bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaporation residue cross sections of superheavy nuclei based on optimized nuclear data*
Authors: Li 李 Jia-Xing 佳星 , Zhang 张 Hong-Fei 鸿飞 
Published: October 2023

Abstract
This study proposes an optimized method for estimating atomic nucleus masses by combining the finite-range droplet model (FRDM) with the support vector machine algorithm. The optimization process significantly improves the accuracy of the FRDM by reducing the root mean square error from 0.606 to 0.253 MeV. The optimized mass data obtained from this method are then used to calculate the evaporation residue cross-sections (ERCSs) for fusion-evaporation reactions, employing the di-nuclear system model. The experimental results for the 48Ca+238U reaction are relatively well reproduced using these optimized mass data. Additionally, the study investigates the impact of mass uncertainties on fusion and survival probabilities. By considering the mass uncertainties, the ERCSs for new elements 119 and 120 are predicted based on the obtained optimized mass data.
Integrated model control simulations of the electron density profile and the implications of using multiple discrete pellet injectors for control
Authors: Bosman T.O.S.J. , Koechl F. , Ho A. , de Baar M.R. , Krishnamoorthy D. , van Berkel M. 
Published: October 2023

Abstract
Pellet injection is regarded as the only realistic actuator for core density control in future reactors such as ITER and DEMO. However, a control strategy that can reliably regulate the plasma close to operational limits using multiple pellet injectors is not yet available. In this paper, we present the first integrated model control simulations where a dedicated model-predictive controller is included in JINTRAC. We show that, when continuous actuators are considered, a simple transport model with a steady-state disturbance rejection paradigm is capable of capturing the particle transport dynamics for multiple transport models and scenarios. This in turn allows the model-predictive controller to deal with the uncertainty and minimize the control error given the limited actuation space. Furthermore, we show that for ITER and DEMO relevant pellet sizes, the discrete, nonlinear dynamics of pellet injection will limit the control performance and jeopardize the constraints if not accounted for by the controller. Hence, we conclude that for high-performance control on future reactors, controllers will have to be developed that explicitly deal with the discrete pellet dynamics.
A 3D-printed blood-brain barrier model with tunable topology and cell-matrix interactions
Authors: Paone Louis S , Benmassaoud Mohammed Mehdi , Curran Aidan , Vega Sebastián L , Galie Peter A 
Published: October 2023

Abstract
Recent developments in digital light processing (DLP) can advance the structural and biochemical complexity of perfusable in vitro models of the blood–brain barrier. Here, we describe a strategy to functionalize complex, DLP-printed vascular models with multiple peptide motifs in a single hydrogel. Different peptides can be clicked into the walls of distinct topologies, or the peptide motifs lining channel walls can differ from those in the bulk of the hydrogel. The flexibility of this approach is used to both characterize the effects of various bioactive domains on endothelial coverage and tight junction formation, in addition to facilitating astrocyte attachment in the hydrogel surrounding the endothelialized vessel to mimic endothelial–astrocyte interaction. Peptides derived from proteins mediating cell-extracellular matrix (e.g. RGD and IKVAV) and cell–cell (e.g. HAVDI) adhesions are used to mediate endothelial cell attachment and coverage. HAVDI and IKVAV-lined channels exhibit significantly greater endothelialization and increased zonula-occluden-1 (ZO-1) localization to cell–cell junctions of endothelial cells, indicative of tight junction formation. RGD is then used in the bulk hydrogel to create an endothelial–astrocyte co-culture model of the blood–brain barrier that overcomes the limitations of previous platforms incapable of complex topology or tunable bioactive domains. This approach yields an adjustable, biofabricated platform to interrogate the effects of cell-matrix interaction on blood–brain barrier mechanobiology.
Human vascularized bile duct-on-a chip: a multi-cellular micro-physiological system for studying cholestatic liver disease
Authors: Du Yu , de Jong Iris E M , Gupta Kapish , Waisbourd-Zinman Orit , Har-Zahav Adi , Soroka Carol J , Boyer James L , Llewellyn Jessica , Liu Chengyang , Naji Ali , Polacheck William J , Wells Rebecca G 
Published: October 2023

Abstract
Exploring the pathogenesis of and developing therapies for cholestatic liver diseases such as primary sclerosing cholangitis (PSC) remains challenging, partly due to a paucity of in vitro models that capture the complex environments contributing to disease progression and partly due to difficulty in obtaining cholangiocytes. Here we report the development of a human vascularized bile duct-on-a-chip (VBDOC) that uses cholangiocyte organoids derived from normal bile duct tissue and human vascular endothelial cells to model bile ducts and blood vessels structurally and functionally in three dimensions. Cholangiocytes in the duct polarized, formed mature tight junctions and had permeability properties comparable to those measured in ex vivo systems. The flow of blood and bile was modeled by perfusion of the cell-lined channels, and cholangiocytes and endothelial cells displayed differential responses to flow. We also showed that the device can be constructed with biliary organoids from cells isolated from both bile duct tissue and the bile of PSC patients. Cholangiocytes in the duct became more inflammatory under the stimulation of IL-17A, which induced peripheral blood mononuclear cells and differentiated Th17 cells to transmigrate across the vascular channel. In sum, this human VBDOC recapitulated the vascular-biliary interface structurally and functionally and represents a novel multicellular platform to study inflammatory and fibrotic cholestatic liver diseases.
Grating assisted temperature insensitive micro-ring resonator biosensor
Authors: Kumar Verma Yogesh , Kumari Soumya , Mani Tripathi Saurabh 
Published: October 2023

Abstract
A grating-assisted temperature-insensitive micro-ring resonator bio-sensor is reported using the finite-difference time-domain simulation method. In addition to choosing a negative thermo-optic coefficient (TOC) material, water, to nullify temperature-induced wavelength shift, optimization of the opto-geometric parameters provided a precisely zero-temperature sensitivity (TS) state of the structure. The negative TOC of water counterbalances the positive shift in resonance wavelength originating from Si waveguides. The grating structure delocalizes the core field into the analyte region, which enhances field–matter interaction to offer high bulk refractive index (RI) and affinity sensing. The advantage of incorporating grating structure in the ring has been demonstrated by comparing the bulk RI sensitivity and affinity sensitivity with and without the grating structure. Without the circular grating array, the bulk RI sensitivity is 214 nm RIU−1, and the affinity sensitivity is 0.139 nm nm−1. Using grating in the ring structure offers an improved bulk RI sensitivity of 525 nm RIU−1 and an adlayer sensitivity of 0.515 nm nm−1. We calculated the system limit of detection of the structure as ∼2

×

10

−
6

RIU. The fabrication tolerance of geometrical parameters, in the form of 10% variation in hole radius and 5% variation in other widths of our sensor, reveals a nominal TS of ∼6 pm ∘C−1. Changing the cladding analyte from pure water to other aqueous solutions, e.g. urine samples, also has a small impact on TS. The present work is useful in RI-dependent monitoring of the constituents present in aqueous medium-based bio-analytes samples in a variable ambient temperature environment.
Relationship between microorganisms and volatile components in each fermentation process in the kusaya gravy that plays an important role in the manufacturing of kusaya, a traditional Japanese fermented fish product
Authors: Kita Kosuke , Unno Ryosuke , Osada Takahiro , Yoshiyama Hiromori , Masaki Sachiko , Nogimura Sakura , Matsutani Minenosuke , Ishikawa Morio , Suzuki Toshihiro 
Published: October 2023

ABSTRACT
The relationship between the microbiota and volatile components of kusaya gravy involved in the manufacturing of kusaya, a traditional Japanese fermented fish product, in the Izu Islands (Niijima and Hachijojima) and the fermentation processes are not clear. In this study, we aimed to investigate the relationship between the microbiota and volatile compounds involved in the manufacturing and management of kusaya gravy. 16S ribosomal RNA (rRNA) gene-based amplicon sequencing revealed that the microbiota in kusaya gravy was significantly different between the two islands, and the microbiota hardly changed during each fermentation process. Gas chromatography–mass spectrometry analysis also revealed that the volatile components were strongly related to the microbiota in kusaya gravy, with Hachijojima samples containing sulfur-containing compounds and Niijima samples containing short-chain fatty acids. Therefore, our findings suggest that kusaya gravy is a characteristic fermented gravy with a stable microbiota, and the fermented pickling gravy is fermented by microorganisms.
Testing the feasibility of a co-designed intervention, comprising self-managed, home-based, exercise training with embedded behavioural support and compression therapy for people with venous leg ulcers receiving treatment at home (FISCU-II)
Authors: Klonizakis Markos , Gumber Anil , McIntosh Emma , Levesley Maria , Horspool Michelle , Logan Pip 
Published: October 2023

Abstract

Background
Venous leg ulcers (VLUs) heal slowly, are painful for patients and are costly for healthcare systems; they also affect patients’ quality of life. Previous work suggests that supervised exercise training used in combination with compression therapy may offer clinical benefits. However, a large population of people with VLUs are unable to access such an intervention due to frailty and age.

Objectives
To assess the feasibility of ‘FISCU Home’ (a co-designed, 12-week home-based self-managed lifestyle programme based on exercise and behaviour support) as an adjunct therapy to compression in people with VLUs.

Methods
Forty people with VLUs, receiving treatment at home, were recruited from community nursing and tissue viability teams, and via a newspaper advertisement. Participants were randomized 1 : 1 either to exercise with behaviour support (three times per week) plus compression therapy or compression only. The feasibility of the programme was assessed using progression criteria that included exercise attendance rate, loss to follow-up, patient preference(s) and adverse events (AEs). Baseline assessments were repeated at 12 weeks and 6 months. Secondary outcomes (i.e. ulcer recurrence, healing rate and healing time) were also documented at these intervals. Intervention and healthcare utilization costs were calculated.

Results
The study recruitment rate was 65%, while 75% of the exercise group participants attended all scheduled exercise sessions. All participants completed compression therapy. No serious AEs or exercise-related AEs were reported. Median (interquartile range) ulcer healing time was shorter in the exercise group [29 (7–108) vs. 42 (6–116) weeks].

Conclusions
The feasibility and acceptability of both a home- and exercise-based lifestyle intervention in conjunction with compression therapy and the study procedures are supported.
Diverse functional interaction driven by control-default network hubs supports creative thinking
Authors: Zhuang Kaixiang , Zeitlen Daniel C , Beaty Roger E , Vatansever Deniz , Chen Qunlin , Qiu Jiang 
Published: October 2023

Abstract
Complex cognitive processes, like creative thinking, rely on interactions among multiple neurocognitive processes to generate effective and innovative behaviors on demand, for which the brain’s connector hubs play a crucial role. However, the unique contribution of specific hub sets to creative thinking is unknown. Employing three functional magnetic resonance imaging datasets (total N = 1,911), we demonstrate that connector hub sets are organized in a hierarchical manner based on diversity, with “control-default hubs”—which combine regions from the frontoparietal control and default mode networks—positioned at the apex. Specifically, control-default hubs exhibit the most diverse resting-state connectivity profiles and play the most substantial role in facilitating interactions between regions with dissimilar neurocognitive functions, a phenomenon we refer to as “diverse functional interaction”. Critically, we found that the involvement of control-default hubs in facilitating diverse functional interaction robustly relates to creativity, explaining both task-induced functional connectivity changes and individual creative performance. Our findings suggest that control-default hubs drive diverse functional interaction in the brain, enabling complex cognition, including creative thinking. We thus uncover a biologically plausible explanation that further elucidates the widely reported contributions of certain frontoparietal control and default mode network regions in creativity studies.
Application of the Aliivibrio fischeri bacterium bioassay for assessing single and mixture effects of antibiotics and copper
Authors: Narciso Alessandra , Barra Caracciolo Anna , Grenni Paola , Rauseo Jasmin , Patrolecco Luisa , Spataro Francesca , Mariani Livia 
Published: October 2023

Abstract
The Aliivibrio fischeri bioassay was successfully applied in order to evaluate the acute effect of sulfamethoxazole (SMX), ciprofloxacin (CIP), chlortetracycline (CTC) and copper (Cu), alone or in binary, ternary, and overall mixture. The toxicity results are reported in terms of both effective concentrations, which inhibited 50% of the bacterium bioluminescence (EC50%), and in Toxic Units (TUs). The TUs were compared with predicted values obtained using the Concentration Addition model (CA). Finally, the toxicity of water extracts from a soil contaminated by the three antibiotics (7 mg Kg−1 each) in the presence/absence of copper (30 mg Kg−1) was also evaluated. Copper was the most toxic chemical (EC50: 0.78 mg L-1), followed by CTC (EC50: 3.64 mg L−1), CIP (96 mg L−1) and SMX (196 mg L−1). Comparing the TU and CA values of the mixtures, additive effects were generally found. However, a synergic action was recorded in the case of the CIP+Cu co-presence and antagonistic effects in the case of CTC+Cu and the ternary mixture (containing each antibiotic at 0.7 mg L−1), were identified. Soil water extracts did not show any toxicity, demonstrating the buffering ability of the soil to immobilize these chemicals.
To cheat or not to cheat: cheatable and non-cheatable virulence factors in Pseudomonas aeruginosa
Authors: Guadarrama-Orozco Katya Dafne , Perez-Gonzalez Caleb , Kota Kokila , Cocotl-Yañez Miguel , Jiménez-Cortés Jesús Guillermo , Díaz-Guerrero Miguel , Hernández-Garnica Mariel , Munson Julia , Cadet Frederic , López-Jácome Luis Esaú , Estrada-Velasco Ángel Yahir , Fernández-Presas Ana María , García-Contreras Rodolfo 
Published: October 2023

Abstract
Important bacterial pathogens such as Pseudomonas aeruginosa produce several exoproducts such as siderophores, degradative enzymes, biosurfactants, and exopolysaccharides that are used extracellularly, benefiting all members of the population, hence being public goods. Since the production of public goods is a cooperative trait, it is in principle susceptible to cheating by individuals in the population who do not invest in their production, but use their benefits, hence increasing their fitness at the expense of the cooperators’ fitness. Among the most studied virulence factors susceptible to cheating are siderophores and exoproteases, with several studies in vitro and some in animal infection models. In addition to these two well-known examples, cheating with other virulence factors such as exopolysaccharides, biosurfactants, eDNA production, secretion systems, and biofilm formation has also been studied. In this review, we discuss the evidence of the susceptibility of each of those virulence factors to cheating, as well as the mechanisms that counteract this behavior and the possible consequences for bacterial virulence.
Genomic insight into the salt tolerance and proteolytic activity of Bacillus subtilis
Authors: Lee Sugyeong , Seo Sumin , Sul Sooyoung , Jeong Do-Won , Lee Jong-Hoon 
Published: October 2023

Abstract
We assessed the salt tolerance and proteolytic activity of 40 genome-published Bacillus subtilis strains isolated from fermented Korean foods to illuminate the genomic background behind the functionality of B. subtilis in high-salt fermentation. On the basis of the salt tolerance and phenotypic proteolytic activity of the 40 strains, we selected five strains exhibiting different phenotypic characteristics. Comparative genomic analyses of these five strains provided genomic insight into the salt tolerance and proteolytic activity of B. subtilis. Two-component system (TCS) genes annotated as ybdGJK and laterally acquired authentic ATP-binding cassette (ABC) transporter system genes of tandem repeat structure might contribute to increase salt tolerance. The additional possession of gene homologs for CAAX protease family proteins and components of Clp (caseinolytic protease) complex, ATP-dependent Clp proteolytic subunit ClpP and AAA+ (ATPases associated with diverse cellular Activities) family ATPases, might determine the proteolytic activity of B. subtilis. This study established the scientific foundation for the viability and functionality of B. subtilis in high-salt fermentation.
Using Physiological System Networks to Elaborate Resilience Across Frailty States
Authors: Hao Meng , Zhang Hui , Li Yi , Hu Xiaoxi , Hu Zixin , Jiang Xiaoyan , Wang Jiucun , Sun Xuehui , Liu Zuyun , Davis Daniel , Jin Li , Wang Xiaofeng 
Published: October 2023

Abstract

Background
Aging is characterized by loss of resilience, the ability to resist or recover from stressors. Network analysis has shown promise in investigating dynamic relationships underlying resilience. We aimed to use network analysis to measure resilience in a longitudinal cohort of older adults and quantify whole-system vulnerabilities associated with frailty.

Methods
We used data from the Rugao Longitudinal Ageing Study, including 71 biomarkers from participants classified as robust, prefrail, or frail. We quantified biomarker correlations and topological parameters. Additionally, we proposed propagation models to simulate damage and recovery dynamics, investigating network resilience under various conditions.

Results
We classified 1 754 individuals into robust (n = 369), prefrail (n = 1 103), and frail (n = 282) groups with 71 biomarkers. Several biomarkers were linked to frailty, including those related to blood pressure, electrocardiogram (ECG), kidney function, platelets, and white blood cells. Each frailty stage was associated with increased network correlations. The frail network showed increased average degree and connectance, decreased average path length and diameter, and reduced modularity compared to robust and prefrail networks. Hub biomarkers, particularly β2-microglobulin and platelet count, played a significant role, potentially propagating dysfunction across physiological systems. Simulations revealed that damage to critical hubs led to longer recovery times in the frail network than robust and prefrail networks.

Conclusions
Network analysis could serve as a valuable tool for quantifying resilience and identifying vulnerabilities in older adults with frailty. Our findings contribute to understanding frailty-related physiological disturbances and offer potential for personalized healthcare interventions targeting resilience in older populations.
Comparison of pharmaceutical properties and biological activities of prednisolone, deflazacort, and vamorolone in DMD disease models
Authors: Liu Grace , Lipari Philip , Mollin Anna , Jung Stephen , Teplova Irina , Li Wencheng , Ying Lanqing , More Vijay , Lennox William , Yeh Shirley , McGann Eric , Moon Young-Choon , Rice Cari , Huarte Eduardo , Gruszka Barbara , Ray Balmiki , Goodwin Elizabeth , Buckendahl Patricia , Yurkow Edward , Braughton Bruce , Narasimhan Jana , Welch Ellen , Voronin Gregory , Weetall Marla 
Published: October 2023

Abstract
Duchenne muscular dystrophy (DMD) is a progressive disabling X-linked recessive disorder that causes gradual and irreversible loss of muscle, resulting in early death. The corticosteroids prednisone/prednisolone and deflazacort are used to treat DMD as the standard of care; however, only deflazacort is FDA approved for DMD. The novel atypical corticosteroid vamorolone is being investigated for treatment of DMD. We compared the pharmaceutical properties as well as the efficacy and safety of the three corticosteroids across multiple doses in the B10-mdx DMD mouse model. Pharmacokinetic studies in the mouse and evaluation of p-glycoprotein (P-gP) efflux in a cellular system demonstrated that vamorolone is not a strong P-gp substrate resulting in measurable central nervous system (CNS) exposure in the mouse. In contrast, deflazacort and prednisolone are strong P-gp substrates. All three corticosteroids showed efficacy, but also side effects at efficacious doses. After dosing mdx mice for two weeks, all three corticosteroids induced changes in gene expression in the liver and the muscle, but prednisolone and vamorolone induced more changes in the brain than did deflazacort. Both prednisolone and vamorolone induced depression-like behavior. All three corticosteroids reduced endogenous corticosterone levels, increased glucose levels, and reduced osteocalcin levels. Using micro-computed tomography, femur bone density was decreased, reaching significance with prednisolone. The results of these studies indicate that efficacious doses of vamorolone, are associated with similar side effects as seen with other corticosteroids. Further, because vamorolone is not a strong P-gp substrate, vamorolone distributes into the CNS increasing the potential CNS side-effects.
Ruxolitinib accelerates influenza A virus adaptation in the Madin-Darby canine kidney (MDCK) cell line
Authors: Malenovská Hana 
Published: October 2023

Abstract

Aim
To investigate the effect of ruxolitinib medium supplement, separately and in combination with trypsin, on influenza A virus (IAV) adaptation and propagation in the Madin-Darby canine kidney (MDCK) cell line.

Methods and results
Two consecutive passages of three egg-based IAV strains were performed in the MDCK cell line with medium (a) without additives; (b) with a combination of ruxolitinib and trypsin; (c) with ruxolitinib; and (d) trypsin. Adaptation without a medium additive failed in both passages. After a single passage, the probability of the IAV adaptation was highly significantly influenced by the type of additive (binomial generalized linear model, χ22 = 23.84, P &lt; 0.00001). The highest probability of adaptation was achieved with the combination of ruxolitinib and trypsin, followed by ruxolitinib alone and trypsin. After the two consecutive passages, the influence of the type of medium additive on the probability of virus adaptation was no longer significant. In two of three IAV MDCK-adapted strains, the type of medium additive had no significant influence on virus yields.

Conclusion
Ruxolitinib accelerates the adaptation of IAV in the MDCK cell line both individually and together with trypsin.