bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS
Authors: Loke Png , zhao mingming , Jankovic Dragana , Hornick Katherine , Link Verena , Souza Camila Oliveira Silva , Belkaid Yasmine , Lack Justin 
Published: January 2024

Abstract

How macrophages in the tissue environment integrate multiple stimuli will depend on the genetic background of the host, but this is poorly understood. Here, we investigated C57BL/6 and BALB/c strain specific in vivo IL-4 activation of tissue-resident macrophages (TRMs) from the peritoneal cavity. C57BL/6 TRMs are more transcriptionally responsive to IL-4 stimulation, with a greater association of induced genes with super enhancers, induced enhancers, and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling revealed BL/6 specific enrichment of NF-κB, IRF, and STAT motifs. Additionally, IL-4-activated BL/6 TRMs demonstrated an augmented synergistic response upon in vitro lipopolysaccharide (LPS) exposure compared to BALB/c TRMs, despite naïve BALB/c TRMs displaying a more robust transcriptional response to LPS than naïve BL/6 TRMs. Single-cell RNA sequencing (scRNA-seq) analysis of mixed bone marrow chimeric mice indicated that transcriptional differences between BL/6 and BALB/c TRMs, and synergy between IL-4 and LPS, are cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming resulting in strain specific synergistic responses to LPS exposure.
Ultrasound-based radiomics model: a potential adjunctive tool for assessing impaired placental function in preeclampsia
Authors: Sun Hongshuang , Jiao Jing , Wang Yicong , Zhu Chen , Wang Shaochun , Ban Bo , Guo Yi , Wang Yuanyuan , Ren Yunyun 
Published: January 2024

Abstract

Purpose
Combined with ultrasound-based radiomics, our research team has successfully developed a novel model that enables the evaluation of placental function in rats with pre-eclampsia.
Material and Methods
We have developed a rat model of preeclampsia induced by L-NAME and evaluated placental dysfunction through the analysis of microstructural alterations and immunoprotein levels in placental tissue. After feature extraction of ultrasound images, the Boruta feature selection method was employed to determine the most effective combination of features, and a ten-fold cross-validation method was utilized to establish the optimal model for classifying placental dysfunction. The accuracy, sensitivity, specificity, and AUC were employed to assess the efficacy of the developed model.
Results
In pregnant rats with preeclampsia, significant changes were observed in the microstructure of placental tissue and the expression of the angiogenic factor in the tissue. Ultrasound images of the placenta yielded a total of 558 radiomics features based on high-throughput mining of quantitative image features. After assessment of impaired placental function, an evaluation model was successfully constructed for assessing placental function in pregnant rats. The evaluation model had an AUC of 0.95, with high sensitivity, specificity, accuracy, positive predictive value, and negative predictive value, reaching 88.7%, 91.5%, 90.2%, 90.4%, and 90.0%, respectively.
Conclusion
Ultrasound-based radiomics could effectively identify abnormal placental features in pregnant rats with preeclampsia, and exhibiting high performance in evaluating normal and poor placental function.
Growing online attention and positive sentiments towards carbon dioxide removal
Authors: Repke Tim , Muller-Hansen Finn , Cox Emilx , Minx Jan 
Published: January 2024

Abstract

Scaling up CO2 removal is crucial to achieve net-zero targets and limit global warming.
Understanding public perception of large-scale carbon dioxide removal (CDR) is vital to avoid opposition that could slow down development, investments, and deployment.

Using Twitter data from 2010 to 2022, we analysed attention and sentiments towards ten CDR methods.
Our study provides up-to-date time series evidence complementing survey studies, capturing the opinions of users with knowledge or awareness of emerging CDR methods.

Attention towards CDR has grown exponentially, particularly in recent years.
Overall, the discourse on CDR has become more positive, except for BECCS.
Conventional CDR methods are the most discussed and receive more positive sentiments.
We examined three user types, each with varying levels of involvement in the discourse.
Infrequent users (assumed less familiar) pay more attention to methods with biological sinks, while frequent users (assumed more familiar) focus more on novel CDR methods.
A cost-effective approach to measurements of fluorophore temperature sensitivity and temperature change
Authors: Cai Matthew , Sun Alexander , Yan Andrea , Ding Zachary , Jiang Melvin Zunyao , Wang Charissa , Yuan Baohong 
Published: January 2024

Abstract
The demand for measuring fluorophore temperature sensitivity and temperature change in chemical or biological samples has spurred the search for effective methods. While infrared (IR) light-based thermal devices are popular, they are limited to surface temperature measurement. Fluorescence-based thermometry, which utilizes intensity, lifetime, polarization, and spectrum change, provides the temperature information directly from the samples and can have high temporal and spatial resolution. However, measuring fluorescence can be tricky and expensive. A cost-effective approach to achieving reasonable accuracy is highly desired. This study introduces such an approach, employing a light-emitting diode (LED) for fluorophore excitation and a laser diode (LD) for sample heating, with a phone camera recording fluorescence changes. A data processing method converts the video into digital data, processed through digital filters. Utilizing a small-volume cuvette enhances heating efficiency. This study serves as a practical guide for inexperienced individuals, including students, instructors, and researchers, facilitating entry into the field and navigating the complexities of fluorescence-based thermometry.
Surface ruptures of the 2022 Guanshan-Chihshang earthquakes in central Longitudinal Valley area, eastern Taiwan
Authors: Wang Yu , Wu Sheng-Han , Chou Hoi-Ling Birdie , Li Yi-Yu , Cheng Wai-San , Ho Andrew , Chen Jian-Ming , Liu Sze-Chieh , Hsieh Chia-Yun , Duan Siang , Min Saw Myat , Myo Ei Mhone Nathar , Tsai Yuan-Lu , Liang Nai-Wun , Liao Jhih-Hao , Lam Tsz-Yau Amundsen , Chang En-Wei , Shyu J. Bruce H. 
Published: January 2024

Abstract
The Mw 6.4 and 6.8 Guanshan-Chihshang earthquakes occurred on 17 and 18 September 2022 resulted in prominent surface ruptures within the Longitudinal Valley in eastern Taiwan, particularly along the Yuli fault in the middle of the valley. Approximately 18 hours after the mainshock, we began to document the surface rupture in the vicinity of Yuli Town, where the rupture transected through the center of the residential area. Our result suggests the surface rupture of the mainshock formed a confined single left-lateral trace in the town of Yuli, characterized by a series of en échelon right-stepping left-lateral faulting geometry. The rupture of 2022 roughly matches the locations of surface ruptures of 1951 inside the Yuli Town, with similar amount of cross-fault left-lateral displacement. North and South of the Yuli residential area, we identified several sections of the surface rupture distributed in the water-saturated paddy fields. The maximum left-lateral displacement recorded across the rupture can reach to 1.4 meters just south of Yuli, with the fault scarp resembles a high-angle west-dipping fault geometry. In addition to the co-seismic surface ruptures, our repeating cross-fault measurements show significant post-seismic shallow after-slip along the Yuli fault. The amount of post-seismic deformation within 3 months after the mainshock is close to, or even higher than the co-seismic cross-fault displacement, consistent with local witness accounts and post-event field photos which showed continuous damage and displacement of building floors and roads after the earthquake. Such shallow post-seismic slips were also observed along the main fault trace in the 2014 South Napa earthquake, and likely represent the shallow elastoplastic behavior of the sub-vertical fault in the young alluvial sediments.
Large scale exploration reveals rare taxa as key members shaping microbial assembly in alkaline lake sediments
Authors: Yu Ke , Qiu Zhiguang , He Shuhang , Lian Chun-Ang , Zhang Qing , Qiao Xuejiao , Yao Ciqin , Mu Rong , Wang Li , Cao Xiao-Ai , Yan Yan 
Published: January 2024

Abstract

Alkaline lakes are typical extreme environments inhabitant for a range of diverse microbial extremophiles. However, the large-scale distribution patterns, environmental adaptations, community assembly processes, and evolutionary dynamics of microbial communities, particularly those with different niches remain largely unexplored. In this study, we investigated the characteristics of microbial communities in terms of rare and abundant taxa within alkaline lake sediments in west and northwest China. We observed the community structure of abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences, supporting by the assembly process of abundant taxa influenced by diffusion limitation, a stochastic process, and rare taxa predominantly driven by heterogeneous selection as a deterministic process due to their broader environmental adaptability. Network analysis indicated that rare taxa as keystone species played a vital role in community interactions, contributing positively to community stability. From an evolutionary perspective, rare taxa were found to have higher specification and transition rate than abundant taxa, implying that rare taxa served as a genetic reservoir and potential candidates to become abundance taxa, and highlighting the crucial role of rare taxa in the maintenance of microbial diversity. These findings provide deeper insights into the dynamics of abundant and rare taxa in alkaline lake ecosystems and underscore the significant influence of rare taxa on microbial diversity and community stability, offering profound implications for ecosystem management and the conservation of biodiversity in alkaline lakes.
Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer
Authors: Xie WenJie , Sun Zhao , Fu Yang 
Published: January 2024

Abstract

BACKGROUND
More than one hundred types of RNA modification involved in nearly all the biological processes. However, the crosstalk among these RNA methylations and their related regulators still remains mysterious in the development and progression of colon adenocarcinoma (COAD).
OBJECTIVE
This study aimed to explore the interactions and prognostic values of RNA methylation regulators in COAD.
METHODS
Subgroups of COAD patients from the TGCA database were determined by consensus clustering. GSVA and GSEA analyses were used to detect the different biological pathways. And algorithms including ssGSEA and ESTIMATE were performed for the immunological analysis. Moreover, the univariate and multivariate Cox analyses based on immunohistochemistry were applied to investigate the prognostic values.
RESULTS
COAD patients were divided into two groups: patients with the worse prognosis were identified with the dysregulated EMT, NF-κB and KRAS signaling pathways and higher stromal scores. NSUN6, the writer of m5C, was further confirmed as a protective protein by immunohistochemistry and multi-datasets analysis suggested that FBXW7 is co-expressed with NSUN6.
CONCLUSIONS
In COAD, interactions among the regulators of m6A, m5C and m1A could be used to distinguish the patients with different prognosis. And the m5C writer NSUN6 can be served as a prognostic biomarker.
Covid-19 and Cholera Co-Infection and Comorbidity in Africa and Asia: A Systematic Review and Meta Analysis
Authors: Akinsulie Olalekan Chris , Olukogbe Oluwagbemisola Oyin , Idris Ibrahim , Joshi Melina , Williams Rhonda , Koku Roberta , Shahzad Sammuel , Babawale Pius , Banwo Olamilekan Gabriel , Gbadegoye Joy Olaoluwa , Ugwu Charles Egede , Fasakin Oluwole , Aliyu Victor Ayodele , Ogunleye Seto Charles , Okedoyin Deborah O 
Published: January 2024

Abstract
In Africa and Asia, the interplay between COVID-19 and cholera has manifested as a dual burden on healthcare systems and economies and as a potential public health threat, necessitating effective intervention. Cholera outbreaks have surged, especially in Africa, compounded by the recent COVID-19 pandemic. Due to a shift in focus towards combating COVID-19 and the consequent weakening of healthcare systems, data on cholera outbreaks are limited in many Asian and African nations in recent times. Here, we conducted a systematic review using available data from published articles on the impact of COVID-19 pandemic on cholera cases in Africa and Asia. Using the keywords “COVID-19”, “Cholera”, and “Endemic region”, we gathered articles from electronic databases while adhering to the established syntax. As a result, 642 articles were identified from PubMed, 4 from the Cochrane Library, and 7 from the Global Index Medicine. Eighteen studies met the inclusion criteria. The meta-analysis showed that COVID-19 and cholera comorbidity and coinfection in both Africa and Asia were strongly positively correlated (95% CI = 0.80, 0.99). These findings suggest that cholera incidence and mortality were elevated during the COVID-19 pandemic in Africa and Asia. The development of measures to prevent cholera outbreaks, especially those strengthening healthcare systems, which were largely overwhelmed during the COVID-19 pandemic, is necessary to bolster public health.
Semi-quantitative analysis of key aroma compounds in fragrant rice bran oil by GC×GC- TOFMS and GC-O
Authors: Wang Yong , Liu Lvrui , Wang Xin , Cao Hongwei , Wang Jing , Jiang Yuanrong , Zhu Zhennan , Guan Xiao 
Published: January 2024

Abstract
The physicochemical and flavor qualities of three types of rice bran oil (RBO) were explored, namely RBO A (rice aroma RBO), RBO B (pressed RBO), and RBO C (refined RBO). Various analyses were employed to critically evaluate the flavor profiles of these oils. In the preliminary findings, no significant differences were observed in the physicochemical properties among them. However, through sensory and instrumental evaluations, RBO A was identified having the optimum flavor. GC×GC-TOFMS and GC-O analysis of the RBO A revealed that 14 key aroma compounds primarily contributed to its flavor. These compounds aligned with the characteristic flavor substances of fragrant rice. Notably, 2-AP and vanillin emerged as the most substantial contributors. This research not only sheds light on the aromatic constitution of RBO A but also bears significant implications for future investigations and industrial applications aimed at enhancing the flavor of RBO.
Evaluation of evidences for dynamic systems based on Bayes factors with an application
Authors: Hashempour Majid , Doostparast Mahdi 
Published: January 2024

Abstract

This paper deals with the computation of Bayes factors (BFs) based on sequential order statistics arising from homogeneous exponential populations. Explicit expressions for the BFs are derived from the chi-square and the Poisson distribution functions. Some approximations for the derived BFs are also proposed. A simulated data set is analyzed using the obtained results. Open problems are also mentioned. The findings of this paper may be used for assessing evidence in the available data in various fields such as reliability analyses of engineering systems and life testing experiments.
Mathematics Subject Classification: 62F15, 62L12, 62N01.
Improvement in the abrasion resistance of cutter blades by laser processing
Authors: Shigemori Keisuke , Hironaka Yoichiro 
Published: January 2024

Abstract

Blades that are mass-produced and distributed as industrial products are indispensable tools in our lives. Some of these inexpensive and convenient blades are considered disposable. However, by improving their performance with a small amount of additional machining, we could reduce waste and improve society. We performed underwater laser machining using a 5-ns pulsed laser to improve the abrasion resistance. By using a mass-produced cutter blade, the cutting edge was laser peened, and a sharpness test was conducted with a sharpness tester. The measured values showed that the abrasion resistance could be approximately doubled. Additionally, in this work, sharpness tester measurements were found to be applicable for evaluating the performance of laser peening effects.
A Scalable Blockchain-based Framework for Efficient IoT Data Management Using Lightweight Consensus
Authors: Haque Ehtisham Ul , Shah Adil , Iqbal Jawaid , Ullah Syed Sajid , Alroobaea Roobaea , Hussain Saddam 
Published: January 2024

Abstract
Recent research has focused on applying blockchain technology to solve security-related problems in Internet of Things (IoT) networks. However, the inherent scalability issues of blockchain technology become apparent in the presence of a vast number of IoT devices and the substantial data generated by these networks. Therefore, in this paper, we use a lightweight consensus algorithm to cater to these problems. We propose a scalable blockchain-based framework for managing IoT data, catering to a large number of devices. This framework utilizes the Delegated Proof of Stake (DPoS) consensus algorithm to ensure enhanced performance and efficiency in resource-constrained IoT networks. DPoS being a lightweight consensus algorithm leverages a selected number of elected delegates to validate and confirm transactions, thus mitigating the performance and efficiency degradation in the blockchain-based IoT networks. In this paper, we implemented an Interplanetary File System (IPFS) for distributed storage, and Docker to evaluate the network’s performance in terms of throughput, latency, and resource utilization. We divided our analysis into four parts: Latency, throughput, resource utilization, and file upload time and speed in distributed storage evaluation. Our empirical findings demonstrate that our framework exhibits low latency, measuring less than 0.976 milliseconds. The proposed technique outperforms Proof of Stake (PoS), representing a state-of-the-art consensus technique. We also demonstrate that the proposed approach is useful in IoT applications where low latency or resource efficiency is required.
Physiologically-based pharmacokinetic/pharmacodynamic modeling of meropenem in critically ill patients
Authors: Yang yujie , Wang Yirong , Zeng Wei , Zhou Jinhua , Xu Min , Lan Ying , Liu Lvye , Shen Jian , Zhang Chuan , He Qin 
Published: January 2024

Abstract

Objectives
The purpose of this study was to develop a physiologically based pharmacokinetic/pharmacodynamic model (PBPK/PD) of meropenem for critically ill patients.
Methods
A PBPK model of meropenem in healthy adults was established using PK-Sim® software and subsequently extrapolated to critically ill patients based on anatomic and physiological parameters. The mean fold error (MFE) and geometric mean fold error (GMFE) method were used to compare the differences between predicted and observed values of pharmacokinetic parameters Cmax, AUC0−∞, CL to evaluate the accuracy of PBPK model. The model was verified by using meropenem plasma samples obtained from the ICU patients, which were determined by HPLC-MS/MS. The PBPK model was thereafter combined with a PKPD model, developed based on f%T > MIC. Monte Carlo simulation was utilized to calculate the probability of target attainment (PTA) in patients.
Results
The developed PBPK model successfully predicted the meropenem disposition in critically ill patients, wherein the MFE average and GMFE of all predicted PK parameters were within 1.25-fold error range. The therapeutic drug monitoring (TDM) of meropenem was conducted 92 blood samples from 31 ICU patients, of which 71 (77.17%) blood samples were consistent with the simulated value. The TDM results showed that we may not need age-specific dose adjustment of meropenem in critically ill patients. Monte Carlo simulations showed that continuous infusion and frequent administration were necessary to achieve curative effect for critically ill patients, whereas excessive infusion time (> 4h) was not necessary.
Conclusion
The PBPK/PD modelling incorporating literature data and prospective study data is able to correctly predict meropenem pharmacokinetics in critically ill patients. Our study provides a reference for realizing clinical personalized medication for critically ill patients.
Animal burrow presence patterns and local shrub density in Central California Deserts
Authors: Owen Ethan , Lortie Christopher J. , Zuliani Mario 
Published: January 2024

Abstract
Background
Ecological resource availability is crucial for the survival of local desert animal communities. Landscape resources such as shrubs and burrows provide several mechanisms that can benefit associating animal species typically through reducing harsh abiotic factors. Since many of these shrubs act as foundational species within desert ecosystems, understanding how these resources, along with those created by local vertebrate species, can provide key insights into habitat utilization. Here, we test to see if there is an association between the presence of burrows created by local desert species and the total density of foundational shrubs, across various Central California deserts. This was tested through a combination of burrow field surveys and satellite imagery. All data was combined to determine if there is a relationship between both resources for desert vertebrate species.
Results
We found that there were significantly more burrows associated with foundational shrub species across Central California deserts and that shrub density positively predicts the presence of burrows. In several of the tested ecosystems, increasing shrub densities positively predicted higher probabilities of burrow presence.
Conclusions
The existence of two highly utilized desert resources, and the relationship between them, signals that areas abundant in both resources can positively impact local animal species.
Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides new insights into its evolution and polysaccharide biosynthesis
Authors: Cui Suxia , Cui Jipeng , Wang Rui , Gu Ruoqing , Chen Minghui , Wang Ziyao , Li Li , Hong Jianming 
Published: January 2024

Abstract

Phragmites australis, widely distributed worldwide, has a vast biomass and a strong ability to adapt to the environment. Its rhizome (known as "Lugen" in Chinese medicine) has been used as a traditional Chinese medicine for over 2,000 years. In this study, we assembled a chromosome-level reference genome of Phragmites australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of reeds genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmites polysaccharides that have important roles in rhizome development. The assembly of the P. australis genome contributes to our understanding of Arundiaceae evolution and polysaccharide biosynthesis in phragmitis rhizoma.