Polynomial regression analysis on electromagnetohydrodynamic hybrid nanofluid flow over a rotating disk: Applications in next-generation thermal systems
Gunisetty Ramasekhar, P.D. Selvi, Hijaz Ahmad
et al.
Thermal systems need effective cooling and heating processes, therefore thermal transfer innovation is critical in modern times, playing an important role in the manufacturing, aerospace, and electronic equipment sectors, in addition to automobiles and other modes of transportation. This study investigates the heat transfer properties of an electromagnetohydrodynamic mixed nanofluid across a porous spinning disk. The primary goal is to develop and validate an efficient engine oil/Cu-CuO hybrid framework that integrates traditional numerical approaches with polynomial regression analysis to accurately predict the flow and thermal features of complex nanofluid systems. The conversion of PDEs into ODEs is achieved by utilizing similarity variables. Thereafter, for graphical purposes, the study employed the bvp4c numerical method. The resultant structure is solved with the bvp4c scheme, and polynomial regression analysis is created to train the solution data for accurate estimation across different parameter (Q, Ec, Rd) settings. The suggested polynomial regression analysis has regression coefficients are 0.98, 0.87, 0.97, indicating high predicted accuracy and effectiveness. The influence of different parameters participating in the mathematical modeling is shown in various graphs and tables. In the result section the investigation noticed the velocity outlines increased, and on the other hand, there was a decreasing tendency in the energy outline for enlarging electric field parameter values. The heat generation and eckert number parameter values are increased, resulting in an improved energy profile. The results of this simulation have the potential to contribute significantly to more advanced study and research in the fields of bioengineering and bio-nanofluid dynamics.
Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach
Patrice Koehl, Marc Delarue, Henri Orland
We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin bridge formalism, which constrains molecular trajectories to reach a prescribed final state within a finite time and yields an efficient low-temperature approximation of the exact bridge equation. To obtain physically meaningful protein transitions, we couple this formulation to a new coarse-grained potential combining a Go-like term that preserves native backbone geometry with a Rouse-type elastic energy term from polymer physics; we refer to the resulting approach as SIDE. We evaluate SIDE on several proteins undergoing large-scale conformational changes and compare its performance with established methods such as MinActionPath and EBDIMS. SIDE generates smooth, low-energy trajectories that maintain molecular geometry and frequently recover experimentally supported intermediate states. Although challenges remain for highly complex motions-largely due to the simplified coarse-grained potential-our results demonstrate that SIDE offers a powerful and computationally efficient strategy for modeling bio-molecular conformational transitions.
en
q-bio.BM, physics.bio-ph
Synthesis of new zwitterionic surfactants and investigation of their surface active and thermodynamic properties
Ahmed S. Mansour, M. M. Abo-Aly, S. A. Rizk
et al.
Abstract This study focused on the synthesis of six bio-based zwitterionic surfactants derived from oleic acid to assess their applicability in different petroleum fields. The final bi-zwitterionic surfactants were synthesized from oleic acid, utilizing the double bond and carboxylic group. Friedel–Crafts alkylation, sulfonation, chlorination, amidation, and quaternization were performed to synthesize six bi-zwitterionic surfactants. The bi-quaternary surfactants derived from benzene are represented by the general formula Bi Q 10, BOAS (Amide), with the symbols BE, BP, and BPh. In contrast, those derived from naphthalene are represented by Bi Q 10, NOAS (Amide), with the symbols NE, NP, and NPh. The structures of these surfactants were confirmed using FT-IR and H1-NMR techniques. The surface activity and thermodynamic properties of the synthesized surfactants were analyzed through surface tension measurements conducted at various temperatures (30, 40, 50, and 60°C). Additionally, CMC, γ CMC , π CMC , Γ max , A min, and Pc 20 were measured. The thermodynamic variables for micellization and adsorption were also measured. The structural effect of the obtained surfactants was assessed. The maximum value of the structural effect was 4.33 KJmol-1, corresponding to BE. The results indicated that the negative values of ΔGads were greater than the negative values of ΔGmic, indicating that these surfactants are absorbed in the interface prior to the formation of micelles. The more negative values of ΔGads suggest that these surfactants are strongly adsorbed onto solid particles, such as sands and rocks, indicating their potential utilization in oil production in different petroleum fields.
Insights into How Degradable Microplastics Enhance Cu<sup>2+</sup> Mobility in Soil Through Interfacial Interaction
Hongjia Peng, Bolun Yu, Zuhong Lin
et al.
The incomplete degradation of degradable plastics may pose potential ecological risks, as it can generate degradable microplastics (DMPs), especially when these DMPs coexist with heavy metals in soil. Taking petrochemical-based poly(butylene adipate-co-terephthalate) (PBAT) and bio-based polylactic acid (PLA) as representative DMPs, this study investigated how DMPs affect the adsorption–desorption behavior of Cu<sup>2+</sup> in soil and the underlying mechanisms via batch equilibrium experiments and characterization analyses. The experiments revealed that ion exchange (accounting for 33.6–34.3%), oxygen-containing functional group complexation, and electrostatic interactions were the primary adsorption driving forces, with chemical adsorption playing the main role. Compared to the soil, the PBAT and PLA had smaller specific surface areas and pore volumes, fewer oxygen-containing functional groups, and especially lacked O-metal functional groups. They can dilute soil, clog its pores, and cover its active sites. 1% DMPs significantly reduced the soil’s equilibrium adsorption capacity (Q<sub>e</sub>) (3.7–4.7%) and increased equilibrium desorption capacity (Q<sub>De</sub>) (1.7–2.6%), thereby increasing the mobility and ecological risk of Cu<sup>2+</sup>. PBAT and PLA had no significant difference in effects on the adsorption, but their specific mechanisms were somewhat distinct. Faced with the prevalent, worsening coexistence of DMPs and heavy metals in soil, these findings contribute to the ecological risk assessment of DMPs.
Digital Twin Calibration for Biological System-of-Systems: Cell Culture Manufacturing Process
Fuqiang Cheng, Wei Xie, Hua Zheng
Biomanufacturing innovation relies on an efficient Design of Experiments (DoEs) to optimize processes and product quality. Traditional DoE methods, ignoring the underlying bioprocessing mechanisms, often suffer from a lack of interpretability and sample efficiency. This limitation motivates us to create a new optimal learning approach for digital twin model calibration. In this study, we consider the cell culture process multi-scale mechanistic model, also known as Biological System-of-Systems (Bio-SoS). This model with a modular design, composed of sub-models, allows us to integrate data across various production processes. To calibrate the Bio-SoS digital twin, we evaluate the mean squared error of model prediction and develop a computational approach to quantify the impact of parameter estimation error of individual sub-models on the prediction accuracy of digital twin, which can guide sample-efficient and interpretable DoEs.
The concept of bio-economic mulching in droughty tropical agroecosystems and its trans-season effects on soil hydro-thermal regime and okra performance
Benedict Odinaka Okorie, Justina O. Obi, Geraldine U. Chioke
et al.
Mulching is an effective soil-water conservation technique in high-evaporative-demand tropical climates. Because of the drawbacks in bulk application of organic mulches, we introduce the concept of bio-economic mulching (BEM), a one-time low-rate application of organic mulch to improve soil productivity while sustaining economic viability. The study evaluated the effects of BEM (dry-grass mulching at 0, 2, 4, and 6 t ha–1) on soil hydrothermal properties of sandy-loam Ultisols using okra growth during 4–9 weeks after sowing in successive rainy-to-dry/partially rainfed season (PRS) and rainy/completely rainfed season (CRS). During the PRS, soil volumetric moisture content (q) increased (10.02%–25.50%), but soil temperature decreased (37.67–26.67°C) as BEM rate increased. A similar q trend (8.71%–18.37%) occurred during the CRS. Soil thermal conductivity (0.78to 4.88 W m–1 K–1), thermal diffusivity (3.95 × 10–7 to 35.97 × 10–7 m2 s–1), and heat flux (15.00 to 85.56 W m–2) generally decreased as q increased with BEM application rate particularly during the PRS; the reverse prevailed for volumetric heat capacity (1.33 × 106 to 2.25 × 106 J m–3 K–1). Okra plant height differed (BEM-6 > BEM-4 > BEM-2/BEM-0) in the PRS, but BEM-6 and BEM-4 gave the tallest and shortest plants, respectively in the CRS. Fruit yield was 1.8- and 9.5-fold higher in BEM-6 than BEM-4 in PRS and CRS, respectively. Mulch treatment-induced temporal variations in soil q influenced okra performance indices of plant height (r2 = 0.85) and total fresh fruit yield (r2 = 0.69). In droughty tropical environments, BEM implementation at 6 t ha−1 could engender soil hydrothermal regime favoring vegetable production beyond the ‘drier’ first season and even more pronouncedly in the second season.
Agriculture, Agriculture (General)
Recent Trend of Nanotechnology Applications to Improve Bio-accessibility of Lycopene by Nanocarrier: A Review
Mohammad Anwar Ul Alam, Mhamuda Khatun, Mohammad Arif Ul Alam
Lycopene, rich in red, yellow, or orange-colored fruits and vegetables, is the most potent antioxidant among the other carotenoids available in human blood plasma. It is evident that regular lycopene intake can prevent chronic diseases like cardiovascular diseases, type-2 diabetes, hypertension, kidney diseases and cancer. However, thermal processing, light, oxygen, and enzymes in gastrointestinal tract (GIT) compromise the bioaccessibility and bioavailability of lycopene ingested through diet. Nanoencapsulation provides a potential platform to prevent lycopene from light, air oxygen, thermal processing and enzymatic activity of the human digestive system. Physicochemical properties evidenced to be the potential indicator for determining the bioaccessibility of encapsulated bioactive compounds like lycopene. By manipulating the size or hydrodynamic diameter, zeta potential value or stability, polydispersity index or homogeneity and functional activity or retention of antioxidant properties observed to be the most prominent physicochemical properties to evaluate beneficial effect of implementation of nanotechnology on bioaccessibility study. Moreover, the molecular mechanism of the bioavailability of nanoparticles is not yet to be understood due to lack of comprehensive design to identify nanoparticles' behaviors if ingested through oral route as functional food ingredients. This review paper aims to study and leverage existing techniques about how nanotechnology can be used and verified to identify the bioaccessibility of lycopene before using it as a functional food ingredient for therapeutic treatments.
T(w)o patch or not t(w)o patch: A novel additional food model
Urvashi Verma, Aniket Banerjee, Rana D. Parshad
A number of top down bio-control models have been proposed where the introduced predators' efficacy is enhanced via the provision of additional food (AF). However, if the predator has a pest dependent monotone functional response, pest extinction is unattainable. In the current manuscript, we propose a model where a predator with pest dependent monotone functional response is introduced into a ``patch" such as a prairie strip with AF, and then disperses or drifts into a neighboring ``patch" such as a crop field, to target a pest. We show the pest extinction state is attainable in the crop field and can be globally attracting. The AF model with patch structure can eliminate predator explosion present therein and can keep pest densities lower than the classical top-down bio-control model. We provide the first proof of the global stability of the interior equilibrium for the classical AF model. We also observe ``patch-specific chaos" - the pest occupying the crop field can oscillate chaotically, while the pest in the prairie strip oscillates periodically. We discuss these results in light of bio-control strategies that utilize state-of-the-art farming practices such as prairie strips and drift and dispersal pressures driven by climate change.
A Novel Power-optimized CMOS sEMG Device with Ultra Low-noise integrated with ConvNet (VGG16) for Biomedical Applications
Ahmed Ayman - Mohamed Sabry
The needle bio-potential sensors for measuring muscle and brain activity need invasive surgical targeted muscle reinnervation (TMR) and a demanding process to maintain, but surface bio-potential sensors lack clear bio-signal reading (Signal-Interference). In this research, a novel power-optimized complementary metal-oxide-semiconductor (CMOS) Surface Electromyography (sEMG) is developed to improve the efficiency and quality of captured bio-signal for biomedical application: The early diagnosis of neurological disorders (Dystonia) and a novel compatible mind-controlled prosthetic leg with human daily activities. A novel sEMG composed of CMOS Op-Amp based PIC16F877A 8-bit CMOS Flash-based Microcontroller is utilized to minimize power consumption and data processing time. sEMG Circuit is implemented with developed analog filter along with infinite impulse response (IIR) digital filter via Fast Fourier Transform (FFT), Z-transform, and difference equations. The analysis shows a significant improvement of 169.2% noise-reduction in recorded EMG signal using developed digital filter compared to analog one according to numerical root mean square error (RMSE). Moreover, digital IIR was tested in two stages: algorithmic and real-world. As a result, IIR's algorithmic (MATLAB) and real-world RMSEs were 0.03616 and 0.05224, respectively. A notable advancement of 20.8% in data processing duration in EMG signal analysis. Optimizing VGG, AlexNet, and ResNet ConvNet as trained and tested on 15 public EEG (62-electrode) and 18 subjects' observed EMG data. The results indicate that VGG16-1D is 98.43% higher. During real testing, the accuracy was 95.8 +/- 4.6% for 16 subjects (6 Amputees-10 Dystonia). This study demonstrates the potential for sEMG, paving the way for biomedical applications.
Regulating the Hydrophobic Domain in Peptide-Catecholamine Coassembled Nanostructures for Fluorescence Enhancement
Ruoyang Zhao, Feng Gao, Maoyu Li
et al.
Hydrophobic domains provide specific microenvironment for essential functional activities in life. Herein, we studied how the coassembling of peptides with catecholamines regulate the hydrophobic domain-containing nanostructures for fluorescence enhancement. By peptide encoding and coassembling with catecholamines of different hydrophilicities, a series of hierarchical assembling systems were constructed. In combination with molecular dynamics simulation, we experimentally discovered the hydrophobic domain of chromophore microenvironment regulates the fluorescence of coassembled nanostructures. Our results shed light on the rational design of fluorescent bio-coassembled nanoprobes for biomedical applications.
Reprogramming Megakaryocytes for Controlled Release of Platelet-like Particles Carrying a Single-Chain Thromboxane A<sub>2</sub> Receptor-G-Protein Complex with Therapeutic Potential
Renzhong Lu, Yan Li, Anna Xu
et al.
In this study, we reported that novel single-chain fusion proteins linking thromboxane A<sub>2</sub> (TXA<sub>2</sub>) receptor (TP) to a selected G-protein α-subunit q (SC-TP-Gαq) or to α-subunit s (SC-TP-Gαs) could be stably expressed in megakaryocytes (MKs). We tested the MK-released platelet-linked particles (PLPs) to be used as a vehicle to deliver the overexpressed SC-TP-Gαq or the SC-TP-Gαs to regulate human platelet function. To understand how the single-chain TP-Gα fusion proteins could regulate opposite platelet activities by an identical ligand TXA<sub>2</sub>, we tested their dual functions—binding to ligands and directly linking to different signaling pathways within a single polypeptide chain—using a 3D structural model. The immature MKs were cultured and transfected with cDNAs constructed from structural models of the individual SC-TP-Gαq and SC-TP-Gαs, respectively. After transient expression was identified, the immature MKs stably expressing SC-TP-Gαq or SC-TP-Gαs (stable cell lines) were selected. The stable cell lines were induced into mature MKs which released PLPs. Western blot analysis confirmed that the released PLPs were carrying the recombinant SC-TP-Gαq or SC-TP-Gαs. Flow cytometry analysis showed that the PLPs carrying SC-TP-Gαq were able to perform the activity by promoting platelet aggregation. In contrast, PLPs carrying SC-TP-Gαs reversed Gq to Gs signaling to inhibit platelet aggregation. This is the first time demonstrating that SC-TP-Gαq and SC-TP-Gαs were successfully overexpressed in MK cells and released as PLPs with proper folding and programmed biological activities. This bio-engineering led to the formation of two sets of biologically active PLP forms mediating calcium and cAMP signaling, respectively. As a result, these PLPs are able to bind to identical endogenous TXA<sub>2</sub> with opposite activities, inhibiting and promoting platelet aggregation as reprogrammed for therapeutic process. Results also demonstrated that the nucleus-free PLPs could be used to deliver recombinant membrane-bound GPCRs to regulate cellular activity in general.
Removal of Cr6+ ions and mordant violet 40 dye from liquid media using Pterocladia capillacea red algae derived activated carbon-iron oxides
Soha Mahrous Ismail Mohamed, Eda Keleş Güner, Murat Yılmaz
et al.
Abstract In recent years, water pollution has become one of the most dangerous problems facing the world. Pollution of water with heavy metals and different dyes has caused many harmful effects on human health, living organisms and our environment. In this study, iron oxide nanomagnetic composite from Pterocladia Capillacea red algae-derived activated carbon (PCAC-IO) was synthesized by co-precipitation method using different iron salts and different base solutions. The synthesized nanocomposite was investigated with various characterization techniques such as FTIR, BET, SEM-EDX, TEM, XRD, and VSM. The obtained PCAC-IO adsorbent was used for Cr6+ ions and Mordant Violet 40 (MV40) dye removal. The adsorption mechanism of Cr6+ ions and MV40 dye on PCAC-IO was examined using several adsorption and kinetic isotherm models. Langmuir and Freundlich models were investigated using experimental data. Pseudo-first-order (PFO), Pseudo-second-order (PSO) and intraparticle diffusion models (IPDM) were applied to identify the adsorption mechanism. It has shown that the PSO kinetic model fits better with the experimental data obtained from PCAC-IO. This result can be interpreted as the adsorption of the adsorbate on the nanocomposite as chemical adsorption. The optimum conditions for maximum Cr6+ ions removal (96.88%) with PCAC-IO adsorbent occur at room temperature, 5 g L−1 adsorbent concentration, 100 mg L−1 initial pollutant concentration, pH 1 and at the end of 180 min, while maximum MV40 dye removal (99.76%), other conditions being the same, unlikely it occurred at pH 2.06 and after 45 min. The most suitable model for Cr6+ ions removal under the conditions of 1 L−1 g adsorbent concentration and 400 mg L−1 adsorbate concentration was Langmuir (Q max = 151.52 mg g−1), while for MV40 removal it was Freundlich (Q max = 303.03 mg g−1). We propose the use of activated carbon-supported iron oxide prepared from bio-waste material, especially from Pterocladia Capillacea red algae, as a promising adsorbent with high efficiency in the removal of Cr6+ ions and MV40 dye from aqueous media.
A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
Robert Haase, Elnaz Fazeli, David Legland
et al.
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the right platform, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.
Pursuit and Evasion Strategy of a Differential Game Based on Deep Reinforcement Learning
Can Xu, Yin Zhang, Weigang Wang
et al.
Since the emergence of deep neural network (DNN), it has achieved excellent performance in various research areas. As the combination of DNN and reinforcement learning, deep reinforcement learning (DRL) becomes a new paradigm for solving differential game problems. In this study, we build up a reinforcement learning environment and apply relevant DRL methods to a specific bio-inspired differential game problem: the dog sheep game. The dog sheep game environment is set on a circle where the dog chases down the sheep attempting to escape. According to some presuppositions, we are able to acquire the kinematic pursuit and evasion strategy. Next, this study implements the value-based deep Q network (DQN) model and the deep deterministic policy gradient (DDPG) model to the dog sheep game, attempting to endow the sheep the ability to escape successfully. To enhance the performance of the DQN model, this study brought up the reward mechanism with a time-out strategy and the game environment with an attenuation mechanism of the steering angle of sheep. These modifications effectively increase the probability of escape for the sheep. Furthermore, the DDPG model is adopted due to its continuous action space. Results show the modifications of the DQN model effectively increase the escape probabilities to the same level as the DDPG model. When it comes to the learning ability under various environment difficulties, the refined DQN and the DDPG models have bigger performance enhancement over the naive evasion model in harsh environments than in loose environments.
RETRACTED: Evaluation of SDS‐coated iron nanostructure on the gene expression of bio surfactant‐producing genes by Pseudomonas aeruginosa
Yaser Ahsani Arani, Zahra Noormohammadi, Behnam Rasekh
et al.
Abstract Bio surfactants are natural surfactants that induce emulsification, displacement, increased solubility, and mobility of hydrophobic organic compounds. In this study, the gene expression of biosurfactant production genes by Pseudomonas aeruginosa in the presence of sodium dodecyl sulfate coated iron nanostructure (Fe/SDS) were evaluated. Emulsification Index and Surface Tension reduction test to check stability and emulsification the rhamnolipid were done. Purification was evaluated using thin layer chromatography (TLC) and expression of rhlA, mvfR, lasR, rhlR genes was determined using q‐PCR technique. Binding of nanoparticles to bio surfactants was confirmed by TEM. The best emulsification index, was by the sample that exposed to 1 mg/L Fe/SDS nanoparticles for 2 days. Rhamnolipid produced in the presence of nanoparticles had an acceptable ability to reduce surface tension. The Rf (retention factor) value obtained was 0.63 by chromatography. q‐PCR results showed that the expression of rhlA, mvfR, lasR, rhlR genes was significantly increased in Fe/SDS treated cells, which indicates the significant positive effect (P < 0.05) of nanoparticles on biosurfactant production of treated cells. While, SDS and Fe alone were not affected significantly (P > 0.05) on the expression of these genes. Our findings indicated the importance of nanoparticles in increasing the expression of genes involved in the bio surfactant production pathway of Pseudomonas aeruginosa.
Evaluation of the Bio-Evolution Microsporidia generic and typing real-time PCR assays for the diagnosis of intestinal microsporidiosis
Moniot Maxime, Nourrisson Céline, Bonnin Virginie
et al.
Cases of intestinal microsporidiosis infection are underestimated and affect both immunocompromized and immunocompetent patients. Real-time PCR is superseding microscopic examination for its diagnosis in medical analysis laboratories. However, few manufacturers include microsporidia in their PCR panel for the diagnosis of infectious gastroenteritis. Here, we evaluated the performances of the real-time PCR assays microsporidia generic and microsporidia typing (Bio-Evolution, France) on the Rotor-Gene Q real-time PCR cycler (Qiagen, France). We included 45 negative and 44 positive stool samples for Enterocytozoon bieneusi (n = 34, with various genotypes), Encephalitozoon intestinalis (n = 4), Encephalitozoon hellem (n = 4), and Encephalitozoon cuniculi (n = 2). We also studied a four-year survey of an inter-laboratory quality control program including 9 centers that used this commercial assay. Sensitivity and specificity of the microsporidia generic assay were 86.4% and 93.3%, respectively. Encephalitozoon hellem and Encephalitozoon cuniculi were detected by the microsporidia generic PCR assay but not by the microsporidia typing PCR assay. These results were consistent with the results of the inter-laboratory quality control program. In conclusion, Bio-Evolution Real-time PCR assays are useful tools for intestinal microsporidiosis, but negative results for microsporidia typing assays require supplementary analyses to confirm E. hellem or E. cuniculi infections.
Infectious and parasitic diseases
Structural optimization of biohydrogen production: Impact of pretreatments on volatile fatty acids and biogas parameters
Mahmood Mahmoodi-Eshkaftakia, Gustavo Mockaitis
The present study aims to describe an innovative approach that enables the system to achieve high yielding for biohydrogen (bio-H$_2$) production using xylose as a by-product of lignocellulosic biomass processing. A hybrid optimization technique, structural modelling, desirability analysis, and genetic algorithm could determine the optimum input factors to maximize useful biogas parameters, especially bio-H$_2$ and CH$_4$. As found, the input factors (pretreatment, digestion time and biogas relative pressure) and volatile fatty acids (acetic acid, propionic acid and butyric acid) had indirectly and significantly impacted the bio-H$_2$ and desirability score. The pretreatment factor had the most effect on bio-H$_2$ and CH$_4$ production among the factors, and after that, were propionic acid and digestion time. The optimization method showed that the best pretreatment was acidic pretreatment, digestion time > 20 h, relative pressure in a range of 300-800 mbar, acetic acid in a range of 90-200 mg/L, propionic acid in a range of 20-150 mg/L, and butyric acid in a range of 250-420 mg/L. These values caused to produce H$_2$ > 10.2 mmol/L, CH$_4$ > 3.9 mmol/L, N$_2$ < 15.3 mmol/L, CO$_2$ < 19.5 mmol/L, total biogas > 0.31 L, produced biogas > 0.10 L, and accumulated biogas > 0.41 L.
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth
et al.
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically when large (bio-)chemical networks are considered where reactions are stereo-specific, rigorous techniques are inevitable. We present an approach using the right Cayley graph of a monoid in order to track atoms concurrently through sequences of reactions and predict their potential location in product molecules. This can not only be used to systematically build hypothesis or reject reaction mechanisms (we will use the ANRORC mechanism "Addition of the Nucleophile, Ring Opening, and Ring Closure" as an example), but also to infer naturally occurring subsystems of (bio-)chemical systems. Our results include the analysis of the carbon traces within the TCA cycle and infer subsystems based on projections of the right Cayley graph onto a set of relevant atoms.
A biologically plausible neural network for Slow Feature Analysis
David Lipshutz, Charlie Windolf, Siavash Golkar
et al.
Learning latent features from time series data is an important problem in both machine learning and brain function. One approach, called Slow Feature Analysis (SFA), leverages the slowness of many salient features relative to the rapidly varying input signals. Furthermore, when trained on naturalistic stimuli, SFA reproduces interesting properties of cells in the primary visual cortex and hippocampus, suggesting that the brain uses temporal slowness as a computational principle for learning latent features. However, despite the potential relevance of SFA for modeling brain function, there is currently no SFA algorithm with a biologically plausible neural network implementation, by which we mean an algorithm operates in the online setting and can be mapped onto a neural network with local synaptic updates. In this work, starting from an SFA objective, we derive an SFA algorithm, called Bio-SFA, with a biologically plausible neural network implementation. We validate Bio-SFA on naturalistic stimuli.
A Novel Tool for Visualization of Water Molecular Structure and Its Changes, Expressed on the Scale of Temperature Influence
Zoltan Kovacs, Bernhard Pollner, George Bazar
et al.
Aquaphotomics utilizes water-light interaction for in-depth exploration of water, its structure and role in aqueous and biologic systems. The aquagram, a major analytical tool of aquaphotomics, allows comparison of water molecular structures of different samples by comparing their respective absorbance spectral patterns. Temperature is the strongest perturbation of water changing almost all water species. To better interpret and understand spectral patterns, the objective of this work was to develop a novel, temperature-scaled aquagram that provides standardized information about changes in water molecular structure caused by solutes, with its effects translated to those which would have been caused by respective temperature changes. NIR spectra of Milli-Q water in the temperature range of 20–70 °C and aqueous solutions of potassium chloride in concentration range of 1 to 1000 mM were recorded to demonstrate the applicability of the proposed novel tool. The obtained results presented the influence of salt on the water molecular structure expressed as the equivalent effect of temperature in degrees of Celsius. The temperature-based aquagrams showed the well-known structure breaking and structure making effects of salts on water spectral pattern, for the first time presented in the terms of temperature influence on pure water. This new method enables comparison of spectral patterns providing a universal tool for evaluation of various bio-aqueous systems which can provide better insight into the system’s functionality.