bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of light-dependent functions of GIGANTEA
Authors: Patnaik Alena , Mishra Priyanka , Dash Anish , Panigrahy Madhusmita , Panigrahi Kishore C S 
Published: November 2024

Abstract
GIGANTEA (GI) is a multifaceted plant-specific protein that originated in a streptophyte ancestor. The current known functions of GI include circadian clock control, light signalling, flowering time regulation, stomata response, chloroplast biogenesis, accumulation of anthocyanin, chlorophyll, and starch, phytohormone signalling, senescence, and response to drought, salt, and oxidative stress. Six decades since its discovery, no functional domains have been defined, and its mechanism of action is still not well characterized. In this review, we explore the functional evolution of GI to distinguish between ancestral and more recently acquired roles. GI integrated itself into various existing signalling pathways of the circadian clock, blue light, photoperiod, and osmotic and oxidative stress response. It also evolved parallelly to acquire new functions for chloroplast accumulation, red light signalling, and anthocyanin production. In this review, we have encapsulated the known mechanisms of various biological functions of GI, and cast light on the evolution of GI in the plant lineage.
The physical properties of two potential targets for space missions: (155140) 2005 UD and (612267) 2001 SG286
Authors: Gherase R M , Popescu M , Vaduvescu O , Wilson T G , de León J , Lorenzi V , Licandro J , Morate D , Simion G , Macías A Aznar , Dumitru B A 
Published: November 2024

ABSTRACT
The ground-based characterization of asteroids is a key step for planning their exploration. The near-Earth asteroid 155140 (2005 UD) is a potential flyby target of Japan Aerospace Exploration Agency’s DESTINY+ (Demonstration and Experiment of Space Technology for INterplanetary voYage with Phaethon fLyby and dUst Science) mission, while (612267) 2001 SG286 has been considered as a possible target for in-situ exploration. We aim to determine their physical properties using the observations obtained with various telescopes from Canary Islands Observatory. For 2005 UD, we confirmed the two peak light curve, a rotation period of 5.224 $\pm$ 0.003 h and an amplitude of 0.34 mag. However, a three peak solution seemed also to fit the light curve, but this was discarded as implausible. Using the obtained visible to near-infrared spectrum we classified it as a Cb type, and we found a spectral matching with heated carbonaceous chondrite meteorites of CM2 type. The thermal emission flux at 2.2 $\mu \mathrm{ m}$ points to an albedo of $p_V = 0.06~\pm ~0.02$. There are significant differences in the spectrum of 2005 UD compared to that of (3200) Phaeton, hypothesized as its parent body. The accurate visible spectrum obtained with the Gran Telescopio Canarias indicate that 2001 SG286 is an S-type asteroid. The photometric data obtained with Isaac Newton Telescope suggest a rotation period of 12.30 $\pm$ 0.01 h and an amplitude of 0.64 mag. With these observations we found its absolute magnitude $H$ = 21.4 $\pm$ 0.3, and estimate its size as 160 $\pm$ 45 m.
RBPWorld for exploring functions and disease associations of RNA-binding proteins across species
Authors: Liao Jian-You , Yang Bing , Shi Chuan-Ping , Deng Wei-Xi , Deng Jin-Si , Cen Mei-Feng , Zheng Bing-Qi , Zhan Zi-Ling , Liang Qiao-Ling , Wang Ji-En , Tao Shuang , Lu Daning , Liang Maojin , Zhang Yu-Chan , Yin Dong 
Published: November 2024

Abstract
RNA-binding proteins (RBPs) play key roles in a wide range of physiological and pathological processes. To facilitate the investigation of RBP functions and disease associations, we updated the EuRBPDB and renamed it as RBPWorld (http://research.gzsys.org.cn/rbpworld/#/home). Leveraging 998 RNA-binding domains (RBDs) and 87 RNA-binding Proteome (RBPome) datasets, we successfully identified 1 393 413 RBPs from 445 species, including 3030 human RBPs (hRBPs). RBPWorld includes primary RNA targets of diverse hRBPs, as well as potential downstream regulatory pathways and alternative splicing patterns governed by various hRBPs. These insights were derived from analyses of 1515 crosslinking immunoprecipitation-seq datasets and 616 RNA-seq datasets from cells with hRBP gene knockdown or knockout. Furthermore, we systematically identified 929 RBPs with multi-functions, including acting as metabolic enzymes and transcription factors. RBPWorld includes 838 disease-associated hRBPs and 970 hRBPs that interact with 12 disease-causing RNA viruses. This provision allows users to explore the regulatory roles of hRBPs within the context of diseases. Finally, we developed an intuitive interface for RBPWorld, facilitating users easily access all the included data. We believe that RBPWorld will be a valuable resource in advancing our understanding of the biological roles of RBPs across different species.
StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization
Authors: Feng Yue , Qaseem Ammar , Moumbock Aurélien F A , Pan Shuling , Kirchner Pascal A , Simoben Conrad V , Malange Yvette I , Babiaka Smith B , Gao Mingjie , Günther Stefan 
Published: November 2024

Abstract
Streptomycetes remain an important bacterial source of natural products (NPs) with significant therapeutic promise, particularly in the fight against antimicrobial resistance. Herein, we present StreptomeDB 4.0, a substantial update of the database that includes expanded content and several new features. Currently, StreptomeDB 4.0 contains over 8500 NPs originating from ∼3900 streptomycetes, manually annotated from ∼7600 PubMed-indexed peer-reviewed articles. The database was enhanced by two in-house developments: (i) automated literature-mined NP–protein relationships (hyperlinked to the CPRiL web server) and (ii) pharmacophore-based NP–protein interactions (predicted with the ePharmaLib dataset). Moreover, genome mining was supplemented through hyperlinks to the widely used antiSMASH database. To facilitate NP structural dereplication, interactive visualization tools were implemented, namely the JSpecView applet and plotly.js charting library for predicted nuclear magnetic resonance and mass spectrometry spectral data, respectively. Furthermore, both the backend database and the frontend web interface were redesigned, and several software packages, including PostgreSQL and Django, were updated to the latest versions. Overall, this comprehensive database serves as a vital resource for researchers seeking to delve into the metabolic intricacies of streptomycetes and discover novel therapeutics, notably antimicrobial agents. StreptomeDB is publicly accessible at https://www.pharmbioinf.uni-freiburg.de/streptomedb.
Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites
Authors: Boileau Etienne , Wilhelmi Harald , Busch Anne , Cappannini Andrea , Hildebrand Andreas , Bujnicki Janusz M , Dieterich Christoph 
Published: November 2024

Abstract
We present Sci-ModoM, the first next-generation RNome database offering a holistic view of the epitranscriptomic landscape. Sci-ModoM has a simple yet powerful interface, underpinned by FAIR data principles, a standardized nomenclature, and interoperable formats, fostering the use of common standards within the epitranscriptomics community. Sci-ModoM provides quantitative measurements per site and dataset, enabling users to assess confidence levels based on score, coverage, and stoichiometry. Data in Sci-ModoM is directly traceable to its sources. Users can Search and Compare over six million modifications across 156 datasets, Browse or download datasets, and retrieve metadata. A comparison tool offers a novel and unique opportunity to compare modifications site-wise across datasets, with the ability to securely upload and compare user data against latest published research. Sci-ModoM empowers researchers, including non-experts, to access a broad spectrum of recent quantitative RNA modification data, thereby enhancing the utility and impact of latest discoveries, and opening new avenues in biological and medical research.
Impact of the US Maternal Tetanus Toxoid, Reduced Diphtheria Toxoid, and Acellular Pertussis (Tdap) Vaccination Program on Preventing Pertussis in Infants 2 to &lt;6 Months of Age: A Case-Control Evaluation
Authors: Skoff Tami H , Rubis Amy B , Kirley Pam Daily , Scherzinger Karen , McMahon Melissa , McGuire Suzanne , Kudish Kathy , Cieslak Paul R , Shang Nong , Hariri Susan 
Published: November 2024

Abstract

Background
To protect infants aged &lt;2 months against pertussis, the United States recommends Tdap (tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis) vaccination during each pregnancy. Data are limited on the strategy's effectiveness against pertussis in infants aged ≥2 months.

Methods
Pertussis case infants aged 2 to &lt;6 months with cough onset between 1 January 2011 and 31 December 2014 were identified in 6 US states. Controls were 2 to &lt;6 months of age, hospital matched, and selected by birth certificate. Mothers were interviewed to collect demographic and healthcare information. Provider-verified vaccination history was obtained for infants and mothers. Adjusted odds ratios (aORs) were calculated using conditional logistic regression; overall vaccine effectiveness (VE) was estimated as (1 − aOR)×100. To describe maternal Tdap VE modified by infant DTaP (diphtheria and tetanus toxoids and acellular pertussis) doses, case-control sets were unmatched, and a time-to-event analysis was conducted through a generalized linear mixed model.

Results
A total of 335 cases and 927 controls were enrolled. The overall adjusted VE estimate for Tdap during pregnancy was 45.6% (95% confidence interval [CI], 5.8%–68.5%) and increased slightly, but not significantly, against infant hospitalization (55.7% [−116.8% to 90.9%]). Although point estimates were not significant, VE was modified by infant DTaP doses (58.8% [95% CI, −6.0% to 84.0%] for 0 DTaP doses, 30.5% [−21.4% to 60.2%] for 1 dose, and 3.2% [−170.8% to 65.4%] for 2 doses).

Conclusions
Our study suggests that there is some benefit of maternal Tdap vaccination beyond the first 2 months of life, however, on-time vaccination of infants remains critical to maintain protection from pertussis.
Prescribing Patterns of High Opioid and Antibiotic Prescribers, Washington State, 2021: Do Some Prescribers Have Trouble Saying No?
Authors: Evans David Trey , Kamenar Katarina , Zering Jessica , D’Angeli Marisa , Stohs Erica J 
Published: November 2024

Abstract
Among Washington State emergency and family medicine physicians, high prescribers of opioids were 2.9 times more likely to be high prescribers of antibiotics in the Medicare Part D population. The inverse relationship showed the same association. Antimicrobial and opioid stewards should collaborate on shared goals to implement effective interventions.
EXECUTER1 and singlet oxygen signaling: A reassessment of nuclear activity
Authors: Liu Kaiwei , Zhao Huan , Lee Keun Pyo , Yu Qing , Di Minghui , Wang Liangsheng , Kim Chanhong 
Published: November 2024

Abstract
Chloroplasts are recognized as environmental sensors, capable of translating environmental fluctuations into diverse signals to communicate with the nucleus. Among the reactive oxygen species produced in chloroplasts, singlet oxygen (1O2) has been extensively studied due to its dual roles, encompassing both damage and signaling activities, and the availability of conditional mutants overproducing 1O2 in chloroplasts. In particular, investigating the Arabidopsis (Arabidopsis thaliana) mutant known as fluorescent (flu) has led to the discovery of EXECUTER1 (EX1), a plastid 1O2 sensor residing in the grana margin of the thylakoid membrane. 1O2-triggered EX1 degradation is critical for the induction of 1O2-responsive nuclear genes (SOrNGs). However, a recent study showed that EX1 relocates from chloroplasts to the nucleus upon 1O2 release, where it interacts with WRKY18 and WRKY40 (WRKY18/40) transcription factors to regulate SOrNG expression. In this study, we challenge this assertion. Our confocal microscopy analysis and subcellular fractionation assays demonstrate that EX1 does not accumulate in the nucleus. While EX1 appears in nuclear fractions, subsequent thermolysin treatment assays indicate that it adheres to the outer nuclear region rather than localizing inside the nucleus. Furthermore, luciferase complementation imaging and yeast 2-hybrid assays reveal that EX1 does not interact with nuclear WRKY18/40. Consequently, our study refines the current model of 1O2 signaling by ruling out the nuclear relocation of intact EX1 as a means of communication between the chloroplast and nucleus.
MYB168 and WRKY20 transcription factors synergistically regulate lignin monomer synthesis during potato tuber wound healing
Authors: Yang Ruirui , Wang Qihui , Wang Ying , Zhang Xuejiao , Zheng Xiaoyuan , Li Yongcai , Prusky Dov , Bi Yang , Han Ye 
Published: November 2024

Abstract
Lignin is a critical component of the closing layer of the potato (Solanum tuberosum L.) tuber during healing; however, the molecular mechanism of its formation remains poorly understood. To elucidate the molecular mechanism of tuber healing, we screened the genes encoding transcription factors that regulate lignin synthesis(StMYB24/49/105/144/168, StWRKY19/20/22/23/34) and the key genes involved in lignin monomer synthesis (PHENYLALANINE AMMONIA LYASE 5 (StPAL5) and CINNAMYL ALCOHOL DEHYDROGENASE 14 (StCAD14)) for induced expression after wounding using transcriptome data. Dual-luciferase assay, yeast one-hybrid, electrophoretic mobility shift assay, and chromatin immunoprecipitation-qPCR assays revealed that StMYB168 could bind directly to the StPAL5 and StCAD14 promoters to activate their expression and that StWRKY20 enhanced this regulation with a synergistic effect. Y2H, bimolecular fluorophore complementation, and coimmunoprecipitation assays showed that StMYB168 interacted with StWRKY20 to form a MYB-WRKY complex. Furthermore, transient overexpression (OE) of StMYB168 and StWRKY20 in Nicotiana benthamiana leaves upregulated the expression of NbPAL and NbCAD10 and promoted lignin accumulation in the leaves. In addition, OE of StWRKY20 and StMYB168 together resulted in higher expression levels of NbPAL and NbCAD10 and higher levels of lignin monomer and total lignin. In contrast, silencing of StMYB168 and StWRKY20 in potato significantly reduced the lignin content of wounded tubers. In conclusion, StMYB168 and StWRKY20 are important regulators of lignin biosynthesis in potato tubers during healing and can positively regulate lignin biosynthesis by forming a complex. The elucidation of this regulatory module provides information on the regulatory mechanism of lignin monomer synthesis in wounded tubers at the transcriptional level.
Kaon Experiments
Authors: Yamanaka Taku 
Published: November 2024

Abstract
After $CP$ violation was discovered in the $K_L \rightarrow \pi ^+ \pi ^-$ decay, many theories were proposed to explain it, and the Kobayashi–Maskawa model and the Superweak model lasted for many years as strong candidates. High-precision kaon experiments with many new techniques and improvements rejected the Superweak model and supported the Kobayashi–Maskawa model in the 1990s. Since then, rare kaon decay experiments have studied $K \rightarrow \pi \nu \overline{\nu }$ decays to search for $CP$ violation caused by new physics beyond the Standard Model. Various techniques have been developed to increase the sensitivity and to suppress backgrounds.
A scoping review of food consumer aspects in transitioning to a safe and just agrifood system
Authors: Moghayer Saeed , Manouchehrabadi Behrang , Tiboldo Giulia , Ferrer-Pérez Hugo , Kozicka Marta , van Dijk Michiel , Farina Giuditta , Castellari Elena , Moro Daniele , Philippidis George 
Published: November 2024

Abstract
The agrifood system holds the key to identifying potential transformative pathways to achieve prosperity for all within the limits of the planet's natural resources, thereby fostering a safe and just operating system (SJOS) for future generations. The agrifood system is currently not on the right track to meet this ambition. Food–consumer processes such as preference shifts toward healthy diets and substantial reductions in food losses and waste could help to avoid severe environmental degradation and decrease overall mortality, although it remains unclear whether such transitional developments are entirely compatible with socially responsible thresholds. In this paper, we conduct a scoping review approach to map the evidence on the underlying drivers of such demand-side processes in the context of an SJOS with the aim to provide insights on how to transform the EU agrifood system. This review specifically examines how consumer aspects influence the SJOS, rather than exploring the bidirectional relationship. We used a scoping review approach to select relevant studies. The selected papers were subjected to quantitative and qualitative analyses. As a result, we extract insights and draw lessons from the role of food–consumer processes in the transition toward a more SJOS for the agrifood system.
Noise test of an electromagnetic antenna for low frequency scattered gravitational waves
Authors: Cruise Adrian Michael , Flack Robert 
Published: November 2024

ABSTRACT
Gravitational waves proved hard to detect experimentally and yet carry high energy fluxes. Conversely, the technology for electromagnetic waves is sophisticated, easily available, and highly sensitive. Various proposals have been made to use the conversion of a gravitational wave into an electromagnetic wave to generate signals that could be detected. We present test results from a novel electromagnetic antenna, efficient at the very low frequencies needed to explore the signals from supermassive black holes mergers. These will eventually be studied by the laser interferometric space antenna (LISA) at wavelengths between $10^{8}$ and $10^{11}$ m. Common forms of electromagnetic antennae are only efficient when the ratio of wavelength, $\lambda$, to antenna length, L, is roughly between 0.1 and 10. This paper proposes a scheme for a realistic ground-based electromagnetic antenna, ‘the resistive antenna’, which operates efficiently at a ratio $\frac{\lambda }{L}$ of more than $10^{6}$. The first estimates of ambient noise at these low frequencies from field trials of such a device are presented. The measured levels of ambient noise result in this detection scheme having a sensitivity much worse than LISA. The antenna design described in this communication may also have application in other fields.
Male fertility is preserved following ixekizumab treatment—a real-life pilot study
Authors: Micu Mihaela C , Farina Nicola , Decean Hana P , Micu Alexandru , Surd Stela , Gîrlovanu Marinela , Andone-Rotaru Bianca , Dagna Lorenzo 
Published: November 2024

Abstract

Introduction
Preserving fertility is crucial when managing male patients with spondyloarthritis (SpA) and/or psoriasis (PsO), especially in young men. Chronic inflammation, hormonal dysregulation and immunosuppressive therapies can negatively impact male fertility. Over the past decades, positive data have emerged regarding the reproductive safety of various therapies in men. Ixekizumab (IXE), a high-affinity monoclonal antibody targeting IL-17A, has shown a safe profile for male fertility in small studies. This pilot study assesses the impact of IXE treatment on sperm parameters in SpA and/or PsO patients in a real-world setting.

Methods
Consecutive adult male SpA and/or PsO patients eligible for or undergoing IXE treatment were prospectively enrolled. Demographic data, disease characteristics, laboratory assessments, comorbidities and previous treatments were recorded. Sperm analysis was conducted after a minimum of 6 months of IXE treatment, and also before treatment inititation in a subgroup of patients. Parallel sperm evaluations were performed in a control group of healthy donors.

Results
Ten patients were enrolled: eight with SpA and two with PsO. After 6 months of IXE treatment, all patients had normal sperm parameters. One SpA and PsO patient with baseline oligozoospermia showed normal parameters at follow-up and achieved a successful pregnancy post-treatment. Compared with controls, IXE-treated patients had lower sperm concentrations but higher vitality.

Conclusion
In our limited-size pilot study on SpA and PsO patients, IXE exposure did not impair male fertility. Sperm parameters remained within normal ranges after a minimum of 6 months of treatment. Early IXE treatment may preserve or potentially reverse fertility impairment.
Taxation of foreign trusts in Greece/Tax incentives for the transfer of residence of individuals to Greece
Authors: Patiti Magdalini 
Published: November 2024

Abstract
The present overview provides a summary of the Greek tax regime applicable to foreign trusts. Up until 2017, the taxation of foreign trusts was largely left unregulated in the Greek tax system, which can be attributed to the fact that trusts, being a common-law concept, are not recognized by Greek legislation. Despite the uncertainties, foreign trusts were often used as structures for wealth management or estate planning. The guidelines provided in 2017 were thus eagerly awaited to provide clarity on a matter that was left unregulated for decades and can therefore only be considered as a very positive development. Nevertheless, certain aspects raise concern. This overview also summarizes the Greek Tax Incentive Regimes, which have been met with great demand from foreign residents seeking to transfer their (tax) residence to Greece.
Epigenetic modification of IGF2/H19 imprinting control region regulates PGC-1α/PI3K/AKT2 pathway in a rat model of intrauterine growth restriction
Authors: Liao Lihong , Zhou Xiuyun , Zhang Meihui , Lin Tulian , Long Wenjun , Yan Yaqin , Ning Qin , Luo Xiaoping 
Published: November 2024

Abstract

Background:
Intrauterine growth restriction (IUGR) is associated with adverse metabolic outcomes during adulthood. Histone modifications and changes in DNA methylation-affected genes are important for fetal development. This study aimed to confirm the epigenetic mechanisms in IUGR.

Methods:
IUGR models were established in Sprague–Dawley rats using a maternal nutritional restriction approach during pregnancy. The abundance of insulin-like growth factor 2 (IGF2), phosphoinositide 3-kinase (PI3K), AKT serine/threonine kinase 2 (AKT2), and PPAR gamma coactivator 1 alpha (PGC-1α) was examined by real-time polymerase chain reaction (RT-PCR) and Western blotting analysis. Chromatin immunoprecipitation RT-PCR was employed to analyze histone modification in CCCTC-binding factor (CTCF)1–4 binding sites of the IGF2/H19 imprinting control region (ICR). The methylation states of CTCF1–4 binding sites were studied by pyrosequencing.

Results:
The IUGR models were constructed successfully. IGF2 mRNA abundance in the placenta, fetal liver, and newborn liver was decreased in the IUGR group (P <0.01). Meanwhile, as compared with the control group, the expression levels of AKT2, PI3K, and PGC-1α were lower in newborn and 8-week-old livers in the IUGR group (P <0.05). In addition, knocking down IGF2 reduced the protein expression levels of AKT2-P and PGC-1α (P <0.05). In CTCF binding sites 1-4 of the IGF2/H19 ICR, AcH3 enrichment was significantly lower in CTCF1-3 in newborn and 8-week-old IUGR rats. H3K4me3 enrichment was significantly lower in the CTCF1–4 of newborn and 8-week-old IUGR groups (P <0.01). H3K9me2 enrichment was significantly higher in the IUGR group (P <0.01). The CpG dinucleotide methylation levels of CTCF1 and CTCF3, but not those of CTCF2 and CTCF4 binding sites in IUGR rat fetal, 4-week old, and 8-week-old livers decreased significantly (P <0.05).

Conclusion:
The methylation status and histone modification in the IGF2/H19 ICR are related to growth and lipid metabolism via the PGC-1α/PI3K/AKT2 pathway in IUGR rats.