Experimental Techniques Research Articles

Highly Selective On‐Surface Dehydrogenative Aromatization of n‐Hexyl to Phenyl Substituents

AbstractDehydrogenative aromatization of alkyl substituents represents a powerful approach to aryl‐substituted functional molecules. However, the inertness of alkyl groups and the need for harsh reaction conditions accompanied by low product selectivity hamper its widespread applications. Here, we demonstrate the highly selective on‐surface thermal aromatization of n‐hexyl substituents on polycyclic aromatic hydrocarbons (PAHs) to their phenyl‐substituted analogues under mild conditions. After depositing two representative precursor molecules, n‐hexyl‐substituted hexaphenylbenzene (HPB‐Hex) and bianthryl octacarboxylic tetraimide (BATI‐Hex), onto a pre‐heated Au(111) substrate, dehydroaromatization of the peripheral n‐hexyl groups into phenyl rings occurs, following the planarization of hexaphenylbenzene and bianthryl core. This process involves sequential intramolecular C−C bond rotations, dehydrogenation, and cyclodehydrogenation reactions, yielding phenyl‐substituted hexabenzocoronene (HBC‐Ph) and bisanthene octacarboxylic tetraimides (BSTI‐Ph). The reaction sequences were monitored using scanning tunneling microscopy (STM) and bond‐resolved non‐contact atomic force microscopy (nc‐AFM), offering structural proof of both intermediates and final products. These experimental techniques were complemented by density functional theory (DFT) simulations, which facilitated the detection of crucial steps in the conversion of n‐hexyl to phenyl groups. Moreover, the effect of alkyl aromatization on the electronic properties of the newly formed aromatic hydrocarbons was elucidated using scanning tunneling spectroscopy (STS).

Increased caveolin 1 by human antigen R exacerbates Porphyromonas gingivali-induced atherosclerosis by modulating oxidative stress and inflammatory responses

Objective: Many different types of infectious oral diseases have been identified clinically, including chronic periodontitis. Porphyromonas gingivalis is the main pathogen causing chronic periodontitis, which is closely related to atherosclerosis (AS) and can promote the expression levels of caveolin 1 (Cav-1) and induced ribonucleic acid (RNA)-binding protein human antigen R (HuR). However, the roles of Cav-1 and its relationship with HuR in P. gingivalis-mediated AS progression remain largely unknown. Here, we aimed to detect the role and molecular mechanisms of Cav-1 in P. gingivalis-mediated AS. Material and Methods: To investigate the role of Cav-1 in P. gingivalis-mediated AS, we infected human umbilical vein endothelial cells (HUVECs) with P. gingivalis at a multiplicity of infection of 100:1 for 6, 12, and 24 h to simulate P. gingivalis-induced AS models in vitro and then transfected them with Cav-1 small interfering RNA to silence Cav-1. Combining molecular biology experimental techniques such as cell counting kit-8 assay, enzyme-linked immunosorbent assay, immunofluorescence staining, flow cytometry, Western blotting, and Oil Red O staining, and apolipoprotein E-deficient AS model mice, the impacts of Cav-1 on cell viability, inflammation, oxidative stress, apoptosis, Cav-1 and intercellular cell adhesion molecule-1 (ICAM-1) levels, and atherosclerotic plaque formation were investigated. Then, the relationship between Cav-1 and HuR was investigated through biotin pull-down and RNA immunoprecipitation assays, reverse transcription quantitative polymerase chain reaction, and Western blot. Results: P. gingivalis can induce Cav-1 expression in a time- and dose-dependent manner (P < 0.05). This effect can inhibit the proliferation of HUVECs (P < 0.05). Cav-1 interference repressed inflammatory response, reactive oxygen species (ROS) and ICAM-1 levels, and apoptosis in the HUVECs (P < 0.05). Cav-1 messenger RNA was stabilized by HuR, which can bind to the 3’ untranslated region of Cav-1. Increase in HuR level reversed the effects of Cav-1 silencing on ROS and ICAM-1 levels and apoptosis in the HUVECs (P < 0.05). In addition, the levels of inflammatory response, oxidative stress, and atherosclerotic plaque formation induced by P. gingivalis in the mouse model were significantly reduced after Cav-1 expression was inhibited (P < 0.05). Conclusion: HuR-activated Cav-1 may promote atherosclerotic plaque formation by modulating inflammatory response and oxidative stress, leading to AS.

Experimental Study on Interlayer Interference Characteristics During Commingled Production in a Multilayer Tight Sandstone Gas Reservoir

In this study, a practical and comprehensive experimental technique has been proposed to investigate the interlayer interference characteristics in multilayer tight sandstone gas reservoirs with multi-pressure systems and different reserves. Firstly, single-layer depletion simulation experiments were conducted to measure the gas flow rate and gas extraction efficiency for each of the six layers. A series of physical simulation experiments were then conducted to monitor gas production and pressure variations in commingled multilayer production scenarios under various conditions. Finally, interlayer interference characteristics and gas extraction efficiencies and the main controlling factors were evaluated, analyzed, and identified. The interlayer pressure differential is found to be the primary factor dictating both interference and gas production, followed by initial gas production rates, and permeability variations in the order of positive significance. A higher interlayer pressure differential, a lower initial gas production rate, and a larger permeability variation result in an increase in interlayer interference and a reduction in gas production during commingled production. Increasing the number of commingled layers leads to an overall increase in gas production losses of 10.95% for two layers to 13.35% for four layers. Layers exhibiting small interlayer pressure difference are positively compatible for commingled production.

SiRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database.

Small interfering RNA (siRNA) has revolutionised biomedical research and drug development through precise post-transcriptional gene silencing technology. Despite its immense potential, siRNA therapy still faces technical challenges, such as delivery efficiency, targeting specificity, and molecular stability. To address these challenges and facilitate siRNA drug development, we have developed siRNAEfficacyDB, a comprehensive database that integrates experimentally validated siRNA efficacy data. This database contains 3544 siRNA records, covering 42 target genes and 5 cell lines. It provides detailed information on siRNA sequences, target genes, inhibition efficiencies, experimental techniques, cell lines, siRNA concentrations, and incubation times. siRNAEfficacyDB offers a user-friendly web interface that makes it easy to query, browse and analyse data, enabling efficient access to siRNA-related information. In summary, siRNAEfficacyDB provides a useful data foundation for siRNA drug design and optimisation, serving as a valuable resource for advancing computer-aided siRNA design research and nucleic acid drug development. siRNAEfficacyDB is freely available at https://cellknowledge.com.cn/siRNAEfficacy for non-commercial use.

Investigation of Erosion and Deposition Due to Flows with Particles.

In this work, we employed experimental technique to study the issue of particle erosion and deposition in multiphase flows involving both particles of micro/meso- and nanoscale (sand particles and iron oxide particles). Especially, liquids with immersed nanoparticles gained a lot of interest in the recent years due to their enhanced thermal properties. At the same time, this type of fluids is still not widely used in practical and engineering applications, and one of the reasons is a risk of leading to erosion and deposition on, for instance, pipe walls. In our experiments, an aluminum plate was subjected to a flow with particles by immersing it in a beaker with a rotating fluid for 530 h. After this, the plate was investigated using scanning electron microscopy (SEM) and atomic force microscopy (AFM), followed by energy dispersive X-ray (EDX) analysis. According to our observations, the erosion was mainly caused by the largest particles (sand particles), while the nanoparticles did not lead to clear erosion but resulted in significant deposition due to strong adhesion, as well as corrosion, resulting in aluminum oxide formation. This issue was also confirmed through theoretical analysis by comparing the momentum response time and the characteristic time of the flow, as well as computational fluid dynamics (CFD) simulations.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals.

In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.

Contemporary music improvisation for silent film

This article explores how contemporary music improvisation for silent film both evokes and challenges the jazz canon by pushing the boundaries of genre, instrumentation, techniques, and collaboration while also engaging with the narrative and cultural contexts of the films. It draws from my practice-led research over the last twenty years, which has consisted of performing free improvised music in response to the screening of silent film, as a solo performer or as part of a jazz ensemble. The corpus of films used in the research spans animated shorts by Dutch director Gerrit van Dijk, surrealist shorts by Man Ray, German expressionist feature film by Fritz Lang and F. W. Murnau, French feminist film by Germaine Dulac, and documentary and amateur archive film of the North West Film Archive in Manchester and the Media Archive for Central England in Lincoln. In the performances, while jazz is taken as primary influence, musicians often incorporate elements of other musics, make use of a broader range of instruments and of non-traditional sound sources beyond the typical jazz ensemble, and employ experimental techniques and unconventional playing methods that challenge and evoke the conventional improvisational norms of jazz. Musicians might opt to follow or contradict the narrative and emotional cues of the film, which can result in processes of music making that prioritize the exploration of the boundaries of storytelling over traditional jazz forms and structures. Across this research, I have observed how silent film improvisation has been attracting diverse audiences. This cross-pollination of audiences can introduce jazz to new fans and challenge preconceived notions about who jazz is for.

N6-methyladenosine modification of circular RNA circASH2L suppresses growth and metastasis in hepatocellular carcinoma through regulating hsa-miR-525-3p/MTUS2 axis.

CircRNAs have been demonstrated to play a crucial role in regulating the growth and progression of various cancers, including hepatocellular carcinoma (HCC). Nevertheless, the circRNA's expression pattern and function in HCC need more investigation. Bioinformatics techniques were used to identify differentially expressed circRNAs in HCC. CircASH2L expression in HCC tissues was assessed through qRT-PCR and ISH analysis. To assess circASH2L's impact on HCC progression, a variety of experiments were carried out both in vitro and in vivo, such as CCK8, colony formation, EdU assay, flow cytometry, transwell assay, and xenograft mouse model. Various experimental techniques including qRT-PCR, dual luciferase reporter assay, FISH, RNA pull-down, and RIP experiments were utilized to evaluate the relationship between circASH2L, miR-525-3p, and MTUS2. Additionally, experiments were conducted to explore the impact of m6A modification on circASH2L expression, including RNA stability assay, m6A RNA immunoprecipitation assay (MeRIP), and Co-IP experiments. We found that circASH2L was downregulated in HCC tissues and the downregulation of circASH2L was significantly correlated with malignant characteristics as well as poor overall survival of patients with HCC. CircASH2L was found to inhibit cells growth, migration and invasion as well as tumorigenesis and metastasis in vivo. Mechanistically, we established that circASH2L directly interacted with miR-525-3p to enhance MTUS2 expression, subsequently leading to tumor suppression. Moreover, the influence of circASH2L on tumor suppression was attenuated by increasing miR-525-3p levels, and MTUS2 was recognized as an essential intermediary in circASH2L-induced tumor suppression. Additionally, N6-methyladenosine (m6A) modification was identified in circASH2L. Our data suggested that METTL3 was responsible for mediating m6A methylation of circASH2L, ultimately regulating circASH2L expression through the promotion of its degradation. These findings collectively highlight the role of circASH2L as a tumor suppressor through a unique circASH2L/miR-525-3p/MTUS2 axis, shedding light on the significance of m6A modification in regulating circASH2L function. The work emphasizes circASH2L as a promising therapeutic target for treating HCC, offering new insights into the role of circRNAs in HCC development.

Green synthesis of fluorescent N-doped carbon quantum dots from castor seeds and their applications in cell imaging and pH sensing.

Water-soluble fluorescent N-doped carbon quantum dots (N-CQDs) were hydrothermally prepared through a green synthesis route using castor seeds as a single precursor and a hydrothermal method. Several experimental techniques have been used to characterize synthesized N-CQDs to confirm their structure and to verify their applicability in cell imaging and pH sensing. The synthesized N-CQDs were found to have are characterized by amorphous nature with a spherical shape with an average particle size of 6.57nm as revealed from XRD and TEM measurements. The FTIR results reveal the presence of carboxylic and hydroxyl functional groups on the surface of the CQDs, which was also confirmed by XPS analysis. The fluorescence characterization of the synthesized N-CQDs showed blue emission and excitation dependence with good photostability. It was found that the optimal excitation and emission wavelengths were (λEx = 360) and (λEm = 432) nm, respectively. The fluorescence quantum yield (QY) of about 9.6% at the optimum excitation wavelength 360nm. Moreover, the fluorescence intensity of N-CQDs showed good linear dependence with the pH values in ranges of 3.5 - 7.5 and 8 - 12 as well as high sensitivity for slight changes of pH values. According to these results, two fluorescent pH sensors were created based on acidic and basic media. The obtained N-CQDs have zeta potential of -21.86 mV and thus have excellent stability in water. Moreover, N-CQDs derived from the castor seeds have antimicrobial activity and exhibits low cytotoxicity to WI-13 cells with IC50 = 394.4 ± 13.8µg/mL. The results of this study demonstrated that the synthesized N-CQDs derived from castor seeds can be used as pH sensing and antimicrobial materials. On the other hand, they are also promising in applications in cell imaging, thermo-sensing and optoelectronics.

A Perspective on the Use of Hydroxyapatites to Improve the Dissolution Behavior of Poorly Water-Soluble Piretanide

Background/Objectives: Interest in drug delivery systems (DDS) based on inorganic substrates has increased in parallel with the increase in the number of poorly water-soluble drugs. Hydroxyapatite is one of the ideal matrices for DDS due to its biocompatibility, low cost, and ease of preparation. Methods: We propose two doped hydroxyapatites, one with Ba on Ca sites another with Si on P sites, with the aim of improving the dissolution rate of piretanide, a diuretic, poorly water-soluble drug. The hybrids were characterized by different physical–chemical techniques, and their formation was demonstrated by infrared spectroscopy, thermal analysis, and electron microanalysis, as well as by comparing the results with those obtained on physical mixtures of HAPs and properly prepared piretanide. Results: Both the hybrids improved the piretanide dissolution rate compared with the physical mixtures and the drug alone. The dose was completely solubilized from the Si-doped hybrid in about 5 min in the three fluids considered. This remarkable improvement can be explained by an increase in the wettability and solubility of the drug loaded in the drug-carrier systems. Conclusions: Different experimental techniques, in particular spectroscopy and electronic microanalysis, proved the successful loading of piretanide onto doped HAP. Pharmaceutical measurements demonstrated rapid drug release in different fluids simulating gastrointestinal conditions after oral administration. These hybrid systems could be a very promising platform for drug delivery.

Investigation of Excellence in Nd-YAG laser cutting of Al6061-T6 Thin sheet using GRA coupled with PCA

Abstract Cutting flying materials with minimum deviations and metallurgical damages is always preferred for airframe work in aircraft industries. In the present scenario, the laser cutting process has become the preferred choice for fine cutting of sheet materials with close tolerances. This paper reports the investigation of excellence in pulsed laser cutting of Al-alloy (Al6061-T6) sheet. Five quality characteristics for quantifying the dimensional accuracy (i.e., kerf width and deviation at the top and bottom side) and metallurgical damage (i.e., heat-affected zone) have been considered for the proposed work. These characteristics depend on the lamp current, laser parameters (pulse width and frequency), and relative motion between the sheetmetal and laser source. The experiments have been performed using the design of experiments technique. Further, the results of laser cutting have been optimized by using grey relational analysis (GRA) coupled with principal component analysis (PCA). The application of GRA-PCA is found capable of optimizing all five process responses at a time. The unevenness within the kerf is reduced by 22% and 32% at the top and bottom sides, respectively.

Vanadium incorporation in 2D-layered MoSe2

Recent advances in experimental techniques have made it possible to manipulate the structural and electronic properties of two-dimensional layered materials (2DM) through interaction with foreign atoms. Using quantum mechanics calculations based on the density functional theory, we explored the dependency of the structural, energetic, electronic, and magnetic properties of the interaction between Vanadium (V) atoms and monolayer and bilayer MoSe2. Spin-polarized metallic behavior was observed for high V concentration, and a semiconductor/metal interface emerged due to V adsorption on top of BL MoSe2. Our research demonstrated that the functionalization of 2D materials makes an important contribution to the design of spintronic devices based on a 2D-layered materials platform.

How to Assess and Predict Electrical Double Layer Properties. Implications for Electrocatalysis.

The electrical double layer (EDL) plays a central role in electrochemical energy systems, impacting charge transfer mechanisms and reaction rates. The fundamental importance of the EDL in interfacial electrochemistry has motivated researchers to develop theoretical and experimental approaches to assess EDL properties. In this contribution, we review recent progress in evaluating EDL characteristics such as the double-layer capacitance, highlighting some discrepancies between theory and experiment and discussing strategies for their reconciliation. We further discuss the merits and challenges of various experimental techniques and theoretical approaches having important implications for aqueous electrocatalysis. A strong emphasis is placed on the substantial impact of the electrode composition and structure and the electrolyte chemistry on the double-layer properties. In addition, we review the effects of temperature and pressure and compare solid-liquid interfaces to solid-solid interfaces.

CRISPRoffT: comprehensive database of CRISPR/Cas off-targets.

The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) programmable nuclease system continues to evolve, with in vivo therapeutic gene editing increasingly applied in clinical settings. However, off-target effects remain a significant challenge, hindering its broader clinical application. To enhance the development of gene-editing therapies and the accuracy of prediction algorithms, we developed CRISPRoffT (https://ccsm.uth.edu/CRISPRoffT/). Users can access a comprehensive repository of off-target regions predicted and validated by a diverse range of technologies across various cell lines, Cas enzyme variants, engineered sgRNAs (single guide RNAs) and CRISPR editing systems. CRISPRoffT integrates results of off-target analysis from 74 studies, encompassing 29 experimental prediction techniques, 368 guide sequences, 226164 potential guide and off-target pairs and 8840 validated off-targets. CRISPRoffT features off-target data from different CRISPR approaches (knockout, base editing and prime editing) applied under diverse experimental conditions, including 85 different Cas/guide RNA (gRNA) combinations used across 34 different human and mouse cell lines. CRISPRoffT provides results of comparative analyses for individual guide sequences, genes, cell types, techniques and Cas/gRNA combinations under different conditions. CRISPRoffT is a unique resource providing valuable insights that facilitate the safety-driven design of CRISPR-based therapeutics, inform experimental design, advance the development of computational off-target prediction algorithms and guide RNA design algorithms.

Exploration of quantum oscillation in antiferromagnetic Weyl semimetal GdSiAl.

GdSiAl single crystal has been investigated by means of magnetic and magneto-transport measurements and compared with ab-initio density functional theory (DFT) calculations. Significant non-saturating magnetoresistance reaching ∼ 18% at 12T and 2K was observed, alongside the presence of Shubnikov-de Haas oscillations with the fundamental frequencies 22.09T and 77.33T. Shubnikov-de Haas oscillations provide the information about the nontrivial π Berry phase in GdSiAl with the Fermi surface areas of 0.00211 Å-2and 0.00739 Å-2. Angle-dependent magnetoresistance shows anisotropy with θ, exhibiting a maximum at 180°. The magnetic susceptibility data for H ∥ c and H ⊥ c reveals that the magnetic moments of Gd3+ions orders antiferromagnetically below 32K along with an another transition occurs at ∼ 8K, which is consistent with the heat capacity measurements where a distinct λ-shaped anomaly has been observed near antiferromagnetic ordering temperature 32K. The high value of Debye temperature indicates the contribution of acoustic phonons. Electronic structure calculations suggest the existence of nested Fermi surface pockets characterized by nesting wave vectors that closely align with the observed magnetic ordering wave vector. Furthermore, DFT calculations reveal the presence of Weyl nodes in close proximity to the Fermi surface. Our findings from combined experimental and theoretical techniques indicate GdSiAl to be a potential candidate for an antiferromagnetic topological Weyl semimetal.

Investigating the Morphology of a Free-Falling Jet with an Accurate Finite Element and Level Set Modeling

This study investigates the morphology of a free-falling liquid jet by using a computational approach with an experimental validation. Numerical simulations are developed by means of the Finite Element Method (FEM) for solving the viscous fluid flow and the level set method in order to track the interface between the fluid and air. Experiments are conducted in order to capture the shape of a free-falling jet of viscous fluid via circular orifice, where the shape is measured optically. The numerical results are found to be in agreement with the experimental data, demonstrating the validity of the proposed approach. Furthermore, we analyze the role of the surface tension by implementing linear as well as nonlinear surface energy models. All computational codes are developed with the aid of open-source packages from FEniCS and made publicly available. The combination of experimental and numerical techniques provides a comprehensive understanding of the morphology of free-falling jets and may be extended to multiphysics problems rather in a straightforward manner.

Highly Selective On-Surface Dehydrogenative Aromatization of n-Hexyl to Phenyl Substituents.

Dehydrogenative aromatization of alkyl substituents represents a powerful approach to aryl-substituted functional molecules. However, the inertness of alkyl groups and the need for harsh reaction conditions accompanied by low product selectivity hamper its widespread applications. Here, we demonstrate the highly selective on-surface thermal aromatization of n-hexyl substituents on polycyclic aromatic hydrocarbons (PAHs) to their phenyl-substituted analogues under mild conditions. After depositing two representative precursor molecules, n-hexyl-substituted hexaphenylbenzene (HPB-Hex) and bianthryl octacarboxylic tetraimide (BATI-Hex), onto a pre-heated Au(111) substrate, dehydroaromatization of the peripheral n-hexyl groups into phenyl rings occurs, following the planarization of hexaphenylbenzene and bianthryl core. This process involves sequential intramolecular C-C bond rotations, dehydrogenation, and cyclodehydrogenation reactions, yielding phenyl-substituted hexabenzocoronene (HBC-Ph) and bisanthene octacarboxylic tetraimides (BSTI-Ph). The reaction sequences were monitored using scanning tunneling microscopy (STM) and bond-resolved non-contact atomic force microscopy (nc-AFM), offering structural proof of both intermediates and final products. These experimental techniques were complemented by density functional theory (DFT) simulations, which facilitated the detection of crucial steps in the conversion of n-hexyl to phenyl groups. Moreover, the effect of alkyl aromatization on the electronic properties of the newly formed aromatic hydrocarbons was elucidated using scanning tunneling spectroscopy (STS).

Effect of High Heat Flux of Helium and Hydrogen Plasma Jet on the Material Properties of Piezoelectric PZT-Ceramics

A set of experimental and measurement techniques to study the influence of a plasma jet on the main material parameters of piezoelectric ceramics has been presented. A series of plasma experiments has been carried out using a pulsed plasma jet system. It allows of a metered-dose exposure to plasma of different composition and fluence with a constant particle flux density of 1021/m2, energy flux density of 0.1 MJ/m2 and average particle energy of 100–200 eV in a pulse duration of 15 μs. The study of the effects that a repeated exposure to an extreme heat flux of helium and hydrogen plasmas has on the near-surface layer structure and basic material parameters of mass-produced piezoelectric ceramic samples has been presented. The main result of the research is an experimental confirmation of the surface micro-structuring starting after just a few cycles of plasma exposure while only a slight decrease of the main material parameters as well as the preservation of polarization has been observed for two types of different compositions of PZT-ceramics. A further increase in the number of exposure pulses leads to practically no change of main material parameters of both ceramics, even showing a tendency for recovery instead.

Tracking the topology of neural manifolds across populations

Neural manifolds summarize the intrinsic structure of the information encoded by a population of neurons. Advances in experimental techniques have made simultaneous recordings from multiple brain regions increasingly commonplace, raising the possibility of studying how these manifolds relate across populations. However, when the manifolds are nonlinear and possibly code for multiple unknown variables, it is challenging to extract robust and falsifiable information about their relationships. We introduce a framework, called the method of analogous cycles, for matching topological features of neural manifolds using only observed dissimilarity matrices within and between neural populations. We demonstrate via analysis of simulations and in vivo experimental data that this method can be used to correctly identify multiple shared circular coordinate systems across both stimuli and inferred neural manifolds. Conversely, the method rejects matching features that are not intrinsic to one of the systems. Further, as this method is deterministic and does not rely on dimensionality reduction or optimization methods, it is amenable to direct mathematical investigation and interpretation in terms of the underlying neural activity. We thus propose the method of analogous cycles as a suitable foundation for a theory of cross-population analysis via neural manifolds.

Graph-based machine learning model for weight prediction in protein–protein networks

Proteins interact with each other in complex ways to perform significant biological functions. These interactions, known as protein–protein interactions (PPIs), can be depicted as a graph where proteins are nodes and their interactions are edges. The development of high-throughput experimental technologies allows for the generation of numerous data which permits increasing the sophistication of PPI models. However, despite significant progress, current PPI networks remain incomplete. Discovering missing interactions through experimental techniques can be costly, time-consuming, and challenging. Therefore, computational approaches have emerged as valuable tools for predicting missing interactions. In PPI networks, a graph is usually used to model the interactions between proteins. An edge between two proteins indicates a known interaction, while the absence of an edge means the interaction is not known or missed. However, this binary representation overlooks the reliability of known interactions when predicting new ones. To address this challenge, we propose a novel approach for link prediction in weighted protein–protein networks, where interaction weights denote confidence scores. By leveraging data from the yeast Saccharomyces cerevisiae obtained from the STRING database, we introduce a new model that combines similarity-based algorithms and aggregated confidence score weights for accurate link prediction purposes. Our model significantly improves prediction accuracy, surpassing traditional approaches in terms of Mean Absolute Error, Mean Relative Absolute Error, and Root Mean Square Error. Our proposed approach holds the potential for improved accuracy in predicting PPIs, which is crucial for better understanding the underlying biological processes.