bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of strong lensing observations to dark matter substructure: a case study with Euclid
Authors: O’Riordan Conor M , Despali Giulia , Vegetti Simona , Lovell Mark R , Moliné Ángeles 
Published: March 2023

ABSTRACTWe introduce a machine learning method for estimating the sensitivity of strong lens observations to dark matter subhaloes in the lens. Our training data include elliptical power-law lenses, Hubble Deep Field sources, external shear, and noise and PSF for the Euclid VIS instrument. We set the concentration of the subhaloes using a vmax–rmax relation. We then estimate the dark matter subhalo sensitivity in 16 000 simulated strong lens observations with depth and resolution resembling Euclid VIS images. We find that with a 3σ detection threshold, 2.35 per cent of pixels inside twice the Einstein radius are sensitive to subhaloes with a mass Mmax ≤ 1010 M⊙, 0.03 per cent are sensitive to Mmax ≤ 109 M⊙, and the limit of sensitivity is found to be Mmax = 108.8 ± 0.2 M⊙. Using our sensitivity maps and assuming CDM, we estimate that Euclid-like lenses will yield $1.43^{+0.14}_{-0.11}[f_\mathrm{sub}^{-1}]$ detectable subhaloes per lens in the entire sample, but this increases to $35.6^{+0.9}_{-0.9}[f_\mathrm{sub}^{-1}]$ per lens in the most sensitive lenses. Estimates are given in units of the inverse of the substructure mass fraction $f_\mathrm{sub}^{-1}$. Assuming fsub = 0.01, one in every 70 lenses in general should yield a detection, or one in every ∼ three lenses in the most sensitive sample. From 170 000 new strong lenses detected by Euclid, we expect ∼2500 new subhalo detections. We find that the expected number of detectable subhaloes in warm dark matter models only changes relative to cold dark matter for models which have already been ruled out, i.e. those with half-mode masses Mhm &gt; 108 M⊙.
Growing the first galaxies’ merger trees
Authors: Nadler Ethan O , Benson Andrew , Driskell Trey , Du Xiaolong , Gluscevic Vera 
Published: March 2023

ABSTRACT
Modelling the growth histories of specific galaxies often involves generating the entire population of objects that arise in a given cosmology and selecting systems with appropriate properties. This approach is highly inefficient when targeting rare systems such as the extremely luminous high-redshift galaxy candidates detected by JWST. Here, we present a novel framework for generating merger trees with branches that are guaranteed to achieve a desired halo mass at a chosen redshift. This method augments extended Press Schechter theory solutions with constrained random processes known as Brownian bridges and is implemented in the open-source semi-analytic model galacticus. We generate ensembles of constrained merger trees to predict the growth histories of seven high-redshift JWST galaxy candidates, finding that these systems most likely merge ≈2 Gyr after the observation epoch and occupy haloes of mass ≳1014 M⊙ today. These calculations are thousands of times more efficient than existing methods, are analytically controlled, and provide physical insights into the evolution of haloes with rapid early growth. Our constrained merger tree implementation is publicly available at https://github.com/galacticusorg/galacticus.
Extremely powerful flare phenomenon of H2O maser in W49N near −40 km s−1
Authors: Volvach A E , Volvach L N , Larionov M G 
Published: March 2023

ABSTRACT
As a result of detailed observations of the water vapour maser at the 22-m Simeiz radio telescope from 2017 June to 2019 December, two powerful flares were recorded in the Galactic source W49N, which occurred near the high-velocity feature −40 km s−1. The extremely powerful flare had an ultrashort duration of about 2 d and reached a flux density of 110 kJy. An ultrashort flare occurred at the top of a less powerful, but ten times longer one. To our knowledge, a flare of a water maser with such extreme characteristics has never been reported before. A correlation between the exponential increase and decrease in the flare flux density and decrease in line widths with increasing flux density, which is characteristic of an unsaturated maser, is found. The maser of the third flare was in a saturated state and provided a large input flux density 9.5 kJy for the occurrence of two powerful flares, the masers of which were in an unsaturated state. New data have been obtained concerning the physical characteristics of the water maser phenomenon during powerful flares.
Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries
Authors: Feng Chao , Wang Jing , Liston Aaron , Kang Ming 
Published: March 2023

AbstractIntrogressive hybridization is widespread in wild plants and has important consequences. However, frequent hybridization between species makes the estimation of the species’ phylogeny challenging, and little is known about the genomic landscape of introgression as it results from complex interactions of multiple evolutionary processes. Here, we reconstructed the phylogeny of ten wild diploid strawberries with whole genome resequencing data and then investigated the influence of recombination rate variation on phylogeny and introgression. We found that genomic regions with low recombination showed reduced levels of incomplete lineage sorting and introgression, and concentrated phylogenetic signals, thus contributing to the most likely species tree of wild diploid strawberries. We revealed complex and widespread introgression across the genus Fragaria, with an average proportion of approximately 4.1% of the extant genome. Introgression tends to be retained in the regions with high recombination rates and low gene density. Furthermore, we identified four SLF genes under selective sweeps that may play potential roles in the possible regain of self-incompatibility by ancient introgression. Altogether, our study yielded novel insights into the evolutionary history and genomic characteristics of introgression in wild diploid strawberries and provides evidence for the role of introgression in plant mating system transitions.
Filament assembly underpins the double-stranded DNA specificity of AIM2-like receptors
Authors: Garg Archit , Stallings Christina M , Sohn Jungsan 
Published: March 2023

AbstractUpon sensing cytosolic- and/or viral double-stranded (ds)DNA, absent-in-melanoma-2 (AIM2)-like-receptors (ALRs) assemble into filamentous signaling platforms to initiate inflammatory responses. The versatile yet critical roles of ALRs in host innate defense are increasingly appreciated; however, the mechanisms by which AIM2 and its related IFI16 specifically recognize dsDNA over other nucleic acids remain poorly understood (i.e. single-stranded (ss)DNA, dsRNA, ssRNA and DNA:RNA hybrid). Here, we find that although AIM2 can interact with various nucleic acids, it preferentially binds to and assembles filaments faster on dsDNA in a duplex length-dependent manner. Moreover, AIM2 oligomers assembled on nucleic acids other than dsDNA not only display less ordered filamentous structures, but also fail to induce the polymerization of downstream ASC. Likewise, although showing broader nucleic acid selectivity than AIM2, IFI16 binds to and oligomerizes most readily on dsDNA in a duplex length-dependent manner. Nevertheless, IFI16 fails to form filaments on single-stranded nucleic acids and does not accelerate the polymerization of ASC regardless of bound nucleic acids. Together, we reveal that filament assembly is integral to nucleic acid distinction by ALRs.
Endogenous retrovirus-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization
Authors: Yu Miao , Hu Xiaoqian , Pan Zihang , Du Cui , Jiang Jing , Zheng Wanshan , Cai Han , Wang Yinan , Deng Wenbo , Wang Haibin , Lu Jinhua , Sun Ming-an , Cao Bin 
Published: March 2023

AbstractEndogenous retroviruses (ERVs) have been proposed as a driving force for the evolution of the mammalian placenta, however, the contribution of ERVs to placental development and the underlying regulatory mechanism remain largely elusive. A key process of placental development is the formation of multinucleated syncytiotrophoblasts (STBs) in direct contact with maternal blood, through which constitutes the maternal-fetal interface critical for nutrient allocation, hormone production and immunological modulation during pregnancy. We delineate that ERVs profoundly rewire the transcriptional program of trophoblast syncytialization. Here, we first determined the dynamic landscape of bivalent ERV-derived enhancers with dual occupancy of H3K27ac and H3K9me3 in human trophoblast stem cells (hTSCs). We further demonstrated that enhancers overlapping several ERV families tend to exhibit increased H3K27ac and reduced H3K9me3 occupancy in STBs relative to hTSCs. Particularly, bivalent enhancers derived from the Simiiformes-specific MER50 transposons were linked to a cluster of genes important for STB formation. Importantly, deletions of MER50 elements adjacent to several STB genes, including MFSD2A and TNFAIP2, significantly attenuated their expression concomitant to compromised syncytium formation. Together, we propose that ERV-derived enhancers, MER50 specifically, fine-tune the transcriptional networks accounting for human trophoblast syncytialization, which sheds light on a novel ERV-mediated regulatory mechanism underlying placental development.
BACH1 deficiency prevents neointima formation and maintains the differentiated phenotype of vascular smooth muscle cells by regulating chromatin accessibility
Authors: Guo Jieyu , Qiu Jingjing , Jia Mengping , Li Qinhan , Wei Xiangxiang , Li Liliang , Pan Qi , Jin Jiayu , Ge Fei , Ma Siyu , He Yunquan , Lin Jiayi , Li Yongbo , Ma Jinghua , Jiang Nan , Zhi Xiuling , Jiang Lindi , Zhang Jianyi , Osto Elena , Jing Qing , Wang Xinhong , Meng Dan 
Published: March 2023

Abstract
The transcription factor BTB and CNC homology 1(BACH1) has been linked to coronary artery disease risk by human genome-wide association studies, but little is known about the role of BACH1 in vascular smooth muscle cell (VSMC) phenotype switching and neointima formation following vascular injury. Therefore, this study aims to explore the role of BACH1 in vascular remodeling and its underlying mechanisms. BACH1 was highly expressed in human atherosclerotic plaques and has high transcriptional factor activity in VSMCs of human atherosclerotic arteries. VSMC-specific loss of Bach1 in mice inhibited the transformation of VSMC from contractile to synthetic phenotype and VSMC proliferation and attenuated the neointimal hyperplasia induced by wire injury. Mechanistically, BACH1 suppressed chromatin accessibility at the promoters of VSMC marker genes via recruiting histone methyltransferase G9a and cofactor YAP and maintaining the H3K9me2 state, thereby repressing VSMC marker genes expression in human aortic smooth muscle cells (HASMCs). BACH1-induced repression of VSMC marker genes was abolished by the silencing of G9a or YAP. Thus, these findings demonstrate a crucial regulatory role of BACH1 in VSMC phenotypic transition and vascular homeostasis and shed light on potential future protective vascular disease intervention via manipulation of BACH1.
Exposure to ambient air pollution and metabolic kidney diseases: evidence from the Northeast China Biobank
Authors: Zhang Yixiao , Xia Yang , Chang Qing , Ji Chao , Zhao Yuhong , Zhang Hehua 
Published: March 2023

ABSTRACT

Background
At present, there is no epidemiological evidence of the association between metabolic kidney diseases (MKD) and exposure to air pollution.

Methods
We investigated the association between exposure to long-term air pollution and the risk of developing MKD using samples from the Northeast China Biobank.

Results
Data from 29 191 participants were analyzed. MKD prevalence was 3.23%. Every standard deviation increment in PM2.5 increased the risk of MKD [odds ratio (OR) = 1.37, 95% confidence interval (CI) 1.19–1.58), diabetic kidney disease (DKD) (OR = 2.03, 95% CI 1.52–2.73), hypertensive kidney disease (BKD) (OR = 1.31, 95% CI 1.11–1.56), hyperlipidemic kidney disease (PKD) (OR = 1.39, 95% CI 1.19–1.63) and obese kidney disease (OKD) (OR = 1.34, 95% CI 1.00–1.81). PM10 increased the risk of MKD (OR = 1.42, 95% CI 1.20–1.67), DKD (OR = 1.38, 95% CI 1.03–1.85), BKD (OR = 1.30, 95% CI 1.07–1.58) and PKD (OR = 1.50, 95% CI 1.26–1.80). Sulfur dioxide increased the risk of MKD (OR = 1.57, 95% CI 1.34–1.85), DKD (OR = 1.81, 95% CI 1.36–2.40), BKD (OR = 1.44, 95% CI 1.19–1.74) and PKD (OR = 1.72, 95% CI 1.44–2.04). Ozone decreased the risk of PKD (OR = 0.83, 95% CI 0.70–0.99). Age, ethnicity and air pollution interacted to affect the risk of MKD, BKD and PKD. Associations between air pollution and CKD or metabolic disease were weaker than those with MKD. The association between air pollution and MKD became stronger when compared with participants with non-metabolic disease.

Conclusions
Air pollution may cause MKD or facilitate the progression from metabolic disease to renal failure.
Polio virotherapy targets the malignant glioma myeloid infiltrate with diffuse microglia activation engulfing the CNS
Authors: Yang Yuanfan , Brown Michael C , Zhang Gao , Stevenson Kevin , Mohme Malte , Kornahrens Reb , Bigner Darell D , Ashley David M , López Giselle Y , Gromeier Matthias 
Published: March 2023

Abstract

Background
Malignant gliomas commandeer dense inflammatory infiltrates with glioma-associated macrophages and microglia (GAMM) promoting immune suppression, evasion, and tumor progression. Like all cells in the mononuclear phagocytic system, GAMM constitutively express the poliovirus receptor, CD155. Besides myeloid cells, CD155 is widely upregulated in the neoplastic compartment of malignant gliomas. Intratumor treatment with the highly attenuated rhino:poliovirus chimera, PVSRIPO, yielded long-term survival with durable radiographic responses in patients with recurrent glioblastoma (Desjardins et al. New England Journal of Medicine, 2018). This scenario raises questions about the contributions of myeloid versus neoplastic cells to polio virotherapy of malignant gliomas.

Methods
We investigated PVSRIPO immunotherapy in immunocompetent mouse brain tumor models with blinded, board-certified neuropathologist review, a range of neuropathological, immunohistochemical, and immunofluorescence analyses, and RNAseq of the tumor region.

Results
PVSRIPO treatment caused intense engagement of the GAMM infiltrate associated with substantial, but transient tumor regression. This was accompanied by marked microglia activation and proliferation in normal brain surrounding the tumor, in the ipsilateral hemisphere and extending into the contralateral hemisphere. There was no evidence for lytic infection of malignant cells. PVSRIPO-instigated microglia activation occurred against a backdrop of sustained innate antiviral inflammation, associated with induction of the Programmed Cell Death Ligand 1 (PD-L1) immune checkpoint on GAMM. Combining PVSRIPO with PD1/PD-L1 blockade led to durable remissions.

Conclusions
Our work implicates GAMM as active drivers of PVSRIPO-induced antitumor inflammation and reveals profound and widespread neuroinflammatory activation of the brain-resident myeloid compartment by PVSRIPO.
Resting-state functional connectivity in lifelong musicians
Authors: Eierud Cyrus , Michael Andrew , Banks David , Andrews Edna 
Published: March 2023

Abstract

Background
It has been postulated that musicianship can lead to enhanced brain and cognitive reserve, but the neural mechanisms of this effect have been poorly understood. Lifelong professional musicianship in conjunction with novel brain imaging techniques offers a unique opportunity to examine brain network differences between musicians and matched controls.

Objective
In this study we aim to investigate how resting-state functional networks (FNs) manifest in lifelong active musicians. We will evaluate the FNs of lifelong musicians and matched healthy controls using resting-state functional magnetic resonance imaging.

Methods
We derive FNs using the data-driven independent component analysis approach and analyze the functional network connectivity (FNC) between the default mode (DMN), sensory-motor (SMN), visual (VSN), and auditory (AUN) networks. We examine whether the linear regressions between FNC and age are different between the musicians and the control group.

Results
The age trajectory of average FNC across all six pairs of FNs shows significant differences between musicians and controls. Musicians show an increase in average FNC with age while controls show a decrease (P = 0.013). When we evaluated each pair of FN, we note that in musicians FNC values increased with age in DMN–AUN, DMN–VSN, and SMN–VSN and in controls FNC values decreased with age in DMN–AUN, DMN–SMN, AUN–SMN, and SMN–VSN.

Conclusion
This result provides early evidence that lifelong musicianship may contribute to enhanced brain and cognitive reserve. Results of this study are preliminary and need to be replicated with a larger number of participants.
Beyond Dividing the Pie: Multi-Issue Bargaining in the Laboratory
Authors: Bochet Olivier , Khanna Manshu , Siegenthaler Simon 
Published: March 2023

Abstract
We design a laboratory experiment to study bargaining behaviour when negotiations involve multiple issues. Parties must discover both trading prices and agreement scopes, giving rise to unexplored information structures and bargaining strategies. We find that bargainers often trade the efficient set of issues despite lacking information about individual aspects. However, beneficial agreements critically hinge on integrated negotiations that allow deals on bundles of issues. Moreover, access to more information boosts agreement rates in small-surplus negotiations but can also backfire as it triggers increased risk-taking and conflicting fairness preferences in large-surplus negotiations. Finally, successful negotiations display a specific bargaining convention that emerges endogenously. It involves alternating offers that meet the other side’s most recent demand halfway.
Cognitive Control System Gates Insula Processing of Affective Stimuli in Early Psychosis
Authors: Koussis Nikitas C , Burgher Bjorn , Jeganathan Jayson , Scott James G , Cocchi Luca , Breakspear Michael 
Published: March 2023

Abstract

Background and Hypothesis
Impairments in the expression, experience, and recognition of emotion are common in early psychosis (EP). Computational accounts of psychosis suggest disrupted top-down modulation by the cognitive control system (CCS) on perceptual circuits underlies psychotic experiences, but their role in emotional deficits in EP is unknown.

Study Design
The affective go/no-go task was used to probe inhibitory control during the presentation of calm or fearful faces in young persons with EP and matched controls. Computational modeling of functional magnetic resonance imaging (fMRI) data were performed using dynamic causal modeling (DCM). The influence of the CCS on perceptual and emotional systems was examined using parametric empirical bayes.

Study Results
When inhibiting motor response to fearful faces, EP participants showed higher brain activity in the right posterior insula (PI). To explain this, we used DCM to model effective connectivity between the PI, regions from the CCS activated during inhibition (dorsolateral prefrontal cortex [DLPFC] and anterior insula [AI]), and a visual input region, the lateral occipital cortex (LOC). EP participants exerted a stronger top-down inhibition from the DLPFC to the LOC than controls. Within the EP cohort, increased top-down connectivity between the LOC and AI was associated with a higher burden of negative symptoms.

Conclusions
Young persons with a recent onset of psychosis show a disturbance in the cognitive control of emotionally salient stimuli and the suppression of irrelevant distractors. These changes are associated with negative symptoms, suggesting new targets for the remediation of emotional deficits in young persons with EP.
Extracellular Vesicles in the Arbuscular Mycorrhizal Symbiosis: Current Understanding and Future Perspectives
Authors: Holland Samuel , Roth Ronelle 
Published: March 2023

The arbuscular mycorrhizal (AM) symbiosis is an ancient and highly conserved mutualism between plant and fungal symbionts, in which a highly specialized membrane-delimited fungal arbuscule acts as the symbiotic interface for nutrient exchange and signaling. As a ubiquitous means of biomolecule transport and intercellular communication, extracellular vesicles (EVs) are likely to play a role in this intimate cross-kingdom symbiosis, yet, there is a lack of research investigating the importance of EVs in AM symbiosis despite known roles in microbial interactions in both animal and plant pathosystems. Clarifying the current understanding of EVs in this symbiosis in light of recent ultrastructural observations is paramount to guiding future investigations in the field, and, to this end, this review summarizes recent research investigating these areas. Namely, this review discusses the available knowledge regarding biogenesis pathways and marker proteins associated with the various plant EV subclasses, EV trafficking pathways during symbiosis, and the endocytic mechanisms implicated in the uptake of these EVs. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
An Accurate and Individualized Preoperative Estimation Method for the Linear Insertion Depth of Cochlear Implant Electrode Arrays Based on Computed Tomography
Authors: Jia Gaogan , Song Zijun , Wu Lingjie , Sun Qiushi , Sheng Yaru , Ni Yusu , Li Huawei , Li Wenyan 
Published: March 2023

Objectives:
Cochlear implantation or auditory brainstem implantation is currently the only accepted method for improving severe or profound sensorineural hearing loss. The length of the electrodes implanted during cochlear implantation is closely related to the degree of hearing improvement of hearing after the surgery. We aimed to explore new methods to accurately estimate the electrode array (EA) linear insertion depth based on computed tomography (CT) images prior surgery, which could help surgeons select the appropriate EA length for each patient.

Design:
Previous studies estimated the linear insertion depth by measuring the length of the lateral wall of the cochlea rather than the electrode’s path in the cochlea duct. Here, we determined the actual position of the EA on the CT image after cochlear surgery in order to predict the path of the EA, and the length of the predicted EA path was measured by the contouring technique (CoT) to estimate the linear insertion depth of the EA. Because CoT can only measure the length of the estimated EA path on a two-dimensional plane, we further modified the measurement by weighting the height of the cochlea and the length of the EA tail (the length of the last stimulating electrode to the end, which cannot be displayed on the CT image), which we termed the modified CoT + height + tail (MCHT) measurement.

Results:
Based on our established method, MCHT could reduce the error to the submillimeter range (0.67 ± 0.37 mm) when estimating the linear insertion depth of various kinds of EAs compared with the actual implant length. The correlation coefficient between the linear insertion depth as predicted by MCHT and the actual was 0.958. The linear insertion depth estimated by this method was more accurate than that estimated using the classical CoT technique (R = 0.442) and using the modified Escudé’s method (R = 0.585).

Conclusions:
MCHT is a method based on CT images that can accurately predict the linear insertion depth of cochlear implants preoperatively. This is the first report that we are aware of a method for predicting linear insertion depth before cochlear implantation with only submillimeter errors and that is tailored to different types of EAs.