bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering
Authors: Mia Md. Mojnu , Sultana Habiba , Amin Md. Al , Hossain Md. Sakhawat , Imam Hasan , Mohiuddin A. K. M. , Mahmud Shahin 
Published: February 2025

ABSTRACTThe field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications.
A computational approach to analyze apple dehydration using hybrid active solar dryer
Authors: Chaturvedi Vedansh , Gaur Manoj Kumar 
Published: February 2025

AbstractIn the present research, the control parameters that is, bed area, water flow rate, and No. of air exchanges of Hybrid Active Solar Dryer integrated with Evacuated Tube Collector located at the solar energy laboratory of Madhav Institute of Technology and Science (MITS) Gwalior (M.P.) India, have been optimized. Moisture removal (mev), convective heat transfer coefficient (hc), evaporative heat transfer coefficient (he) and drying rate (Rd) have been taken as response parameters. Experiments have been conducted in different seasons according to Taguchi's L9 orthogonal array (OA). Response data has been analyzed independently and simultaneously. With the help of signal‐to‐noise (S/N) ratio, optimal parameter setting has been determined for good performance in different seasons. Entropy measuring techniques are used to determine the entropy weightage of each response. Gray relational analysis integrates several responses into a single one, that is, gray relational grade (GRG). The value of predicted S/N ratio for GRG as per optimal parameter setting is −0.04706 which is higher than the experimental S/N ratio which is −0.48614, indicating the successful implementation of this approach.
Thermal and acoustic properties of lime‐based sustainable insulation materials produced from hemp fibers modified with boron
Authors: Yıldız Ali , Yıldız Esra , Koçak Ahmet Burak 
Published: February 2025

AbstractThe importance of using natural materials in the construction field within the framework of sustainable and environmentally friendly approaches is increasing day by day. In this context, this study was aimed to develop a hemp fiber‐based insulating building material. The boron doped fibers were characterized by thermogravimetric and differential thermal analysis (DTA/TGA) and field emission environmental scanning electron microscopy (FE‐ESEM). The materials were produced by mixing undoped, 10% and 15% boric acid doped hemp fibers separately with lime. The fiber:binder ratio was determined as 1:4 by weight in all samples. To determine the thermal and acoustic properties of the produced samples; thermal conductivity test with heat flow plate method, sound absorption and sound transmission loss tests with impedance tube method were carried out. In order to determine the mechanical strength of the materials, a three‐point bending tests were performed. As a result of the analyses, the thermal conductivity coefficients of the samples produced using hemp fibers, which are undoped, doped with 10% and 15% boric acid solution, were determined as 0.0935, 0.1926, and 0.1863 W/mK, respectively; noise reduction coefficients (NRCs) were measured as 0.425, 0.443, and 0.385, respectively; the highest sound transmission loss values were recorded as 27.17, 33.50, and 46.92 dB, respectively; and the flexural strength (σf) values were determined as 1.922, 1.992, and 2.578 MPa, respectively.
Multi‐Objective Optimization of a Spherical Thermal Storage Tank Using a Student Psychology‐Based Approach
Authors: Wang Xi , Carriveau Rupp , Ting David S.‐K. , Brown David , McGillis Andrew 
Published: February 2025

ABSTRACTEnergy storage technologies often store heat, with water as a preferred medium due to its availability and low cost. However, maintaining water in a liquid state at high temperatures requires large pressure vessels, posing significant design challenges. Balancing thermal storage capacity with pressure constraints is essential. This paper explores the dynamics of thermal storage water tanks, aiming to optimize their design using a multi‐criteria approach. An equilibrium thermodynamic model was developed to evaluate the impact of geometric structure and operating parameters. The results show that optimizing a single variable is insufficient to minimize pressure swing, reduce heat loss, and maximize storage capacity. To address these trade‐offs, a multi‐objective student psychology‐based optimization (SPBO) algorithm was employed for three‐objective optimization, outperforming particle swarm optimization (PSO) in convergence. The technique for order preference by similarity to ideal solution (TOPSIS) method was applied to the Pareto frontier, yielding ideal solutions using both data‐driven and manually weighted approaches. Compared with the initial design, the data‐driven weighted (entropy‐weighted and coefficient of variation methods) optimal designs improved all objectives, reducing pressure swing by 12.8% and 19.8%, respectively. A manually weighted approach reduced pressure swing by up to 86.7%, albeit with a decrease in thermal storage capacity.
Elastic Nanoparticle‐Reinforced, Conductive Structural Color Hydrogel With Super Stretchability, Self‐Adhesion, Self‐Healing as Electrical/Optical Dual‐Responsive Visual Electronic Skins
Authors: Xu Min , Liao Junlong , Li Jiajia , Shi Yu , Zhang Ziyu , Fu Yifu , Gu Zhongze , Xu Hua 
Published: February 2025

ABSTRACTDeveloping smart hydrogel with excellent physicochemical properties and multiple signal output capability for interactively electronic skin still remains challenging. Here, conductive structural color hydrogels with desirable physicochemical properties (including high stretchability and robustness, self‐adhesion and self‐healing) were developed to provide synchronous electronic and visual color signals for e‐skins. Highly charged elastic nanoparticles were elaborately used as building units for structural color and the hydrogel were prepared by the self‐assembly of the nanoparticle to form a non‐close‐packed array in a mixture comprised of acrylamide, silkworm silk fiber proteins (SF), reduced graphene oxide (rGO) and then photopolymerization. Benefiting from the improved interfacial compatibility between flexible hydrogel network and elastic nanoparticle, covalent cross‐linking network structure and synergistic multiple non‐covalent bonding interactions, the hydrogel exhibits extraordinary mechanical properties, excellent self‐adhesion to diverse substrates and self‐healing at room temperature. In addition, the hydrogel exhibited sensitive resistance changes and synchronous structural color changes under strain. As a proof‐to‐concept, the hydrogel displayed superior capability for the color‐response and the electrical signal response of various human motions, the spatial distribution of external mechanical stimuli as well as identification of different external stimuli, indicating promising applications in the fields of interactive visual electronic skin, wearable devices, and human–machine interfaces.
Contributions of Genetic Variation in Astrocytes to Cell and Molecular Mechanisms of Risk and Resilience to Late‐Onset Alzheimer's Disease
Authors: Lee Hyo , Pearse Richard V. , Lish Alexandra M. , Pan Cheryl , Augur Zachary M. , Terzioglu Gizem , Gaur Pallavi , Liao Meichen , Fujita Masashi , Tio Earvin S. , Duong Duc M. , Felsky Daniel , Seyfried Nicholas T. , Menon Vilas , Bennett David A. , De Jager Philip L. , Young‐Pearse Tracy L. 
Published: February 2025

ABSTRACTReactive astrocytes are associated with Alzheimer's disease (AD), and several AD genetic risk variants are associated with genes highly expressed in astrocytes. However, the contribution of genetic risk within astrocytes to cellular processes relevant to the pathogenesis of AD remains ill‐defined. Here, we present a resource for studying AD genetic risk in astrocytes using a large collection of induced pluripotent stem cell (iPSC) lines from deeply phenotyped individuals with a range of neuropathological and cognitive outcomes. IPSC lines from 44 individuals were differentiated into astrocytes followed by unbiased molecular profiling using RNA sequencing and tandem mass tag‐mass spectrometry. We demonstrate the utility of this resource in examining gene‐ and pathway‐level associations with clinical and neuropathological traits, as well as in analyzing genetic risk and resilience factors through parallel analyses of iPSC‐astrocytes and brain tissue from the same individuals. Our analyses reveal that genes and pathways altered in iPSC‐derived astrocytes from individuals with AD are concordantly dysregulated in AD brain tissue. This includes increased levels of prefoldin proteins, extracellular matrix factors, COPI‐mediated trafficking components and reduced levels of proteins involved in cellular respiration and fatty acid oxidation. Additionally, iPSC‐derived astrocytes from individuals resilient to high AD neuropathology show elevated basal levels of interferon response proteins and increased secretion of interferon gamma. Correspondingly, higher polygenic risk scores for AD are associated with lower levels of interferon response proteins in astrocytes. This study establishes an experimental system that integrates genetic information with a matched iPSC lines and brain tissue data from a large cohort of individuals to identify genetic contributions to molecular pathways affecting AD risk and resilience.
Pseudo‐MRI Engine for MRI‐Free Electromagnetic Source Imaging
Authors: Jaiswal Amit , Nenonen Jukka , Parkkonen Lauri 
Published: February 2025

ABSTRACTStructural head MRIs are a crucial ingredient in MEG/EEG source imaging; they are used to define a realistically shaped volume conductor model, constrain the source space, and visualize the source estimates. However, individual MRIs are not always available, or they may be of insufficient quality for segmentation, leading to the use of a generic template MRI, matched MRI, or the application of a spherical conductor model. Such approaches deviate the model geometry from the true head structure and limit the accuracy of the forward solution. Here, we implemented an easy‐to‐use tool, pseudo‐MRI engine, which utilizes the head‐shape digitization acquired during a MEG/EEG measurement for warping an MRI template to fit the subject's head. To this end, the algorithm first removes outlier digitization points, densifies the point cloud by interpolation if needed, and finally warps the template MRI and its segmented surfaces to the individual head shape using the thin‐plate‐spline method. To validate the approach, we compared the geometry of segmented head surfaces, cortical surfaces, and canonical brain regions in the real and pseudo‐MRIs of 25 subjects. We also tested the MEG source reconstruction accuracy with pseudo‐MRIs against that obtained with the real MRIs from individual subjects with simulated and real MEG data. We found that the pseudo‐MRI enables comparable source localization accuracy to the one obtained with the subject's real MRI. The study indicates that pseudo‐MRI can replace the need for individual MRI scans in MEG/EEG source imaging for applications that do not require subcentimeter spatial accuracy.
Flow Boiling Analysis for HFE‐7100 in a Vertical Porous Tube
Authors: Saihood Raed G. , Nima Mohammed A. 
Published: February 2025

ABSTRACTMuch recent research has focused on dielectric fluids in engineering applications because of their physical properties. In this study, the use of HFE‐7100 as a working fluid in a porous pipe exposed to thermal conditions like solar radiation conditions in Baghdad city was studied. The two‐phase mixture model with Local Thermal Non‐Equilibrium assumption was applied to analyze the flow boiling of a subcooled HFE‐7100 in a vertical pipe filled with high porosity metal foam. The Finite volume approach with MATLAB code was used to solve the governing equations like continuity, momentum based on Forchheimer‐extended Darcy model and energy equations. The results displayed that the heat transfer rises with the rise in pore density, porosity and the heat flux while the liquid saturation reduces with the raise in heat flux and pore density and the decrease in porosity of the metal foam. PPI effect is more effective at low porosity, as it increases the heat transfer coefficient by 101%, 95%, and 88% at 0.8, 0.9, and 0.95 porosity, respectively. But the effect of porosity is very small compared to PPI effect on the liquid saturation where it decreases by 4% when the porosity decreases from 0.95 to 0.85, while it decreases by 23% when the pore density increases from 10 to 110 PPI.
Reciprocal Associations Between Positivity and Positive Affect During the COVID‐19 Pandemic
Authors: Caprara Mariagiovanna , Contreras Antonio , Suárez‐Falcón Juan C. , Caprara Gian Vittorio , Pozo Pilar , Cabras Emilia , Tavolucci Simone , Alessandri Guido 
Published: February 2025

ABSTRACTIn this study, the associations between positivity and positive affect were examined at five time points between January 2020 and September 2021, a period of turmoil associated with the COVID‐19 pandemic. Data were collected from 1401 students (73.45% women) attending an online university in Spain, commencing at the outbreak of the pandemic and then at four different time points up to the time it was considered to have been controlled. The results of a cross‐lagged panel model revealed that participants who maintained higher general positivity were also those who reported more intense overall positive affect. At the same time, above‐average positive affect predicted higher‐than‐usual levels of positivity. By pointing to the reciprocal relationships between positivity and positive affect, the results corroborate and go beyond previous findings by highlighting a virtuous cycle in which positivity and positive affect reciprocally influence each other over time. These data are in accordance with a dynamic view of how self‐focused, positive evaluative dispositions and chronic positive affective states operate in concert to enhance adaptation and well‐being. The practical implications of these findings are discussed.
Concept for Design And Implementation Of Mobile, Computer‐Generated Display Systems
Authors: Horowitz Paul 
Published: February 2025

AbstractThe purpose of this report is to discuss several computer generated display concepts that appear to be suitable for use in tactical operations centers. The report does not present a survey or review of data display “state‐of‐the‐art”, but attempts to set forth the human and subsystem requirements of tactical centers in general, as well as some that may be unique to a particular system. The display subsystem design described in the report is within the current state‐of‐the‐art and could be available without an extensive research and development program.
Correction of Non‐Uniform Rotational Distortion in the Proximally Controlled Endoscopic OCTA
Authors: Guan Zehua , Li Qiang , Niu Chen , Fan Shuhao , Yu Huanhuan , Wu Wenjuan , Feng Xiangfei , Dai Cuixia 
Published: February 2025

ABSTRACTEndoscopic Optical Coherence Tomography (OCT) can provide high‐resolution cross‐sectional images for internal organ tissues. Combining the endoscopic imaging with Optical Coherence Tomography Angiography (OCTA), information of blood vessels in superficial lumen tissues is expected to be acquired. However, in endoscopic OCT systems using proximal scanning probes, performance of OCTA encounters significant challenges due to non‐uniform rotational distortion (NURD) caused by the non‐constant rotation of the distal imaging unit. In this study, we proposed a registration method for endoscopic OCTA imaging in a proximally controlled OCT System. Global registration and A‐line registration were employed to correct the distortion caused by mechanical friction between the catheter sheath and torque coil. Experimental performances in both microfluidic channel and rat rectum show significant correction of NURD. Our study achieved the first implementation of endoscopic OCTA under a spiral B‐scan rotation scheme in a proximally controlled OCT system, facilitating clear visualization of blood flow.
KDM1A Acts as an Oncogene and Facilitates the Epithelial Mesenchymal Transition Process in Gastric Cancer
Authors: Huang Rongjie , Cai Yichen , Chen Qiuxian , Sun Yuqin , Lian Mingqiao , Lian Mingjie , Cai Lisheng 
Published: February 2025

ABSTRACTBackgroundThis study is performed to research the biological role of KDM1A in the epithelial mesenchymal transition (EMT) of gastric cancer and investigate the mechanism involved.MethodsThe KDM1A, Vimentin and E‐cadherin levels were studied, as well as the correlation among them in gastric cancer samples. Gastric cancer cells were transfected with KDM1A overexpression and knockdown, and the cellular infiltration, motility, morphology and F‐actin expression were subsequently identified. For the protein level assessment of EMT, the western blot analysis combined with immunofluorescence was employed. The effect of KDM1A on TGF‐β/Notch signaling was also detected.ResultsKDM1A was overexpressed in gastric cancer tumor tissues. In the clinical gastric carcinoma samples, the level of KDM1A was linked negatively to the expression of E‐cadherin, while positively to the expression of Vimentin. Among the gastric carcinoma population, the expression of KDM1A was linked to the lymph node metastasis, TNM stage and tumor differentiation. The KDM1A downregulation prohibited the cellular motility, infiltration and F‐actin expression, and suppressed EMT process. KDM1A overexpression exhibited promoting effect on EMT in gastric cancer cells. KDM1A regulated TGF‐β/Notch signaling to affect EMT in gastric cancer cells.ConclusionKDM1A acts as an oncogene and facilitates the epithelial mesenchymal transition process by regulating TGF‐β/Notch signal pathway in gastric cancer cells.
A Review on miRNAs in Enteric Bacteria‐mediated Host Pathophysiology: Mechanisms and Implications
Authors: Doghish Ahmed S. , Elazazy Ola , Mohamed Hend H. , Mansour Reda M. , Ghanem Aml , Faraag Ahmed H. I. , Elballal Mohammed S. , Elrebehy Mahmoud A. , Elesawy Ahmed E. , Abdel Mageed Sherif S. , Saber Sameh , Nassar Yara A. , Abulsoud Ahmed I. , Abdel‐Reheim Mustafa Ahmed , Elawady Alaa S. , Ali Mohamed A. , Basiouny Mohamed Salah , Hemdan Mohamed , Lutfy Radwa H. , Awad Farah A. , El‐Sayed Salma A. , Ashour Mohamed M. , El‐Sayyad Gharieb S. , Mohammed Osama A. 
Published: February 2025

ABSTRACTRecently, many studies focused on the billions of native bacteria found inside and all over the human body, commonly known as the microbiota, and its interactions with the eukaryotic host. One of the niches for such microbiota is the gastrointestinal tract (GIT), which harbors hundreds to thousands of bacterial species commonly known as enteric bacteria. Changes in the enteric bacterial populations were linked to various pathologies such as irritable bowel syndrome and obesity. The gut microbiome could affect the health status of individuals. MicroRNAs (miRNAs) are one of the extensively studied small‐sized noncoding RNAs (ncRNAs) over the past decade to explore their multiple roles in health and disease. It was proven that miRNAs circulate in almost all body fluids and tissues, showing signature patterns of dysregulation associated with pathologies. Both cellular and circulating miRNAs participate in the posttranscriptional regulation of genes and are considered the potential key regulators of genes and participate in cellular communication. This manuscript explores the unique interplay between miRNAs and enteric bacteria in the gastrointestinal tract, emphasizing their dual role in shaping host‐microbiota dynamics. It delves into the molecular mechanisms by which miRNAs influence bacterial colonization and host immune responses, linking these findings to gut‐related diseases. The review highlights innovative therapeutic and diagnostic opportunities, offering insights for targeted treatments of dysbiosis‐associated pathologies.
Nicotinamide Phosphoribosyltransferase Acetylation Mediating Muscle Dysfunction Contributes to Sleep Apnoea in Obesity
Authors: Zhang Liu , Yan Ya Ru , Li Shi Qi , Lin Ying Ni , Wang Yi , Wang Yu Qing , Li Ning , Lu Fang Ying , Sun Xian Wen , Zhang Li Yue , Zhou Jian Ping , Ding Yong Jie , Li Qing Yun 
Published: February 2025

ABSTRACTBackgroundObstructive sleep apnoea (OSA) occurs frequently among individuals with obesity, which is attributed to upper airway muscle dysfunction. Muscle function is regulated by the dynamic balance of the nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH), which is controlled by the enzyme nicotinamide phosphoribosyltransferase (NAMPT). Elevated NAMPT levels have been found in individuals with obesity. However, the role of NAMPT in obesity‐induced muscle impairment has not been fully clarified.MethodsA total of 110 participants (70 moderate‐to‐severe OSA vs. 40 mild or no OSA) underwent electrical impedance mammography and polysomnography. C57BL/6J mice with high‐fat diet‐induced obesity (DIO) and control group were utilized for their characterizations, which included forced running wheel tests, glucose tolerance tests, haematoxylin and eosin staining, immunostaining, magnetic resonance imaging, whole‐body plethysmography, electromyographic techniques, western blot, NAMPT enzymatic activity assays and NAD+/NADH ratio measurements.ResultsPatients with moderate–severe OSA have a significant decrease in lean mass percentage of upper airway muscles compared with those in controls (p < 0.01). In vivo, a high‐fat diet reduced the levels of NAD‐dependent deacetylase sirtuin‐1 (SIRT1) (p < 0.01), which plays a crucial role in the deacetylation of NAMPT. The reduction in SIRT1‐mediated NAMPT deacetylation (p < 0.001) resulted in decreased NAMPT activity (p < 0.01), leading to a decrease in NAD+/NADH ratio (p < 0.05) and decreased the myosin heavy chain isoform (MyHC) I level (p < 0.05), thereby affecting the effectiveness of upper airway muscle and ultimately leading to upper airway collapse (101.0 vs. 81.7 pixels, p = 0.02). The introduction of estradiol mitigated high‐fat diet‐induced muscle dysfunction by enhancing expression of SIRT1 and inhibiting the acetylation of NAMPT, reducing upper airway collapse (81.7 vs. 96.7 pixels, p = 0.06).ConclusionsThese findings highlight the crucial role of SIRT1‐mediated NAMPT deacetylation on obesity‐induced muscle dysfunction, suggesting targeting NAMPT has the potential to reverse the obesity induced muscle dysfunction and provide effective treatment options for OSA.