bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breast cancer malignancy is governed by regulation of the macroH2A2/TM4SF1 axis, the AKT/NF‐κB pathway, and elevated MMP13 expression
Authors: Jin Yunho , Eum Da‐Young , Lee Chaeyoung , Park Soon Yong , Shim Jae Woong , Choi Yoo Jin , Choi Si Ho , Kim Joong‐Gook , Heo Kyu , Park Seong‐Joon 
Published: January 2024

AbstractThe histone variant, macroH2A (mH2A) influences gene expression through epigenetic regulation. Tumor suppressive function of mH2A isoforms has been reported in various cancer types, but few studies have investigated the functional role of mH2A2 in breast cancer pathophysiology. This study aimed to determine the significance of mH2A2 in breast cancer development and progression by exploring its downstream regulatory mechanisms. Knockdown of mH2A2 facilitated the migration and invasion of breast cancer cells, whereas its overexpression exhibited the opposite effect. In vivo experiments revealed that augmenting mH2A2 expression reduced tumor growth and lung metastasis. Microarray analysis showed that TM4SF1 emerged as a likely target linked to mH2A2 owing to its significant suppression in breast cancer cell lines where mH2A2 was overexpressed among the genes that exhibited over twofold upregulation upon mH2A2 knockdown. Suppressing TM4SF1 reduced the migration, invasion, tumor growth, and metastasis of breast cancer cells in vitro and in vivo. TM4SF1 depletion reversed the increased aggressiveness triggered by mH2A2 knockdown, suggesting a close interplay between mH2A2 and TM4SF1. Our findings also highlight the role of the mH2A2/TM4SF1 axis in activating the AKT/NF‐κB pathway. Consequently, activated NF‐κB signaling leads to increased expression and secretion of MMP13, a potent promoter of metastasis. In summary, we propose that the orchestrated regulation of the mH2A2/TM4SF1 axis in conjunction with the AKT/NF‐κB pathway and the subsequent elevation in MMP13 expression constitute pivotal factors governing the malignancy of breast cancer.
RapidBrachyTG43: A Geant4‐based TG‐43 parameter and dose calculation module for brachytherapy dosimetry
Authors: Kalinowski Jonathan , Enger Shirin A. 
Published: January 2024

AbstractBackgroundThe AAPM TG‐43U1 formalism remains the clinical standard for dosimetry of low‐ and high‐energy ‐emitting brachytherapy sources. TG‐43U1 and related reports provide consensus datasets of TG‐43 parameters derived from various published measured data and Monte Carlo simulations. These data are used to perform standardized and fast dose calculations for brachytherapy treatment planning.PurposeMonte Carlo TG‐43 dosimetry parameters are commonly derived to characterize novel brachytherapy sources. RapidBrachyTG43 is a module of RapidBrachyMCTPS, a Monte Carlo‐based treatment planning system, designed to automate this process, requiring minimal user input to prepare Geant4‐based Monte Carlo simulations for a source. RapidBrachyTG43 may also perform a TG‐43 dose to water‐in‐water calculation for a plan, substantially accelerating the same calculation performed using RapidBrachyMCTPS's Monte Carlo dose calculation engine.MethodsTG‐43 parameters , , , and were calculated using three commercial source models, one each of I, Ir, and Co, and were benchmarked to published data. TG‐43 dose to water was calculated for a clinical breast brachytherapy plan and was compared to a Monte Carlo dose calculation with all patient tissues, air, and catheters set to water.ResultsTG‐43 parameters for the three simulated sources agreed with benchmark datasets within tolerances specified by the High Energy Brachytherapy Dosimetry working group. A gamma index comparison between the TG‐43 and Monte Carlo dose‐to‐water calculations with a dose difference and difference to agreement criterion of 1%/1 mm yielded a 98.9% pass rate, with all relevant dose volume histogram metrics for the plan agreeing within 1%. Performing a TG‐43‐based dose calculation provided an acceleration of dose‐to‐water calculation by a factor of 165.ConclusionsDetermination of TG‐43 parameter data for novel brachytherapy sources may now be facilitated by RapidBrachyMCTPS. These parameter datasets and existing consensus or published datasets may also be used to determine the TG‐43 dose for a plan in RapidBrachyMCTPS.
Modeling dynamic cracks initiation and propagation with the local to global approach
Authors: Ma Zhaoyang , Guo Yuchao , Liu Wei , Zhang Xiaofei , Guo Xingming 
Published: January 2024

AbstractThe recently proposed local to global (L2G) method shows an excellent ability of modeling complex arbitrary cracking problem with high efficiency and robustness. Here, we extend the L2G to model dynamic cracks initiation and propagation, in which additional nodes are dynamically introduced to capture displacement discontinuities induced by cracks' propagation, but displacements/accelerations of additional nodes are obtained by solving local nonlinear problems of cracked elements associated with a crack. This unique operation removes the divergence risks caused by adding nodes, and improves the numerical efficiency by decreasing iteration times of the global problem. Crack branching problem is also taken into consideration in current work. Numerical examples for dynamic cracks propagation are provided to demonstrate the effectiveness and robustness of the proposed method.
Contact framework for total Lagrangian smoothed particle hydrodynamics using an adaptive hybrid kernel scheme
Authors: Wiragunarsa I Made , Zuhal Lavi Rizki , Dirgantara Tatacipta , Putra Ichsan Setya 
Published: January 2024

AbstractTotal Lagrangian SPH (TLSPH) offers many advantages that can overcome instability and computational time issues. However, it is not naturally applicable to problems with contact. Many problems in solid dynamics and structural analysis require contact definition. In order to use the total Lagrangian formulation, further development for the contact algorithm is required. This research proposes an algorithm to implement inter‐particle contact in TLSPH using an adaptive hybrid‐kernel scheme for the first time. A combination of the updated and total Lagrangian formulations at the contact surface is introduced, in which the kernel type change automatically when particles from a different body are detected. In kernel change from the updated to the total Lagrangian formulation, the gradient correction cannot be performed using a common correction method because different frames of reference are used. Therefore, a hybrid‐kernel correction technique is proposed to maintain the zeroth‐ and first‐order completeness. Then, the contact force is obtained from the inter‐particle force using the conservation of momentum. The proposed method does not require a user‐defined parameter that makes the application straightforward. Based on the test, the proposed method agrees well with the data available in published literature and the finite element method. Compared with the contact method in classical SPH, the proposed TLSPH shows a significant stability improvement.
Worldwide prevalence and associated factors of nursing staff turnover: A systematic review and meta‐analysis
Authors: Wu Feixia , Lao Yuewen , Feng Ying , Zhu Jiaqing , Zhang Yating , Li Liuyan 
Published: January 2024

AbstractAimsTo systematically assess the worldwide prevalence of nurse turnover and discuss its influencing factors.DesignSystematic review and meta‐analysis.MethodsPubMed, the Cochrane Library, Web of Science, CINAHL, China Knowledge Resource Integrated Database, Wanfang Database were searched from their commencement date to 25 March 2021. Two authors independently reviewed the studies. Stata 15.0 software package was used for statistical analysis, with estimates of data on the prevalence of nurse turnover using a random‐effects model. This review was performed according to the Joanna Briggs Institute (JBI) manual for evidence synthesis and the Preferred Reporting Items for Systematic Review and Meta‐Analysis (PRISMA) Statement. PROSPERO Registration Number:CRD42020208873.ResultsA total of 15 studies covering 852,317 nurses were included in the analyses. The pooled prevalence of nurse turnover was 18% (95% CI: 11% to 26%, I2 = 99.86%, p < 0.0001). Geographic regions (Asia), published years (2001 to 2010) and respondents (new nurses) were significantly associated with the prevalence of nurse turnover. Additionally, several risk factors for turnover were identified in the literature, involving demographic factors (young, single, have short working hours, lower level of education and male nurses), organizational factors (small‐scale hospitals, low salary levels, larger workload, developed region and absence of labour union), satisfaction (dissatisfaction with organization, profession, job and competence).
Effect of planned pauses versus continuous energy restriction on weight loss and attrition: a systematic review
Authors: Wren Gina M. , Koutoukidis Dimitrios A. , Scragg Jadine , Tsompanaki Elena , Hobson Alice , Jebb Susan A. 
Published: January 2024

AbstractObjectiveThe objective of this study was to investigate whether pausing a weight loss program for a defined period of time could enhance weight loss and reduce attrition.MethodsFive databases and two trial registries were searched from inception to July 2023. Randomized‐controlled trials of adults with overweight and/or obesity were included if they compared planned‐pause interventions with continuous energy restriction (CER), usual care, or a minimal intervention. To be included, the weight loss intervention must have incorporated a pause of at least 1 week. Pooled mean differences for weight change and risk ratios for attrition were calculated using random‐effects meta‐analyses.ResultsNine intervention arms (N = 796 participants, 77% female) were included. Pooled results did not detect a significant difference in weight change between planned pauses and CER interventions at the end of the active intervention at a median 26 weeks (planned pauses vs. CER mean: −7.09 vs. −7.0 kg; mean difference: −0.09 kg; 95% CI: −1.10 to 0.93) or at final follow‐up at a median 52 weeks (planned pauses vs. CER mean: −6.91 vs. −6.19 kg; mean difference: −0.72 kg; 95% CI: −2.92 to 1.48). There was no difference in attrition between planned pauses and CER interventions at the end of the active intervention (risk ratio: 1.20, 95% CI: 0.82 to 1.75) or at final follow‐up (risk ratio: 1.04, 95% CI: 0.89 to 1.22).ConclusionsPlanned pauses were consistently found to be no more or less effective than CER for weight loss or attrition.
The effect of lemborexant on insomnia in patients with psychiatric disorders: Detailed evaluation using the Athens Insomnia Scale
Authors: Murayama Tomonori , Ito Yuji , Narita Kenji , Ishida Tetsuro , Hinotsu Shiro , Fujita Masahiko 
Published: January 2024

AbstractAimChronic insomnia disorder is common and associated with reduced quality of life. Benzodiazepine hypnotics are commonly prescribed for insomnia, but have potential side effects such as concentration impairment, somnolence, and dependence. Lemborexant (LEM) is an orexin receptor antagonist considered to have fewer side effects than benzodiazepine hypnotics. This study evaluated the effect of LEM on sleep in detail and examined whether benzodiazepine hypnotics can be gradually tapered by adding LEM.MethodsWe retrospectively examined the effectiveness of LEM in 28 outpatients with insomnia. Insomnia symptoms were assessed using the Athens Insomnia Scale (AIS) before and after LEM administration. We also attempted to taper benzodiazepine hypnotics and assessed benzodiazepine dose using diazepam equivalents for some patients taking benzodiazepine hypnotics. Wilcoxon's signed‐rank test was used for statistical analysis.ResultsThe mean AIS score was significantly improved after LEM treatment (8.7 ± 5.2 vs. 3.8 ± 3.3; P < 0.01). Among the AIS subitems, significant improvement was observed for six items: sleep induction, awakenings during the night, sleep quality, well‐being, functioning capacity, and sleepiness during the day. The mean benzodiazepine dose was significantly lower after LEM treatment (4.6 ± 5.0 mg vs. 2.1 ± 3.3 mg; P < 0.01).ConclusionsThis study indicated the potential of LEM for improving insomnia and reducing benzodiazepine dose.
Ion chemistry and ionic thin film deposition from HMDS‐photochemistry induced by VUV‐radiation from an atmospheric plasma
Authors: Winzer Tristan , Benedikt Jan 
Published: January 2024

AbstractInjection of precursor molecules into a plasma often results in particle generation or deposition in the source, compromising film quality and plasma operation. We present here a study of ion chemistry and ionic film deposition from hexamethyldisilane (HMDS) using a novel device utilizing vacuum ultraviolet (VUV)‐radiation from a remote atmospheric plasma. Infrared spectroscopy showed that ‐like films were obtained at the lowest admixture, where impurities are more important and VUV‐photons reach the substrate, while only slightly oxidized films were deposited at high admixtures. Photoionization mainly forms the monomer ion due to collisional stabilization and possibly slow polymerization reactions as found by ion mass spectrometry. The more detailed photochemistry of HMDS‐related ions is discussed based on mass spectra for different admixtures.
Building an inclusive botany: The “radicle” dream
Authors: Mabry Makenzie E. , Caomhanach Nuala , Abrahams R. Shawn , Gaynor Michelle L. , Pham Kasey Khanh , Williams Tanisha M. , Murphy Kathleen S. , Smocovitis Vassiliki Betty , Soltis Douglas E. , Soltis Pamela S. 
Published: January 2024

Societal Impact StatementIt is important to recognize how our current understanding of plants has been shaped by diverse cultural contexts, as this underscores the importance of valuing and incorporating contributions from all knowledge systems in scientific pursuits. This approach emphasizes the ongoing bias, including within scientific practices, and the necessity of discussing problematic histories within spaces of learning. It is crucial to acknowledge and address biases, even within scientific endeavors. Doing so fosters a more inclusive and equitable scientific community. This article, while not comprehensive, serves as a starting point for conversation and an introduction to current work on these topics.SummaryIn response to a global dialog about systemic racism, ongoing inequalities, appeals to decolonize science, and the many recent calls for diversity, equity, accessibility, and inclusion, we draw on the narratives of plants to revisit the history of botany. Our goal is to uncover how exclusionary practices have functioned in the past and persist today. We also explore the numerous opportunities and challenges that arise in the era of information as we strive to establish a more inclusive field of botany. This approach recognizes and honors the contributions of historically marginalized groups, such as Black and Indigenous communities. We hope that this article can serve as a catalyst for raising awareness, fostering contemplation, and driving action toward a more equitable and just scientific community.
Neural respiratory drive assessment and its correlation with inspiratory muscle strength in patients undergoing open‐heart surgery: A cross‐sectional study
Authors: Pongpanit Karan , Laosiripisan Jitanan , Songsorn Preeyaphorn , Charususin Noppawan , Yuenyongchaiwat Kornanong 
Published: January 2024

AbstractBackground and PurposePulmonary dysfunction and inspiratory muscle weakness are frequently observed after cardiac surgery. Understanding the load on and capacity of respiratory muscles can provide valuable insights into the overall respiratory mechanics and neural regulation of breathing. This study aimed to assess the extent of neural respiratory drive (NRD) and determine whether admission‐to‐discharge differences in NRD were associated with inspiratory muscle strength changes among patients undergoing open‐heart surgery.MethodsThis cross‐sectional study was conducted on 45 patients scheduled for coronary artery bypass graft or heart valve surgery. NRD was measured using a surface parasternal intercostal electromyogram during resting breathing (sEMGpara tidal) and maximal inspiratory effort (sEMGpara max). Maximal inspiratory pressure (MIP) was used to determine inspiratory muscle strength. Evaluations were performed on the day of admission and discharge.ResultsThere was a significant increase in sEMGpara tidal (6.9 ± 3.6 μV, p < 0.001), sEMGpara %max (13.7 ± 11.2%, p = 0.008), and neural respiratory drive index (NRDI, the product of EMGpara %max and respiratory rate) (337.7 ± 286.8%.breaths/min, p < 0.001), while sEMGpara max (−43.6 ± 20.4 μV, p < 0.01) and MIP (−24.4 ± 10.7, p < 0.001) significantly decreased during the discharge period. Differences in sEMGpara tidal (r = −0.369, p = 0.045), sEMGpara %max (r = −0.646, p = 0.001), and NRDI (r = −0.639, p = 0.001) were significantly associated with a reduction in MIP.DiscussionThe findings indicate that NRD increases after open‐heart surgery, which corresponds to a decrease in inspiratory muscle strength.
Comparative study of GQ and QG indices as potentially favorable molecular descriptors
Authors: Kumar Virendra , Das Shibsankar 
Published: January 2024

AbstractIn chemical graph theory, several degree‐based topological indices are introduced and put forward in the development of quantitative structure‐property relationships (QSPR)/quantitative structure‐activity relationships (QSAR) studies. However, only a few of them are considered employable in the prediction of physical and chemical properties and biological activities of molecular compounds. Here, we focus our attention on some foremost characteristics of newly defined Geometric–Quadratic and Quadratic–Geometric indices such as prediction power, degeneracy and structure sensitivity. Based on these attributes, we discuss their comparison with other well‐established degree‐based topological indices with the help of statistical analysis and computational techniques on the data sets of octane, nonane and decane isomers. Some of the graphical approaches, statistical outcomes and computational tests exhibit the dominating nature of the and indices over other topological indices.
Thermoelectric properties of two‐dimensional ternary transition metal nitrides HfNF
Authors: Zhang Zi‐Meng , Chang Wen‐Li , Sun Zi‐Qi , He Xin‐Huan , Zhang Ji‐Long , Wei Xiao‐Ping , Tao Xiaoma 
Published: January 2024

AbstractThe exceptional electron transfer properties and low thermal conductivity of two‐dimensional layered materials render them a promising choice for thermoelectric applications. In this study, we explore the stability, electronic properties, and thermoelectric characteristics of materials composed of two‐dimensionally layered transition metal nitride HfNF. Our research findings show that the structure of HfNF is stable and exhibits the properties of a direct bandgap semiconductor. Furthermore, we employ the Boltzmann transport theory and Slack model to investigate the thermoelectric properties of HfNF within the temperature range of 300 to 900 K. The HfNF materials exhibit relatively large thermoelectric dominance values ( values), with the ‐type HfNF demonstrating a maximum value of 1.46. Furthermore, utilizing the quasi‐harmonic Debye model, thermodynamic properties such as heat capacity, coefficient of thermal expansion, and bulk modulus within the 6 GPa and 600 K range are estimated. Based on these calculations, it is predicted that two‐dimensional HfNF materials will serve as promising new materials for thermoelectric applications spanning from 300 to 900 K.
Evaluation of the electronic density at critical points of hydrogen bonds: PM7 a good alternative to ab‐initio methods
Authors: Soriano‐Agueda Luis 
Published: January 2024

AbstractHydrogen bonds are of vital importance in the formation and functioning of organic molecules; their characterization with theoretical tools is a task of interest to the scientific community. Commonly, the electron density at the bond critical point is used to characterize bonds. Generally this task is carried out with ab‐initio methods. In this study, the PM7 semi‐empirical approach is used to evaluate the quality of the electron density at the hydrogen bond critical points (HBCPs). The research takes into account dimers, nucleobases and alpha‐helices bonded by hydrogen bonds: , , , , , and . The results are compared with second‐order Møller–Plesset and density functional theory. The findings demonstrate that PM7 is a reliable alternative for explaining the electron density trends at the HBCPs.
NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data
Authors: Ma Tianxing , Zhao Zetong , Li Haochen , Wei Lei , Zhang Xuegong 
Published: January 2024

AbstractComplicated molecular alterations in tumors generate various mutant peptides. Some of these mutant peptides can be presented to the cell surface and then elicit immune responses, and such mutant peptides are called neoantigens. Accurate detection of neoantigens could help to design personalized cancer vaccines. Although some computational frameworks for neoantigen detection have been proposed, most of them can only detect SNV‐ and indel‐derived neoantigens. In addition, current frameworks adopt oversimplified neoantigen prioritization strategies. These factors hinder the comprehensive and effective detection of neoantigens. We developed NeoHunter, flexible software to systematically detect and prioritize neoantigens from sequencing data in different formats. NeoHunter can detect not only SNV‐ and indel‐derived neoantigens but also gene fusion‐ and aberrant splicing‐derived neoantigens. NeoHunter supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate neoantigens. These strategies utilize binding characteristics, existing biological big data, and T‐cell receptor specificity to ensure accurate detection and prioritization. We applied NeoHunter to the TESLA dataset, cohorts of melanoma and non‐small cell lung cancer patients. NeoHunter achieved high performance across the TESLA cancer patients and detected 79% (27 out of 34) of validated neoantigens in total. SNV‐ and indel‐derived neoantigens accounted for 90% of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%. Gene fusion‐derived neoantigens were detected in one patient. NeoHunter is a powerful tool to ‘catch all’ neoantigens and is available for free academic use on Github (XuegongLab/NeoHunter).
A comprehensive review of Langya virus and framework for future zoonotic disease control
Authors: Thien Dang Huu , Tran Hoang Bao , Uyen Nguyen Ngoc Phuong , Thao Huynh Lai Phuong , Tam Huynh Thi My , Quan Nguyen Khoi , Huy Nguyen Tien 
Published: January 2024

AbstractFirst reported in August 2022, the Langya virus (LayV) has emerged as a potential global health threat in the post‐COVID‐19 era. Preliminary reports show that 35 patients near Shandong and Henan, China experienced a febrile acute LayV infection. We conducted this review following the PRISMA protocol to synthesise current knowledge on LayV's characteristics in terms of molecular, clinical, and public health perspectives. This virus belongs to the Paramyxoviridae family and carries a non‐segmented, single‐stranded negative‐sense RNA genome. Shrews may be the natural reservoir of the virus. Clinical symptoms range from mild flu‐like symptoms to severe manifestations involving pneumonia, haematological disorders, and organ dysfunction. Diagnostic methods include PCR and ELISA assays. Despite the absence of established treatments, antiviral drugs such as ribavirin and chloroquine may be useful in some cases. In light of prevention, a comprehensive approach that emphasises multidisciplinary collaboration is crucial for early surveillance and response. Urgent global efforts are needed for vaccine development and preparedness against this potential pandemic threat. As the viral dynamics remain uncertain, a proactive approach is vital to mitigate the impact of not only LayV but also future threats on a large scale in long term.