bluuebunny/crossref_metadata_2025_split huggingface dataset:
JustRNA: a database of plant long noncoding RNA expression profiles and functional network
Authors: Tseng Kuan-Chieh , Wu Nai-Yun , Chow Chi-Nga , Zheng Han-Qin , Chou Chin-Yuan , Yang Chien-Wen , Wang Ming-Jun , Chang Song-Bin , Chang Wen-Chi 
Published: June 2023

Abstract
Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.
The swansong of petal cell death: insights into the mechanism and regulation of ethylene-mediated flower senescence
Authors: Parveen Shazia , Altaf Foziya , Farooq Sumira , Lone Mohammad Lateef , ul Haq Aehsan , Tahir Inayatullah 
Published: June 2023

AbstractFlower senescence is a fundamental aspect of the developmental trajectory in flowers, occurring after the differentiation of tissues and maturation of petals, and preceding the growth and development of seeds. It is accompanied by various alterations at the cytological, physiological, and molecular levels, similar to other forms of programmed cell death (PCD). It involves an intricate interplay of various plant growth regulators, with ethylene being the key orchestrator in ethylene-dependent petal senescence. Petal senescence mediated by ethylene is marked by various changes such as petal wilting, amplified oxidative stress, degradation of proteins and nucleic acids, and autophagy. Ethylene crosstalks with other growth regulators and triggers genetic and/or epigenetic reprogramming of genes during senescence in flowers. While our understanding of the mechanism and regulation of petal senescence in ethylene-sensitive species has advanced, significant knowledge gaps still exist, which demand critical reappraisal of the available literature on the topic. A deeper understanding of the various mechanisms and regulatory pathways involved in ethylene-dependent senescence has the capacity to facilitate a more precise regulation of the timing and site of senescence, thus leading to optimized crop yields, enhanced product quality, and extended longevity.
The flavour of grape colour: anthocyanin content tunes aroma precursor composition by altering the berry microenvironment
Authors: Rodríguez-Lorenzo Maite , Mauri Nuria , Royo Carolina , Rambla José L , Diretto Gianfranco , Demurtas Olivia , Hilbert Ghislaine , Renaud Christel , Tobar Vanessa , Huete Joaquín , Delrot Serge , Granell Antonio , Martínez-Zapater José Miguel , Carbonell-Bejerano Pablo 
Published: June 2023

Abstract
Anthocyaninless (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, and this conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed comparisons of microenvironment, transcriptomics, and metabolomics of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was as much as 3.5 ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the up-regulation of photosynthesis-related and other light-responsive genes and by their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles, and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced expression of pathogen defence genes in the berry skin and increased accumulation of C6-derived alcohol and ester volatiles and γ-aminobutyric acid. Collectively, our results indicate that anthocyanin depletion has side-effects on grape composition by altering the internal microenvironment of the berry and the partitioning of the phenylpropanoid pathway. Our findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.
A dynamical survey of the trans-Neptunian region − II. On the nature of chaotic diffusion
Authors: Kővári E , Forgács-Dajka E , Kovács T , Kiss Cs , Sándor Zs 
Published: June 2023

ABSTRACT
On long enough time-scales, chaotic diffusion has the potential to significantly alter the appearance of a dynamical system. The Solar system is no exception: diffusive processes take part in the transportation of small bodies and provide dynamical pathways even for the distant trans-Neptunian objects to reach the inner Solar system. In this letter, we carry out a thorough investigation of the nature of chaotic diffusion. We analyse the temporal evolution of the mean squared displacement of 10 000 ensembles of test particles and quantify in each case the diffusion exponent (enabling the classification between normal, sub-, and superdiffusion), the generalized diffusion coefficient, and a characteristic diffusion time-scale, too. This latter quantity is compared with an entropy-based time-scale, and the two approaches are studied in light of direct computations as well. Our results are given in the context of two-dimensional maps, thereby facilitating the understanding of the relationship between the typical phase space structures and the properties of chaotic diffusion.
IXPE and NICER view of black hole X-ray binary 4U 1630–47: First significant detection of polarized emission in thermal state
Authors: Kushwaha Ankur , Jayasurya Kiran M , Agrawal Vivek K , Nandi Anuj 
Published: June 2023

ABSTRACT
We present a detailed spectro-polarimetric study of black hole X-ray binary 4U 1630−47 during its 2022 outburst with IXPE and NICER observations. The source is observed in disc dominated thermal state (kTin ≈ 1.4 keV) with clear detection of absorption features at 6.69 ± 0.01 keV and 6.97 ± 0.01 keV from both NICER as well as IXPE spectra, likely indicating a coupling of disc-wind. A significant degree of polarization (PD) $= 8.33\pm 0.17~{{\ \rm per\ cent}}$ and polarization angle (PA) =17.78° ± 0.60° in the energy range of 2 − 8 keV are measured with IXPE. PD is found to be an increasing function of energy whereas PA remains roughly same within the energy range. Simultaneous energy spectra from NICER in the range of 0.5 − 12 keV are modelled to study the spectral properties. Furthermore, the spin parameter of the black hole is estimated with spectro-polarimetric data as a$_{\ast }=0.920\pm 0.001\, (1\sigma)$ which is corroborated by NICER observations. Finally, we discuss the implications of our findings.
GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
Authors: Yu Hao , Wang Yuqing , Zhang Xi , Wang Zheng 
Published: June 2023

Abstract
Large-scale single-cell RNA sequencing (scRNA-seq) has emerged as a robust method for dissecting cellular heterogeneity at single-cell resolution. However, to meet the increasingly high computational demands of non-programming experts, a user-friendly, scalable, and accessible online platform for analyzing scRNA-seq data is urgently needed. Here, we have developed a web-based platform GRACE (GRaphical Analyzing Cell Explorer) (http://grace.flowhub.com.cn or http://grace.jflab.ac.cn:28080) that enables online massive single-cell transcriptome analysis, improving interactivity and reproducibility using high-quality visualization frameworks. GRACE provides easy access to interactive visualization, customized parameters, and publication-quality graphs. Furthermore, it comprehensively integrates preprocessing, clustering, developmental trajectory inference, cell-cell communication, cell-type annotation, subcluster analysis, and pathway enrichment. In addition to the website platform, we also provide a Docker version that can be easily deployed on private servers. The source code for GRACE is freely available at (https://github.com/th00516/GRACE). Documentation and video tutorials are accessible from website homepage (http://grace.flowhub.com.cn). GRACE can analyze massive scRNA-seq data more flexibly and be accessible to the scientific community. This platform fulfills the major gap that exists between experimental (wet lab) and bioinformatic (dry lab) research.
EPIC-0307-mediated selective disruption of PRADX–EZH2 interaction and enhancement of temozolomide sensitivity to glioblastoma via inhibiting DNA repair and MGMT
Authors: Xin Lei , Tan Yanli , Zhu Yuanxue , Cui Xiaoteng , Wang Qixue , Zhao Jixing , Tian Shaohui , Xu Can , Xiao Menglin , Hong Biao , Xu Jianglong , Yuan Xiaoye , Wang Changsheng , Kang Chunsheng , Fang Chuan 
Published: June 2023

Abstract

Background
Temozolomide (TMZ) treatment efficacy in glioblastoma (GBM) has been limited by resistance. The level of O-6-methylguanine-DNA methyltransferase (MGMT) and intrinsic DNA damage repair factors are important for the TMZ response in patients. Here, we reported a novel compound, called EPIC-0307, that increased TMZ sensitivity by inhibiting specific DNA damage repair proteins and MGMT expression.

Methods
EPIC-0307 was derived by molecular docking screening. RNA immunoprecipitation (RIP), and chromatin immunoprecipitation by RNA (ChIRP) assays were used to verify the blocking effect. Chromatin immunoprecipitation (ChIP) and co-immunoprecipitation (Co-IP) assays were performed to explore the mechanism of EPIC-0307. A series of in vivo and in vitro experiments were designed to evaluate the efficacy of EPIC-0307 in sensitizing GBM cells to TMZ.

Results
EPIC-0307 selectively disrupted the binding of PRADX to EZH2 and upregulated the expression of P21 and PUMA, leading to cell cycle arrest and apoptosis in GBM cells. EPIC-0307 exhibited a synergistic inhibitory effect on GBM when combined with TMZ by downregulating TMZ-induced DNA damage repair responses and epigenetically silencing MGMT expression through modulating the recruitment of ATF3-pSTAT3-HDAC1 regulatory complex to the MGMT promoter. EPIC-0307 demonstrated significant efficacy in suppressing the tumorigenesis of GBM cells, restoring TMZ sensitivity.

Conclusion
This study identified a potential small-molecule inhibitor (SMI) EPIC-0307 that selectively disrupted the PRADX–EZH2 interaction to upregulate expressions of tumor suppressor genes, thereby exerting its antitumor effects on GBM cells. EPIC-0307 treatment also increased the chemotherapeutic efficacy of TMZ by epigenetically downregulating DNA repair-associate genes and MGMT expression in GBM cells.
Full-parameter omnidirectional transformation optical devices
Authors: Gao Yuan , Luo Yu , Zhang Jingjing , Huang Zhengjie , Zheng Bin , Chen Hongsheng , Ye Dexin 
Published: June 2023

ABSTRACT
Transformation optics (TO) provides an unprecedented technique to control electromagnetic (EM) waves by engineering the constitutive parameters of the surrounding medium through a proper spatial transformation. In general, ideal transformation optical devices require simultaneous electric and magnetic responses along all three dimensions. To ease the practical implementation, previous studies usually made use of reduced parameters or other simplified approaches, which inevitably introduce extra reflection or unwanted phase shift. Up to today, experimental realizations of full-parameter transformation optical devices in free space are still quite limited. Here, a general design strategy is proposed to solve this problem. As a specific example, a full-parameter spatial-compression TO medium with constitutive parameters taking the diagonal form diag(a, a, 1/a) for the TM wave incidence was designed and realized experimentally. Such spatial-compression TO media were then applied to the implementation of an ideal omnidirectional invisibility cloak capable of concealing a large-scale object over a wide range of illumination angles. Both the simulation and experiment confirm that the cloak allows for nearly unity transmission of EM waves in the forward direction without introducing extra scattering or phase shift. This work constitutes an important stepping stone for future practical implementation of arbitrary full-parameter omnidirectional transformation optical devices.
Prototheca Infection: A Descriptive Study
Authors: Cullen Grace D , Yetmar Zachary A , Fida Madiha , Abu Saleh Omar M 
Published: June 2023

Abstract
Prototheca is a microalgae known to cause infections in humans, with protothecosis most commonly presenting as olecranon bursitis or localized soft tissue infection. Disseminated disease can be seen in immunocompromised patients. In this retrospective single-institution case series, we describe our experience with 7 patients with Prototheca infections.
Poor Sensitivity of Stool Culture Compared to Polymerase Chain Reaction in Surveillance for Vibrio cholerae in Haiti, 2018–2019
Authors: Guillaume Yodeline , Debela Meti , Slater Damien , Vissieres Kenia , Ternier Ralph , Franke Molly F , Harris Jason B , Ivers Louise C 
Published: June 2023

Abstract
We report on the sensitivity and specificity of stool culture compared to polymerase chain reaction for detecting Vibrio cholerae in Haiti during the waning period of the initial outbreak in 2018–2019. We found that stool culture (with a sensitivity of 33.3% and specificity of 97.4%) may not be sufficiently robust in this context.
Optimizing the Use of Beta-Lactam Antibiotics in Clinical Practice: A Test of Time
Authors: Tilanus Alwin , Drusano George 
Published: June 2023

Abstract
Despite their limitations, the pharmacokinetics (PK) and pharmacodynamics (PD) indices form the basis for our current understanding regarding antibiotic development, selection, and dose optimization. Application of PK-PD in medicine has been associated with better clinical outcome, suppression of resistance, and optimization of antibiotic consumption. Beta-lactam antibiotics remain the cornerstone for empirical and directed therapy in many patients. The percentage of time of the dosing interval that the free (unbound) drug concentration remains above the minimal inhibitory concentration (MIC) (%fT &gt; MIC) has been considered the PK-PD index that best predicts the relationship between antibiotic exposure and killing for the beta-lactam antibiotics. Time dependence of beta-lactam antibiotics has its origin in the acylation process of the serine active site of penicillin-binding proteins, which subsequently results in bacteriostatic and bactericidal effects during the dosing interval. To enhance the likelihood of target attainment, higher doses, and prolonged infusion strategies, with/or without loading doses, have been applied to compensate for subtherapeutic levels of antibiotics related to PK-PD changes, especially in the early phase of severe sepsis. To minimize resistance and maximize clinical outcome, empirical therapy with a meropenem loading dose followed by high-dose-prolonged infusion should be considered in patients with high inoculum infections presenting as severe (Gram negative) sepsis. Subsequent de-escalation and dosing of beta-lactam antibiotics should be considered as an individualized dynamic process that requires dose adjustments throughout the time course of the disease process mediated by clinical parameters that indirectly assess PK-PD alterations.
Prognostic Value of ctDNA Detection in Patients With Locally Advanced Rectal Cancer Undergoing Neoadjuvant Chemoradiotherapy: A Systematic Review and Meta-analysis
Authors: Chang Lele , Zhang Xuemei , He Lei , Ma Qian , Fang Tianyuan , Jiang Chengzhi , Ma Zhigang , Li Qingwei , Wu Chunlong , Tao Ji 
Published: June 2023

Abstract

Background
Circulating tumor DNA (ctDNA) is increasingly used as a biomarker for metastatic rectal cancer and has recently shown promising results in the early detection of recurrence risk.

Methods
We conducted a systematic review and meta-analysis to explore the prognostic value of ctDNA detection in LARC patients undergoing neoadjuvant chemoradiotherapy (nCRT). We systematically searched electronic databases for observational or interventional studies that included LARC patients undergoing nCRT. Study selection according to the PRISMA guidelines and quality assessment of the REMARK tool for biomarker studies. The primary endpoint was the impact of ctDNA detection at different time points (baseline, post-nCRT, post-surgery) on relapse-free survival (RFS) and overall survival (OS). The secondary endpoint was to study the association between ctDNA detection and pathological complete response(pCR) at different time points.

Results
After further review and analysis of the 625 articles initially retrieved, we finally included 10 eligible studies. We found no significant correlation between ctDNA detection at baseline and long-term survival outcomes or the probability of achieving a pCR. However, the presence of ctDNA at post-nCRT was associated with worse RFS (HR = 9.16, 95% CI, 5.48-15.32), worse OS (HR = 8.49, 95% CI, 2.20-32.72), and worse pCR results (OR = 0.40, 95%CI, 0.18-0.89). The correlation between the presence of ctDNA at post-surgery and worse RFS was more obvious (HR = 14.94; 95% CI, 7.48-9.83).

Conclusions
Our results suggest that ctDNA detection is a promising biomarker for the evaluation of response and prognosis in LARC patients undergoing nCRT, which merits further evaluation in the following prospective trials.
Drastic reduction of the population distribution of White Storks predicted in absence of landfills
Authors: López-García Alejandro , Gil-Tapetado Diego , Aguirre José I 
Published: June 2023

AbstractOrganic waste production has greatly increased following human sprawl and led to the development of landfills in recent decades. This abundant and reliable anthropogenic food source has favored several species, some of which consequently became overabundant. Landfills present hazards to wildlife, which may suffocate on plastic materials, tangle on cords, and get exposed to pollutants and pathogens. In response to environmental and public health concerns over the maintenance of landfills, the European Commission proposed to close the landfills. Our objective was to determine the impact of Landfill European Directive on the White Stork (Ciconia ciconia) whose population recovery and growth was linked to landfill exploitation. We implemented species distribution models to project future distribution in the absence of landfills in the Community of Madrid (Spain). Habitat suitability was estimated based on nest occurrence and we included data from land cover types, human population density, and two different climate change scenarios (i.e. emissions in low and high shared socioeconomic pathways). Given that protection measures, particularly implemented in protected areas, were associated with population recovery, we also evaluated the overlapping degree between protected areas and projected distribution. Our models predicted a sharp decline in breeding population distribution with landfill closure, reaching values similar to the 1984 breeding census when the species was categorized as threatened. Our results also suggest a decrease in maximum habitat suitability. Climate change also contributed to a reduction in breeding population distribution given model predictions for the extreme emission pathway (ssp5). Measures such as gradual change in landfill management, continuous monitoring of breeding populations, and evaluation of the White Stork use of natural feeding areas before and after landfill closure, should be considered.
Low temperature-induced regulatory network rewiring via WRKY regulators during banana peel browning
Authors: Zhu Wenjun , Li Hua , Dong Pengfei , Ni Xueting , Fan Minlei , Yang Yingjie , Xu Shiyao , Xu Yanbing , Qian Yangwen , Chen Zhuo , Lü Peitao 
Published: June 2023

Abstract
Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer–promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.
Simulation study of ultrahigh-precision single-ion extraction from a linear Paul trap
Authors: Muroo Kento , Okamoto Hiromi , Miyawaki Nobumasa , Yuri Yosuke 
Published: June 2023

AbstractA detailed simulation study is conducted to explore the possibility of transporting a single ion precisely along a particular design orbit. As a practically useful example, we consider nitrogen ions sympathetically cooled with ultracold calcium ions produced in a linear Paul trap (LPT) by the Doppler laser-cooling technique. A single nitrogen almost completely frozen in the laboratory frame is extracted from the LPT by manipulating the axial potential barriers. A similar idea was recently implemented by Groot-Berning et al. [New J. Phys. 23, 063067 (2021)] to create nitrogen-vacancy centers in diamond as a platform for some important quantum technologies. We here perform systematic 3D simulations taking a standard LPT structure into account and figure out the necessary conditions to achieve the ultrahigh-precision irradiation of a single nitrogen onto any target. In addition to the string Coulomb crystal used in the previous work above, we show that even the shell crystalline structure can be employed for our purpose. When several specific conditions are satisfied, a normalized root-mean-squared emittance of ejected nitrogen ions can be made of the order of 10−16 m·rad in transverse dimensions perpendicular to the design orbit.