bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoadjuvant therapy increases the risk of metabolic disorders and osteosarcopenia in patients with early breast cancer
Authors: Zhang Yan , Kang Hua , Zhao Jing , Wang Yajun , Cai Wei , Zhang Xiaoli , Li Kaifu , Zhao Ye 
Published: May 2024

Abstract

Background
The purpose of this study is to evaluate the effects of neoadjuvant therapy on glucose and lipid metabolism, bone mineral density (BMD) and muscle, and to explore the relationship between metabolic disorders and changes in body composition, so as to provide better health management strategies for breast cancer survivors.

Methods
The clinical data of 43 patients with breast cancer who received neoadjuvant therapy in Xuanwu Hospital from January 2020 to June 2021 were analyzed retrospectively. The biochemical results, including albumin, blood glucose, triglyceride and cholesterol, were collected before neoadjuvant therapy and before surgery. The pectoral muscle area, pectoral muscle density and cancellous bone mineral density of the 12th thoracic vertebra were also measured by chest CT.

Results
After neoadjuvant therapy, fasting blood glucose, triglyceride and cholesterol were significantly increased, albumin was decreased. At the same time, pectoral muscle area, pectoral muscle density and T12 BMD were decreased. After treatment, BMD was positively correlated with pectoral muscle area, R2 = 0.319, P = 0.037, and BMD was also positively correlated with pectoral muscle density, R2 = 0.329, P = 0.031. Multivariate analysis showed that BMD and pectoral muscle density were correlated with menstrual status, and pectoral muscle area was correlated with body mass index before treatment, none of which was related to glucose and lipid metabolism.

Conclusion
Neoadjuvant therapy can cause glucose and lipid metabolism disorder, BMD decrease and muscle reduction. BMD was positively correlated with muscle area and density after treatment, suggesting that patients had an increased chance of developing osteosarcopenia.
Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses
Authors: Luo Xiaopeng , Jiang Xinqiang , Schmitt Vivian , Kulkarni Shubhada R , Tran Huy Cuong , Kacprzak Sylwia M , Van Breusegem Frank , Van Aken Olivier , Vandepoele Klaas , De Clercq Inge 
Published: May 2024

Abstract
Plants, being sessile organisms, constantly need to respond to environmental stresses, often leading to the accumulation of reactive oxygen species (ROS). While ROS can be harmful, they also act as second messengers guiding plant growth and stress responses. Because chloroplasts are sensitive to environmental changes and are both a source and a target of ROS during stress conditions, they are important in conveying environmental changes to the nucleus, where acclimation responses are coordinated to maintain organellar and overall cellular homeostasis. ANAC102 has previously been established as a regulator of β-cyclocitral-mediated chloroplast-to-nucleus signaling, protecting plants against photooxidative stress. However, debates persist about where ANAC102 is located—in chloroplasts or in the nucleus. Our study, utilizing the genomic ANAC102 sequence driven by its native promoter, establishes ANAC102 primarily as a nuclear protein, lacking a complete N-terminal chloroplast-targeting peptide. Moreover, our research reveals the sensitivity of plants overexpressing ANAC102 to severe superoxide-induced chloroplast oxidative stress. Transcriptome analysis unraveled a dual role of ANAC102 in negatively and positively regulating genome-wide transcriptional responses to chloroplast oxidative stress. Through the integration of published data and our own study, we constructed a comprehensive transcriptional network, which suggests that ANAC102 exerts direct and indirect control over transcriptional responses through downstream transcription factor networks, providing deeper insights into the ANAC102-mediated regulatory landscape during oxidative stress.
Analysis of sulfide signaling in rice highlights specific drought responses
Authors: Zhang Jing , Aroca Angeles , Hervás Manuel , Navarro José A , Moreno Inmaculada , Xie Yanjie , Romero Luis C , Gotor Cecilia 
Published: May 2024

Abstract
Hydrogen sulfide regulates essential plant processes, including adaptation responses to stress situations, and the best characterized mechanism of action of sulfide consists of the post-translational modification of persulfidation. In this study, we reveal the first persulfidation proteome described in rice including 3443 different persulfidated proteins that participate in a broad range of biological processes and metabolic pathways. In addition, comparative proteomics revealed specific proteins involved in sulfide signaling during drought responses. Several proteins are involved in the maintenance of cellular redox homeostasis, the tricarboxylic acid cycle and energy-related pathways, and ion transmembrane transport and cellular water homeostasis, with the aquaporin family showing the highest differential levels of persulfidation. We revealed that water transport activity is regulated by sulfide which correlates with an increasing level of persulfidation of aquaporins. Our findings emphasize the impact of persulfidation on total ATP levels, fatty acid composition, levels of reactive oxygen species, antioxidant enzymatic activities, and relative water content. Interestingly, the role of persulfidation in aquaporin transport activity as an adaptation response in rice differs from current knowledge of Arabidopsis, which highlights the distinct role of sulfide in improving rice tolerance to drought.
Protein kinase SnRK2.6 phosphorylates transcription factor bHLH3 to regulate anthocyanin homeostasis during strawberry fruit ripening
Authors: Huang Fuli , Sun Mimi , Yao Zhijin , Zhou Jing , Bai Qian , Chen Xuexue , Huang Yun , Shen Yuanyue 
Published: May 2024

Abstract
Strawberry (Fragaria × ananassa) is a model plant for studying non-climacteric fruit ripening regulated by abscisic acid (ABA); however, the signaling of ABA in the regulation of fruit coloration is not fully understood. In this study, we identified the transcription factor BASIC HELIX-LOOP-HELIX 3 (bHLH3) as being key to fruit coloration via yeast two-hybrid library screening using the bait SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2 (SnRK2.6), which is a core ABA signaling component that negatively regulates ripening. The interaction was also confirmed by firefly luciferase complementation assays and pull-down assays. RT-qPCR and western blot analysis confirmed that bHLH3 is expressed ubiquitously in strawberry tissues, and it is expressed stably during fruit development. Overexpression and RNAi of both bHLH3 and SnRK2.6 demonstrated that bHLH3 and SnRK2.6 promote and inhibit strawberry fruit coloration, respectively. Using EMSAs, we showed that bHLH3 promotes the expression of UDP-GLUCOSE: FLAVONOL-O-GLUCOSYLTRANSFERASE (UFGT), a key gene for anthocyanin biosynthesis, by directly binding to its promoter. We determined that SnRK2.6 can phosphorylate bHLH3 and that this inhibits its binding to the UFGT promoter, consequently suppressing expression. Altogether, we propose that increased ABA content during strawberry fruit ripening leads to decreased expression of SnRK2.6, which in turn releases the phosphorylation of bHLH3 and thereby enhances UFGT expression, ultimately promoting the coloration of the fruit.
Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway
Authors: Akyuz Turumtay Emine , Turumtay Halbay , Tian Yang , Lin Chien-Yuan , Chai Yen Ning , Louie Katherine B , Chen Yan , Lipzen Anna , Harwood Thomas , Satish Kumar Kavitha , Bowen Benjamin P , Wang Qian , Mansfield Shawn D , Blow Matthew J , Petzold Christopher J , Northen Trent R , Mortimer Jenny C , Scheller Henrik V , Eudes Aymerick 
Published: May 2024

Abstract
Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.
Full spectroscopic model and trihybrid experimental-perturbative-variational line list for NH
Authors: Perri Armando N , McKemmish Laura K 
Published: May 2024

ABSTRACT
Imidogen (NH) is a reactive molecule whose presence in astrochemical environments is of interest due to its role in the formation of nitrogen-containing molecules and as a potential probe of nitrogen abundance. Spectroscopic NH monitoring is useful for Earth-based combustion and photolysis processes of ammonia and other nitrogen-containing species. NH is also relevant to ultracold molecular physics and plasma studies. To enable these diverse applications, high-quality molecular spectroscopic data are required. Here, a new line list with significant advantages over existing data is presented. Most notably, this line list models isotopologue spectroscopy and forbidden transitions (important for NH visible absorption), alongside some overall improvements to accuracy and completeness. This approach takes advantage of existing experimental data (from a previous MARVEL compilation) and perturbative line lists together with new MRCI ab initio electronic data. These are used to produce a novel variational spectroscopic model and trihybrid line list for the main 14N1H isotopologue, as well as isotopologue-extrapolated hybrid line lists for the 14N2H, 15N1H, and 15N2H isotopologues. The new 14N1H ExoMol-style trihybrid line list, kNigHt, comprises 4076 energy levels (1078 experimental) and 327 014 transitions up to 47 500 cm−1 (211 nm) between five low-lying electronic states (X 3Σ−, a 1Δ, b 1Σ+, A 3Π, and c 1Π). For most anticipated applications aside from far-infrared studies, this line list will be of sufficient quality; any improvements should focus on the b 1Σ+ energies, and the a 1Δ – A 3Π and b 1Σ+ – A 3Π spin–orbit couplings.
Lung ultrasound in the assessment of interstitial lung disease in patients with connective tissue disease: Performance in comparison with high-resolution computed tomography
Authors: Watanabe Shinji , Yomono Keina , Yamamoto Shintaro , Suzuki Mikito , Gono Takahisa , Kuwana Masataka 
Published: May 2024

ABSTRACT

Objective
To investigate clinical relevance of performing lung ultrasound (LUS) in patients with connective tissue disease (CTD)-associated interstitial lung disease (ILD) in comparison with high-resolution computed tomography (HRCT).

Methods
This single-centre study enrolled eligible patients with CTD-ILD from the prospective LUS registry. Total B-lines were detected by assessment at 14 sites via LUS. Forced vital capacity, diffusing lung capacity for carbon monoxide (DLCO), DLCO/alveolar volume, 6-minute walking distance, and the ILD-GAP index were used as ILD prognostic parameters. Correlations were examined using single and multiple regression analyses.

Results
Sixty-seven patients were enrolled, including 29 with idiopathic inflammatory myopathy or anti-synthetase syndrome, 25 with systemic sclerosis (SSc), 10 with rheumatoid arthritis, and 3 with mixed CTD. The total number of B-lines correlated with ILD extent on HRCT in patients with CTD-ILD (r = 0.66; P &lt; .001), particularly in patients with SSc-ILD (r = 0.78; P &lt; .001). Total B-lines and ILD extent on HRCT showed comparable correlations with prognostic parameters, while multiple regression analysis revealed the limited benefit of performing LUS in addition to HRCT in predicting correlations with prognostic factors.

Conclusions
LUS serves as an alternative tool for assessing the severity and prognosis of patients with CTD-ILD.
Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility
Authors: Hanke Dustin M , Wang Yiqing , Dagan Tal 
Published: May 2024

Abstract
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.
Biochemical properties of chromatin domains define genome compartmentalization
Authors: Lucini Federica , Petrini Cristiano , Salviato Elisa , Pal Koustav , Rosti Valentina , Gorini Francesca , Santarelli Philina , Quadri Roberto , Lembo Giovanni , Graziano Giulia , Di Patrizio Soldateschi Emanuele , Tagliaferri Ilario , Pinatel Eva , Sebestyén Endre , Rotta Luca , Gentile Francesco , Vaira Valentina , Lanzuolo Chiara , Ferrari Francesco 
Published: May 2024

Abstract
Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics
Authors: Elizarraras John M , Liao Yuxing , Shi Zhiao , Zhu Qian , Pico Alexander R , Zhang Bing 
Published: May 2024

Abstract
Enrichment analysis, crucial for interpreting genomic, transcriptomic, and proteomic data, is expanding into metabolomics. Furthermore, there is a rising demand for integrated enrichment analysis that combines data from different studies and omics platforms, as seen in meta-analysis and multi-omics research. To address these growing needs, we have updated WebGestalt to include enrichment analysis capabilities for both metabolites and multiple input lists of analytes. We have also significantly increased analysis speed, revamped the user interface, and introduced new pathway visualizations to accommodate these updates. Notably, the adoption of a Rust backend reduced gene set enrichment analysis time by 95% from 270.64 to 12.41 s and network topology-based analysis by 89% from 159.59 to 17.31 s in our evaluation. This performance improvement is also accessible in both the R package and a newly introduced Python package. Additionally, we have updated the data in the WebGestalt database to reflect the current status of each source and have expanded our collection of pathways, networks, and gene signatures. The 2024 WebGestalt update represents a significant leap forward, offering new support for metabolomics, streamlined multi-omics analysis capabilities, and remarkable performance enhancements. Discover these updates and more at https://www.webgestalt.org.
LowTempGAL: a highly responsive low temperature-inducibleGALsystem inSaccharomyces cerevisiae
Authors: Lu Zeyu , Shen Qianyi , Bandari Naga Chandra , Evans Samuel , McDonnell Liam , Liu Lian , Jin Wanli , Luna-Flores Carlos Horacio , Collier Thomas , Talbo Gert , McCubbin Tim , Esquirol Lygie , Myers Chris , Trau Matt , Dumsday Geoff , Speight Robert , Howard Christopher B , Vickers Claudia E , Peng Bingyin 
Published: May 2024

AbstractTemperature is an important control factor for biologics biomanufacturing in precision fermentation. Here, we explored a highly responsive low temperature-inducible genetic system (LowTempGAL) in the model yeast Saccharomyces cerevisiae. Two temperature biosensors, a heat-inducible degron and a heat-inducible protein aggregation domain, were used to regulate the GAL activator Gal4p, rendering the leaky LowTempGAL systems. Boolean-type induction was achieved by implementing a second-layer control through low-temperature-mediated repression on GAL repressor gene GAL80, but suffered delayed response to low-temperature triggers and a weak response at 30°C. Application potentials were validated for protein and small molecule production. Proteomics analysis suggested that residual Gal80p and Gal4p insufficiency caused suboptimal induction. ‘Turbo’ mechanisms were engineered through incorporating a basal Gal4p expression and a galactose-independent Gal80p-supressing Gal3p mutant (Gal3Cp). Varying Gal3Cp configurations, we deployed the LowTempGAL systems capable for a rapid stringent high-level induction upon the shift from a high temperature (37–33°C) to a low temperature (≤30°C). Overall, we present a synthetic biology procedure that leverages ‘leaky’ biosensors to deploy highly responsive Boolean-type genetic circuits. The key lies in optimisation of the intricate layout of the multi-factor system. The LowTempGAL systems may be applicable in non-conventional yeast platforms for precision biomanufacturing.
Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families
Authors: Hoikkala Ville , Graham Shirley , White Malcolm F 
Published: May 2024

Abstract
Recognition of RNA from invading mobile genetic elements (MGE) prompts type III CRISPR systems to activate an HD nuclease domain and/or a nucleotide cyclase domain in the Cas10 subunit, eliciting an immune response. The cyclase domain can generate a range of nucleotide second messengers, which in turn activate a diverse family of ancillary effector proteins. These provide immunity by non-specific degradation of host and MGE nucleic acids or proteins, perturbation of membrane potentials, transcriptional responses, or the arrest of translation. The wide range of nucleotide activators and downstream effectors generates a complex picture that is gradually being resolved. Here, we carry out a global bioinformatic analysis of type III CRISPR loci in prokaryotic genomes, defining the relationships of Cas10 proteins and their ancillary effectors. Our study reveals that cyclic tetra-adenylate is by far the most common signalling molecule used and that many loci have multiple effectors. These typically share the same activator and may work synergistically to combat MGE. We propose four new candidate effector protein families and confirm experimentally that the Csm6-2 protein, a highly diverged, fused Csm6 effector, is a ribonuclease activated by cyclic hexa-adenylate.
Treatment strategies of the thromboembolic risk in kidney failure patients with atrial fibrillation
Authors: Genovesi Simonetta , Camm A John , Covic Adrian , Burlacu Alexandru , Meijers Björn , Franssen Casper , Luyckx Valerie , Liakopoulos Vassilios , Alfano Gaetano , Combe Christian , Basile Carlo 
Published: May 2024

ABSTRACT
The incidence and prevalence of atrial fibrillation (AF) in patients affected by kidney failure, i.e. glomerular filtration rate &lt;15 ml/min/1.73 m2, is high and probably underestimated. Numerous uncertainties remain regarding how to prevent thromboembolic events in this population because both cardiology and nephrology guidelines do not provide clear recommendations. The efficacy and safety of oral anticoagulant therapy (OAC) in preventing thromboembolism in patients with kidney failure and AF has not been demonstrated for either vitamin K antagonists (VKAs) or direct anticoagulants (DOACs). Moreover, it remains unclear which is more effective and safer, because estimated creatinine clearance &lt;25–30 ml/min was an exclusion criterion in the randomized controlled trials (RCTs). Three RCTs comparing DOACs and VKAs in kidney failure failed to reach the primary endpoint, as they were underpowered. The left atrial appendage is the main source of thromboembolism in the presence of AF. Left atrial appendage closure (LAAC) has recently been proposed as an alternative to OAC. RCTs comparing the efficacy and safety of LAAC versus OAC in kidney failure were terminated prematurely due to recruitment failure. A recent prospective study showed a reduction in thromboembolic events in haemodialysis patients with AF and undergoing LAAC compared with patients taking or not taking OAC. We review current treatment standards and discuss recent developments in managing the thromboembolic risk in kidney failure patients with AF. The importance of shared decision-making with the multidisciplinary team and the patient to consider individual risks and benefits of each treatment option is underlined.