bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remove First Detect Later: a counter-intuitive approach for detecting radio frequency interference in radio sky imagery
Authors: van Zyl Daniel J , Grobler Trienko L 
Published: April 2024

ABSTRACT
The modern era has witnessed a rapid uptake of technological use – from air travel to mobile cellphones. Technological advancement has however come at the cost of radio spectrum crowding and as such the efficient detection of radio frequency interference (RFI) from radio sky images has become more paramount. Detecting RFI is a complex task that blends semantic segmentation and anomaly detection, further complicated by the limited availability of public data sets with accurate ground truth labels. Recent studies show that deep learning models improve RFI detection compared to current state-of-the-art tools. However, many astronomers are hesitant to adopt these models, possibly due to the dependence of these models on noisy labels from existing tools when accurate ground truth labels are largely unavailable in the public domain. This study argues that utilizing large weakly labelled training data sets yields lower performance than appropriately employing a modest set of expertly annotated samples. Further, Remove First Detect Later (RFDL), an augmented deep learning framework, is proposed. First, counter-intuitively, removing RFI with inpainting, RFDL feeds the difference between the original and inpainted images into existing detection models. RFDL’s performance is benchmarked against current state-of-the-art deep learning methods and the prevalent AOFlagger pipeline, using AUROC, AUPRC, and F1 score metrics. It is shown that RFDL significantly outperforms the state-of-the-art while only necessitating the use of 20 expertly labelled images.
MeerKAT and ALMA view of the AGAL045.804 − 0.356 clump
Authors: Seidu Mavis , Chibueze J O , Fuller Gary A , Avison A , Asabre Frimpong N 
Published: April 2024

ABSTRACT
This study presents a detailed analysis of the GAL045.804 − 0.356 massive star-forming clump. A high-angular resolution and sensitivity observations were conducted using MeerKAT at 1.28 GHz and ALMA interferometer at 1.3 mm. Two distinct centimetre radio continuum emissions (source A and source B) were identified within the clump. A comprehensive investigation was carried out on source A, the G45.804 − 0.355 star-forming region (SFR) due to its association with Extended Green Object (EGO), 6.7 GHz methanol maser and the spatial coincidence with the peak of the dust continuum emission at 870 µm. The ALMA observations revealed seven dense dust condensations (MM1–MM7) in source A. The brightest (Sν ∼ 87 mJy) and massive main dense core, MM1, was co-located with the 6.7 GHz methanol maser. Explorations into the kinematics revealed gas motions characterized by a velocity gradient across the MM1 core. Furthermore, molecular line emission showed the presence of an extended arm-like structure, with a physical size of 0.25 pc × 0.18 pc (∼ 50 000 au × 30 000 au) at a distance of 7.3 kpc. Amongst these arms, two arms were prominently identified in both the dust continuum and some of the molecular lines. A blue-shifted absorption P-Cygni profile was seen in the H2CO line spectrum. The findings of this study are both intriguing and new, utilizing data from MeerKAT and ALMA to investigate the characteristics of the AGAL45 clump. The evidence of spiral arms, the compact nature of the EGO and &lt; 2 km s−1 velocity gradient are all indicative of G45.804 − 0.355 being oriented face-on.
SIDE-real: Supernova Ia Dust Extinction with truncated marginal neural ratio estimation applied to real data
Authors: Karchev Konstantin , Grayling Matthew , Boyd Benjamin M , Trotta Roberto , Mandel Kaisey S , Weniger Christoph 
Published: April 2024

ABSTRACT
We present the first fully simulation-based hierarchical analysis of the light curves of a population of low-redshift type Ia supernovæ (SNæ Ia). Our hardware-accelerated forward model, released in the Python package slicsim, includes stochastic variations of each SN’s spectral flux distribution (based on the pre-trained BayeSN model), extinction from dust in the host and in the Milky Way, redshift, and realistic instrumental noise. By utilizing truncated marginal neural ratio estimation (TMNRE), a neural network-enabled simulation-based inference technique, we implicitly marginalize over 4000 latent variables (for a set of ≈100 SNæ Ia) to efficiently infer SN Ia absolute magnitudes and host-galaxy dust properties at the population level while also constraining the parameters of individual objects. Amortization of the inference procedure allows us to obtain coverage guarantees for our results through Bayesian validation and frequentist calibration. Furthermore, we show a detailed comparison to full likelihood-based inference, implemented through Hamiltonian Monte Carlo, on simulated data and then apply TMNRE to the light curves of 86 SNæ Ia from the Carnegie Supernova Project, deriving marginal posteriors in excellent agreement with previous work. Given its ability to accommodate arbitrarily complex extensions to the forward model, e.g. different populations based on host properties, redshift evolution, complicated photometric redshift estimates, selection effects, and non-Ia contamination, without significant modifications to the inference procedure, TMNRE has the potential to become the tool of choice for cosmological parameter inference from future, large SN Ia samples.
The relationship between Behçet’s disease and the quality of life for pediatric patients and their parents
Authors: Şahin Nihal , Bayrak Yunus E , Sönmez Hafize E , Sözeri Betül 
Published: April 2024

ABSTRACT

Objectives
Chronic diseases impact people’s quality of life (QoL). Behçet’s disease (BD) is a multisystemic chronic disease characterized by vasculitis of various vessels. We aimed to assess QoL in paediatric BD (PEDBD) patients and their parents.

Methods
We conducted a cross-sectional study from June to December 2022, including PEDBD patients meeting classification criteria. We recorded clinical characteristics and assessed QoL using PedsQL for patients and WHOQOL-Bref for parents.

Results
A study of 38 patients (60.5% girls, 39.5% boys), median age 15.5 years (range 10–17), with oral aphthae and various mucocutaneous symptoms: genital ulcers (78.9%), pseudofolliculitis (76.3%), erythema nodosum (23.6%), and some with uveitis (13.1%), vascular (13.1%), neurological (10.5%), and gastrointestinal (5.2%) involvement. All were in remission under treatment. Median PedsQL scores: total 74.5 (range 40–94.8), physical health 76.5 (43–100), psychosocial health 75 (25–92); 14 patients scored below cutoff. Girls had lower physical health scores (P = .004), and disease duration correlated negatively with PedsQL score (r = -0.648, P = .001). Median WHOQOL score for parents: 50 (25–100), with 20 scoring below cutoff.

Conclusion
One-third of PEDBD children and over half of their parents had low QoL. Disease duration and gender, as with many chronic illnesses, correlated with QoL in PEDBD.
Self-amplifying RNAs generated with the modified nucleotides 5-methylcytidine and 5-methyluridine mediate strong expression and immunogenicity in vivo
Authors: Azizi Hiva , Renner Tyler M , Agbayani Gerard , Simard Bryan , Dudani Renu , Harrison Blair A , Iqbal Umar , Jia Yimei , McCluskie Michael J , Akache Bassel 
Published: April 2024

Abstract
When utilized in therapeutic applications, synthetic self-amplifying RNA (saRNA) can lead to higher and more sustained expression than standard messenger RNA (mRNA). This feature is particularly important for gene replacement therapy applications where prolonged expression could reduce the dose and frequency of treatments. The inclusion of modified nucleotides in synthetic non-amplifying mRNA has been shown to increase RNA stability, reduce immune activation and enhance gene expression. Preclinical and clinical studies with saRNA have so far exclusively relied on RNA containing the canonical nucleotides adenosine, cytidine, guanosine and uridine. For the first time, we show that noncanonical nucleotides, such as 5-methylcytidine (m5C) and 5-methyluridine (m5U), are sufficiently compatible with a replicon derived from Venezuelan equine encephalitis alphavirus mediating protein translation in vitro, while those containing N1-methylpseudouridine in place of uridine show no detectable expression. When administered in vivo, saRNA generated with m5C or m5U mediates sustained gene expression of the luciferase reporter gene, with those incorporating m5U appearing to lead to more prolonged expression. Finally, distinct antigen-specific humoral and cellular immune responses were induced by modified saRNA encoding the model antigen ovalbumin. The use of modified nucleotides with saRNA-based platforms could enhance their potential to be used effectively in a variety of applications.
Efficacy of Lamivudine Plus Dolutegravir vs Dolutegravir-Based 3-Drug Regimens in People With HIV Who Are Virologically Suppressed
Authors: Borghetti Alberto , Ciccullo Arturo , Lombardi Francesca , Giannarelli Diana , Passerotto Rosa Anna , Lamanna Francesco , Carcagnì Antonella , Farinacci Damiano , Dusina Alex , Baldin Gianmaria , Zazzi Maurizio , Di Giambenedetto Simona 
Published: April 2024

Abstract

Background
Lamivudine + dolutegravir maintenance dual therapy (DT) could be less effective than 3-drug therapy (TT) in the context of resistance-associated mutations to nucleoside reverse transcriptase inhibitors (NRTIs). The ARCA database was queried to test this hypothesis with a trial emulation strategy.

Methods
People with HIV taking 2 NRTIs plus a protease inhibitor or a non-NRTI who switched to DT or dolutegravir-based TT were followed up from the first HIV RNA &lt;50 copies/mL (baseline) to virologic failure (VF; ie, 2 consecutive HIV RNA ≥50 copies/mL or 1 HIV RNA ≥200 copies/mL). Those switching to DT within 6 months were assigned to the treatment arm and all other patients to the control arm. Each participant was also cloned, assigned to the opposite strategy, and censored at the time of deviation from that strategy. Using inverse probability of censoring weight Cox regression models, we calculated hazard ratios of VF for DT vs TT stratified for the presence of resistance-associated mutations.

Results
Overall 626 people were analyzed: 204 with DT and 422 with TT (73% men; mean age, 44 years). Ten and 31 VFs occurred with DT and TT, respectively, over a median 5.8 years. When compared with a fully active TT, the DT had similar efficacy (adjusted hazard ratio, 0.88; 95% CI, .29–2.61; P = .812) when full susceptibility was confirmed at historical genotype. When previous M184V/I was present in both groups, the risk of VF was higher for DT vs TT but was not statistically significant (adjusted hazard ratio, 3.06; 95% CI, .45–20.84; P = .252).

Conclusions
DT was not associated with a significantly higher risk of VF than dolutegravir-based TT.
Syndromic Gastrointestinal Panel Diagnostic Tests Have Changed our Understanding of the Epidemiology of Yersiniosis—Foodborne Diseases Active Surveillance Network, 2010-2021
Authors: Ray Logan C , Payne Daniel C , Rounds Joshua , Trevejo Rosalie T , Wilson Elisha , Burzlaff Kari , Garman Katie N , Lathrop Sarah , Rissman Tamara , Wymore Katie , Wozny Sophia , Wilson Siri , Francois Watkins Louise K , Bruce Beau B , Weller Daniel L 
Published: April 2024

Abstract

Background
In the US, yersinosis was understood to predominantly occur in winter and among Black or African American infants and Asian children. Increased use of culture-independent diagnostic tests (CIDTs) has led to marked increases in yersinosis diagnoses.

Methods
We describe differences in the epidemiology of yersiniosis diagnosed by CIDT versus culture in 10 US sites, and identify determinants of health associated with diagnostic method.

Results
Annual reported incidence increased from 0.3/100 000 in 2010 to 1.3/100 000 in 2021, particularly among adults ≥18 years, regardless of race and ethnicity, and during summer months. The proportion of CIDT-diagnosed infections increased from 3% in 2012 to 89% in 2021. An ill person’s demographic characteristics and location of residence had a significant impact on their odds of being diagnosed by CIDT.

Conclusions
Improved detection due to increased CIDT use has altered our understanding of yersinosis epidemiology, however differential access to CIDTs may still affect our understanding of yersinosis.
APX2 Is an Ascorbate Peroxidase–Related Protein that Regulates the Levels of Plastocyanin in Chlamydomonas
Authors: Caccamo Anna , Vega de Luna Félix , Misztak Agnieszka E , Pyr dit Ruys Sébastien , Vertommen Didier , Cardol Pierre , Messens Joris , Remacle Claire 
Published: April 2024

Abstract
The function of ascorbate peroxidase–related (APX-R) proteins, present in all green photosynthetic eukaryotes, remains unclear. This study focuses on APX-R from Chlamydomonas reinhardtii, namely, ascorbate peroxidase 2 (APX2). We showed that apx2 mutants exhibited a faster oxidation of the photosystem I primary electron donor, P700, upon sudden light increase and a slower re-reduction rate compared to the wild type, pointing to a limitation of plastocyanin. Spectroscopic, proteomic and immunoblot analyses confirmed that the phenotype was a result of lower levels of plastocyanin in the apx2 mutants. The redox state of P700 did not differ between wild type and apx2 mutants when the loss of function in plastocyanin was nutritionally complemented by growing apx2 mutants under copper deficiency. In this case, cytochrome c6 functionally replaces plastocyanin, confirming that lower levels of plastocyanin were the primary defect caused by the absence of APX2. Overall, the results presented here shed light on an unexpected regulation of plastocyanin level under copper-replete conditions, induced by APX2 in Chlamydomonas.
The Arabidopsis Mitochondrial Nucleoid–Associated Protein WHIRLY2 Is Required for a Proper Response to Salt Stress
Authors: Negroni Yuri L , Doro Irene , Tamborrino Alberto , Luzzi Irene , Fortunato Stefania , Hensel Götz , Khosravi Solmaz , Maretto Laura , Stevanato Piergiorgio , Lo Schiavo Fiorella , de Pinto Maria Concetta , Krupinska Karin , Zottini Michela 
Published: April 2024

Abstract
In the last years, plant organelles have emerged as central coordinators of responses to internal and external stimuli, which can induce stress. Mitochondria play a fundamental role as stress sensors being part of a complex communication network between the organelles and the nucleus. Among the different environmental stresses, salt stress poses a significant challenge and requires efficient signaling and protective mechanisms. By using the why2 T-DNA insertion mutant and a novel knock-out mutant prepared by CRISPR/Cas9–mediated genome editing, this study revealed that WHIRLY2 is crucial for protecting mitochondrial DNA (mtDNA) integrity during salt stress. Loss-of-function mutants show an enhanced sensitivity to salt stress. The disruption of WHIRLY2 causes the impairment of mtDNA repair that results in the accumulation of aberrant recombination products, coinciding with severe alterations in nucleoid integrity and overall mitochondria morphology besides a compromised redox-dependent response and misregulation of antioxidant enzymes. The results of this study revealed that WHIRLY2-mediated structural features in mitochondria (nucleoid compactness and cristae) are important for an effective response to salt stress.
Multiple Roles of Brassinosteroid Signaling in Vascular Development
Authors: Furuya Tomoyuki , Ohashi-Ito Kyoko , Kondo Yuki 
Published: April 2024

Abstract
Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for transporting water and nutrients throughout the plant body, initially establishes a tissue pattern during primary development and then dramatically increases the number of vascular cells during secondary development. This complex developmental process is properly regulated by a network consisting of various hormonal signaling pathways. Genetic studies have revealed that mutants that are defective in BR biosynthesis or the BR signaling cascade exhibit a multifaceted vascular development phenotype. Furthermore, BR crosstalk with other plant hormones, including peptide hormones, coordinately regulates vascular development. Recently, the involvement of BR in vascular development, especially in xylem differentiation, has also been suggested in plant species other than the model plant Arabidopsis thaliana. In this review, we briefly summarize the recent findings on the roles of BR in primary and secondary vascular development in Arabidopsis and other species.
ATML1 Regulates the Differentiation of ER Body–Containing Large Pavement Cells in Rosette Leaves of Brassicaceae Plants
Authors: Wilkens Alwine , Czerniawski Paweł , Bednarek Paweł , Libik-Konieczny Marta , Yamada Kenji 
Published: April 2024

Abstract
Endoplasmic reticulum (ER)–derived organelles, ER bodies, participate in the defense against herbivores in Brassicaceae plants. ER bodies accumulate β-glucosidases, which hydrolyze specialized thioglucosides known as glucosinolates to generate bioactive substances. In Arabidopsis thaliana, the leaf ER (LER) bodies are formed in large pavement cells, which are found in the petioles, margins and blades of rosette leaves. However, the regulatory mechanisms involved in establishing large pavement cells are unknown. Here, we show that the ARABIDOPSIS THALIANA MERISTEM L1 LAYER (ATML1) transcription factor regulates the formation of LER bodies in large pavement cells of rosette leaves. Overexpression of ATML1 enhanced the expression of LER body–related genes and the number of LER body–containing large pavement cells, whereas its knock-out resulted in opposite effects. ATML1 enhances endoreduplication and cell size through LOSS OF GIANT CELLS FROM ORGANS (LGO). Although the overexpression and knock-out of LGO affected the appearance of large pavement cells in Arabidopsis, the effect on LER body–related gene expression and LER body formation was weak. LER body–containing large pavement cells were also found in Eutrema salsugineum, another Brassicaceae species. Our results demonstrate that ATML1 establishes large pavement cells to induce LER body formation in Brassicaceae plants and thereby possibly contribute to the defense against herbivores.
The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot
Authors: Wang Ying-Gang , Zhang Yu-Min , Wang Ya-Hui , Zhang Kai , Ma Jing , Hang Jia-Xin , Su Yu-Ting , Tan Shan-Shan , Liu Hui , Xiong Ai-Sheng , Xu Zhi-Sheng 
Published: April 2024

Abstract
Little is known about the factors regulating carotenoid biosynthesis in roots. In this study, we characterized DCAR_032551, the candidate gene of the Y locus responsible for the transition of root color from ancestral white to yellow during carrot (Daucus carota) domestication. We show that DCAR_032551 encodes a REPRESSOR OF PHOTOSYNTHETIC GENES (RPGE) protein, named DcRPGE1. DcRPGE1 from wild carrot (DcRPGE1W) is a repressor of carotenoid biosynthesis. Specifically, DcRPGE1W physically interacts with DcAPRR2, an ARABIDOPSIS PSEUDO-RESPONSE REGULATOR2 (APRR2)-like transcription factor. Through this interaction, DcRPGE1W suppresses DcAPRR2-mediated transcriptional activation of the key carotenogenic genes phytoene synthase 1 (DcPSY1), DcPSY2, and lycopene ε-cyclase (DcLCYE), which strongly decreases carotenoid biosynthesis. We also demonstrate that the DcRPGE1W–DcAPRR2 interaction prevents DcAPRR2 from binding to the RGATTY elements in the promoter regions of DcPSY1, DcPSY2, and DcLCYE. Additionally, we identified a mutation in the DcRPGE1 coding region of yellow and orange carrots that leads to the generation of alternatively spliced transcripts encoding truncated DcRPGE1 proteins unable to interact with DcAPRR2, thereby failing to suppress carotenoid biosynthesis. These findings provide insights into the transcriptional regulation of carotenoid biosynthesis and offer potential target genes for enhancing carotenoid accumulation in crop plants.
Trk-fused gene plays a critical role in diet-induced adipose tissue expansion and is also involved in thyroid hormone action
Authors: Yamamotoya Takeshi , Ohata Yukino , Akasaka Yasuyuki , Hasei Shun , Inoue Masa-Ki , Nakatsu Yusuke , Kanna Machi , Yamazaki Hiroki , Kushiyama Akifumi , Fujishiro Midori , Ono Hiraku , Sakoda Hideyuki , Yamada Tetsuya , Ishihara Hisamitsu , Asano Tomoichiro 
Published: April 2024

Abstract
Mutations in the Trk-fused gene (TFG) cause hereditary motor and sensory neuropathy with proximal dominant involvement, which reportedly has high co-incidences with diabetes and dyslipidemia, suggesting critical roles of the TFG in metabolism as well. We found that TFG expression levels in white adipose tissues (WATs) were elevated in both genetically and diet-induced obese mice and that TFG deletion in preadipocytes from the stromal vascular fraction (SVF) markedly inhibited adipogenesis. To investigate its role in vivo, we generated tamoxifen-inducible adipocyte-specific TFG knockout (AiTFG KO) mice. While a marked down-regulation of the peroxisome proliferator-activated receptor gamma target, de novo lipogenesis (DNL), and mitochondria-related gene expressions were observed in subcutaneous WAT (scWAT) from AiTFG KO mice, these effects were blunted in SVF-derived adipocytes when the TFG was deleted after differentiation into adipocytes, implying cell nonautonomous effects. Intriguingly, expressions of thyroid hormone receptors, as well as carbohydrate responsive element-binding protein β, which mediates the metabolic actions of thyroid hormone, were drastically down-regulated in scWAT from AiTFG KO mice. Reduced DNL and thermogenic gene expressions in AiTFG KO mice might be attributable to impaired thyroid hormone action in vivo. Finally, when adipocyte TFG was deleted in either the early or the late phase of high-fat diet feeding, the former brought about an impaired expansion of epididymal WAT, whereas the latter caused prominent adipocyte cell death. TFG deletion in adipocytes markedly exacerbated hepatic steatosis in both experimental settings. Collectively, these observations indicate that the TFG plays essential roles in maintaining normal adipocyte functions, including an enlargement of adipose tissue, thyroid hormone function, and thermogenic gene expressions, and in preserving hypertrophic adipocytes.