bluuebunny/crossref_metadata_2025_split huggingface dataset:
scRNA-seq profiling of neonatal and adult thymus-derived CD4+ T cells by a T cell origin-time tracing model
Authors: Han Yuheng , Ouyang Xinxing , Chen Yao , Lai Shujing , Sun Hongxiang , Wu Ningbo , Ruan Chun , Lu Limin , Su Bing 
Published: December 2022

ABSTRACT
It is well documented that the neonatal thymus-derived (neonatal-TD) regulatory T cells (Treg) are essential to prevent lethal autoimmune diseases and allergies, and neonatal and adult thymus possesses distinct output potentials for naïve T cells, including Treg. However, the molecular features and detailed functional differences between neonatal-TD and adult thymus-derived (adult-TD) T cells in terms of their ability to maintain immune homeostasis during long-term environmental influences are still largely unknown, partially due to the lack of appropriate animal models to precisely trace these cells at specific time points. In this study, neonatal-TD and adult-TD CD4+ T cells from the spleen and Peyer's patches were traced for 9 weeks by a T cell origin-time tracing mouse model and analysed by single-cell RNA sequencing. More Treg but fewer naïve T cells were found in neonatal-TD CD4+ T cells from both tissues than those from adult-TD counterparts. Interestingly, the neonatal-TD Treg in both the spleen and Peyer's patches exhibited augmented expression of Foxp3, Gata3, Ctla4, Icos, Il2ra, Tgfb1, and Nrp1, as well as enriched Gene Ontology terms like T cell activation and tolerance induction, indicating an enhanced immunosuppressive function. These results were further confirmed by flow cytometry analysis and in vitro immune suppression assays. Flow cytometry also revealed a significantly higher proportion of neonatal-TD Treg in total Treg than that of adult-TD counterparts, suggesting the longer lifespan of neonatal-TD Treg. To investigate the intrinsic features of neonatal-TD and adult-TD CD4+ T cells, a shortened tracing time was performed. Surprisingly, the neonatal-TD and adult-TD CD4+ T cells had similar proportions of Treg and did not exhibit significant differences in Foxp3, Gata3, Ctla4, Icos, Il2ra, and Tgfb1 expression levels after tracing for 12 days. On the other hand, neonatal-TD Treg present an increased Nrp1 expression level compared with adult-TD counterparts, indicating the enhanced stability. Together, our work reveals that the neonatal-TD Treg are more immunosuppressive, which is likely shaped primarily by environmental factors.
The InternationalOryzaMap Alignment Project (IOMAP): the Americas—past achievements and future directions
Authors: Alsantely Aseel , Gutaker Rafal , Navarrete Rodríguez María E , Arrieta-Espinoza Griselda , Fuchs Eric J , Costa de Oliveira Antonio , Tohme Joe , Zuccolo Andrea , Wing Rod A , Fornasiero Alice 
Published: December 2022

AbstractThe wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of &gt;600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of ‘IOMAP: the Americas’ is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
Central concentration of asymmetric features in post-starburst galaxies at z ∼ 0.8
Authors: Himoto Kazuharu G , Kajisawa Masaru 
Published: December 2022

ABSTRACT
We present morphological analyses of post-starburst galaxies (PSBs) at 0.7 &lt; z &lt; 0.9 in the COSMOS field. We fitted ultraviolet to mid-infrared multiband photometry of objects with i &lt; 24 from COSMOS2020 catalogue with population synthesis models assuming non-parametric, piece-wise constant function of star formation history, and selected 94 of those galaxies that have high specific star formation rates (SSFRs) of more than 10−9.5 yr−1 in 321–1000 Myr before observation and an order-of-magnitude lower SSFRs within recent 321 Myr. We devised a new non-parametric morphological index which quantifies concentration of asymmetric features, CA, and measured it as well as concentration C and asymmetry A on the Hubble Space Telescope/Advanced Camera for Surveys IF814W-band images. While relatively high C and low A values of PSBs are similar to those of quiescent galaxies rather than star-forming galaxies, we found that PSBs show systematically higher values of CA than both quiescent and star-forming galaxies; 36 per cent of PSBs have log CA &gt; 0.8, while only 16 per cent (2 per cent) of quiescent (star-forming) galaxies show such high CA values. Those PSBs with high CA have relatively low overall asymmetry of A ∼ 0.1, but show remarkable asymmetric features near the centre. The fraction of those PSBs with high CA increases with increasing SSFR in 321–1000 Myr before observation rather than residual ongoing star formation. These results and their high surface stellar mass densities suggest that those galaxies experienced a nuclear starburst in the recent past, and processes that cause such starbursts could lead to the quenching of star formation through rapid gas consumption, supernova/active galactic nucleus feedback, and so on.
A Small Change With a Twist Ending: A Single Residue in EGF-CFC Drives Bilaterian Asymmetry
Authors: Truchado-García Marta , Perry Kimberly J , Cavodeassi Florencia , Kenny Nathan J , Henry Jonathan Q , Grande Cristina 
Published: December 2022

Abstract
Asymmetries are essential for proper organization and function of organ systems. Genetic studies in bilaterians have shown signaling through the Nodal/Smad2 pathway plays a key, conserved role in the establishment of body asymmetries. Although the main molecular players in the network for the establishment of left-right asymmetry (LRA) have been deeply described in deuterostomes, little is known about the regulation of Nodal signaling in spiralians. Here, we identified orthologs of the egf-cfc gene, a master regulator of the Nodal pathway in vertebrates, in several invertebrate species, which includes the first evidence of its presence in non-deuterostomes. Our functional experiments indicate that despite being present, egf-cfc does not play a role in the establishment of LRA in gastropods. However, experiments in zebrafish suggest that a single amino acid mutation in the egf-cfc gene in at least the common ancestor of chordates was the necessary step to induce a gain of function in LRA regulation. This study shows that the egf-cfc gene likely appeared in the ancestors of deuterostomes and “protostomes”, before being adopted as a mechanism to regulate the Nodal pathway and the establishment of LRA in some lineages of deuterostomes.
Mutations in CmVPS41 controlling resistance to cucumber mosaic virus display specific subcellular localization
Authors: Real Núria , Villar Irene , Serrano Irene , Guiu-Aragonés Cèlia , Martín-Hernández Ana Montserrat 
Published: December 2022

AbstractResistance to cucumber mosaic virus (CMV) in melon (Cucumis melo L.) has been described in several exotic accessions and is controlled by a recessive resistance gene, cmv1, that encodes a vacuolar protein sorting 41 (CmVPS41). cmv1 prevents systemic infection by restricting the virus to the bundle sheath cells, preventing viral phloem entry. CmVPS41 from different resistant accessions carries two causal mutations, either a G85E change, found in Pat-81 and Freeman’s cucumber, or L348R, found in PI161375, cultivar Songwhan Charmi (SC). Here, we analyzed the subcellular localization of CmVPS41 in Nicotiana benthamiana and found differential structures in resistant and susceptible accessions. Susceptible accessions showed nuclear and membrane spots and many transvacuolar strands, whereas the resistant accessions showed many intravacuolar invaginations. These specific structures colocalized with late endosomes. Artificial CmVPS41 carrying individual mutations causing resistance in the genetic background of CmVPS41 from the susceptible variety Piel de Sapo (PS) revealed that the structure most correlated with resistance was the absence of transvacuolar strands. Coexpression of CmVPS41 with viral movement proteins, the determinant of virulence, did not change these localizations; however, infiltration of CmVPS41 from either SC or PS accessions in CMV-infected N. benthamiana leaves showed a localization pattern closer to each other, with up to 30% cells showing some membrane spots in the CmVPS41SC and fewer transvacuolar strands (reduced from a mean of 4 to 1–2) with CmVPS41PS. Our results suggest that the distribution of CmVPS41PS in late endosomes includes transvacuolar strands that facilitate CMV infection and that CmVPS41 re-localizes during viral infection.
Determinants of health-related quality of life across the spectrum of connective tissue diseases using latent profile analysis: results from the LEAP cohort
Authors: Dyball Sarah , Reynolds John A , Herrick Ariane L , Haque Sahena , Chinoy Hector , Bruce Ellen , Naz Sophia , Parker Ben , Bruce Ian N 
Published: December 2022

Abstract

Objectives
Poor health-related quality of life (HRQoL) is well recognized in patients with CTD. We hypothesized that subgroups of patients across the spectrum of CTD experience different HRQoL patterns and aimed to determine patient-level characteristics associated with these different subgroups.

Methods
Using the eight continuous domains of the Medical Outcomes Study 36-item Short Form (SF-36) questionnaire we performed data-driven clustering to derive latent profiles (LPs) of patients with distinct HRQoL patterns. Multivariable ordinal logistic regression was used to determine patient-level characteristics associated with each HRQoL subgroup identified.

Results
A total of 309 CTD patients completed the SF-36 questionnaire. The most impaired SF-36 domains in each disease group were vitality, general health and bodily pain. The physical component of the SF-36 was consistently more impaired compared with the mental component, with similar scores across disease groups. Three LPs were identified with poor [n = 89 (29%)], average [n = 190 (61.4%)] and excellent [n = 30 (9.7%)] HRQoL. LPs were not associated with diagnostic grouping or autoantibody profiles. Black background [odds ratio (OR) 0.22 (95% CI 0.08, 0.63)], Indo-Asian background [OR 0.39 (95% CI 0.19, 0.78)], concomitant fibromyalgia [OR 0.40 (95% CI 0.20, 0.78)], sicca symptoms [OR 0.56 (95% CI 0.32, 0.98)] and multimorbidity [Charlson Comorbidity Index; OR 0.81 (95% CI 0.67, 0.97)] were associated with the ‘poor’ HRQoL LP.

Conclusion
Distinct HRQoL subgroups exist that are not primarily driven by a specific diagnosis or autoantibody profiles. We identified a number of key demographic and clinical factors associated with poor HRQoL. These factors need to be addressed across the whole CTD spectrum as part of a holistic management approach aimed at improving overall patient outcomes.
Endoscopic Ultrasound-guided Transluminal Gallbladder Drainage in Patients With Acute Cholecystitis
Authors: Irani Shayan S. , Sharma Neil R. , Storm Andrew C. , Shah Raj J. , Chahal Prabhleen , Willingham Field F. , Swanstrom Lee , Baron Todd H. , Shlomovitz Eran , Kozarek Richard A. , Peetermans Joyce A. , McMullen Edmund , Ho Evelyne , van der Merwe Schalk W. 
Published: December 2022

Objective:
To evaluate the safety and efficacy of endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) using a lumen-apposing metal stent (LAMS).

Background:
For patients with acute cholecystitis who are poor surgical candidates, EUS-GBD using a LAMS is an important treatment alternative to percutaneous gallbladder drainage.

Methods:
We conducted a regulatory-compliant, prospective multicenter trial at 7 tertiary referral centers in the United States of America and Belgium. Thirty consecutive patients with mild or moderate acute cholecystitis who were not candidates for cholecystectomy were enrolled between September 2019 and August 2021. Eligible patients had a LAMS placed transmurally with 30 to 60-day indwell if removal was clinically indicated, and 30-day follow-up post-LAMS removal. Endpoints included days until acute cholecystitis resolution, reintervention rate, acute cholecystitis recurrence rate, and procedure-related adverse events (AEs).

Results:
Technical success was 93.3% (28/30) for LAMS placement and 100% for LAMS removal in 19 patients for whom removal was attempted. Five (16.7%) patients required reintervention. Mean time to acute cholecystitis resolution was 1.6±1.5 days. Acute cholecystitis symptoms recurred in 10.0% (3/30) after LAMS removal. Five (16.7%) patients died from unrelated causes. Procedure-related AEs were reported to the FDA in 30.0% (9/30) of patients, including one fatal event 21 days after LAMS removal; however, no AEs were causally related to the LAMS.

Conclusions:
For selected patients with acute cholecystitis who are at elevated surgical risk, EUS-GBD with LAMS is an alternative to percutaneous gallbladder drainage. It has high technical and clinical success, with low recurrence and an acceptable AE rate. Clinicaltrials.gov, Number: NCT03767881.
PD-L1 regulates inflammatory macrophage development from human pluripotent stem cells by maintaining interferon-gamma signal
Authors: Cao Handi , Xiang Yang , Zhang Shihui , Chao Yiming , Guo Jilong , Ho Joshua W. K. , Huang Yuanhua , Liu Pentao , Sugimura Ryohichi 
Published: December 2022

AbstractPD-L1 (programmed death-ligand 1) serves as a pivotal immune checkpoint in both the innate and adaptive immune systems. PD-L1 is expressed in macrophages in response to interferon-gamma (IFNγ). We examined whether PD-L1 might regulate macrophage development. We establishedPD-L1-/-human pluripotent stem cells, differentiated them into macrophages, and observed a 60% reduction of CD11B+CD45+macrophages inPD-L1-/-, orthogonally verified with PD-L1 inhibitor BMS-1166 reduced macrophages to the same fold. Single-cell RNA sequencing further confirmed the 60% reduction of macrophages as well as the down-regulation of macrophage-defining transcription factorsSPI1, KLF6, andMAFB. Further,PD-L1-/-macrophages reduced the level of inflammatory signals such as NFκB, TNF, and chemokines CXCL and CCL families. Whilst anti-inflammatory TGF-β was upregulated. Finally, we identified thatPD-L1-/-macrophages significantly down-regulated interferon-stimulated genes (ISGs) despite IFNγ in differentiation media. Mechanistically,PD-L1-/-macrophages reducedIFNGR1expression explaining that cells could not respond to IFNγ. These data suggest that PD-L1 regulates inflammatory macrophage development by maintaining the IFNγ signal.
The impact of study design choices on significance and generalizability of canonical correlation analysis in neuroimaging studies
Authors: Pigeau Grace , Costantino Manuela , Devenyi Gabriel A. , Bussy Aurelie , Parent Olivier , Chakravarty M. Mallar 
Published: December 2022

AbstractThis technical note describes the effects of different data reduction methods and sample sizes for neuroimaging studies in the context of canonical correlation analysis (CCA). CCA is a multivariate statistical technique which has gained increasing popularity in neuroimaging research in recent years. Here, we investigate the parcellation methods’ impact on elucidating neuroanatomical relationships (based on cortical thickness) with known risk factors related to Alzheimer’s disease risk using data from the UK Biobank. The cortical thickness values were parcellated using four common methods in neuroimaging (atlas-based parcellation, spectral clustering, principal component analysis, and independent component analysis) and results from CCA were compared. The results show that the choice of parcellation technique impacts the strength and significance of the correlation between the brain and behaviours. Principal component analysis and independent component analysis result in the strongest correlations.Additionally, we show that regardless of parcellation technique, smaller sample sizes of participants result in inflated correlation strength and significance.
Towards a General Approach for Bat Echolocation Detection and Classification
Authors: Aodha Oisin Mac , Martínez Balvanera Santiago , Damstra Elise , Cooke Martyn , Eichinski Philip , Browning Ella , Barataud Michel , Boughey Katherine , Coles Roger , Giacomini Giada , Swiney G. M. Cristina Mac , Obrist Martin K. , Parsons Stuart , Sattler Thomas , Jones Kate E. 
Published: December 2022

AbstractAcoustic monitoring is an effective and scalable way to assess the health of important bioindicators like bats in the wild. However, the large amounts of resulting noisy data requires accurate tools for automatically determining the presence of different species of interest. Machine learning-based solutions offer the potential to reliably perform this task, but can require expertise in order to train and deploy.We propose BatDetect2, a novel deep learning-based pipeline for jointly detecting and classifying bat species from acoustic data. Distinct from existing deep learning-based acoustic methods, BatDetect2’s outputs are interpretable as they directly indicate at what time and frequency a predicted echolocation call occurs. BatDetect2 also makes use of surrounding temporal information in order to improve its predictions, while still remaining computationally efficient at deployment time.We present experiments on five challenging datasets, from four distinct geographical regions (UK, Mexico, Australia, and Brazil). BatDetect2 results in a mean average precision of 0.88 for a dataset containing 17 bat species from the UK. This is significantly better than the 0.71 obtained by a traditional call parameter extraction baseline method.We show that the same pipeline, without any modifications, can be applied to acoustic data from different regions with different species compositions. The data annotation, model training, and evaluation tools proposed will enable practitioners to easily develop and deploy their own models. BatDetect2 lowers the barrier to entry preventing researchers from availing of effective deep learning bat acoustic classifiers. Open source software is provided at:https://github.com/macaodha/batdetect2
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants
Authors: Fu Yunfan , Bedő Justin , Papenfuss Anthony T. , Rubin Alan F. 
Published: December 2022

AbstractEvaluating the impact of amino acid variants has been a critical challenge for studying protein function and interpreting genomic data. High-throughput experimental methods like deep mutational scanning (DMS) can measure the effect of large numbers of variants in a target protein, but because DMS studies have not been performed on all proteins, researchers also model DMS data computationally to estimate variant impacts by predictors. In this study, we extended a linear regression-based predictor to explore whether incorporating data from alanine scanning (AS), a widely-used low-throughput mutagenesis method, would improve prediction results. To evaluate our model, we collected 146 AS datasets, mapping to 54 DMS datasets across 22 distinct proteins. We show that improved model performance depends on the compatibility of the DMS and AS assays, and the scale of improvement is closely related to the correlation between DMS and AS results.
Histology-associated transcriptomic heterogeneity in ovarian folliculogenesis revealed by quantitative single-cell RNA-sequencing for tissue sections with DRaqL
Authors: Ikeda Hiroki , Miyao Shintaro , Nagaoka So , Yamamoto Takuya , Kurimoto Kazuki 
Published: December 2022

ABSTRACTHigh-quality single-cell RNA-sequencing (RNA-seq) with spatial resolution remains challenging. Laser capture microdissection (LCM) is a widely used, potent approach to isolate arbitrarily targeted cells from tissue sections for comprehensive transcriptomics. Here, we developed DRaqL (direct RNA recovery and quenching for LCM), an experimental approach for efficient lysis of single cells isolated by LCM from alcohol- and formalin-fixed sections without RNA purification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable to that of profiling from freshly dissociated cells, together with effective exon– exon junction profiling. Furthermore, the combination of DRaqL and protease treatment enabled robust and efficient single-cell transcriptome analysis from tissue sections strongly fixed with formalin. Applying this method to mouse ovarian sections, we revealed a transcriptomic continuum of growing oocytes quantitatively associated with oocyte size, and detected oocyte-specific splice isoforms. In addition, our statistical model revealed heterogeneity of the relationship between the transcriptome of oocytes and their size, resulting in identification of a size–transcriptome relationship anomaly in a subset of oocytes. Finally, we identified genes that were differentially expressed in granulosa cells in association with the histological affiliations of granulosa cells to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ–soma relationship. Thus, we developed a versatile, efficient approach for robust single-cell cDNA amplification from tissue sections and provided an experimental platform conducive to high-quality transcriptomics, thereby revealing histology-associated transcriptomic heterogeneity in folliculogenesis in ovarian tissues.
Flattening the Curve is Imperative: When China Relaxes the Dynamic Zero COVID-19 Policy
Authors: Zhao Shilei , Sha Tong , Xue Yongbiao , Chen Hua 
Published: December 2022

AbstractSince December 7, 2022, China relaxed the strict dynamic zero COVID-19 policy. Here we quantitatively analyze its potential impacts on COVID-19 trend with the epidemiological model SUVQC using the population and parameter settings of Beijing as a case. Our results indicate that if non-pharmacological interventions are completely ceased, the ICU bed demand number will peak in 26 days at ∼23.88 thousand, which is 18 times the total number of ICU beds in Beijing. COVID-19 Omicron will cause 31,817 deaths in Beijing in the first year. We urge that the flattening curve strategy is necessary to slow down the infection and avoid overwhelming the healthcare system.