bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multimodal stacked ensemble model for breast cancer prognosis prediction: a proposed CNN hyperparameter optimization using the Tug of War (TWO) algorithm
Authors: Maigari Aminu , Zainol Zurinahni , Xinying Chew 
Published: February 2024

Abstract
Breast cancer (BC) is a global health challenge that affects millions of women worldwide and leads to significant mortality. Recent advancements in next-generation sequencing technology have enabled comprehensive diagnosis and prognosis determination using multiple data modalities. Deep learning methods have shown promise in utilizing these multimodal data sources, outperforming single-modal models. However, integrating these heterogeneous data sources poses significant challenges in clinical decision-making. This study proposes an optimized multimodal CNN for a stacked ensemble model (OMCNNSE) for breast cancer prognosis. Our novel method involves the integration of the Tug of War (TWO) algorithm to optimize the hyperparameters of a convolutional neural network (CNN), enhancing feature extraction from three distinct multimodal datasets: clinical profile data, copy number alteration (CNA), and gene expression data. Specifically, we employ the TWO algorithm to optimize separate CNN models for each dataset, identifying optimal values for the hyperparameters. We then trained the three baseline CNN models using the optimized values through 10-fold cross-validation. Finally, we utilize an ensemble learning approach to integrate the models' predictions and apply an SVM classifier for the final prediction. To evaluate the proposed method, we conducted experiments on the METABRIC breast cancer dataset comprising diverse patient profiles. Our results demonstrated the effectiveness of the OMCNNSE approach for predicting breast cancer prognosis. The model achieved high AUC, accuracy, sensitivity, precision, and MCC, outperforming traditional single-modal models and other state-of-the-art methods.
Determination of some quality properties of ice cream fermented with kefir culture and flavored with mint (Menthaspicata L.)
Authors: Öztürk-Yalçın Feyza , Ürkek Bayram , Şengül Mustafa 
Published: February 2024

Abstract
Kefir is a healthy fermented dairy product, while ice cream is one of the most consumed dairy products. In this study, the mint flavor was added in different proportions (0 (KI), 0.2% (KIM2), 0.4% (KIM4), and 0.6% (KIM6)) to ice cream fermented with kefir culture. The study investigated the microbiological, antioxidant, thermal, rheological, textural, compositional, and sensory properties of kefir ice cream samples during 45-day storage. The lactic bacilli, lactic cocci, and Leuconostoc counts of samples were around 8 log CFU/g, while the yeast counts were less than 4 log CFU/g. The addition of mint flavor did not have a negative effect on the microbiological properties of the samples. Values of IC50 and total phenolic content (except for samples KIM2 and KIM6) values did not differ significantly among samples and during storage (P<0.05). The pH and melting rate values of the samples decreased with the addition of mint flavor, while acidity values increased. Sample KI usually had the lowest values for thermal properties. The overrun, a*, WI, and hardness values of the samples decreased based on the mint flavor concentration, whereas the viscosity (at 50 rpm) and consistency coefficient values increased. Samples KI and KIM2 were scored higher than other samples for all sensory properties. As a result, 0.2% mint flavored kefir ice cream could be produced.
Vaccination Model: self-protective behavior in the face of Ransomware Attack in SMEs
Authors: Rechavi Amit , Berenblum Tamar 
Published: February 2024

Abstract
In today's business environment, the reliance of business processes on information technology (IT) has never been stronger, making the maintenance and security of IT systems crucial for organizations. Ransomware attacks present a significant cybersecurity risk, yet many existing solutions primarily focus on technology, overlooking the critical role of human behavior in system security. To address this gap, we experimented to assess the impact of controlled exposure to ransomware attacks on users' protection motivation and behavior. Unlike traditional security training, our approach actively engaged users in real-life scenarios and hands-on security events. The results demonstrated that controlled exposure to ransomware significantly heightened users' vigilance and improved their ability to recognize and respond to phishing campaigns. These findings indicate that hands-on exposure experiences enhance learning and boost protection motivation, sustaining positive effects on cybersecurity behavior. Our study underscores the importance of addressing the human factor in cybersecurity and introduces a promising approach to fortifying resilience against cyber threats. The vaccination model exemplifies a practical and effective strategy for improving cybersecurity readiness within authentic organizational environments by shaping users' mindsets and actions through real threat demonstrations.
Effects of NaOH Addition on Cellulose Nanocrystal Functionalization with 2,4-Dichlorophenoxyacetic Acid
Authors: Clouse Delaney E. , Collins Elise G. , Rahman Tanmay , Khodakovskaya Mariya V. , Davis Virginia A. 
Published: February 2024

Abstract
This article investigates the necessity of sodium hydroxide (NaOH) addition for the amine functionalization of sulfated cellulose nanocrystals (CNCs) and its effect on nanocrystal reactivity with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). The use of CNCs as a nanocarrier of active biomolecules has grown in the past decade. Previously, CNCs were produced by laboratory sulfuric acid hydrolysis protocols that imparted sulfate half-ester groups with hydrogen counterions. Because of this, researchers cited the need to add a deprotonating base such as NaOH before amination, a common precursor reaction for further biomolecule functionalization. However, current commercially produced sulfated CNCs have a sodium counterion instead of hydrogen. This work explores whether the use of commercial sulfated CNCs negates the need for sodium hydroxide addition in amine functionalization. We investigated the effect of 10 wt% sodium hydroxide solution on the amination of 1 wt% and 2 wt% CNC dispersions. Following this step, CNCs were then further modified via EDC/NHS chemistry to attach 2,4-D. Thermogravimetric analysis coupled with infrared spectroscopy was used to qualitatively confirm attachment. Elemental analysis determined that the degree of amine substitution for all dispersions ranged from 5.4–6.7%. 2,4-D attachment to amine groups varied from 3.9–6.5% when NaOH was present to 7.1% when NaOH was not added. These results highlight how the evolution in CNC extraction methods has resulted in NaOH addition no longer being necessary for successful reactions when using commercially sourced sulfated CNCs with a sodium counterion.
Molecular Dynamics Simulation and Molecular Docking Study on the Conversion of Ginsenosides by β-Glucanase
Authors: Yao Xiangyu , Pan Hong , Hong Yinan , Wang Xiaojun , Lu Tianwen 
Published: February 2024

Abstract
Enzymatic conversion is an important method for producing rare ginsenosides. In order to explore the molecular mechanisms underlying the interaction of β-Glucanase during the conversion process of rare ginsenoside CK, this study employed high-performance liquid chromatography, infrared spectroscopy, ultraviolet spectroscopy, and fluorescence spectroscopy to investigate the ability of β-Glucanase to convert ginsenoside Rb1 into ginsenoside CK. Changes in the secondary structure quantity of the enzyme before and after conversion were characterized. Additionally, this study accurated binding sites of β-Glucanase with ginsenoside Rb1, as well as optimal conformations, were identified through molecular dynamics simulations and molecular docking. Spectroscopic experiments revealed a reduction in the α-helix and β-fold content of β-Glucanase in acetic acid buffer. Molecular dynamics and docking results indicated that spontaneous interactions between β-Glucanase and ginsenosides Rb1, Rd, and F2, characterized by strong binding forces and high dissociation rates. In summary, the spectroscopic experiments, molecular simulations, and docking validations collectively demonstrate structural changes in the enzyme itself and the generation of some secondary bonds between the enzyme and ginsenosides during the process of converting ginsenoside Rb1 to CK. This study provides theoretical support for the conversion of ginsenoside Rb1 by β-Glucanase, elucidating the mechanisms of enzyme immobilization and catalytic reactions of β-Glucanase, offering new insights into the interaction between proteins and small molecule ligands.
The Association between Mediterranean Diet Adherence and Behavioral Outcomes among Urban Teenagers
Authors: Julvez Jordi , Pinar Ariadna , Ruiz Marina , Ayala Nicolas , Pacual-Rubio Vicenç , Fabregat-Sanjuan Albert , Casanova-Molla Jordi , Solà-Valls Nuria , Contreras Oren , Romaguera Dora , Fernádez-Barrés Sílvia 
Published: February 2024

Abstract
Objective: We examined the association between Mediterranean diet and psychosocial functioning among high school students from Barcelona, Spain.
Methods: This is a sample of healthy teenagers (11 to 16 years old) recruited during 2016–2017 from 12 high schools in Barcelona. The 622 participants responded the Mediterranean Diet Quality Index for Children and Adolescents (KIDMED) and the Strengths and Difficulties Questionnaire (SDQ). Multivariable linear regression models were applied to assess the associations between KIDMED and SDQ scores and adjusting for potential confounders.
Results: KIDMED score was negatively associated with SDQ total problem score (β = -0.20 (95% CI = -0.38; -0.02)) and conduct problem score (β = -0.08 (95% CI = -0.14; -0.03)). KIDMED score was positively associated with prosocial behavior subscale score (0.08 (0.03; 0.14)).
Conclusion: Adherence to Mediterranean diet is beneficial for some domains of psychosocial functioning. Dietary patterns are important for mental health during the adolescence.
Age-related histone H3.3 accumulation associates with a repressive chromatin in mouse tibialis anterior muscle
Authors: Masuzawa Ryo , Flete Hemilce Karina Rosa , Shimizu Junya , Kawano Fuminori 
Published: February 2024

Abstract

Age-related alterations in epigenetic regulation are postulated to result in the disorganization of cellular functions of skeletal muscles. The accumulation of the non-canonical histone variant H3.3 increases with age in several organs and exhibits tissue-specific patterns of histone modifications. However, it is unclear how histone distribution and modifications in skeletal muscle are affected by aging. The present study aimed to investigate age-related changes in H3.3 and its role in the aging process of mouse skeletal muscles. We first analyzed age-related changes in the morphology of the tibialis anterior muscle and age-related changes in gene expression and histone distribution at target loci in the tibialis anterior muscles in mice of various ages. A significant decrease in muscle weight and the number of myonuclei was observed at 53-wk-old. H3.3 levels significantly increased with age and correlated with H3K27me3 levels. Chromatin immunoprecipitation analysis showed similar changes at both transcriptionally upregulated and downregulated loci. Next, we assessed the effect of acute exercise on gene expression and histone distribution between 8- and 53-wk-old mice. No upregulation in gene expression in response to acute exercise was noted in 53-wk-old mice. H3K27me3 levels were increased in certain loci in response to acute exercise in 8-wk-old mice. However, in 53-wk-old mice, H3.3 and H3K27me3 levels were increased at rest and were not affected by acute exercise. Furthermore, we assessed the effects of forced H3.3 expression in the skeletal muscles of 8-wk-old mice. The mice were given a viral vector expressing H3.3 under the control of a skeletal muscle-specific promoter. The latency to fall in the rotarod test significantly improved in mice with forced H3.3 expression. Downregulation of gene expression was noted in the tibialis anterior muscle of mice with forced H3.3 expression. H3.3 incorporation into the nucleosomes at these loci was promoted by forced H3.3 expression, although H3K27me3 distribution was reduced at these loci. Collectively, these results suggest that H3.3 accumulation increased with age in skeletal muscle and induced the formation of repressive chromatin in association with H3K27me3. Further, these results also suggest that H3.3 accumulation plays a positive role in muscle function if H3K27me3 is unmodified.
When Quantum Dots Meet Blue Phase Liquid Crystal Elastomers: Visualized Full-Color and Mechanically-Switchable Circularly Polarized Luminescence
Authors: Li Quan , Li Shan , Tang Yuqi , Fan Qingyan , Li Ziyuan , Zhang Xinfang , Wang Jingxia , Guo Jinbao 
Published: February 2024

Abstract

Polymer-based circularly polarized luminescence (CPL) materials with the advantage of diversified structure, easy fabrication, high thermal stability, and tunable properties have garnered considerable attention. However, adequate and precise tuning over CPL in polymer-based materials remains challenging due to the difficulty in regulating chiral structures. Herein, visualized full-color CPL is achieved by doping red, green, and blue quantum dots (QDs) into reconfigurable blue phase liquid crystal elastomers (BPLCEs). In contrast to the CPL signal observed in cholesteric liquid crystal elastomers (CLCEs), the chiral 3D cubic superstructure of BPLCEs induces an opposite CPL signal. Notably, this effect is entirely independent of photonic bandgaps (PBGs) and results in a high glum value, even without matching between PBGs and the emission bands of QDs. Meanwhile, the lattice structure of the BPLCEs can be reversibly switched via mechanical stretching force, inducing on-off switching of the CPL signals, and these variations can be further fixed using dynamic disulfide bonds in the BPLCEs. Moreover, the smart polymer-based CPL systems using the BPLCEs for anti-counterfeiting and information encryption have been demonstrated, suggesting the great potential of the BPLCEs-based CPL active materials.
Synergistic effects of anlotinib and DDP synergy in breast cancer treatment: inhibiting of cell growth and migration, and augmenting apoptosis and autophagy via modulation of the VEGF/JAK2/STAT3 axis
Authors: Zhang Hongmei , Liu Chunling , Jin Ye , Wang Zheng , Jia Zhenxian , Cui Tong , Zhang Zhi , Zhang Xuemei 
Published: February 2024

Abstract
Anlotinib has been shown to have good anti-tumor effects in a variety of tumors, including breast cancer (BRCA); however, the combined anti-tumor efficacy of anlotinib and DDP in BRCA, as well as the underlying mechanism, remain to fully elucidated. This study aims to explore the role of VEGFA expression in BRCA and the therapeutic efficacy of anlotinib, alone and in combination with cisplatin (DDP), in treating BRCA. BRCA cells were treated with or without anlotinib and/or DDP. The proliferation, migration and invasion capabilities of BRCA cells were evaluated using CCK-8 assays, clone formation assays, wound healing assays and transwell assays. Cell apoptosis was detected by Hoechst33342 fluorescence staining and flow cytometry technique. The potential mechanism of anlotinib in the development of BRCA was predicted through bioinformatics analysis, and the mRNA or protein levels were subsequently quantified using qPCR and western blot. The anti-breast cancer efficacy of anlotinib was evaluated in vivo using a xenograft tumor model. Our findings reveal that increased VEGFA expression in BRCA patients is associated with a poorer prognosis, underscoring the need for targeted therapeutic strategies. We demonstrate that both anlotinib and DDP independently inhibit BRCA cell growth, migration, and invasion. Their combination exhibits a synergistic effect, significantly enhancing the inhibition of these oncogenic processes. This synergy is further evident in the induction of apoptosis and autophagy within BRCA cells. Mechanistically, anlotinib's effectiveness is attributed to its inhibition of the JAK2/STAT3 pathway, a critical axis in BRCA progression. In vivo studies reinforce these findings, anlotinib markedly inhibits tumor growth in mice xenografted. This study confirms the efficacy of anlotinib or in combination with DDP and elucidates the mechanism behind anlotinib's effectiveness, highlighting its role in inhibiting the JAK2/STAT3 pathway. These findings pave the way for further clinical exploration and development of anlotinib-based therapies, offering hope for improved outcomes in breast cancer management.
Numerical approach for brain tumor growth model using higher order compact finite difference scheme
Authors: Das Hirak Jyoti , Sen Shuvam 
Published: February 2024

Abstract
In this article, we focus on analyzing the reaction-diffusion model applied to brain gliomas, incorporating two distinct types of growth functions. To gain a comprehensive understanding, we extend our analysis to different types of tissue environments. We explore scenarios where the diffusion coefficient remains constant, reflecting a homogeneous tissue environment. Additionally, we investigate cases where the diffusion coefficient becomes spatially variable, introducing heterogeneity into the model. This spatial variability accounts for the varying properties of different regions within the brain. Subsequently, we extend our investigation to heterogeneous tissue environments in $2$-dimensions. Our analysis of simulation results reveals differences in growth patterns based on the parameters utilized.
Bioinformatics and machine learning-based screening of key genes in Alzheimer's disease.
Authors: Hou Meng-ting , Li Xi-yu , Li Jia-xing , Bao Juan 
Published: February 2024

Abstract
Objective
To analyze differentially expressed genes (DEGs) related to mitophagy between Alzheimer's disease (AD) patients and normal controls using bioinformatics and machine learning methods and to screen for key genes to provide theoretical support for the study of AD pathogenesis and therapeutic targets.
Methods
Data microarrays related to AD were obtained from the GEO database, and DEGs were obtained by differential expression analysis of gene expression data using R. The DEGs were intersected with mitophagy-related genes to obtain the genes of interest, and then the group of genes was enriched for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways. A machine-learning model was constructed at the same time to screen key genes, construct risk prediction models and predict transcription factors based on key genes. In addition, consistent clustering analysis was performed on AD samples, followed by immunization and pathway analysis for each subtype.
Results
Seven key genes were finally screened from 38 mitophagy-related DEGs, and the risk prediction model constructed on the basis of these 7 genes had an AUC of 0.877. Cluster analysis classified the AD samples into two subtypes, and the immune infiltration between the two subtypes was also significantly different.
Conclusion
This study screened the key genes of AD based on bioinformatics, which provides a new perspective and potential therapeutic targets for exploring the potential mechanism of mitophagy affecting AD as well as a new idea and direction for individualized treatment of AD.
Sedimentation of large, soluble proteins up to 140 kDa for 1H-detected MAS NMR and 13C DNP NMR – practical aspects
Authors: Bell Dallas , Lindemann Florian , Gerland Lisa , Aucharova Hanna , Klein Alexander , Friedrich Daniel , Hiller Matthias , Grohe Kristof , Rossum Barth van , Diehl Anne , Hughes Jon , Mueller Leonard J. , Linser Rasmus , Miller Anne-Frances , Oschkinat Hartmut 
Published: February 2024

Abstract
Solution NMR is typically applied to biological systems with molecular weights < 40 kDa whereas magic-angle-spinning (MAS) solid-state NMR traditionally targets very large, oligomeric proteins and complexes exceeding 500 kDa in mass, including fibrils and crystalline protein preparations. Here, we propose that the gap between these size regimes can be filled by the approach presented that enables investigation of large, soluble and fully protonated proteins in the range of 40–140 kDa. As a key step, ultracentrifugation produces a highly concentrated, gel-like state, resembling a dense phase in spontaneous liquid-liquid phase separation (LLPS). By means of three examples, a Sulfolobus acidocaldarius bifurcating electron transfer flavoprotein (SulfETF), tryptophan synthases from Salmonella typhimurium (StTS) and the dimeric β-subunits from Pyrococcus furiosus (PfTrpB), we show that such samples yield well-resolved proton-detected 2D and 3D NMR spectra at 100 kHz MAS without heterogeneous broadening, similar to diluted liquids. Herein, we provide practical guidance on centrifugation conditions and tools, sample behavior, and line widths expected. We demonstrate that the observed chemical shifts correspond to those obtained from µM/low mM solutions or crystalline samples, indicating structural integrity. Nitrogen line widths as low as 20–30 Hz are observed. The presented approach is advantageous for proteins or nucleic acids that cannot be deuterated due to the expression system used, or where relevant protons cannot be re-incorporated after expression in deuterated medium, and it circumvents crystallization. Importantly, it allows the use of low-glycerol buffers in dynamic nuclear polarization (DNP) NMR of proteins as demonstrated with the cyanobacterial phytochrome Cph1.
Efficacy of a Self-help Parenting Program on Parental Outcomes: a Randomized Controlled Trial
Authors: de Jong S. R. C. , Hoofdakker Barbara J. , Veen-Mulders Lianne , Veenman Betty Y. , Oosterlaan Jaap , Luman Marjolein 
Published: February 2024

Abstract
The efficacy of our newly developed self-help parenting program on children’s externalizing behavior was recently shown. The present study investigated its efficacy on parental outcomes, which is understudied in clinical trials. Using a randomized controlled trial, 110 parents were allocated to an intervention condition (either with or without telephonic support) or a waitlist condition. Outcomes included the Parenting Practices Interview (PPI; positive and negative parenting practices), Parenting Sense of Competence Scale (PSOC), Parenting Stress Index (PSI) and Eyberg Child and Behavior Inventory - Problem Scale (ECBI-P; the number of child behaviors that parents perceive as troublesome). All measures were collected at baseline (T0) and post intervention (after 15 weeks, T2); PPI and ECBI-P were also collected at week 8 (T1) and 28 (T3). Using longitudinal multi-level regression analyses, we compared the intervention and waitlist condition at T2. Furthermore, the support and no support conditions were exploratively compared at T2 and T3. Comparing intervention to waitlist, results showed medium-sized effects on PPI and ECBI-P scores and a small-sized effect on PSI scores, and no differences between the conditions on PSOC scores. No differences were found between the support and the no-support condition. The results indicate that our self-help program improved parenting practices and parents’ perception of child behavior, in addition to previous findings on child outcomes. This confirms that self-help parenting programs may be a promising alternative to face-to-face programs, although future studies should focus on determining for whom and in which settings which parenting programs are most helpful..