bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propeller-Ice Contact modelling with Peridynamics
Authors: Han Kang , Wang Chao , Yang Zeyu , Guo Chunyu , Wang Chunhui 
Published: August 2023

Abstract
Ice loads pose a significant threat to ice-class propellers in frozen waters, making it crucial to analyse the magnitude of ice loads. However, the complex mechanical properties of ice and its failure process make it challenging to investigate the correlation between ice-propeller contact phenomena and ice loads. This paper uses a PC3 class propeller blade to study the propeller-ice contact process. This study involves developing ice failure and propeller blade models based on ordinary and non-ordinary state-based peridynamics theory and validating them using experimental. Convergence analysis was performed before blade ice loads evaluation. Additionally, we investigate the effect of the pitch angle on the ice-milling process.
Numerical Investigation of the Propulsive Efficiency of a Containership under Load Variation
Authors: Yeh T H , Chen S H , Lin T Y , Chau S W 
Published: August 2023

Abstract
The International Towing Tank Conference (ITTC) suggests that determining the variations of propulsion efficiency can be achieved by model tests that may be costly and inefficient. This is the reason why this paper investigates the variation of propulsion factors under various ship loading conditions by computational fluid dynamics (CFD). This study proposed a non-iterative method for load variation tests that reduced the computational time. The CFD software Star-CCM+ was used to solve the transient free-surface Reynolds-averaged Navier–Stokes equations. To further reduce the computational time, the propeller was modeled using the actuator disk method. The resistance augmentation, wake fraction, and propeller efficiency of a container ship model KCS with propeller KP505 were studied. These values were used to calculate the load variation coefficient of the shaft revolution speed ζN
and load variation coefficient of the delivered power ζP
at full scale. The results showed that as the resistance increased, the rotation rate correspondingly increased to maintain the service speed. As the ship resistance increased, the hull and open water efficiencies decreased, and when the actuator disk model assumed a relative rotative efficiency of 1.0, the quasi-propulsion efficiency also decreased.
Investigating capacitive force sensors with 3D printed flexible structures as dielectric layers
Authors: Lin Chien-Hung , Guo Bo-Yi 
Published: August 2023

Abstract
The utilization of a three dimension (3D) printing for the fabrication of micro-electromechanical system (MEMS) sensors presents various advantages including low cost, customization, simplicity, and speed. This study involved conducting mechanical and electrical analyses on three types of dielectric layer structures using the finite element method. Capacitive force sensors were produced through 3D printing using fused deposition modeling (FDM). The sensitivity and stiffness of the sensors were determined by measuring their capacitance and displacement changes under force using a self-made measurement system. The experimental results indicate that pre-heating the dielectric layer can reduce the hysteresis effects. In terms of more complex structures, stringing phenomena during the printing process can compromise the reliability of the sensor. A suitable dielectric layer structure can be designed based on the measurement range and sensitivity of the sensor. The results of this study demonstrate the potential for additive manufacturing to replace conventional MEMS processes in sensor production. With the advancement of FDM printing technology, it is increasingly feasible to apply 3D printing technology to sensor manufacturing in the future.
Helicobacter pylori–negative mucosa-associated lymphoid tissue (MALT) lymphoma of the stomach: A clinicopathologic analysis
Authors: Gu Sean X , Siddon Alexa J , Huntington Scott F , Jain Dhanpat 
Published: August 2023

Abstract

Objectives
Gastric mucosa-associated lymphoid tissue (MALT) lymphoma is historically associated with Helicobacter pylori (HP) infections in more than 80% of patients. However, the incidence of HP-negative MALT lymphoma has been increasing. The clinicopathologic features have not been well studied, and optimal management strategies remain unclear.

Methods
The pathology database was searched for primary gastric MALT lymphomas diagnosed from 2000 to 2017. The clinical data and the slides were reviewed. The cases were divided for analysis into those with a background of chronic gastritis with HP, chronic gastritis without HP, and without either a background of chronic gastritis or HP.

Results
Of 70 gastric MALT lymphoma cases identified, 26 (37% of total) had chronic gastritis and were positive for HP histologically (n = 23) or were HP positive by additional laboratory testing (n = 3). The remaining 44 (63% of total) cases were HP negative by histology. Within the HP-negative cases, 5 (11% of HP-negative cases) showed histologic gastritis while 39 (89% of HP-negative cases) did not have sufficient evidence of gastritis through review of slides (n = 18) or based on available pathology reports (n = 21). The HP-negative cases without gastritis had higher propensities to show a mass lesion on endoscopy compared with HP-positive cases (37.5% vs 11.1%, P = .02) at the initial diagnosis. The immunophenotype and rate of positive B-cell gene rearrangement were not significantly different between the 2 groups. While all HP-positive patients received antibiotics for HP eradication, treatment in the HP-negative group varied among antibiotics, radiation, rituximab, or chemotherapy. Among HP-negative patients with available follow-up, 13 (39%) showed disease recurrence, similar to the recurrence rate in HP-positive patients; however, no individual from either group has died of the disease thus far.

Conclusions
The incidence of HP-negative MALT lymphoma is increasing, and in our practice, it is currently more common than HP-associated MALT lymphomas. The pathophysiology of HP-negative MALT lymphoma without chronic gastritis remains unclear. Follow-up data in our study suggest that the prognosis of these cases is excellent despite varied management modalities.
Multinucleated tumor cells in clear cell renal cell carcinoma
Authors: Pacheco Richard R , Binboga Kurt Busem , Kosemehmetoglu Kemal , Rothrock Aimi T , Lightle Andrea , Akgul Mahmut 
Published: August 2023

Abstract

Objectives
Multinucleated tumor cells (MTCs) in clear cell renal cell carcinoma (ccRCC) are not well understood.

Methods
Our study included ccRCC cases in a single institution between 2010 and 2019. We classified MTC as MTC with degenerative atypia (MTCD), MTC with no anaplasia (MTCNA), and MTC with anaplasia (MTCA). Clinicopathologic characteristics and outcomes were compared between MTC groups.

Results
In all, 92 of 256 people (36%) with ccRCC had MTC. People with ccRCC with MTCD and those with ccRCC but no MTC had similar clinicopathologic characteristics and outcomes. Also, MTCNA and MTCA were associated with larger tumor size, advanced pathologic tumor stage, higher World Health Organization/International Society of Urologic Pathologists nuclear grade, and higher metastatic potential (P &lt; .001 for each parameter). Overall, MTCA was associated with an increased rate of recurrence (P = .004), higher metastatic potential (P &lt; .001), and shorter time to metastasis (P = .033), regardless of tumor stage. Univariate Cox regression revealed MTCNA as a significant predictor of metastasis at 5 years (hazard ratio [HR], 4.171; 95% CI, 1.934-8.998); moreover, MTCA was a significant predictor of recurrence (HR, 5.723; 95% CI, 2.495-13.124), metastasis (HR, 12.024; 5.966-24.232), and death (HR, 5.661; 95% CI, 2.688-11.924) at 5 years.

Conclusions
Although MTCD may not be relevant in tumor grading, MTCNA and MTCA are associated with adverse outcomes.
The effect of exogenous dihydroxyacetone and methylglyoxal on growth, anthocyanin accumulation, and the glyoxalase system in Arabidopsis
Authors: Zhao Maoxiang , Nakamura Toshiyuki , Nakamura Yoshimasa , Munemasa Shintaro , Mori Izumi C , Murata Yoshiyuki 
Published: August 2023

ABSTRACT
Dihydroxyacetone (DHA) occurs in wide-ranging organisms, including plants, and can undergo spontaneous conversion to methylglyoxal (MG). While the toxicity of MG to plants is well-known, the toxicity of DHA to plants remains to be elucidated. We investigated the effects of DHA and MG on Arabidopsis. Exogenous DHA at up to 10 mm did not affect the radicle emergence, the expansion of green cotyledons, the seedling growth, or the activity of glyoxalase II, while DHA at 10 mm inhibited the root elongation and increased the activity of glyoxalase I. Exogenous MG at 1.0 mm inhibited these physiological responses and increased both activities. Dihydroxyacetone at 10 mm increased the MG content in the roots. These results indicate that DHA is not so toxic as MG in Arabidopsis seeds and seedlings and suggest that the toxic effect of DHA at high concentrations is attributed to MG accumulation by the conversion to MG.
MLNGCF: circRNA–disease associations prediction with multilayer attention neural graph-based collaborative filtering
Authors: Wu Qunzhuo , Deng Zhaohong , Zhang Wei , Pan Xiaoyong , Choi Kup-Sze , Zuo Yun , Shen Hong-Bin , Yu Dong-Jun 
Published: August 2023

Abstract

Motivation
CircRNAs play a critical regulatory role in physiological processes, and the abnormal expression of circRNAs can mediate the processes of diseases. Therefore, exploring circRNAs–disease associations is gradually becoming an important area of research. Due to the high cost of validating circRNA–disease associations using traditional wet-lab experiments, novel computational methods based on machine learning are gaining more and more attention in this field. However, current computational methods suffer to insufficient consideration of latent features in circRNA–disease interactions.

Results
In this study, a multilayer attention neural graph-based collaborative filtering (MLNGCF) is proposed. MLNGCF first enhances multiple biological information with autoencoder as the initial features of circRNAs and diseases. Then, by constructing a central network of different diseases and circRNAs, a multilayer cooperative attention-based message propagation is performed on the central network to obtain the high-order features of circRNAs and diseases. A neural network-based collaborative filtering is constructed to predict the unknown circRNA–disease associations and update the model parameters. Experiments on the benchmark datasets demonstrate that MLNGCF outperforms state-of-the-art methods, and the prediction results are supported by the literature in the case studies.

Availability and implementation
The source codes and benchmark datasets of MLNGCF are available at https://github.com/ABard0/MLNGCF.
Distinct tau folds initiate templated seeding and alter the post-translational modification profile
Authors: Tarutani Airi , Kametani Fuyuki , Tahira Marina , Saito Yuko , Yoshida Mari , Robinson Andrew C , Mann David M A , Murayama Shigeo , Tomita Taisuke , Hasegawa Masato 
Published: August 2023

Abstract
Pathological tau accumulates in the brain in tauopathies such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy and corticobasal degeneration, and forms amyloid-like filaments incorporating various post-translational modifications (PTMs). Cryo-electron microscopic (cryo-EM) studies have demonstrated that tau filaments extracted from tauopathy brains are characteristic of the disease and share a common fold(s) in the same disease group. Furthermore, the tau PTM profile changes during tau pathology formation and disease progression, and disease-specific PTMs are detected in and around the filament core. In addition, templated seeding has been suggested to trigger pathological tau amplification and spreading in vitro and in vivo, although the molecular mechanisms are not fully understood. Recently, we reported that the cryo-EM structures of tau protofilaments in SH-SY5Y cells seeded with patient-derived tau filaments show a core structure(s) resembling that of the original seeds. Here, we investigated PTMs of tau filaments accumulated in the seeded cells by liquid chromatography/tandem mass spectrometry and compared them with the PTMs of patient-derived tau filaments. Examination of insoluble tau extracted from SH-SY5Y cells showed that numerous phosphorylation, deamidation and oxidation sites detected in the fuzzy coat in the original seeds were well reproduced in SH-SY5Y cells. Moreover, templated tau filament formation preceded both truncation of the N-/C-terminals of tau and PTMs in and around the filament core, indicating these PTMs may predominantly be introduced after the degradation of the fuzzy coat.
p53 promotes the expansion of regulatory T cells via DNMT3a- and TET2- mediated Foxp3 expression in sepsis
Authors: Zhang Hui , Wu Tiantian , Ren Chao , Dong Ning , Wu Yao , Yao Yongming 
Published: August 2023

Abstract

Background
Immunosuppression is an important characteristic of sepsis and is closely related to poor outcomes. Regulatory T cells (Tregs) contribute to immune suppression by inhibiting effector T cell (Teff) proliferation and differentiation. We aimed to investigate the role of p53 in Treg expansion after sepsis.

Methods
We constructed a sepsis model in wild-type (WT) and p53f/f/CD4-Cre+ mice by cecal ligation and puncture (CLP) and evaluated the proportions of CD4+CD25+ Foxp3+ Tregs by flow cytometry. The expression levels of forkhead/winged helix transcription factor p3 (Foxp3), DNA methyltransferase enzyme (DMNT)3a and ten–eleven translocation (TET)2 were examined using quantitative real-time PCR and Western blot analysis. Treg-specific demethylation region (TSDR) methylation sites in cells were analyzed by bisulfite-sequencing PCR. Furthermore, the direct binding of p53 to the Dnmt3a and TET2 promoters was illustrated using a luciferase assay. The suppressive ability of Tregs was indicated by enzyme-linked immunosorbent assay analysis of cytokine levels and the proliferation of cocultured Teffs. Finally, mortality rates after CLP were compared among WT and p53f/f/CD4-Cre+ mice.

Results
The proportion of CD4+CD25+ Foxp3+ Tregs was significantly reduced in p53f/f/CD4-Cre+ mice compared to WT mice after CLP. The enhanced expression of Foxp3 in WT mice was downregulated in the p53f/f/CD4-Cre+ group. We found decreased DMNT3a and increased TET2 levels after CLP. However, the dysregulation of DNMT3a and TET2 was significantly reversed in p53f/f/CD4-Cre+ mice. TSDR underwent increased demethylation in p53f/f/CD4-Cre+ mice. Luciferase activity indicated direct binding of p53 to the promoter regions of DNMT3a and TET2 to regulate their transcription. Consequently, Tregs from p53f/f/CD4-Cre+ CLP mice exhibited limited suppressive ability, as indicated by the reduced production of transforming growth factor-β and interleukin 10 (IL-10). In the coculture system, Teffs showed preserved production of IL-2, differentiation into Th1 cells and proliferation in the presence of Tregs isolated from p53f/f/CD4-Cre+ CLP mice. Finally, the mortality rate of the p53f/f/CD4-Cre+ group after CLP was significantly reduced in comparison to that of the WT group.

Conclusion
p53 appears to be critical for Foxp3 expression and consequent Treg expansion by regulating the induction of DNMT3a and TET2, thereby resulting in Foxp3-TSDR demethylation in the context of sepsis.
Development of human hippocampal subfield microstructure and relation to associative inference
Authors: Vinci-Booher Sophia , Schlichting Margaret L , Preston Alison R , Pestilli Franco 
Published: August 2023

Abstract
The hippocampus is a complex brain structure composed of subfields that each have distinct cellular organizations. While the volume of hippocampal subfields displays age-related changes that have been associated with inference and memory functions, the degree to which the cellular organization within each subfield is related to these functions throughout development is not well understood. We employed an explicit model testing approach to characterize the development of tissue microstructure and its relationship to performance on 2 inference tasks, one that required memory (memory-based inference) and one that required only perceptually available information (perception-based inference). We found that each subfield had a unique relationship with age in terms of its cellular organization. While the subiculum (SUB) displayed a linear relationship with age, the dentate gyrus (DG), cornu ammonis field 1 (CA1), and cornu ammonis subfields 2 and 3 (combined; CA2/3) displayed nonlinear trajectories that interacted with sex in CA2/3. We found that the DG was related to memory-based inference performance and that the SUB was related to perception-based inference; neither relationship interacted with age. Results are consistent with the idea that cellular organization within hippocampal subfields might undergo distinct developmental trajectories that support inference and memory performance throughout development.
Box–Behnken Design-Aided Validation and Optimization of a Stability-Indicating Reverse Phase-HPLC Method for the Estimation of Tamoxifen Citrate in Lipidic Nano-Vesicles
Authors: Kumar Gautam , Mullick Prashansha , Nandakumar Krishnadas , Mutalik Srinivas , Chamallamudi Mallikarjuna Rao 
Published: August 2023

Abstract
Stability indicating a reverse-phase HPLC analytical method for the quantification of tamoxifen citrate (TMX) in the bulk and lipidic nano-vesicles (LNVs) was developed. The optimized method was validated according to the ICH Q2 (R1) guidelines by following a three-factor interaction Box–Behnken design using Design-Expert® software. The responses measured at 236 nm were retention time (Rt), peak area, tailing factor (TF) and the number of theoretical plates. TMX was eluted best using the Luna® C18 LC Column along with a mobile phase of methanol (MeOH) and ammonium acetate buffer (AAB pH 4.5) 80:20 v/v mixture at 25 ± 2°C temperature. The currently developed method was linear in 100-5,000 ng/mL range with a detection limit of 4.55 ng/mL and a quantification limit of 13.78 ng/mL. The optimized method was utilized to evaluate the stability of TMX in different stress conditions by performing forced degradation studies. The results from the degradation study stipulated that on exposure to various stressors namely acid, alkali, oxidative, thermal and UV light, the TMX did not show considerable degradation except for UV light exposure. Further, the method was successfully used for the quantification of TMX in LNVs.
Cost-Effectiveness of Universal Asymptomatic Preoperative SARS-CoV-2 Polymerase Chain Reaction Screening: A Cost-Utility Analysis
Authors: Uno Shunsuke , Goto Rei , Honda Kimiko , Uchida Sho , Uwamino Yoshifumi , Namkoong Ho , Yoshifuji Ayumi , Mikita Kei , Takano Yaoko , Matsumoto Morio , Kitagawa Yuko , Hasegawa Naoki 
Published: August 2023

Abstract

Background
An early report has shown the clinical benefit of the asymptomatic preoperative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening test, and some clinical guidelines recommended this test. However, the cost-effectiveness of asymptomatic screening was not evaluated. We aimed to investigate the cost-effectiveness of universal preoperative screening of asymptomatic patients for SARS-CoV-2 using polymerase chain reaction (PCR) testing.

Methods
We evaluated the cost-effectiveness of asymptomatic screening using a decision tree model from a payer perspective, assuming that the test-positive rate was 0.07% and the screening cost was 8500 Japanese yen (JPY) (approximately 7601 US dollars [USD]). The input parameter was derived from the available evidence reported in the literature. A willingness-to-pay threshold was set at 5 000 000 JPY/quality-adjusted life-year (QALY).

Results
The incremental cost of 1 death averted was 74 469 236 JPY (approximately 566 048 USD) and 291 123 368 JPY/QALY (approximately 2 212 856 USD/QALY), which was above the 5 000 000 JPY/QALY willingness-to-pay threshold. The incremental cost-effectiveness ratio fell below 5 000 000 JPY/QALY only when the test-positive rate exceeded 0.739%. However, when the probability of developing a postoperative pulmonary complication among SARS-CoV-2–positive patients was below 0.22, asymptomatic screening was never cost-effective, regardless of how high the test-positive rate became.

Conclusions
Asymptomatic preoperative universal SARS-CoV-2 PCR screening is not cost-effective in the base case analysis. The cost-effectiveness mainly depends on the test-positive rate, the frequency of postoperative pulmonary complications, and the screening costs; however, no matter how high the test-positive rate, the cost-effectiveness is poor if the probability of developing postoperative pulmonary complications among patients positive for SARS-CoV-2 is sufficiently reduced.
Why do we keep ignoring sex in kidney disease?
Authors: Jankowska Magdalena , Soler María José , Stevens Kate I , Torra Roser 
Published: August 2023

ABSTRACT
Throughout the history of nephrology, little attention has been paid to the sex and gender differences in kidney disease. This lack of awareness prevents optimal diagnosis and management of kidney disease. In today's world of precision medicine, it is imperative to appreciate the differential factors regarding gender and kidney disease.
This editorial summarizes the up-to-date literature regarding sex and gender differences in kidney disease and considers areas where knowledge is incomplete and where further research is needed. We address sex-specific effects on chronic kidney disease epidemiology; risks of dialysis underdosing and medication overdosing in women; unexplained loss of female sex advantage in life expectancy during dialysis, and impact of sex on diagnosis and management of genetic kidney disease. We also aim to highlight the impact of gender on kidney health and raise awareness of disparities that may be faced by women, and transgender and gender-diverse persons when a male-model approach is used by healthcare systems. By understanding the link between sex and kidney disease, kidney specialists can improve the care and outcomes of their patients. In addition, research on this topic can inform the development of targeted prevention and intervention strategies that address the specific needs and risk factors of different populations.
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria
Authors: Zielezinski Andrzej , Dobrychlop Wojciech , Karlowski Wojciech M 
Published: August 2023

Abstract
The TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRG-associated, unique features, and characteristics of bacterial organisms.
Database URL www.combio.pl/trgdb