bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast EndoG prevents genome instability by degrading cytoplasmic DNA
Authors: Ira Grzegorz , Yu Yang , Wang Xin , Fox Jordan , Yu Ruofan , McCauley Brenna , Nikoloutsos Nic , Li Qian , Hastings Philip , Dang Weiwei , Chen Kaifu , Thakre Pilendra 
Published: January 2024

Abstract

In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease 1. Cytoplasmic nucleases degrade these DNA species to limit inflammation 2,3. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nuclear mtDNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
Knowledge Spillovers from Clean Innovation. A Tradeoff between Growth and Climate?
Authors: Verhoeven Dennis , Martin Ralf 
Published: January 2024

Abstract
Allocating scarce public funds to clean R&D might mean forfeiting higher economic gains from supporting other sectors, creating a tradeoff between economic and environmental goals. Our analysis of knowledge spillovers – the primary pathway for growth via innovation policy – suggests no such tradeoff: subsidy return rates are higher in Clean than in most other fields. But designing clean innovation policy based on national interests alone is inefficient, with EU-wide coordination boosting EU returns by 25% and global coordination raising worldwide returns by over 60%. Our analysis of cross-border knowledge spillovers suggests the EU could significantly benefit from US clean-focused policies like the Inflation Reduction Act.
Gut-derived memory γδT17 cells exacerbate sepsis-induced acute lung injury
Authors: Zhang Jiancheng , Xie Bing , Wang Mengyuan , Zhang Xinyu , Zhang Yujing , Qi Hong , Liu Hong , Wu Yuming , Wen Xiaoyue , Chen Xiaoyan , Han Mengqi , Xu Dan , Sun Xueqiang , Zhang Xue , Zhao Xin , Shang You , Yuan Shiying 
Published: January 2024

Abstract

Sepsis, a worldwide health crisis, is notorious for its high mortality rate, often attributed to the development of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS)1. The possible roles of the gut-lung axis mediated by the gut microbiota and its metabolites in the context of ALI have been documented2–4. However, the direct migration of intestinal immune cells to the lung as a mediator of ALI remains unclear. Here we report that sepsis prompted γδT17 cell migration from the small intestine to the lung, subsequently triggering an overwhelming inflammatory response dominated by IL-17A. The activated Wnt signaling in the alveolar macrophages during sepsis was identified as a driving factor for the subsequent CCL1 upregulation, which prompted the migration of small intestinal γδT17 cells to the lung. Small intestinal memory γδT17 cells (CD44+ Ly6C– IL-7Rhigh CD8low) were the major subtype of γδT17 cells that migrated from the small intestine to the lung and aggravated ALI. Esketamine alleviated ALI through dampening pulmonary Wnt/β-catenin signaling-mediated migration of small intestinal γδT17 cells to the lung. This study highlights the significant contribution of the direct migration of immune cells from the small intestine to the lung in sepsis-induced ALI, and clarifies the pathological significance of the localized elevation of IL-17A in the lung.
Predicting Labor and Delivery Complications: Dual Application of Logistic Regression and Supervised Machine Learning Algorithms
Authors: Alemayoh Fisha Mehabaw , Taye Getu Tadele , Abraha Hiluf Ebuy , Gebrehiwot Teklit Gebretsadik , Ebrahim Mohamedawel Mohamedniguss 
Published: January 2024

Abstract
Background
Prediction involves the use of data to learn, build knowledge, and improve predictive capacity through time from historical data to forecast future events. Predicting labor and delivery complications at an early stage could save the mother and baby from health challenges even death. This study aimed to identify determinants of and predict labor and delivery complications using machine learning techniques.
Methods
Data were collected using a data extraction sheet adopted from the Federal Ministry of Health Integrated antenatal, labor, delivery, and postnatal care card from Ayder Comprehensive Specialized Hospital, Ethiopia from April to July 2020. These samples were grouped using an 80% by 20% ratio on stratified outcome variables into training and test datasets. Descriptive, bivariate, and multivariate regression analyses were performed using Statistical Package for Social Science (SPSS). The synthetic minority oversampling technique (SMOTE) was used to balance the training dataset. Python and scikit learn were utilized to implement extreme gradient boosting (XGB), random forest, decision tree (DT), support vector machine (SVM), and K-nearest-neighbors (KNN) to develop predictive models for predicting labor and delivery complications. The confusion matrix, accuracy, precision, recall, receiver operating characteristics (ROC) curve, and F1-score test were used to compare the classification algorithms' prediction performance.
Results
A total of 320 (16%) mothers experienced labor and delivery complications. Models developed with KNN, SVM, random forest, DT, and XGB predicted the occurrence of labor and delivery complications with accuracy levels of 82%, 82%, 80%, 82% and 85%, respectively. The model developed using XGB scored the highest accuracy level.
Conclusions
Age, history of hypertension, history of preeclampsia, history of abortion, vaginal bleeding in the current pregnancy, history of diabetes mellitus, presentation of fetus, and Rh status were found to be determinants of labor and delivery complications. The model developed using the XGB algorithm has performed better in terms of predictive performance.
Characterizing pain in patients with Fabry disease: Findings from a web-based cross-sectional survey in the US
Authors: Wallace Eric , Laney Dawn , Warsi Ibrahim , Baldwin Connie , Johnson Jack , Kupferman Joseph , DasMahapatra Pronabesh , Lyn Nicole 
Published: January 2024

Abstract

Background:Fabry disease (FD) is a rare, progressive disorder caused by pathogenic variants of theGLAgene resulting in the accumulation of toxic metabolites. Pain is a hallmark of FD, and patients often present with heterogeneous pain profiles. This cross-sectional, web-based survey was conducted to characterize pain and pain crises in patients with FD in the United States and explore the effects of sex, disease phenotypes, and treatment on pain.Results:A total of 66 participants (mean [±SD] age: 44.0 [±12.7] years; females: 59.1%) completed the survey. Participants reported experiencing pain in upper (34.8%) and lower (43.9%) extremities several times a day and abdominal pain (31.8%) a few times a week. Overall, participants reported the nature of their pain as triggered (upper extremities: 47.0%; abdomen: 51.5%) or sudden (lower extremities: 57.6%). Female participants reported experiencing pain in upper (46.2%) and lower (48.7%) extremities several times a day and described it as sudden or triggered (48.7%) in upper extremities and sudden (61.5%) in lower extremities. Pain crises were reported in the lower extremities (80.0%), followed by the upper extremities (66.7%) and the abdomen (51.1%), and were often characterized as burning, tingling, or stabbing. A higher proportion of female participants (84.6%) than that of male participants (73.7%) reported pain crises in lower extremities. The duration of pain crises varied from 30 minutes to several days for different subgroups depending on sex and FD phenotypes. Most participants (81.0%) reported symptom improvement after 12 months of FD-specific treatment. With agalsidase beta as the most recent medication, participants reported improvement in neuropathic symptoms (burning in hands, 45.9%), with an overall mean (±SD) satisfaction score of 7.2 (±1.7).Conclusions:Pain was largely reported to be triggered across all subgroups. Consistent pain profiles were noted in participants across sex and FD phenotypes. Female participants reported pain burden similar to that of male participants, and pain crisis experience was heterogeneous across the subgroups. Most participants reported improvement in symptoms after FD-specific treatment and a high treatment satisfaction score with agalsidase beta.
dFLASH; dual FLuorescent transcription factor Activity Sensor for Histone integrated live-cell reporting and high-content screening
Authors: Bersten David , Allen Timothy , Roennfeldt Alison , Reckdharajkumar Moganalaxmi , Liu Miaomiao , Quinn Ronald , Russell Darryl , Peet Daniel J , Whitelaw Murray 
Published: January 2024

Abstract

Live-cell reporting of regulated transcription factor (TF) activity has a wide variety of applications in synthetic biology, drug discovery, and functional genomics. As a result, there is high value in the generation of versatile, sensitive, robust systems that can function across a range of cell types and be adapted toward diverse TF classes. Here we present the dual FLuorescent transcription factor Activity Sensor for Histone integrated live-cell reporting (dFLASH), a modular sensor for TF activity that can be readily integrated into cellular genomes. We demonstrate readily modified dFLASH platforms that homogenously, robustly, and specifically sense regulation of endogenous Hypoxia Inducible Factor (HIF) and Progesterone receptor (PGR) activities, as well as regulated coactivator recruitment to a synthetic DNA-Binding Domain-Activator Domain fusion proteins. The dual-colour nuclear fluorescence produced normalised dynamic live-cell TF activity sensing with facile generation of high-content screening lines, strong signal:noise ratios and reproducible screening capabilities (Z’ = 0.68-0.74). Finally, we demonstrate the utility of this platform for functional genomics applications by using CRISPRoff to modulate the HIF regulatory pathway, and for drug screening by using high content imaging in a bimodal design to isolate activators and inhibitors of the HIF pathway from a ~1600 natural product library.
Impact of cellulose supramolecular structure on its carboxymethylation reaction activity
Authors: Yuldoshov Sherzod , Yunusov Khaydar , Goyipnazarov Ilkhom , Sarymsakov Abdushkur , Rashidova Sayyora , Guohua Jiang 
Published: January 2024

Abstract
The reaction activity of cellulose samples is determined according to their supramolecular structure, especially the degree of crystallinity. The carboxymethylation reaction kinetics of cotton cellulose (CC), powder cellulose (PC) and microcrystalline cellulose (MCC), with different degrees of crystallinity, were studied by the solid-phase method and in an ethanol-water solution medium. In the row of CC, MCC, and PC with different supramolecular structures, it was found that with decreasing crystallinity degree of the raw materials, during carboxymethylation by the solid-phase method and in an ethanol-water solution medium, the degree of substitution (DS) of sodium carboxymethylcellulose (Na-CMC) increased. In this row the activation energy values of the carboxymethylation reaction of CC, MCC, and PC were 31.12, 19.75, and 15.72 kJ/mol, respectively, by the solid-phase method. Furthermore, the activation energies of the carboxymethylation reaction of CC, MCC, and PC were 59.95, 26.15, and 23.68 kJ/mol, respectively, in an ethanol-water solution medium. Decreasing activation energies led to an increase in the reaction activity, which, after CC, MCC, and PC carboxymethylation, the DS of Na-CMC reached 0.61, 0.80, and 0.87, respectively, using the solid-phase method. In an ethanol solution medium, the DS values of Na-CMC reached 0.86, 1.04, and 1.24 after carboxymethylation of the CC, MCC, and PC, respectively.
Assessment of seismic hazard incorporating site-specific study for Assam, North-East India
Authors: Borah Mayuri , Sharma Mukat Lal , Dubey Ramanand 
Published: January 2024

Abstract
In conjunction with site-specific studies, probabilistic seismic hazard assessment (PSHA) is crucial in formulating site-specific response spectra to provide valuable insights into local seismic hazard variations. A site-specific seismic hazard assessment is presented considering a classical probabilistic approach incorporating ground response analysis for Assam, North-East (NE) India. NE India Region is classified into ten seismic source zones depending on the seismicity and tectonics. An updated homogenized earthquake catalogue for 1897–2022 has been used. The seismicity parameters have been calculated with the complete catalogue for each source zone. A topography-based Vs30 model has been considered, and for the application of ground motion prediction equations (GMPEs), a logic tree approach using the log-likelihood method (LLH) has been considered. The hazard maps for Assam are prepared at the bedrock level in terms of peak ground acceleration (PGA) and spectral acceleration (Sa) values. The PGA values vary between 0.23–0.34 g and 0.33–0.51 g for 475 and 2475 years of return period, respectively. The hazard curves and uniform hazard spectra (UHS) have also been presented for ten headquarters of Assam, along with disaggregation studies for Guwahati. Further, borehole data from Guwahati have been considered for evaluating ground responses with the assignment of proper soil conditions. The surface level PGA for Guwahati gets amplified significantly up to 0.41 g and 0.56 g for 475 and 2475 years of return period, respectively. Finally, the surface-level responses have been presented for Guwahati city, one of the ten headquarters of Assam, considering the controlling earthquake.
A novel method for neutron energy spectrum measurement base on Single Event Upset of Static Random Access Memories
Authors: Liu Yuxuan , Qiu Yanyan , Tan Zhixin , Chen Yonghao , Yi Han , He Yongning , Zhao Xiaolong , Fan Ruirui 
Published: January 2024

Abstract
Without the time-of-flight, the neutron energy spectrum measurements are difficult. Bonner sphere spectrometer and threshold detectors are normally employed for this neutron field measurement. The complexity and budget of these systems restrict their applications. According to the investigation of SRAMs’ (Static Random Access Memories) Single Event Upset (SEU) cross-sections, a novel method of neutron energy spectrum measurement up to tens of MeV energy range is proposed in this paper, which is more available and lower cost. From a series of the published SRAM cross-section results by previous work and the upset rate of these SRAMs, the unknown neutron energy spectrum can be evaluated. A SVD (singular value decomposition) method is used for deriving the energy spectrum. In further research, the relationship between the quantity of SRAMs and the resolve accuracy is studied with the theory of information entropy. It proves that the energy spectrum accuracy is highly depended on the SEU cross-sections active range and the number of different SRAMs.
A mouse model of sporadic Alzheimer’s disease with elements of major depression
Authors: Bobkova N.V. , Chuvakova L.N. , Kovalev V.I. , Zdanova D.Y. , Chaplygina A.V. , Rezvykh A.P. , Evgen'ev M.B. 
Published: January 2024

Abstract
Animals after bulbectomy are often used as a model of major depression or sporadicAlzheimer’s disease and, hence, the status of this model is still disputable. To elucidate the nature of alterations in the expression of the genome after the operation we analyzed transcriptomes (RNA-seq data) of the cortex, hippocampus, and cerebellum of olfactory bulbectomized (OBX) mice. Analysis of the functional significance of genes in the brain of OBX mice indicates that the balance of the GABA/glutamatergic systems is disturbed with hyperactivation of the latter in the hippocampus leading to the development of excitotoxicity and induction of apoptosis on the background of severe mitochondrial dysfunction and astrogliosis. On top of this, the synthesis of neurotrophic factors decreases leading to the disruption of the cytoskeleton of neurons, an increase in the level of intracellular calcium, and activation of tau protein hyperphosphorylation and beta-amyloid depositions. Moreover, the acetylcholinergic system is deficient in the background of hyperactivation of acetylcholinesterase. Importantly, the activity of the dopaminergic, endorphin, and opiate systems in OBX mice decreases leading to hormonal dysfunction. Genes responsible for the regulation of circadian rhythms, cell migration, and impaired innate immunity are activated in OBX animals. All this takes place on the background of drastic down-regulation of ribosomal protein genes in the brain. The obtained results indicate that OBX mice represent a model of Alzheimer's disease with elements of major depression. This model can be tentatively attributed to AD subtype B2 in humans.
Distinguishing High-Metastasis-Potential Circulating Tumor Cells through Fluidic Shear Stress in a Bloodstream-Like Microfluidic Circulatory System
Authors: Yang Michael , LI Wenxiu , Guo Zhengjun , Zhou Zhihang , Zhou Zhengdong , He Huimin , Sun Jiayu , Zhou Xiaoyu , Chin Y Rebecca , Zhang Liang 
Published: January 2024

Abstract

Circulating tumor cells (CTCs) play a critical role as initiators in tumor metastasis, which unlocks an irreversible process of cancer progression. Regarding the fluid environment of intravascular CTCs, a comprehensive understanding of the impact of hemodynamic shear stress on CTCs is of profound significance but remains vague. Here, we report a microfluidic circulatory system that can emulate CTC microenvironment to research responses of typical liver cancer cells to varying levels of fluid shear stress (FSS). We find that survived HepG2 cells in the microfluidic circulatory system exhibit marked overexpression on TLR4 and TPPP3 genes, which are shown to be associated with the colony formation, migration, and anti-apoptosis abilities of HepG2. Furthermore, overexpression of these two genes in another liver cancer cell line with low TLR4 and TPPP3 expression, SK-Hep-1 cells, by lentivirus-mediated transfection also confirm the critical role of TLR4 and TPPP3 on improving SK-Hep-1 cells’ colony formation, migration, and survival capability under fluid environment. Interestingly, in vivo study further shows SK-Hep-1 cells overexpressed with these genes have enhanced metastatic potential to liver and lung organs via tail vein injection in mouse models. These results reveal CTCs can adapt to fluid environment though altering genetic makeup and corresponding cellular behaviors, which may provide novel therapeutic strategies for cancer diagnosis and treatment.
Porous silicon and silica carriers for delivery of peptide therapeutics
Authors: Yan Jiachen , Siwakoti Prakriti , Kokil Ganesh , Kumeria Tushar 
Published: January 2024

Abstract
Peptides have gained tremendous popularity as biological therapeutic agents in recent years due to their favourable specificity, diversity of targets, well-established screening methods, ease of production, and lower cost. However, their poor physiological and storage stability, pharmacokinetics, and fast clearance have limited their clinical translation. Novel nanocarrier-based strategies have shown promise in overcoming these issues. In this direction, porous silicon (pSi) and mesoporous silica nanoparticles (MSNs) have been widely explored as potential carriers for the delivery of peptide therapeutics. These materials possess several advantages, including large surface areas, tunable pore sizes, and adjustable pore architectures, which make them attractive carriers for peptide delivery systems. In this review, we cover pSi and MSNs as drug carriers focusing on their use in peptide delivery. The review provides a brief overview of their fabrication, surface modification, and interesting properties that make them ideal peptide drug carriers. The review provides a systematic account of various studies that have utilised these unique porous carriers for peptide delivery describing significant in vitro and in vivo results. We have also provided a critical comparison of the two carriers in terms of their physicochemical properties and short-term and long-term biocompatibility. Lastly, we have concluded the review with our opinion of this field and identified key areas for future research for clinical translation of pSi and MSN-based peptide therapeutic formulations.
Transferable Channels for Fair Micropurchases
Authors: Payeras-Capellà M. Magdalena , Mut-Puigserver Macià , Pericàs-Gornals Rosa 
Published: January 2024

Abstract

The development of e-commerce applications, involving small-value transactions for the exchange of goods or services introduces notable security and privacy challenges. Micropurchases, commonly referred to as micropayments, offer a pragmatic solution that provides a balance between efficiency and security for small-value transactions. The increasing demand for this payment approach, particularly with the advent of technologies such as the Internet of Things (IoT), underscores the need for innovative solutions.This paper introduces a novel micropurchase protocol making use of transferable payment channels. The protocol facilitates equitable and fair exchanges betweenminimal monetary units (μ-coins) and desired goods or services, allowing efficient payments of low values. The proposed transferable channels enable off-chain transactions, minimizing the reliance on on-chain transactions to achieve essential security features. The protocol defines the process of performing purchases, handling received payments, incorporating functionalities for the transfer and reutilization of payment channels for both customers and merchants. Furthermore, the proposed scheme specifies the procedures for redeeming the earned μ-coins by the merchant and refundingthe unused μ-coins by the customer.