bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modified CTAB method for the extraction of high-quality RNA from mono-and dicotyledonous plants rich in secondary metabolites
Authors: Kiss Tibor , Karácsony Zoltán , Gomba-Tóth Adrienn , Szabadi Kriszta Lilla , Spitzmüller Zsolt , Hegyi-Kaló Júlia , Cels Thomas , Otto Margot , Golen Richárd , Hegyi Ádám István , Geml József , Váczy Kálmán Zoltán 
Published: May 2024

Abstract
Background
High-quality RNA extraction from woody plants is difficult because of the presence of polysaccharides and polyphenolics that bind or co-precipitate with the RNA. The CTAB (cetyl trimethylammonium bromide) based method is widely used for the isolation of nucleic acids from polysaccharide-rich plants. Despite the widespread use of the CTAB method, it is necessary to adapt it to particular plant species, tissues and organs. Here we described a simple and generalized method for RNA isolation from mature leaf tissues of several economically important woody (17) and herbaceous plants (2) rich in secondary metabolites. High yields were achieved from small amount (up to 50 mg) of plant material. Two main modifications were applied to the basic protocol: an increase in β-mercaptoethanol concentration (to 10%v/v) and the use of an effective DNase treatment. As opposed to similar studies, we tried to describe a more detailed protocol for isolating RNA, including the exact quantity and concentration of the reagents were used.

Results
Our modified CTAB method is proved to be efficient in extracting the total RNA from a broad range of woody and herbaceous species. The RNA yield was ranged from 2.37 to 91.33 µg/µl. The A260:A280 and A260:A230 absorbance ratios were measured from 1.77 to 2.13 and from 1.81 to 2.22. The RIN value (RNA Integrity Number) of the samples fell between 7.1 and 8.1, which indicated that a small degree of RNA degradation occurred during extraction. The presence of a single peak in the melt curve analyses and low standard errors of the Ct values of replicated measurements indicated the specificity of the primers to bind to the cDNA.

Conclusions
Our RNA isolation method, with fine-tuned and detailed instructions, can produce high quality RNA from a small amount of starting plant material that is suitable for use in downstream transcriptional analyses. The use of an increased concentration of the reducing agent β-mercaptoethanol in the extraction buffer, as well as the application of DNaseI-treatment resulted in a method suitable for a wide range of plants without the need of further optimalization, especially in Rhus typhina (Staghorn sumac), for which molecular-genetic studies have not yet been sufficiently explored.
The deubiquitinase USP7 and E3 ligase TRIM21 regulate vasculogenic mimicry and malignant progression of RMS by balancing SNAI2 homeostasis
Authors: Zhang Ruyue , Zhang Daidi , Han Fugen , Song Xiaorui , Zhang Yaodong , Zhang Jie , Zhu Qingwen , Qin Yanru 
Published: May 2024

Abstract
Background
Rhabdomyosarcoma (RMS) is a rare malignancy and the most common soft tissue sarcoma in children. Vasculogenic mimicry (VM) is a novel tumor microcirculation model different from traditional tumor angiogenesis, which does not rely on endothelial cells to provide sufficient blood supply for tumor growth. In recent years, VM has been confirmed to be closely associated with tumor progression. However, the ability of RMS to form VM has not yet been reported.

Methods
Immunohistochemistry, RT-qPCR and western blot were used to test the expression level of SNAI2 and its clinical significance. The biological function in regulating vasculogenic mimicry and malignant progression of SNAI2 was examined both in vitro and in vivo. Mass spectrometry, co-immunohistochemistry, immunofluorescence staining, and ubiquitin assays were performed to explore the regulatory mechanism of SNAI2.

Results
Our study indicated that SNAI2 was abnormally expressed in patients with RMS and RMS cell lines and promoted the proliferation and metastasis of RMS. Through cell tubule formation experiments, nude mice Matrigel plug experiments, and immunohistochemistry (IHC), we confirmed that RMS can form VM and that SNAI2 promotes the formation of VM. Due to SNAI2 is a transcription factor that is not easily drugged, we used Co-IP combined with mass spectrometry to screen for the SNAI2-binding protein USP7 and TRIM21. USP7 depletion inhibited RMS VM formation, proliferation and metastasis by promoting SNAI2 degradation. We further demonstrated that TRIM21 is expressed at low levels in human RMS tissues and inhibits VM in RMS cells. TRIM21 promotes SNAI2 protein degradation through ubiquitination in the RMS. The deubiquitinase USP7 and E3 ligase TRIM21 function in an antagonistic rather than competitive mode and play a key role in controlling the stability of SNAI2 to determine the VM formation and progression of RMS.

Conclusion
Our findings reveal a previously unknown mechanism by which USP7 and TRIM21 balance the level of SNAI2 ubiquitination, determining RMS vasculogenic mimicry, proliferation, and migration. This new mechanism may provide new targeted therapies to inhibit the development of RMS by restoring TRIM21 expression or inhibiting USP7 expression in RMS patients with high SNAI2 protein levels.
Brief Educational Workshops in Secondary Schools Trial (BESST trial), a school-based cluster randomised controlled trial of the DISCOVER workshop for 16–18-year-olds: recruitment and baseline characteristics
Authors: James Kirsty , Lisk Stephen , Payne-Cook Chloe , Farishta Zamena , Farrelly Maria , Sheikh Ayesha , Slusarczyk Monika , Byford Sarah , Day Crispin , Deighton Jessica , Evans Claire , Fonagy Peter , Saunders David , Sclare Irene , Shearer James , Stallard Paul , Weaver Timothy , Yarrum Jynna , Carter Ben , Brown June S. L. 
Published: May 2024

Abstract
Background
The Brief Educational Workshops in Secondary Schools Trial (BESST) is an England-wide school-based cluster randomised controlled trial assessing the clinical and cost-effectiveness of an open-access psychological workshop programme (DISCOVER) for 16–18-year-olds. This baseline paper describes the self-referral and other recruitment processes used in this study and the baseline characteristics of the enrolled schools and participants.

Method
We enrolled 900 participants from 57 Secondary schools across England from 4th October 2021 to 10th November 2022. Schools were randomised to receive either the DISCOVER day-long Stress workshop or treatment as usual which included signposting information. Participants will be followed up for 6 months with outcome data collection at baseline, 3-month, and 6-month post randomisation.

Results
Schools were recruited from a geographically and ethnically diverse sample across England. To reduce stigma, students were invited to self-refer into the study if they wanted help for stress. Their mean age was 17.2 (SD = 0.6), 641 (71%) were female and 411 (45.6%) were from ethnic minority groups. The general wellbeing of our sample measured using the Mood and Feelings Questionnaire (MFQ) found 314 (35%) of students exhibited symptoms of depression at baseline. Eighty percent of students reported low wellbeing on the Warwick Edinburgh Mental Wellbeing Scale (WEMWBS) suggesting that although the overall sample mean is below the cut-off for depression, the self-referral approach used in this study supports distressed students in coming forward.

Conclusion
The BESST study will continue to follow up participants to collect outcome data and results will be analysed once all the data have been collected.

Trial registration
ISRCTN registry ISRCTN90912799. Registered on 28 May 2020.
Mayaro virus, a potential threat for Europe: vector competence of autochthonous vector species
Authors: Brustolin Marco , Bartholomeeusen Koen , Rezende Tatiana , Ariën Kevin K. , Müller Ruth 
Published: May 2024

Abstract
Background
Mayaro virus (MAYV) is an emerging alphavirus, primarily transmitted by the mosquito Haemagogus janthinomys in Central and South America. However, recent studies have shown that Aedesaegypti, Aedesalbopictus and various Anopheles mosquitoes can also transmit the virus under laboratory conditions. MAYV causes sporadic outbreaks across the South American region, particularly in areas near forests. Recently, cases have been reported in European and North American travelers returning from endemic areas, raising concerns about potential introductions into new regions. This study aims to assess the vector competence of three potential vectors for MAYV present in Europe.

Methods
Aedesalbopictus from Italy, Anophelesatroparvus from Spain and Culexpipiens biotype molestus from Belgium were exposed to MAYV and maintained under controlled environmental conditions. Saliva was collected through a salivation assay at 7 and 14 days post-infection (dpi), followed by vector dissection. Viral titers were determined using focus forming assays, and infection rates, dissemination rates, and transmission efficiency were calculated.

Results
Results indicate that Ae.albopictus and An.atroparvus from Italy and Spain, respectively, are competent vectors for MAYV, with transmission possible starting from 7 dpi under laboratory conditions. In contrast, Cx.pipiens bioform molestus was unable to support MAYV infection, indicating its inability to contribute to the transmission cycle.

Conclusions
In the event of accidental MAYV introduction in European territories, autochthonous outbreaks could potentially be sustained by two European species: Ae.albopictus and An.atroparvus. Entomological surveillance should also consider certain Anopheles species when monitoring MAYV transmission.

Graphical abstract
Rheumatoid arthritis disease activity significantly impacts on the severity of interstitial lung disease
Authors: Ito Yuhei , Ichikawa Yasutaka , Murashima Shuichi , Sakuma Hajime , Nakajima Ayako 
Published: May 2024

Abstract
Objectives
Rheumatoid arthritis (RA) related interstitial lung disease (ILD) impacts on the treatment strategy and its prognosis in patients with RA. However, the relationship between RA disease activity and the severity of comorbid ILD has not been fully investigated. This study aimed to investigate the impact of RA disease activity on the severity of comorbid ILD in detail based on currently established visual scoring method along with physiological severity.

Methods
Consecutive patients with RA visiting to our Rheumatology Centre between December 2020 and December 2023 were analysed. The radiological severity of ILD was evaluated by averaging the extent of the combined lesion of ground glass opacity, reticulation and honeycombing in 5% increments in six representative high-resolution computed tomography slices ranging from 0% (no involvement) to 100% (all lung fields affected) according to Goh and Walsh’s method. Associations between the radiological and physiological severity of ILD and patients’ features were investigated using linear regression analysis.

Results
Among 124 patients (32 men, 92 women), the median age was 70 years, and the median disease duration was 2.92 years. Radiological severity of ILD was 0% (without ILD) in 107 (86.2%), ILD with extent < 10% in nine (7.2%), ILD with extent ≥10% and < 20% in three (2.4%), ILD with extent ≥20% in five (4.0%). Both disease activity score (DAS)28-erythrocyte sedimentation rate (ESR) (standardized coefficient = 0.199, P = 0.03) and rheumatoid factor titre (standardized coefficient = 0.247, P = 0.01) were significantly associated with the radiological quantitative severity of ILD in multivariate analysis adjusted for age, sex, disease duration, smoking status and anti-citrullinated peptide antibody titre. DAS28-ESR was significantly associated with forced vital capacity% predicted (standardized coefficient = -0.230, P = 0.047).

Conclusions
Disease activity of RA was significantly associated with the severity of RA-ILD both radiologically and physiologically.
Clinical validity of the Italian adaptation of the Uniform Data Set Neuropsychological Test Battery (I-UDSNB) in Mild Cognitive Impairment and Alzheimer’s Disease
Authors: Conca Francesca , Esposito Valentina , Catricalà Eleonora , Manenti Rosa , L’Abbate Federica , Quaranta Davide , Giuffrè Guido Maria , Rossetto Federica , Solca Federica , Orso Beatrice , Inguscio Emanuela , Crepaldi Valeria , De Matteis Maddalena , Rotondo Emanuela , Manera Marina , Caruso Giulia , Catania Valentina , Canu Elisa , Rundo Francesco , Cotta Ramusino Matteo , Filippi Massimo , Fundarò Cira , Piras Federica , Arighi Andrea , Tiraboschi Pietro , Stanzani Maserati Michelangelo , Pardini Matteo , Poletti Barbara , Silani Vincenzo , Marra Camillo , Di Tella Sonia , Cotelli Maria , Lodi Raffaele , Tagliavini Fabrizio , Cappa Stefano Francesco 
Published: May 2024

Abstract
Background
The identification and staging of Alzheimer’s Disease (AD) represent a challenge, especially in the prodromal stage of Mild Cognitive Impairment (MCI), when cognitive changes can be subtle. Worldwide efforts were dedicated to select and harmonize available neuropsychological instruments. In Italy, the Italian Network of Neuroscience and Neuro-Rehabilitation has promoted the adaptation of the Uniform Data Set Neuropsychological Test Battery (I-UDSNB), collecting normative data from 433 healthy controls (HC).
Here, we aimed to explore the ability of I-UDSNB to differentiate between a) MCI and HC, b) AD and HC, c) MCI and AD.

Methods
One hundred thirty-seven patients (65 MCI, 72 AD) diagnosed after clinical-neuropsychological assessment, and 137 HC were included. We compared the I-UDSNB scores between a) MCI and HC, b) AD and HC, c) MCI and AD, with t-tests. To identify the test(s) most capable of differentiating between groups, significant scores were entered in binary logistic and in stepwise regressions, and then in Receiver Operating Characteristic curve analyses.

Results
Two episodic memory tests (Craft Story and Five Words test) differentiated MCI from HC subjects; Five Words test, Semantic Fluency (vegetables), and TMT-part B differentiated AD from, respectively, HC and MCI.

Conclusions
Our findings indicate that the I-UDSNB is a suitable tool for the harmonized and concise assessment of patients with cognitive decline, showing high sensitivity and specificity for the diagnosis of MCI and AD.
An adversarial environment reinforcement learning-driven intrusion detection algorithm for Internet of Things
Authors: Mahjoub Chahira , Hamdi Monia , Alkanhel Reem Ibrahim , Mohamed Safa , Ejbali Ridha 
Published: May 2024

AbstractThe increasing prevalence of Internet of Things (IoT) systems has made them attractive targets for malicious actors. To address the evolving threats and the growing complexity of detection, there is a critical need to search for and develop new algorithms that are fast and robust in detecting and classifying dangerous network traffic. In this context, deep reinforcement learning (DRL) is gaining recognition as a prospective solution in numerous fields as it enables autonomous agents to cooperate with their environment for decision-making without relying on human experts. This article presents an innovative approach to intrusion detection in IoT systems using an adversarial reinforcement learning (RL) algorithm known for its exceptional predictive capabilities. The predictive process relies on a classifier, implemented as a streamlined and highly efficient neural network. Embedded within this classifier is a policy function meticulously trained using an innovative RL model. Importantly, this model ensures that the environment’s behavior is dynamically fine-tuned simultaneously with the learning process, improving the overall effectiveness of the intrusion detection approach. The efficiency of our proposal was assessed using the Bot-IoT database, consisting of a mixture of legitimate IoT network traffic and simulated attack scenarios. Our scheme shows superior performance compared to existing ones. Therefore, our approach to IoT intrusion detection can be considered a valuable alternative to existing methods, capable of significantly improving the IoT systems’ security.
Energy efficiency as a driver of the circular economy and carbon neutrality in selected countries of Southern Europe: a soft computing approach
Authors: Ramčilović Jesih Alma , Šimić Goran , Konatar Ljubiša , Brljak Zoran , Šprajc Polona 
Published: May 2024

Abstract

Background
The main goal of the paper is to define the level of energy efficiency in the economies of selected countries in the Balkan region that have opted for the EU Green Deal, a circular economy, and a transition to carbon neutrality. Energy efficiency, as a determinant of carbon neutrality, was selected as an indicator for analysis because it records particularly unfavorable indicators in the region under observation. The research was carried out on a sample of seven Balkan countries and their surrounding areas. An initial qualitative analysis was followed by a quantitative analysis based on a combination of statistical methods and soft computing. Six indicators were selected for the analysis covering a period of 30 years (1990–2020).

Results
A significant obstacle to the green transition and the region’s transition to a circular economy and carbon neutrality is energy efficiency and energy related pollution—the reliance of most countries on coal-fired thermal power plants for electricity generation. The research results showed the following: (a) the degree of economic development and membership in the European Union are not significantly related to the level of energy efficiency; (b) most of the sampled countries are in the initial stages of introducing activities to achieve carbon neutrality; and (c) only Slovenia has documented consistent indicators and evident advancements in its efforts to achieve carbon neutrality. Based on the research findings, proposals for improvements were made in the direction of policymaking and in a methodological sense.

Conclusions
The implementation of circularity and carbon neutrality as a long-term goal of the European Union is not necessarily related to the level of economic development, nor can its trajectory be exclusively ascertained by means of data processing and monitoring. A more precise understanding of a carbon-neutral future can be achieved through the incorporation of qualitative data to a greater extent, a realistic evaluation of historical facts and their repercussions, as well as projections of the effects that reality and global developments after 2022 will have on each country.
Nomogram for predicting the risk of postoperative delirium in elderly patients undergoing orthopedic surgery
Authors: Fan Yunping , Yang Tingjun , Liu Yuhan , Gan Haibin , Li Xiaohua , Luo Yanrong , Yang Xuping , Pang Qianyun 
Published: May 2024

Abstract
Objective
To retrospectively analyze the risk factors for postoperative delirium (POD) after orthopedic surgery in elderly patients and establish an individualized nomogram to predict the risk of POD.

Methods
The data of 1011 patients who underwent orthopedic surgery from January 2019 to January 2022 were retrospectively analyzed. Univariate and multivariate logistic analyses were used to screen for independent risk factors. Stepwise regression was conducted to screen risk factors to construct a nomogram to predict the risk of POD after orthopedic surgery in elderly individuals, and nomogram validation analyses were performed.

Results
The logistic regression results showed that age (≥ 75 years old vs. < 75 years old; odds ratio (OR) = 2.889; 95% confidence interval (CI), 1.149, 7.264), sex (male vs. female, OR = 2.368; 95% CI, 1.066, 5.261), and preoperative cognitive impairment (yes vs. no, OR = 13.587; 95% CI, 4.360, 42.338) were independent risk factors for POD in elderly patients who underwent orthopedic surgery (P < 0.05). A nomogram was constructed using 7 risk factors, i.e., age, American Society of Anesthesiologists (ASA) classification, sex, preoperative hemoglobin (Hb), preoperative pulmonary disease, cognitive impairment, and intraoperative infusion volume. The area under the curve (AUC) showed good discrimination (0.867), the slope of the calibration curve was 1.0, and the optimal net benefit of the nomogram from the decision curve analysis (DCA) was 0.01–0.58.

Conclusion
This study used 7 risk factors to construct a nomogram to predict the risk of POD after major orthopedic surgery in elderly individuals, and the nomogram had good discrimination ability, accuracy, and clinical practicability.
Insights into the abundance, expression and diversity of key denitrification genes in an ecologically managed greenhouse agricultural soil
Authors: Hernández Maqueda R. , Ballesteros I. , Meca D. , Linacero R. , del Moral F. 
Published: May 2024

AbstractUnderstanding the bacteria associated with nitrification and denitrification is crucial for comprehending the processes that lead to nitrous oxide emissions in agricultural greenhouse soils. Therefore, it is important to determine their abundance and expression to gain insight into these processes.The aim of this study was to explore the bacterial communities associated with denitrification in a greenhouse agricultural soil amended with crop residues and manure for six years. For this purpose, we proceeded to detect and quantify the genes nirK and nirS and the gene nosZ through clone library construction, sequencing, phylogenetic analysis, and quantitative polymerase chain reaction (qPCR). Sequence analysis based on the clone library revealed that many of the nirS or nirK genes detected were not closely related to known denitrifier bacteria, but some of the nosZ sequences were related to the genera such as Pseudomonas, Halomonas, and Marinobacter. Furthermore, the qPCR revealed a high abundance of DNA copies in nirK, 6.08 × 109 ± 1.16 × 109, while nirS and nosZ showed lower values, 9.05 × 106 ± 1.65 × 106 and 8.71 × 106 ± 1.44 × 106, respectively. However, the highest expression rate was observed for nirS (mRNA/DNA ratio = 3.10 × 10− 3), while nirK and nosZ showed 10-fold lower expression rates (4.4 × 10− 4 and 3.5 × 10− 4, respectively). The results of this work provide a preliminary overview of the diversity, abundance and expression of key genes associated with the denitrification process in this type of soil and are a starting point for further studies to understand how this type of soil management can influence the denitrification process.
Homoharringtonine: updated insights into its efficacy in hematological malignancies, diverse cancers and other biomedical applications
Authors: Khatua Somanjana , Nandi Sudeshna , Nag Anish , Sen Surjit , Chakraborty Nilanjan , Naskar Arghya , Gürer Eda Sönmez , Calina Daniela , Acharya Krishnendu , Sharifi-Rad Javad 
Published: May 2024

AbstractHHT has emerged as a notable compound in the realm of cancer treatment, particularly for hematological malignancies. Its multifaceted pharmacological properties extend beyond traditional applications, warranting an extensive review of its mechanisms and efficacy. This review aims to synthesize comprehensive insights into the efficacy of HHT in treating hematological malignancies, diverse cancers, and other biomedical applications. It focuses on elucidating the molecular mechanisms, therapeutic potential, and broader applications of HHT. A comprehensive search for peer-reviewed papers was conducted across various academic databases, including ScienceDirect, Web of Science, Scopus, American Chemical Society, Google Scholar, PubMed/MedLine, and Wiley. The review highlights HHT's diverse mechanisms of action, ranging from its role in leukemia treatment to its emerging applications in managing other cancers and various biomedical conditions. It underscores HHT's influence on cellular processes, its efficacy in clinical settings, and its potential to alter pathological pathways. HHT demonstrates significant promise in treating various hematological malignancies and cancers, offering a multifaceted approach to disease management. Its ability to impact various physiological pathways opens new avenues for therapeutic applications. This review provides a consolidated foundation for future research and clinical applications of HHT in diverse medical fields.