bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetically Encoded DNA-RNA Segregation Stimulates Biomimetic Multiphase Compartments
Authors: Shum Ho , Guo Wei , Li Xiufeng , Kinghorn Andrew , Pan Yi , Lau Kwan , Mao Tianjiao , Wang Fang , Yang Zhenyu , Chen Feipeng , Li Xiaolai , Chen Ying , Zhang Yage , Song Yang 
Published: February 2024

Abstract
DNA and RNA are compartmentalized into distinct, heterogeneous structures within cells. However, the separation between RNA and DNA, especially in the absence of modern transcription machinery, is inherently hindered by thermodynamic constraints such as complementary base pairing and entropic mixing. Here, we demonstrate that atomic-level molecular difference between single-stranded DNA and RNA bearing identical sequences can drive the separation of DNA and RNA when complexed with peptides. This molecular mechanism is exploited to develop a family of oligonucleotides that enables DNA-RNA segregation within coacervates, resulting in a library of genetically encoded multiphase droplets containing coexisting DNA- and RNA-rich phases. These droplets emulate the structures and functions of multiphase nuclear compartments found in cells. Our results underscore the significance of pentose sugar mutation in DNA and RNA, which affect the genetic material organization in contemporary cells and could provide an evolutionary advantage during the transition from RNA to DNA genomes.
Management of acute cholecystitis in patients older than the expected life expectancy: Is the Tokyo Guidelines 2018 still practical?
Authors: CHANG YAUREN , Wu Yu-Tung , Chen Szu-An , Fu Chih-Yuan , Hsu Chih-Po , Cheng Chi-Tung , Kuo Ling-Wei , Huang Jen-Fu , Liao Chien-Hung , Hsieh Chi-Hsun 
Published: February 2024

Abstract

Background
As the global population ages, the incidence of acute cholecystitis is increasing. Tokyo Guidelines 2018 are established as the standard for managing this condition. However, the applicability in elderly patients, who often have comorbidities and higher surgical risks, is uncertain. This study assesses the feasibility of using the guidelines to manage acute cholecystitis in patients aged 85 and older.
Methods
We conducted a retrospective analysis on patients aged ≥ 85 diagnosed with acute cholecystitis between 2011 and 2021. Patient demographics, disease severity, comorbidities, and treatment outcomes were examined. Patients were categorized into three groups based on severity and adherence to recommendations.
Results
Among 166 elderly patients with acute cholecystitis, guideline compliance varied by severity. Adherence to the guidelines resulted in better outcomes, including shorter hospital stays and fewer complications, for mild (group I) and moderate (group II) cases. Severe cases (group III) had similar outcomes regardless of guideline adherence.
Conclusions
This study suggests that the Tokyo Guidelines 2018 is applicable to elderly patients aged 85 and older with acute cholecystitis. Better outcomes were observed when patients followed the guidelines, particularly in mild and moderate cases. Tailoring treatment to individual needs is paramount for optimizing outcomes in severe cases within this age group.
16S rRNA gene amplicon-based gut microbiome signature in cerebral vasospasm and delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage: A prospective nested case-control pilot study
Authors: Klepinowski Tomasz , Skonieczna-Żydecka Karolina , Łoniewski Igor , Pettersson Samuel , Wierzbicka-Woś Anna , Kaczmarczyk Mariusz , Palma Joanna , Sawicki Marcin , Poncyljusz Wojciech , Taterra Dominik , Alshafai Nabeel , Stachowska Ewa , Ogilvy Christopher , Sagan Leszek 
Published: February 2024

Abstract

A recent systematic review indicated that gut-microbiota-brain axis contributes to growth and rupture of intracranial aneurysms. However, gaps were detected in the role of intestinal microbiome in cerebral vasospasm (CVS) after aneurysmal subarachnoid hemorrhage (aSAH). This is the first pilot study aiming to test study feasibility and identify differences in gut microbiota between subjects with and without CVS following aSAH. A prospective nested case-control study with 1:1 matching was conducted recruiting subjects with aSAH: cases with CVS; and controls without CVS based on the clinical picture and structured bedside transcranial Doppler (TCD). Fecal samples for microbiota analyses by means of 16S rRNA gene amplicon sequencing were collected within the first 96 hours after ictus. Operational taxonomic unit tables were constructed, diversity metrics calculated, phylogenetic trees built, and differential abundance analysis (DAA) performed. At baseline, the groups did not differ significantly in basic demographic and aneurysm-related characteristics (p > 0.05). Alpha-diversity (richness and Shannon Index) was significantly reduced in cases of middle cerebral artery (MCA) vasospasm (p < 0.05). In DAA, relative abundance of genus Acidaminococcus was associated with MCA vasospasm (p = 0.00013). Two butyrate-producing genera, Intestinimonas and Butyricimonas, as well as [Clostridium] innocuum group had the strongest negative correlation with the mean blood flow velocity in anterior cerebral arteries (p < 0.01; rho = -0.63; -0.57, and − 0.57, respectively). In total, 16 gut microbial genera were identified to correlate with TCD parameters, and two intestinal genera correlated with outcome upon discharge. In this pilot study, we prove study feasibility and present the first preliminary evidence of gut microbiome signature associating with CVS as a significant cause of stroke in subjects with aSAH.
Preparing pure 43Ca+ samples in an ion trap with photoionization and parametric excitations
Authors: Kuo Chun-Hsien , Hsiao Yuan-Chih , Jhang Chen-Yu , Chen Yi-Dong , Tung Shih-Kuang 
Published: February 2024

Abstract

We present a practical scheme for the efficient preparation of laser-cooled 43Ca+ ions in an ion trap. Our approach integrates two well-established methods: isotope-selective photoionization and isotope-specific parametric excitation. Drawing inspiration from the individual merits of each method, we have successfully integrated these techniques to prepare extended chains of 43Ca+ ions, overcoming the challenge posed by their low natural abundance of 0.135% in a natural source. Furthermore, we explore the subtleties of our scheme, focusing on the influence of different factors on the purification process. Our investigation contributes to a broader understanding of the technique and highlights the adaptability of established methods in addressing specific isotopic challenges.
miR-223 Accelerates Lipid Droplets Clearance in Microglia following Spinal Cord Injury by Upregulating ABCA1
Authors: Ou Zhilin , Cheng Yongquan , Ma Hao , Chen Kai , Lin Qiong , Chen Jiayu , Guo Ruqin , Huang Zhiping , Cheng Qixian , Alaeiilkhchi Nima , Zhu Qingan , Huang Zucheng , Jiang Hui 
Published: February 2024

Abstract

Background Spinal cord injury (SCI) is characterized by extensive demyelination and inflammatory responses. Facilitating the clearance of lipid droplets (LDs) within microglia contributes to creating a microenvironment that favors neural recovery and provides essential materials for subsequent remyelination. Therefore, investigating MicroRNAs (miRNAs) that regulate lipid homeostasis after SCI and elucidating their potential mechanisms in promoting LDs clearance in microglia have become focal points of SCI research.Methods We established a subacute C5 hemicontusion SCI model in mice and performed transcriptomic sequencing on the injury epicenter to identify differentially expressed genes and associated pathways. Confocal imaging was employed to observe LDs accumulation. Multi-omics analyses were conducted to identify differentially expressed mRNA and miRNA post-SCI. Pathway enrichment analysis and protein-protein interaction network construction were performed using bioinformatics methods, revealing miR-223-Abca1 as a crucial miRNA-mRNA pair in lipid metabolism regulation. BV2 microglia cell lines overexpressing miR-223 were engineered, and immunofluorescence staining, western blot, and other techniques were employed to assess LDs accumulation, relevant targets, and inflammatory factor expression, confirming its role in regulating lipid homeostasis in microglia.Results Histopathological results of our hemicontusion SCI model confirmed LDs aggregation at the injury epicenter, predominantly within microglia. Our transcriptomic analysis during the subacute phase of SCI in mice implicated ATP-binding cassette transporter A1 (Abca1) as a pivotal gene in lipid homeostasis, cholesterol efflux and microglial activation. Integrative mRNA-miRNA multi-omics analysis highlighted the crucial role of miR-223 in the neuroinflammation process following SCI, potentially through the regulation of lipid metabolism via Abca1. In vitro experiments using BV2 cells engineered to overexpress miR-223 showed that increased miR-223 levels enhanced ABCA1 expression in LPS-induced BV2 cells, promoting LDs clearance and inducing a shift towards an anti-inflammatory M2 phenotype.Conclusions In summary, our study unveils the critical regulatory role of miR-223 in lipid homeostasis following SCI. The mechanism by which this occurs involves the upregulation of ABCA1 expression, which facilitates LDs clearance, consequently alleviating the lipid burden, and inhibiting inflammatory polarization in microglia. These findings suggest that strategies to enhance miR-223 expression and target Abca1, thereby augmenting LDs clearance, may emerge as appealing new clinical targets for treating SCI.
A Genome Wide CRISPR Profiling Approach Identifies Mechanisms of Cisplatin Resistance in Head and Neck Squamous Cell Carcinoma
Authors: Ludwig Megan , Birkeland Andrew , Smith Joshua , Gensterblum-Miller Elizabeth , Zhai JIngyi , Kulkarni Aditi , Jiang Hui , Brenner Chad 
Published: February 2024

Abstract
Background
Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with poor survival rates, especially for cancers arising in the oral cavity or larynx. Cisplatin is a key chemotherapeutic for HNSCC; however poor survival rates may be partially due to cisplatin resistance observed in some HNSCCs. Here, we examined the utility of genome-wide CRISPR knockout profiling for nominating pivotal mechanisms of cisplatin resistance in HNSCC models.
Methods
We characterized the cisplatin sensitivity of 18 HNSCC cell lines. Next, we used a genome-wide CRISPR/Cas9 library to identify genes involved in cisplatin resistance. We next performed validation assays in the UM-SCC-49 cell line model.
Results
Our data prioritized 207 genes as pivotal for cisplatin resistance in HNSCC, including novel genes VGLL3, CIRHA1, NCOR1, SPANXA1, MAP2K7, ULK1, and CDK16. Gene set enrichment analysis identified several NOTCH family genes comprising the top pathway driving cisplatin resistance, which we then validated using a targeted NOTCH1 knockout model. Interestingly, we noted that HNSCC models with natural NOTCH pathway alterations including single allele mutations and/or frameshift alterations had diverse responses to cisplatin treatment suggesting that complex and multi-faceted mechanisms contribute to cisplatin resistance in HNSCC.
Conclusions
Collectively, our study validates a genome-wide CRISPR/Cas9 approach for the discovery of resistance mechanisms in HNSCC, adds to the growing evidence that NOTCH1 status should be evaluated as a biomarker of cisplatin response and provides a framework for future work aimed at overcoming cisplatin resistance.
Associations among early health-related quality of life, mental resilience, and social support in patients after surgery for osteoporotic vertebral compression fractures: a longitudinal study
Authors: Wang Anqi , Tang Di , Zhao Jianghan , Yang Shuo , Fang Haiqin , Jiang Liying 
Published: February 2024

Abstract

Background
The level of health-related quality of life (HRQoL) in postoperative osteoporotic vertebral compression fractures (OVCFs) patients through a longitudinal investigation, as well as the influential factors on life quality were explored. The mediation effect between mental resilience and social support were also examined.
Methods
This study assessed the HRQoL, mental resilience, and social support of patients at baseline 1 day post-surgery (T1), 1 month post-surgery (T2), and 3 months post-surgery (T3) through evaluation. A total of 155 postoperative OVCFs patients completed the baseline survey, with 150 and 140 participants completing the follow-up surveys at T2 and T3, respectively. Correlation analyses were conducted to explore the relationship at each time point. Multiple linear regression was performed to identify those potential influential factors. A structural equation model was utilized to construct a comprehensive longitudinal path model for longitudinal mediation analysis.
Results
Although the level of HRQoL, mental resilience, and social support still remain at relatively lower level at 3 time points, they gradually elevated with time. Mental resilience (r = 0.293, P < 0.01) and social support (r = 0.257, P < 0.01) show significant correlations with HRQoL. Multiple linear regression analysis of T3 indicates that the history of smoking (β=−0.137, P < 0.001), gender (β=−0.154, P < 0.001), and diabetes (β = 0.126, P = 0.001) are independent factors related to the HRQoL of patients after OVCFs surgery. Longitudinal mediation analysis suggests that social support affects HRQoL through mental resilience (β = 1.017, P < 0.001).
Conclusion
Mental resilience and social support are strongly intertwined with HRQoL of OVCFs patients after surgery in the early postoperative stage. Public health initiatives could be provided to promote social support and strengthen their mental resilience, thereby improving their life quality after OVCFs surgery.
Automatic Osteotomy Preoperative Planning for Forearm with Congenital Radioulnar Synostosis: A Dual Hierarchical Optimization Strategy
Authors: Zhou Tianfeng , Cui Ying , Guo Yubing , Zhou Xinhua , Liu Lu , Chen Shanlin 
Published: February 2024

Abstract

Congenital radioulnar synostosis (CRUS) presents a complex forearm deformity, requiring precise osteotomy planning for anatomical restoration. This study proposes an automatic osteotomy preoperative planning method for forearms with CRUS. Proximal forearm bones are first aligned with the template forearm and then a dual hierarchical optimization (DHO) strategy is used to optimize the spatial transformation parameters of the distal fragment. The subsequent optimization aims to maximize the overlap of cross-sections between proximal and distal fragments. Rotational simulations are ultimately conducted to predict postoperative forearm rotational functionality. The DHO strategy effectively restores ideal forearm morphology, with maximum deviations of 1.66 and 2.13 mm for the ulna and radius, respectively. The deformity angles of forearm bones are reduced to 1.35°, 1.39°, 4.83°, 1.20°, 1.03°, and 8.56°. Rotation function analysis reveals a noticeable improvement in achievable rotation range compared to plans by senior surgeons. Automated mobilization osteotomy planning, using the DHO strategy, shows potential for individualized CRUS corrective surgery, offering comprehensive and precise preoperative guidance.
Mechanism and experimental verification of non-uniform pressure in viscous pressure forming
Authors: Wang Zeyu , Wang Zhongjin , Li Zexin 
Published: February 2024

Abstract

The plastic deformation of the complex thin-walled components is not uniform. Applying a non-uniform load can decrease the thickness reduction and improve the thickness uniformity. In recent years, the application of non-uniform pressure to deform the sheet (such as magnetorheological pressure forming and viscous pressure forming) has attracted researchers’ attention. However, the characteristics of the non-uniform pressure have not been researched. Control of the non-uniform pressure in the forming process lacks theoretical support. In this study, the mechanism of the non-uniform pressure in the viscous pressure bulge test is investigated. The pressure-carrying medium, called viscous medium, is semi-solid and flowable. The inhomogeneous flow behavior of the medium produces non-uniform pressure when the maximum is at the bulged pole. The inhomogeneous deformation behavior of the medium produces non-uniform pressure when the minimum is at the bulged pole. The effects of flow and deformation are opposite. The non-uniform pressure function is derived, and the evolution of the pressure is presented. During forming, the viscosity of the medium increases with the pressure, so the effect of the flow behavior increases, and the pressure weight at the pole increases. Viscous pressure bulge tests are carried out to verify the theory. The gradient and evolution of the pressure can be controlled by the loading velocity and the property of the medium. The results provide theoretical guidance for the control of the pressure in viscous pressure forming, and the methodology is expected to analyze the non-uniform pressure in other flexible die forming processes.
In vitro experiments confirm that CX3CR1 can be used as a biomarker for the diagnosis and treatment of osteoarthritis
Authors: +Huang jun pu , Zheng xifan , Meng jinzhi , Wang Hongtao , Chen lingyun , Yao Jun 
Published: February 2024

Abstract

Background: Osteoarthritis (OA) is a chronic joint disease characterized by degenerative changes in the articular cartilage and secondary osteophytes. However, the molecular mechanisms involved in osteoarthritis have not yet been fully elucidated. This study aims to screen genes associated with osteoarthritis and analyze the molecular mechanisms associated with it, aiming to find credible biomarkers.
Methods: The signature gene (CX3CR1) was obtained by downloading the microarray expression profiling dataset from the Gene Expression Omnibus (GEO) public database and screened using R software. The CX3CR1-related DEGs were obtained by correlation analysis and were analysed by gene ontology (GO) and kyoto encyclopedia of genes and genomes pathway (KEGG), and gene set enrichment analysis (GSEA) for enrichment and immunocorrelation analyses. In addition, a ceRNA network was constructed. qRT-PCR, Western blot, and immunohistochemistry were used to verify CX3CR1 expression in vitro.
Results:CX3CR1 was used as the signature gene by screening in this research. And CX3CR1 was found to affect the development of osteoarthritis mainly through lipid metabolism-related functions and pathways. The number of immune cells, such as mast cells activated may have an impact on the progression of OA. The results of qRT-PCR, Western blot, and Immunohistochemical analyses demonstrated the high expression of CX3CR1 in the OA group.
Conclusions:CX3CR1 and its related molecules may play an important role in the development of osteoarthritis and can be used as biomarkers for the diagnosis and treatment of osteoarthritis.
Prosthetic infection caused by Ruminococcus gnavus following total knee arthroplasty. Challenges in anaerobic bacteria identification
Authors: Tristancho-Baró Alexander , Viñeta-Valdelvira Victor , García-Lechuz Juan Manuel , Rezusta Antonio 
Published: February 2024

Abstract

Background Ruminococcus gnavus is a Gram positive, non-sporulated, obligate anaerobe diplococci. It was first described in 1974 by Moore et al from faeces and contents of the gastrointestinal tract of humans and it is a relatively common member of the human gut microbiota, nevertheless its role as a pathogenic bacteria has not been completely elucidated yet and it seems to depend of numerous factors, including those of the host. Here we present a case of prosthetic joint infection following total knee arthroplasty by R. gnavus.Case presentation A 74 years old patient was admitted to the emergency department (day 0) presenting with acute onset of left knee pain and swallowing 20 days after total left knee arthroplasty due to erythema and oedema without signs of fluctuation or purulent discharge from the surgical wound and elevated inflammatory reactants. Perilesional skin swab and synovial fluid were taken for bacterial culture and antibiotic treatment with ceftazidime and daptomycin was established. Examination of samples revealed abundant polymorphonuclear leucocytes, without visualizing bacteria on both Gram smears. After four days of incubation, the anaerobic culture of the synovial fluid exhibit growth of small, grey, umbilicated colonies in pure culture on Schaedler agar. The microorganism was identified as Ruminococcus gnavus by MALDI-TOF and 16S ribosomal bacterial sequence. The isolated showed susceptibility to all anaerobicidal drugs except for Clindamycin. Wound healing required vacuum assisted therapy and the patient was discharged after six weeks with a 4-month course of oral amoxicillin as consolidation therapy.Conclusions Ruminococcus gnavus have been reported as the causal microorganism in a range of human infections, nevertheless its identification remains challenging. Infection of prosthetic joints by anaerobic microorganisms is uncommon and is not considered in its empirical antibiotic treatment, thus, correct and swift identification of anaerobic bacteria in these cases is paramount.
Design of customized mouthguards with superior protection using digital-based technologies and impact tests
Authors: Nasrollahzadeh Naser , Pioletti Dominique P. , Broome Martin 
Published: February 2024

Abstract
Background: In contact sports, an impact on the jaw can generate destructive stress on the tooth-bone system. Mouthguards can be beneficial in reducing the injury risk by changing the dynamics of the trauma. The material properties of mouthguards and their geometrical/structural attributes influence their protective performance. Custom-made mouthguards are the gold standard, and different configurations have been proposed to improve their protection and comfort. However, the effects of different design variables on the performance of customized mouthguards are not well understood.
Results: Herein, we developed a reliable finite element model to analyze contributing factors to the design of custom-made mouthguards. Accordingly, we evaluated the isolated and combined effect of layers' stiffness, thickness, and space inclusion on the protective capability of customized mouthguards. Our simulations revealed that a harder frontal region could distribute load and absorb impact energy through bending if optimally combined with a space inclusion. Moreover, a softer layer could enlarge the time of impact and absorb its energy by compression. We also showed that mouthguards present similar protection with either permanently bonded or mechanically interlocked components. We 3D-printed different mouthguards with commercial resins and performed impact tests to experimentally validate our simulation findings. The impact tests revealed that significantly higher dental protection could be achieved with 3D-printed configurations than conventionally fabricated customized mouthguards. In particular, the strain on the impacted incisor was attenuated around 50% more with a 3D-printed mouthguard incorporating a hard insert and space in the frontal region than a conventional Playsafe® Heavypro mouthguard.
Conclusions: The protective performance of a mouthguard could be maximized by optimizing its structural and material properties to reduce the risk of sports-related dental injuries. Combining finite element simulations, additive manufacturing, and impact tests provides an efficient workflow for developing functional mouthguards with higher protectiveness and athlete comfort. We envision the future with 3D-printed custom mouthguards presenting distinct attributes in different regions that are personalized by the user based on the sport and associated harshness of the impact incidences.