposed therapies and the rapidly emerging interest in AI-based drug discovery, DrugMAP was highly expected to act as an indispensable supplement to existing databases facilitating drug discovery, which was accessible at: https://idrblab.org/drugmap/.
IRescue: uncertainty-aware quantification of transposable elements expression at single cell level
Authors: Polimeni Benedetto , Marasca Federica , Ranzani Valeria , Bodega Beatrice
Published: September 2024

Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present IRescue (Interspersed Repeats single-cell quantifier), a software capable of estimating the expression of TE subfamilies at the single-cell level. IRescue incorporates a unique UMI deduplication algorithm to rectify sequencing errors and employs an Expectation-Maximization procedure to effectively redistribute the counts of multi-mapping reads. Our study showcases the precision of IRescue through analysis of both simulated and real single cell and nuclei RNA-seq data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection and recovery. By linking the expression patterns of TE signatures to specific conditions and biological contexts, we unveil insights into their potential roles in cellular heterogeneity and disease progression.
FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models
Authors: Trapotsi Maria-Anna , van Lopik Jasper , Hannon Gregory J , Czech Nicholson Benjamin , Bornelöv Susanne
Published: September 2024

PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are essential for transposon control in animal gonads. In Drosophila ovarian somatic cells, piRNAs are transcribed from large genomic regions called piRNA clusters, which are enriched for transposon fragments and act as a memory of past invasions. Despite being widely present across Drosophila species, somatic piRNA clusters are difficult to identify and study due to their lack of sequence conservation and limited synteny. Current identification methods rely on either extensive manual curation or availability of high-throughput small RNA sequencing data, limiting large-scale comparative studies. We now present FlaHMM, a hidden Markov model developed to automate genomic annotation of flamenco-like unistrand piRNA clusters in Drosophila species, requiring only a genome assembly and transposon annotations. FlaHMM uses transposable element content across 5- or 10-kb bins, which can be calculated from genome sequence alone, and is thus able to detect candidate piRNA clusters without the need to obtain flies and experimentally perform small RNA sequencing. We show that FlaHMM performs on par with piRNA-guided or manual methods, and thus provides a scalable and efficient approach to piRNA cluster annotation in new genome assemblies. FlaHMM is freely available at https://github.com/Hannon-lab/FlaHMM under an MIT licence.
Approaches for prevention of tumors in patients with rhabdoid tumor predisposition syndrome
Authors: Geethadevi Anupa , Raabe Eric H
Published: September 2024

Patients with rhabdoid tumor predisposition syndrome (RTPS) harbor germline alterations in the epigenetic regulator genes SMARCB1 or SMARCA4. Patients usually present with atypical teratoid/rhabdoid tumor (AT/RT) of the brain or malignant rhabdoid tumor (MRT) arising outside the central nervous system. Intensive treatment can lead to remissions, however tumors frequently recur or synchronous or metachronous tumors appear. A maintenance or secondary prevention regimen may prevent these aggressive tumors. Potential maintenance regimens may include low-dose traditional chemotherapy or different epigenetic therapies designed to target the epigenetic imbalance that drives RTs. We here review several potential maintenance regimens that may be useful in RTPS.
Perspectives on phase engineering of nanomaterials
Authors: Shi Zhenyu , Wu Yuxuan , Ruan Xinyang , Zhai Wei , Li Zijian , Zhai Li , Zhang An , Zhang Hua
Published: September 2024

This perspective highlights the representative progress of phase engineering of nanomaterials (PEN) with an emphasis on noble metals and transition metal dichalcogenides, and proposes future directions in this emerging field.
Targeted imaging of lysosomal zinc ions with a tetrahedral DNA framework fluorescent reporter
Authors: Gao Yue , Liu Xia , Li Wei , Chen Yuncong , Zhu Shitai , Yan Qinglong , Geng Shanshan , Zhang Jichao , Guan Yong , Li Qian , Jia Sisi , Wang Lihua , Li Jiang , He Weijiang , Fan Chunhai , Guo Zijian , Zhu Ying
Published: September 2024

Abnormal levels of zinc ions within endo-lysosomes have been implicated in the progression of Alzheimer's disease (AD), yet the detection of low-concentration zinc ions at the organelle level remains challenging. Here we report the design of an endo-lysosome-targeted fluorescent reporter, Znluorly, for imaging endogenous zinc ions. Znluorly is constructed from an amphiphilic DNA framework (DNF) with programmable size and shape, which can encapsulate zinc-responsive fluorophores within its hydrophobic nanocavity. We find that the tetrahedral DNFs of 20 bp in the edge length are effectively located within endo-lysosomes, which can detect zinc ions with a detection limit of ∼31.9 nM (a sensitivity that is ∼2.5 times that of the free fluorophore). Given the organelle-targeting ability and high zinc sensitivity of Znluorly, we employ it to detect endogenous endo-lysosomal zinc ions in neuron cells. We monitor the dynamics of zinc levels in AD model cells and zebrafish, corroborating the positive correlation between zinc levels and AD hallmarks including Aβ aggregates and learning/memory impairments. Our study provides a generalizable strategy for organelle-specific theranostic applications.
Local social vulnerability as a predictor for cancer-related mortality among US counties
Authors: Uduba Raymond , Rath Divya , Gillum Richard
Published: September 2024

This letter to the editor comments on the report by Chen et al that examined county-level social vulnerability index and age adjusted cancer mortality rates using linear regression models.
Informative priors can account for location uncertainty in stop-level analyses of the North American Breeding Bird Survey, allowing fine-scale ecological analyses
Authors: Burner Ryan C , Kirschbaum Alan , Hostetler Jeffrey A , Ziolkowski David J , Anich Nicholas M , Turek Daniel , Striegel Eli D , Niemuth Neal D
Published: September 2024

Ecological inferences are often based on the locations at which species are present, but many species records have substantial uncertainty in spatial metadata, limiting their utility for fine-scale analyses. This is especially prevalent in historical records such as museum specimens, and in some citizen-science data. For example, the North American Breeding Bird Survey (BBS) has 55+ years of bird data from regular transects (“routes”) across the continent but was not designed to capture the spatial component of point count events, limiting analyses of species-habitat relationships for which it would otherwise be well suited. We present a new methodology for quantifying location uncertainty in BBS records using digitized estimated stop locations, deriving the corresponding environmental covariate uncertainty distributions, and incorporating this information into hierarchical species distribution models using informative Bayesian priors. This approach allows for estimation of species–environment relationships in a way that fully accounts for underlying spatial uncertainty. We quantify stop-location uncertainty in BBS data across the central United States, model bird–land cover relationships in the upper Midwest, and validate our method by comparing posterior land cover estimates to known covariate values for a subset of Global Positioning System (GPS)-digitized stop locations. We provide code for implementing this method in R. Posterior land cover estimates (forest, grass/hay, and developed land cover), based on our informative priors, were highly correlated with known land cover values from GPS-digitized stop locations. Our approach thus makes it possible to responsibly leverage large historical and citizen-science databases, such as the BBS, for fine-scale ecological analyses.
Climate change and languages: the threat of climate-induced migration to the world’s vulnerable languages
Authors: Brown Jason , Middleton John
Published: September 2024

The concepts of “loss” and “damage” relate to the effects of anthropogenic climate changes that affect people’s livelihoods. This short communication proposes that these concepts should be broadened to include cultural intangibles such as language. Migration caused by climate change is a known phenomenon, as are the potentially negative effects migration has on language vitality. We link these concepts together to argue that climate change can have a direct negative impact on the relative health of endangered languages. Focusing on Pacific islands and atolls, it is demonstrated that migration away from these homelands results in decline of use of the associated language. With the effects of climate change on these islands well documented, there is a distinct possibility that climate migration could cause language loss in the near future. We suggest that culturally protective public policies alongside climate policies are needed to support languages (and by extension, cultures) from “loss” and “damage”.
Simultaneous spectroscopic and TESS observations of the short-period Algol-type system: U Coronae Borealis
Authors: Narusawa Shin-ya , Nagai Kazuo , Maeno Syota , Nishimura Masayoshi , Maehara Hiroyuki
Published: September 2024

The H$\alpha$ spectra of the short-period Algol-type system U Corona Borealis were obtained in the primary minima during an observational period of the Transiting Exoplanet Survey Satellite (TESS) satellite. A profile was subtracted from another one that was observed after 11 orbits in the same orbital phase. The resulting H$\alpha$ “difference profile” of U CrB revealed the presence of circumstellar matter. On the other hand, because apparent disturbances did not appear in the light curve obtained from TESS, circumstellar matter observed in this study has no influence on the light curve, at least in the observational pass-band of TESS and the orbital period. The new ephemeris for the primary minimum has been determined.
La pharmacothérapie en fonction des gènes chez les enfants et les adolescents qui prennent des médicaments psychoactifs
Authors: Verstegen Ruud H J , Cohn Iris , Feldman Mark E , Gorman Daniel , Ito Shinya
Published: September 2024

Les médicaments psychoactifs sont de plus en plus utilisés pour traiter les enfants et les adolescents ayant des troubles de santé mentale, mais la variabilité des réponses individuelles fait ressortir l’importance d’une médecine personnalisée. Les tests pharmacogénétiques sont un volet important d’un tel type de médecine. Le nombre d’entreprises de tests pharmacogénétiques commerciaux qui font la promotion de tests de ce genre et promettent un traitement efficace et individualisé des troubles de santé mentale se multiplie depuis quelques années. Les preuves scientifiques en appui à l’utilisation de la pharmacogénétique sont limitées, particulièrement dans les populations pédiatriques. Le présent point de pratique souligne les étapes qui orientent le recours à ces tests pour la prise de médicaments psychoactifs en milieu clinique et présente des ressources de soutien importantes. Il existe des directives cliniques sur les variants des pharmacogènes qui encodent les enzymes de métabolisation du cytochrome P450 (p. ex., CYP2C19, CYP2D6, CYP2C9), lesquels sont l’un des déterminants des concentrations pharmacologiques dans le sang et peuvent appuyer à la fois le choix du médicament et la stratégie posologique de certains antipsychotiques, antidépresseurs et antiépileptiques. Les effets indésirables de certains médicaments antiépileptiques (p. ex., la carbamazépine et la phénytoïne) sont associés à certains types d’antigènes d’histocompatibilité humaine et à des variants de l’ADN polymérase gamma (POLG; acide valproïque). Les données probantes sont limitées à l’égard des variants génétiques des protéines qui ciblent les médicaments, et c’est pourquoi il est difficile de déterminer quels patients présenteraient une réponse altérée au traitement à une concentration sanguine thérapeutique.
Améliorer la sécurité à vélo chez les enfants et les adolescents
Authors: Rosenfield Daniel , Fuselli Pamela , Beno Suzanne
Published: September 2024

Le vélo demeure une activité populaire pour les enfants et les adolescents du monde entier; elle combine le plaisir de se déplacer rapidement et de nombreux avantages pour la santé et la société. Cependant, le vélo est également associé à un risque de blessures graves et de décès. Depuis dix ans, les recherches démontrent de plus en plus que l’amélioration de la sécurité des cyclistes dépend en grande partie de l’environnement dans lequel ils se déplacent et de mesures de sécurité individuelles comme le port du casque. Pour de nombreux enfants et adolescents, la pandémie a accru les possibilités de faire du vélo et, et elle ramené l’attention du public vers des infrastructures cyclables sécuritaires, telles que des voies cyclables réservées. Le présent document de principes passe en revue les données probantes en appui à des infrastructures cyclables plus sécuritaires pour les enfants et les adolescents, de même que les bienfaits du vélo pour la santé physique et mentale. Les avantages du transport actif chez les jeunes et l’influence de l’environnement bâti sur la sécurité et l’adoption du vélo sont exposés. Un aperçu des mesures que chacun peut prendre pour améliorer la sécurité à vélo est suivi de recommandations pour les cliniciens, la communauté des cyclistes, les parents et les décideurs.
A leucine-rich-repeat receptor-like kinase regulates pollen aperture formation in rice
Authors: Zhang Xu , Kim Yu-Jin , Tan Qian , Jung Ki Hong , Liang Wanqi
Published: September 2024

Apertures in pollen grains exhibit species-specific patterns and provide an ideal model for studying cell surface patterning. Pollen apertures are critical for cereal crop fertility, and while DEFECTIVE IN APERTURE FORMATION1 (OsDAF1) and INAPERTURATE POLLEN1 (OsINP1) have been documented to participate in pollen aperture formation in rice (Oryza sativa), the molecular transduction pathway regulating aperture formation is largely unknown. Here, we report that a leucine-rich-repeat receptor-like kinase (LRR-RLK), APERTURE MISSING1 (AM1), plays a key role in rice pollen aperture formation. Mutations of OsAM1 lead to complete sterility due to the disappearance of the pollen aperture and failure in pollen tube germination. OsAM1 encodes a LRR-RLK that belongs to the STRUBBELIG-receptor family. Similar to other reported aperture regulators, OsAM1 assembles to future aperture sites on tetrads after meiosis to regulate aperture formation. The extracellular and intracellular domain of OsAM1 interacts with OsINP1 and OsDAF1, respectively. However, despite their interaction and the absence of aperture formation in osam1 pollen grains, OsINP1 and OsDAF1 localize to future aperture sites at the tetrad stage. Mutation of OsINP1, however, disrupts normal localization of OsAM1, indicating that OsAM1 acts downstream of OsINP1. Our findings reveal the role of a LRR-RLK protein in pollen aperture formation and shed light on the regulatory network of pollen aperture formation.
The Sure Thing Principle leads to instability
Authors: Gallow J Dmitri
Published: September 2024

Orthodox causal decision theory is unstable. Its advice changes as you make up your mind about what you will do. Several have objected to this kind of instability and explored stable alternatives. Here, I’ll show that explorers in search of stability must part with a vestige of their homeland. There is no plausible stable decision theory which satisfies Savage’s Sure Thing Principle. So those in search of stability must learn to live without it.
Between Decentralization and Asymmetry: Explaining Preferences toward the Division of Power in Canada
Authors: Chassé Philippe , Jacques Olivier , Scott Colin
Published: September 2024

In most federations, the division of power between central and subnational governments represents an important cleavage dividing voters and structuring party systems. Yet we lack a robust body of research regarding individuals’ preferences for different forms of devolved decision-making such as decentralization and asymmetrical federalism. This article contributes to this research agenda by analyzing the effects of identity and grievances on public opinion toward the division of powers in Canada. Leveraging four waves of the Confederation of Tomorrow survey, we find that respondents who identify predominantly with their province are more likely to prefer decentralization and asymmetrical federalism, whereas those who hold grievances against the federation prefer decentralization. Studying provincial variations in the impact of our main variables, we point to the role of the political context by showing that in certain provinces, the political mobilization of grievances strengthens the relationship between provincial identity and support for decentralization.
Enhancing vitamin D levels in care homes: the role of healthy building design in preventing respiratory infections
Authors: Putra Andi Andre Pratama
Published: September 2024

The recent article by Willcox et al. in the Journal of Public Health highlights the effectiveness of antiviral prophylaxis and high-dose vitamin D supplementation in reducing acute respiratory infections (ARIs) in care homes. This correspondence extends the discussion by emphasizing the critical role of healthy building design in enhancing vitamin D levels, which is vital for immune function and ARI prevention. Many care home residents suffer from vitamin D deficiency due to limited sunlight exposure. Incorporating architectural elements such as large windows, skylights, and outdoor spaces can significantly increase natural light exposure, thereby boosting vitamin D levels and potentially reducing ARI susceptibility. Despite the benefits of supplementation, addressing environmental factors through healthy building design offers a sustainable, long-term strategy that aligns with public health goals of preventive care and environmental sustainability. Prioritizing such design principles in care home planning and renovation can enhance residents’ health and resilience against infections like influenza and COVID-19.
‘Sleeping with the enemy’: a cross-sectional study on psychological and emotional violence among couples living in Portugal during the COVID-19 pandemic
Authors: Aguiar Ana , Santos Cordeiro Daniel , Gaio Rita , Soares Sara , Vieira Mariana , Pinto Marta , Duarte Raquel
Published: September 2024

Objective

This study aimed to evaluate psychological and emotional violence in relation with sociodemographic characteristics and anxiety and depression symptoms during the COVID-19 pandemic in a sample of Portuguese residents.

Methods

A cross-sectional online study using snowball sampling collected data on demographics, socioeconomic factors, mental health (anxiety and depression symptoms) and couple psychological and emotional violence. The study spanned three months and included 519 individuals aged 18 or above in a relationship since January 2020 or earlier. Data analysis involved descriptive statistics, t-tests, chi-squared tests, logistic regression models (Odds-Ratio [OR] and 95% Confident Interval [CI]), and cluster analysis (K-medoids) using R software (significance threshold of 0.05).

Results

The sample was predominantly composed of women (78.8%) with an average age of 36.8 years and 79% holding higher education degrees. Two clusters emerged: Cluster 1 (n = 420) presented fewer psychological and emotional violence victims, while Cluster 2 (n = 99) presented more. Older age (OR = 1.026, 95%CI 1.000–1.052) and depression symptoms (OR = 1.163, 95%CI 1.080–1.252) increased the likelihood of psychological and emotional abuse. Men also had 2.87 times higher odds of being victims (95%CI 0.203–0.599).

Conclusions

The study underscores the need for comprehensive interventions and prevention measures to address psychological and emotional violence by acknowledging it as a public health concern and pushing for interdisciplinary methods.