bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing the impact of physical and virtual manipulatives in different science domains among preschoolers
Authors: Pavlou Yvoni , Zacharia Zacharias C. , Papaevripidou Marios 
Published: April 2024

AbstractThis study aimed to investigate whether the presence (when using physical manipulatives [PMs]) or absence (when using virtual manipulatives [VMs]) of haptic sensory feedback (i.e., open‐ended haptic manipulation of physical materials with the use of the hands) during experimentation can impact preschoolers’ conceptual understanding of concepts concerning three different subject domains (i.e., balance beam, sinking/floating, and springs). The participants were 132 preschoolers (5–6 years old), 44 per subject domain, who were equally divided into two conditions differing in the means of experimentation (PM or VM) they used. The data of this exploratory study were collected through clinical interviews and analyzed both qualitatively and quantitatively. The findings indicated that preschoolers’ mean score improved in both conditions for each subject domain, (probably) as a result of their participation in the experimentation phase of the interviews, across all domains and conditions. No statistically significant difference in preschoolers’ learning between the two conditions was found in the balance beam domain. In the sinking/floating domain, VM were found to be more conducive to preschoolers’ learning than PM, whereas in the springs domain PM were found to have enhanced preschoolers’ learning more than VM did. These findings have important implications for science teaching and learning in the early childhood years. First, we provide information on when PM or VM is conducive to kindergarteners’ science learning. Second, we report on how prior embodied knowledge, established through haptic sensory input and related to the task at hand, affects learning through PM or VM experimentation.
Synergistic Effects of Doping and Strain in Bismuth Catalysts for CO2 Electroreduction
Authors: Wei Yang , Xu Xin , Shi Dehuan , Jiang Yaming , Zheng Chaoyang , Tan Li , Liu Zheyuan , Zhong Shenghong , Yu Yan 
Published: April 2024

AbstractDoping is a recognized method for enhancing catalytic performance. The introduction of strains is a common consequence of doping, although it is often overlooked. Differentiating the impact of doping and strain on catalytic performance poses a significant challenge. In this study, Cu‐doped Bi catalysts with substantial tensile strain are synthesized. The synergistic effects of doping and strain in bismuth result in a remarkable CO2RR performance. Under optimized conditions, Cu1/6‐Bi demonstrates exceptional formate Faradaic efficiency (>95%) and maintains over 90% across a wide potential window of 900 mV. Furthermore, it delivers an industrial‐relevant partial current density of −317 mA cm−2 at −1.2 VRHE in a flow cell, while maintaining its selectivity. Additionally, it exhibits exceptional long‐term stability, surpassing 120 h at −200 mA cm−2. Through experimental and theoretical mechanistic investigations, it has been determined that the introduction of tensile strain facilitates the adsorption of *CO2, thereby enhancing the reaction kinetics. Moreover, the presence of Cu dopants and tensile strain further diminishes the energy barrier for the formation of *OCHO intermediate. This study not only offers valuable insights for the development of effective catalysts for CO2RR through doping, but also establishes correlations between doping, lattice strains, and catalytic properties of bismuth catalysts.
Study on stress–strain curve and damage evolution model of expanded perlite concrete under uniaxial compression
Authors: Jia Zhiwen , Li Dongwei , Chen Tao , Zhong Shiming , Chen Guanren , Wang Zecheng , Wang Hongqi , Wang Yinjia , Feng Zhangbiao 
Published: April 2024

AbstractThis study investigates the influence of expanded perlite (EP) replacement rate and curing methods on the compressive strength of concrete at different ages through the uniaxial compression test. The stress–strain full curve model of concrete considering EP replacement rate is established, and a damage evolution model considering curing conditions, EP replacement rate and load effects is developed based on the damage theory. The results show that: (1) The lack of water in concrete curing will have a huge negative impact on its mechanical properties, and the internal curing effect of pre‐wet EP can effectively alleviate the phenomenon of incomplete hydration. (2) Under dry curing, the addition of EP will reduce the early compressive strength of concrete, while its internal curing effect can improve the compressive strength of concrete in the later stages. (3) The C & C model and the Guozhenhai model are used to construct the segmented model in the rising and falling sections, and the model parameter formula is deduced by the replacement rate. The model can fully describe the stress–strain relationship of expanded perlite concrete (EPC). (4) The damage evolution model of EPC shows an “S” shape growth curve. Dry curing and EP replacement can both reduce the development rate of damage, while the former has a more significant impact.
Assessing potential barriers to migratory Walleye in the Sandusky River, Ohio
Authors: Myers Madison R. , Hunkins Taylor E. , Bossenbroek Jonathan M. , Mayer Christine M. , Weimer Eric J. 
Published: April 2024

Abstract

Objective
The Sandusky River, Ohio, is one of the major Lake Erie tributaries that supports migratory Walleye Sander vitreus reproduction. Following the construction of the Ballville Dam in 1913, Walleye spawning was limited to an area downstream near Fremont, Ohio. After the removal of the dam in 2018, several natural and human-made features were identified that may impede Walleye passage by collecting woody debris and altering flow conditions. In this study, we use hydrologic modeling and migratory sampling to understand the spatial and temporal dynamic nature of the blockages caused by the remaining anthropogenic and natural barriers.

Methods
We created a fine-scale Hydrologic Engineering Center's River Analysis System (HEC-RAS) model to examine these potential natural and human-made barriers to Walleye passage during spawning. Using our model, we compared swim speeds (10 min maintained and burst) of small, medium, and large Walleye under three flow scenarios with five levels of blockage to assess whether the area was passable. Further, we conducted electrofishing surveys during annual spawning runs from 2020 to 2021 to assess Walleye presence upstream and downstream after dam removal.

Result
Our model predicted that Walleye were able to pass the barriers under most of the scenarios by maintaining burst swim speed. Additionally, we captured Walleye above the former dam site in 2021, suggesting that Walleye can access newly available spawning habitat during certain river conditions.

Conclusion
Removing the Ballville Dam restored fish passage, increased access to spawning habitat, and could improve Walleye production in the Sandusky River.
PTPN7 mediates macrophage‐polarization and determines immunotherapy in gliomas: A single‐cell sequencing analysis
Authors: Ji Xiang , Cheng Jingsong , Su Jing , Wen Rong , Zhang Qi , Liu Guodong , Peng Yun , Mao Jinning 
Published: April 2024

AbstractBackgroundProtein tyrosine phosphatase non‐receptor type 7 (PTPN7) is a signaling molecule that regulates a multitude of cellular processes, spanning cell proliferation, cellular differentiation, the mitotic cycle, and oncogenic metamorphosis. However, the characteristic of PTPN7 in the glioma microenvironment has yet to be elucidated.MethodsThe prognostic value, genomic features, immune characteristics, chemotherapy prediction, and immunotherapy prediction of PTPN7 were systematically explored at the bulk sequencing level. The cell evolution trajectory, cell communication pattern, and cell metabolic activity related to PTPN7 were systematically explored at the single‐cell sequencing level. HMC3 and M0 cells were cocultured with U251 and T98G cells, and flow cytometry was carried out to investigate the polarization of HMC3 and M0. Transwell assay and CCK‐8 assay were performed to explore the migration and proliferation activity of U251 and T98G.ResultsThe expression level of PTPN7 is significantly elevated in glioma and indicates malignant features. PTPN7 expression predicts worse prognosis of glioma patients. PTPN7 is associated with genome alteration and immune infiltration. Besides, PTPN7 plays a crucial role in modulating metabolic and immunogenic processes, particularly by influencing the activity of microglia and macrophages through multiple signaling pathways involved in cellular communication. Specifically, PTPN7 actively mediates inflammation‐resolving‐polarization of macrophages and microglia and protects glioma from immune attack. PTPN7 could also predict the response of immunotherapy.ConclusionsPTPN7 is critically involved in inflammation‐resolving‐polarization mediated by macrophage and microglia and promotes the immune escape of glioma cells.
Integrative analysis of the bladder cancer from a cell cycle NCAM1 perspective at both single cell and bulk resolution
Authors: Zeng Xiangju , Su Hao , Liu Ziqi , Wang Yinhuai , Lu Zhijie , Cheng Shunhua 
Published: April 2024

AbstractIntroductionBladder cancer (BLCA) is a prevalent and deadly form of urinary cancer, and there is a need for effective therapies, particularly for muscle‐invasive bladder cancer (MIBC). Cell cycle inhibitors show promise in restoring control of the cell cycle in BLCA cells, but their clinical prognosis evaluation is limited.MethodsTranscriptome and scRNA‐seq data were collected from the Cancer Genome Atlas Program (TCGA)‐BLCA and GSE190888 cohort, respectively. R software and the Seurat package were used for data analysis, including cell quality control, dimensionality reduction, and identification of differentially expressed genes. Genes related to the cell cycle were obtained from the genecards website, and a protein–protein interaction network analysis was performed using cytoscape software. Functional enrichment analysis, immune infiltration analysis, drug sensitivity analysis, and molecular docking were conducted using various tools and packages. BLCA cell lines were cultured and transfected for in vitro experimental assays, including RT‐qPCR analysis, and CCK‐8 cell viability assays.ResultsWe identified 32 genes as independent risk or protective factors for BLCA prediction. Functional enrichment analysis revealed their involvement in cell cycle regulation, apoptosis, and various signaling pathways. Using these genes, we developed a nomogram for predicting BLCA survival, which displayed high prognosis stratification efficacy in BLCA patients. Four cell cycle associated key genes identified, including NCAM1, HBB, CKD6, and CTLA4. We also identified the main cell types in BLCA patients and investigated the functional differences between epithelial cells based on their expression levels of key genes. Furthermore, we observed a high positive correlative relationship between the infiltration of cancer‐associated fibroblasts and the risk score value. Finally, we conducted in vitro experiments to demonstrate the suppressive role of NCAM1 in BLCA cell proliferation.ConclusionThese findings suggest that cell cycle associated genes could serve as potential biomarkers for predicting BLCA prognosis and may represent therapeutic targets for the development of more effective therapies. Hopefully, these findings provide valuable insights into the molecular mechanisms and potential therapeutic targets in BLCA from the perspective of cell cycle. Moreover, NCAM1 was a novel cell proliferation suppressor in the BLCA carcinogenesis.
Advancing predictive markers in lung adenocarcinoma: A machine learning‐based immunotherapy prognostic prediction signature
Authors: Li Zhongyan , Pei Shengbin , Wang Yanjuan , Zhang Ge , Lin Haoran , Dong Shiyang 
Published: April 2024

AbstractThe prognosis of lung adenocarcinoma (LUAD) is generally poor. Immunotherapy has emerged as a promising therapeutic modality, demonstrating remarkable potential for substantially prolonging the overall survival of individuals afflicted with LUAD. However, there is currently a lack of reliable signatures for identifying patients who would benefit from immunotherapy. We conducted a comparative analysis of two immunotherapy cohorts (OAK and POPLAR) and utilized single‐factor COX regression to identify genes that significantly impact the prognosis of LUAD. Based on the TCGA‐LUAD dataset, we employed a combination of 101 machine learning algorithms to construct a model and selected the optimal model. The model was validated on five GEO datasets and compared with 144 previously published signatures to assess its performance. Subsequently, we explored the underlying biological mechanisms through tumor mutation burden analysis, enrichment analysis, and immune infiltration analysis. An immunotherapy prognostic prediction signature (IPPS) was constructed based on 13 genes, showing robust performance in the TCGA‐LUAD dataset. IPPS exhibited consistent predictive accuracy in the validation cohorts. Compared to 144 previously published signatures, IPPS consistently ranked among the top in terms of C‐index values. Further exploration revealed differences between high and low‐IPPS groups in terms of tumor mutation burden, pathway enrichment, and immune infiltration. IPPS demonstrates strong predictive capabilities for the prognosis of LUAD patients, offering the potential to identify suitable candidates for immunotherapy and contribute to precision treatment strategies for LUAD.
The effects of case/control ratio and sample size on genome‐wide association studies: A simulation study
Authors: Turgut Ali Osman , Koca Davut 
Published: April 2024

AbstractBackgroundGenome‐wide association studies (GWAS) is a useful tool for the detection of disease or quantitative trait‐related genetic variations in the veterinary field. For a binary trait, a case/control experiment is designed in GWAS. However, there is limited information on the optimal case/control and sample size in GWAS.ObjectivesIn this study, it was aimed to detect the effects of case/control ratio and sample size for GWAS using computer simulation under certain assumptions.MethodUsing the PLINK software, we simulated three different disease scenarios. In scenario 1, we simulated 10 different case/control ratios with increasing ratio of cases to controls. In scenario 2, we did versa of scenario 1 with the increasing ratio of controls to cases. In scenarios 1 and 2, sample size gradually was increased with the change case/control ratios. In scenario 3, the total sample size was fixed to 2000 to see real effects of case/control ratio on the number of disease‐related single nucleotide polymorphisms (SNPs).ResultsThe results showed that the number of disease‐related SNPs were the highest when the case/control ratio is close to 1:1 in scenarios 1 and 2 and did not change with an increase in sample size. Similarly, the number of disease‐related SNPs was the highest in case/control ratios 1:1 in scenario 3. However, unbalanced case/control ratio caused the detection of lower number of disease‐related SNPs in scenario 3. The estimated average power of SNPs was highest when case/control ratio is 1:1 in all scenarios.ConclusionsAll findings led to the conclusion that an increase in sample size may enhance the statistical power of GWAS when the number of cases is small. In addition, case/control ratio 1:1 may be the optimal ratio for GWAS. These findings may be valuable not only for veterinary field but also for human clinical experiments.
Diffusion models in protein structure and docking
Authors: Yim Jason , Stärk Hannes , Corso Gabriele , Jing Bowen , Barzilay Regina , Jaakkola Tommi S. 
Published: April 2024

AbstractGenerative AI is rapidly transforming the frontier of research in computational structural biology. Indeed, recent successes have substantially advanced protein design and drug discovery. One of the key methodologies underlying these advances is diffusion models (DM). Diffusion models originated in computer vision, rapidly taking over image generation and offering superior quality and performance. These models were subsequently extended and modified for uses in other areas including computational structural biology. DMs are well equipped to model high dimensional, geometric data while exploiting key strengths of deep learning. In structural biology, for example, they have achieved state‐of‐the‐art results on protein 3D structure generation and small molecule docking. This review covers the basics of diffusion models, associated modeling choices regarding molecular representations, generation capabilities, prevailing heuristics, as well as key limitations and forthcoming refinements. We also provide best practices around evaluation procedures to help establish rigorous benchmarking and evaluation. The review is intended to provide a fresh view into the state‐of‐the‐art as well as highlight its potentials and current challenges of recent generative techniques in computational structural biology.This article is categorized under:
Data Science > Artificial Intelligence/Machine Learning
Structure and Mechanism > Molecular Structures
Software > Molecular Modeling
Enhanced sampling strategies for molecular simulation of DNA
Authors: Mohr Bernadette , van Heesch Thor , Pérez de Alba Ortíz Alberto , Vreede Jocelyne 
Published: April 2024

AbstractMolecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time. Using current computer architectures, time scales of tens of microseconds are feasible with contemporary all‐atom force fields. However, these timescales are insufficient to accurately characterize large conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale challenge. The first approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The path‐metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi‐dimensional CV space. The second strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are generally fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two‐dimensional Müller–Brown potential. DNA applications are featured for two different processes: the Watson–Crick–Franklin to Hoogsteen transition in adenine–thymine base pairs and the binding of a DNA‐binding protein domain to DNA.This article is categorized under:
Molecular and Statistical Mechanics Molecular Dynamics and Monte‐Carlo Methods
Molecular and Statistical Mechanics Free Energy Methods
Software Simulation Methods
Sex differences in CD8+ T cell responses during adaptive immunity
Authors: Layug Paul Jerard , Vats Harman , Kannan Kamali , Arsenio Janilyn 
Published: April 2024

AbstractBiological sex is an important variable that influences the immune system's susceptibility to infectious and non‐infectious diseases and their outcomes. Sex dimorphic features in innate and adaptive immune cells and their activities may help to explain sex differences in immune responses. T lymphocytes in the adaptive immune system are essential to providing protection against infectious and chronic inflammatory diseases. In this review, T cell responses are discussed with focus on the current knowledge of biological sex differences in CD8+ T cell mediated adaptive immune responses in infectious and chronic inflammatory diseases. Future directions aimed at investigating the molecular and cellular mechanisms underlying sex differences in diverse T cell responses will continue to underscore the significance of understanding sex differences in protective immunity at the cellular level, to induce appropriate T cell‐based immune responses in infection, autoimmunity, and cancer.This article is categorized under:
Immune System Diseases > Molecular and Cellular Physiology
Infectious Diseases > Molecular and Cellular Physiology
Theatrical Distribution or Online Streaming? Release Strategies in Europe in Times of Disruption and Change
Authors: Smits Roderik 
Published: April 2024

AbstractThis chapter provides insight into the development of streaming-related release strategies during the Covid-19 pandemic, with particular reference to the European market. I am particularly interested in the relationship between streaming platforms and theatrical cinema exhibitors, a relationship that is often described in terms of conflict and tension. For some in the industry, streaming platforms are perceived as a threat to the theatrical cinema sector. For others in the industry, streaming platforms are symptomatic of the way that the modern era of film exhibition is taking shape, with different distribution systems co-existing to enable different routes to market for different films. This chapter draws on trade press and news coverage to analyse how the relationship between streaming platforms and cinema exhibitors developed during the pandemic. What sort of release strategies for films became common when lockdowns and other policy restrictions were imposed on cinema exhibitors? How did changing circumstances impact release windows for films, and in particular the theatrical cinema window? And has the pandemic brought about structural changes to the film distribution and exhibition businesses in Europe and beyond?
Stunt Scooter and Educational Commons: A German Case Study
Authors: Jäde Sylvia , Eßer Florian , von der Heyde Judith 
Published: April 2024

AbstractThe chapter focuses on the results of the German case studies dealing with the appropriation of public space through youth cultural practices. The focus of the German sub-project is on how children and young people move in public space with stunt scooters and utilize it for their own purposes. As in the SMOOTH project in general the approach of the educational commons serves as a theoretical frame of reference. In this chapter we will describe commoning practices that have emerged during the realized case studies. Besides the aspects of sharing and caring, there were also practices of cooperation and engaged citizenship. All these aspects have a political dimension, which became apparent in different ways in the case studies and in the researched field. Overall, the case studies have shown that the children and young people involved in joint political processes as commoners require a high degree of transparency on the part of the adults involved as to what scope the children and young people involved have for shaping these processes.