ARTICLE | doi:10.20944/preprints202310.1558.v1
Subject: Physical Sciences, Biophysics Keywords: Computational haemodynamics; Intracranial aneurysms; Circle of Willis; Wall shear stress; Boundary conditions
Online: 24 October 2023 (17:32:53 CEST)
Haemodynamic simulations are increasingly used to study vascular diseases like Intracranial Aneurysms (IA) and to further develope treatment options. However, due to limited data, some aspects must rely on heuristics, especially at the simulation’s distal ends. In literature, Murray’s Law is often used to model the outflow split based on vessel cross-section area, but this poses challenges for the communicating arteries in the Circle of Willis (CoW). In this study, we contribute by assessing the impact of Murray’s Law in patient-specific geometries featuring IA at the posterior communication. We simulate different domain extensions, representing common modelling choices. We establish Full CoW simulations as a baseline to evaluate the effect of these modelling assumptions on haemodynamic indicators, focusing on IA growth and rupture-related factors like Wall Shear Stress (WSS) and Oscillatory Shear Index (OSI). Our findings reveal qualitative alterations in haemodynamics when not modeling posterior communication. Comparisons between computing the anterior circulation and computing the whole Circle of Willis reveal quantitative changes in WSS may reach up to 80%, highlighting the significance of modelling choices in assessing IA risks and treatment strategies.
ARTICLE | doi:10.20944/preprints202310.0074.v1
Subject: Physical Sciences, Biophysics Keywords: collagen; water; hydration; radius of gyration; SASA; hydrogen-bond; residence time
Online: 3 October 2023 (02:48:14 CEST)
Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer, of water molecules hydrogen-bonded to the backbone-carbonyl (bb-CO) oxygen atoms. This originates from the following observations. The radius of gyration attests that the PPG triplets are organized along a straight line, so that all triplets (excepting the ends) are equivalent. The solvent accessible surface area (SASA) for the bb-CO oxygens shows a repetitive regularity for every triplet. This leads to bb-CO⋯HOH occupancy following a similar regularity, similar also to the crystal-phase 0-2-1 water occupancy in the P-P-G triplet. The regularity is maintained in spite of the sub-nsec water exchange rate, because the bb-CO sites rarely remain vacant. The manifested ordered first-shell water molecules are expected to produce a cylindrical electrostatic potential around the peptide, that might guide cation diffusion in its vicinity.
REVIEW | doi:10.20944/preprints202309.2143.v1
Subject: Physical Sciences, Biophysics Keywords: Self-organisation; prediction; symbols; observation; ritualisation; information; models; causality; decision; activity; homoclinic orbit
Online: 30 September 2023 (05:36:59 CEST)
Living organisms are active open systems far from thermodynamic equilibrium. The ability to behave actively corresponds to dynamical metastability: minor but supercritical internal or external effects may trigger major substantial actions such as gross mechanical motion, dissipating internally accumulated energy reserves. Gaining selective advantage from beneficial use of activity requires a consistent combination of sensual perception, memorised experience, statistical or causal prediction models, and resulting favourable decisions on actions. This information processing chain originated from mere physical interaction processes prior to life, here denoted as structural information exchange. From there, the self-organised transition to symbolic information processing marks the beginning of life, evolving by novel purposivity of trial-and-error feedback and accumulation of symbolic information. The emergence of symbols and prediction models can be described as a ritualisation transition, a symmetry-breaking kinetic phase transition of the 2nd kind previously known from behavioural biology. The related new symmetry is the neutrally stable arbitrariness, conventionality or code invariance of symbols with respect to their meaning. The meaning of such symbols is given by the structural effect they ultimately unleash, directly or indirectly, by deciding on which actions to take. The early genetic code represents the first symbols. The genetically inherited symbolic information is the first prediction model for activities sufficient for survival under the condition of environmental continuity, sometimes understood as a “final causality” property of the model.
REVIEW | doi:10.20944/preprints202309.2094.v1
Subject: Physical Sciences, Biophysics Keywords: nonequilibrium thermodynamics; entropy production rate; Lyapunov function; complexity; extremal principle; fractal dimension; biological phase transitions
Online: 29 September 2023 (09:36:32 CEST)
An overview of the link between nonequilibrium thermodynamics and complexity theory is offered. It is shown how the rate of entropy production can be quantified through the spectrum of the Lyapunov exponents. It was shown how the entropy production per unit of time meets the necessary and sufficient conditions to be a Lyapunov function and constitutes per se an extremal principle. The entropy production fractal dimension conjecture was established. It is shown how the rate of entropy production as a non-extremal criterion represents an alternative way of sensitivity analysis of differential equations. Finally, an extension to biophysical-chemical systems, on the one hand, the use of the dissipation function is shown, as a thermodynamic potential out of equilibrium, in the characterization of biological phase transitions. On the other hand, it was evidenced how the rate of entropy production represents a physical quantity to evaluate the complexity and robustness of cancer.
ARTICLE | doi:10.20944/preprints202309.2016.v1
Subject: Physical Sciences, Biophysics Keywords: X-ray; DNA; X-ray diffraction; attosecond pulse; USP; Nick(DNA); bending DNA.
Online: 29 September 2023 (04:55:17 CEST)
It is well known that X-ray crystallography is based on X-ray diffraction (XRD) by atoms and molecules. The diffraction pattern arises as a result of scattering of incident radiation, which makes it possible to determine the structure of the scattering substance. With the advent of ultrashort radiation sources, the theory and interpretation of X-ray diffraction analysis remained the same. This work shows that when an attosecond laser pulse is scattered on a DNA molecule, including during its nicking and bending, the pulse duration is an important characteristic of the scattering. In this case, the diffraction pattern changes significantly compared to the previously known scattering theory. The results obtained must be used in XRD theory to study DNA structures, their mutations and damage, since the previously known theory can produce large errors and, therefore, the DNA structure can be “deciphered” incorrectly.
ARTICLE | doi:10.20944/preprints202309.1225.v1
Subject: Physical Sciences, Biophysics Keywords: genetics; molecular biology; biophysics; quantum mechanics
Online: 19 September 2023 (05:18:03 CEST)
This study investigates the impact of temperature-induced quantum proton tunneling probability on DNA amplification during polymerase chain reactions (PCR). Using a simulation model based on a Gaussian wavefunction and finite-difference time-domain method, quantum tunneling of protons across square potential barriers is examined. The results unveil consistent probability distributions for quantum tunneling across various PCR temperatures, with distinct oscillation patterns emerging post-barrier crossing. Acknowledging limitations in initial conditions due to temperature-dependent proton energy, the study highlights the need for refined models and experimental validation. These findings accentuate the potential interplay between quantum mechanics and biological systems, prompting further research to understand quantum tunnelling’s comprehensive effect on genetic variations and molecular processes.
ARTICLE | doi:10.20944/preprints202309.0963.v1
Subject: Physical Sciences, Biophysics Keywords: edge of chaos; intermittency; difference mapping; Lyapunov exponent; consciousness; thesaurus; memristor; forth phase of water; proton; Grotthuss mechanism; gap junctions; excitation; inhibition; neuron; brain; fields of hippocampus
Online: 14 September 2023 (11:16:53 CEST)
Consciousness is a special type of interaction between subjects exchanging by lingua quanta (phonemes). A set of lingua quanta composes a thesaurus placed on the edge of chaos. Its library is a memory, modification of which is due to tuning of memristive neural elements scattered in the brain volume. The memristive neural model takes into consideration two types of neurons - excitatory and inhibitory and the current leakage, all at the body temperature, T = 309 K. At such temperatures only heavy ions like hydrogen ions - protons can pass robustly through the water medium of the brain. The robust ion transport is proton water wires supported by the Grotthuss mechanism. Final aims of the ions are the gap junctions (electric synapses) linking nearest neurons. Following these observations, a model of excitable nervous tissue is constructed. Namely, a difference mapping on the basis of sigmoid curves can reproduce chaotic modes of neural activity proved by positive values of the Lyapunov exponent. The edge of chaos is placed near the bifurcation boundary dividing the chaos and the periodic convulsive activity typical at the epileptic discharges. In this region the self-sustained spiral waves occur. An intermittent activity of the competing excitatory and inhibitory neurons is observed on the edge of chaos. The intermittent electrical activity of neural tissues is demonstrated by records both from different literature issues and records made by the author together with DR. A. Dudkin on slices of CA1 field of the hippocampus.
REVIEW | doi:10.20944/preprints202308.2176.v1
Subject: Physical Sciences, Biophysics Keywords: Liquid biopsy; electrochemical sensors; Lab On Chip; miniaturization; sensors integration; microfabrication
Online: 31 August 2023 (10:40:48 CEST)
Screening and early diagnosis of diseases are crucial for a patient's treatment to be successful and to improve their survival rate, especially in cancer. The development of non-invasive analytical methods able to detect biomarkers of pathologies is a critical point to define a successful treat-ment and a good outcome. This study extensively reviews electrochemical methods used for the development of biosensors in liquid biopsy, owing to their ability to provide rapid response, pre-cise detection, and low detection limits. We also discuss new developments in electrochemical biosensors, which can improve the specificity and sensitivity of standard analytical procedures. Electrochemical biosensors demonstrate remarkable sensitivity in detecting minute quantities of analytes, encompassing proteins, nucleic acids, and circulating tumor cells, even within challeng-ing matrices such as urine, serum, blood, and various other body fluids. Among the various de-tection techniques used for the detection of cancer biomarkers, even in the picogram range, volt-ammetric sensors are deeply discussed in this review because of their advantages and technical characteristics. This widespread utilization stems from their ability to facilitate quantitative de-tection of ions and molecules with exceptional precision. The comparison of each electrochemical technique is discussed to provide the selection of appropriate analytical methods.
ARTICLE | doi:10.20944/preprints202308.0804.v1
Subject: Physical Sciences, Biophysics Keywords: Sensorimotor Integration; Spinal muscle atrophy; cognition; Fitts’s Law; Motor; Sensory
Online: 10 August 2023 (03:36:20 CEST)
Previous studies have found that individuals with limited motor capabilities due to acquired neurological injury (e.g., spinal cord injury and stroke) can make accurate action possibility judgements for neurologically healthy individuals. Previous studies have shown that people with limited motor capabilities may rely on previous motor experience (i.e., pre-injury) when making action possibility judgments for others. In the present study, we examined whether having severely limited previous motor experience from birth, as a consequence of spinal muscle atrophy (SMA), alters the action possibility judgments made for neurologically healthy individuals. Participants with SMA and Neurologically Healthy (NH) sex- and age-matched controls performed a perceptual-motor judgment task using the Fitts’s law paradigm (see Fitts, 1954). Participants observed apparent motion videos of reciprocal aiming movements with varying indices of difficulty (ID, see: Manson et al., 2014). For each movement, participants predicted the shortest movement time (MT) at which a neurologically healthy young adult could perform the task while maintaining accuracy. Between-group comparisons revealed that participants with SMA predicted significantly longer MTs compared to controls. Regression analyses revealed that predicted MTs of both NH and SMA participants exhibited a Fitts’s law relationship (i.e., the predicted MTs significantly increased as movement difficulty increased). A supplementary analysis on the SMA group revealed no differences in predicted MTs between the participants with some and no motor function as assessed by the SMA health index. Overall, these results provide evidence that participants with SMA who have limited or no motor experience may make more conservative action possibility judgments for others. Critically, our finding that the pattern of action possibility judgements (e.g., the slopes of the regression lines) were not different between SMA and NH groups provides evidence that limited previous motor experience may not completely impair action possibility judgements.
ARTICLE | doi:10.20944/preprints202308.0305.v1
Subject: Physical Sciences, Biophysics Keywords: ovarian cancer; lysophosphatidic acid; gelsolin; actin; lipid-protein interaction; predictive molecular modelling
Online: 3 August 2023 (10:07:10 CEST)
Lysophosphatidic acid (LPA) is a promising biomarker candidate to screen for ovarian cancer (OC) and potentially stratify and treat patients according to disease stage. LPA is known to target actin-binding protein gelsolin that is a key regulator of actin filament assembly. Previous studies have shown that the phosphate headgroup of LPA alone is inadequate to bind to the short chain of amino acids in gelsolin known as the PIP2-binding domain. Thus, the molecular-level detail of the mechanism of LPA binding is poorly understood. Here, we model LPA binding to the PIP2-binding domain of gelsolin in the gelsolin-actin complex through extensive ten microsecond atomistic molecular dynamics (MD) simulations. We predict that LPA binding causes a local conformational rearrangement due to LPA interactions with both gelsolin and actin residues. These conformational changes are a result of the amphipathic nature of LPA, where the anionic phosphate, polar glycerol and ester groups, and lipophilic aliphatic tail mediate LPA binding via charged electrostatic, hydrogen bonding, and van der Waals interactions. The negatively-charged LPA headgroup binds to the PIP2-binding domain of gelsolin-actin while its hydrophobic tail is inserted into actin, creating a strong LPA-insertion pocket that weakens the gelsolin–actin interface. The computed structure, dynamics, and energetics of the ternary gelsolin–LPA–actin complex confirms that a quantitative OC assay is possible based on LPA-triggered actin release from the gelsolin-actin complex.
ARTICLE | doi:10.20944/preprints202307.1476.v1
Subject: Physical Sciences, Biophysics Keywords: COVID-19 mathematical model; Vaccination; Stochastic Asymptotic stability; Legendre-Gauss-Lobatto points; Spectral Method
Online: 21 July 2023 (07:13:53 CEST)
Coronavirus disease 2019 (COVID-19) is a high contagious respiratory infectious disease that has afiected millions of people worldwide. Initially, basic public health measures were implemented to control specially the spread of such virus. However, vaccination has emerged as a highly efiective strategy in combating COVID-19 and reducing its transmission. Several efiective and safe vaccines have been approved to prevent the inadvertent spread of the disease. In this study, a modeling approach is used to analyze the impact of these vaccines on the dynamics of COVID-19. By applying a higher-order numerical method, the model is solved based on reported cases in Pakistan. A spectral method is employed for the numerical solution, and the model is simulated to assess the efiects of vaccination. The Next-generation method is used to calculate the threshold quantity, known as R0, which indicates the potential for disease transmission. The study also includes a detailed stability analysis, examining the invariance properties of the model solution and discussing equilibrium points and their stability in disease-free and endemic states. Furthermore, the study presents graphical representations of the influence of special parameters on the dynamics of the pandemic.
ARTICLE | doi:10.20944/preprints202307.0983.v1
Subject: Physical Sciences, Biophysics Keywords: entropy; DNA; biomolecules; polyelectrolyte; fluctuations; charge inversion; correlations; field theory; one-loop order
Online: 14 July 2023 (08:18:04 CEST)
The entropy and charge distributions have been calculated for a simple model of polyelectrolytes attached to the surface of DNA using a field-theoretic method that includes fluctuations to the lowest one-loop order beyond mean-field theory. Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. In our model, the condensed polyelectrolytes are taken to be doubly charged dimers of length comparable to the distance between sites along the phosphate chains. Within this lattice-gas model, each adsorption site is assumed to have either a vacancy or a positively-charged dimer attached with the dimer oriented either parallel or perpendicular to the double helix DNA chain. We find that the inclusion of the fluctuation terms decreases the entropy by ∼50% in the weak binding regime. There, the bound dimer concentration is low because the dimers are repelled from the DNA molecule, which competes with the chemical potential driving them from the solution to the DNA surface. Surprisingly, this decrease in entropy due to correlations is so significant that it overcompensates for the entropy increase at the mean field level, so that the total entropy is even lower than in the absence of interactions between lattice sites. As a bonus, we present a transparent exposition of the methods used that could be useful to students and others wishing to use this formulation to extend this calculation to more realistic models.
ARTICLE | doi:10.20944/preprints202307.0582.v1
Subject: Physical Sciences, Biophysics Keywords: inhomogeneous spontaneous curvature; catenoidal necks; stress on curved fluid membranes
Online: 10 July 2023 (11:14:31 CEST)
The mechanical effects of membrane compositional inhomogeneities are analyzed in a process analogous of neck formation in cellular membranes. We cast on the Canham-Helfrich model of fluid membranes with both the spontaneous curvature and the surface tension being non-homogeneous functions along the cell membrane. The inhomogeneous distribution is determined by the equilibrium mechanical equations and the boundary conditions as considered in the axisymmetric setting compatible with the necking process. To establish the role played by mechanical inhomogeneity, we focus on the catenoid, a surface of zero mean curvature. Analytic solutions are shown to exist for the spontaneous curvature and the constrictive forces in terms of the border-radii. Our theoretical analysis shows that the inhomogeneous distribution of spontaneous curvature in a mosaic-like neck constrictional forces potentially contributing to the membrane scission under minimized work in living cells.
ARTICLE | doi:10.20944/preprints202307.0134.v1
Subject: Physical Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; epidemiology; lattice simulation; infection diffusion; epidemics; control measures
Online: 4 July 2023 (03:58:33 CEST)
Our aim is to provide an insight of the procedures and the dynamics that lead the spread of contagious diseases through populations. Our simulation tool can increase our understanding on the spatial parameters which affect the diffusion of a virus. SIR models are based on the hypothesis that populations are “well mixed”. Our model constitutes an attempt to focus on the effects of the specific distribution of the initially infected individuals through the population and provide insights, considering the stochasticity of the transmission process. For this purpose, we represent the population using a square lattice of nodes. Each node represents an individual that may or may not carry the virus. Nodes that carry the virus can only transfer it to susceptible neighboring nodes. This important revision of the common SIR model provides a very realistic property: the same number of initially infected individuals can lead to multiple paths, depending on their initial distribution in the lattice. This property creates better predictions and probable scenarios to construct a probability function and appropriate confidence intervals. Finally, this structure permits realistic visualizations of the results to understand the procedure of contagion and spread of a disease and the effects of any measures applied.
ARTICLE | doi:10.20944/preprints202306.1319.v1
Subject: Physical Sciences, Biophysics Keywords: urine analysis; digital holographic microscopy bacteria detection; urinary tract infection; biofluid sample screening
Online: 19 June 2023 (08:24:09 CEST)
Urinary tract infections are among the most frequent infectious diseases and require screening of a great amount of urine samples from patients. However, a high percentage of samples results as negative after urine culture plate test (CPT), demanding a simple and fast preliminary technique to screen out the negative samples. We propose a digital holographic microscopy (DHM) method to inspect fresh urine samples flowing in a glass capillary for 3 minutes, recording holograms at 2 frames per second. After digital reconstruction, bacteria, white and red blood cells, epithelial cells and crystals were identified and counted and the samples were classified as negative or positive according to clinical cutoff values. Taking CPT as reference, we processed 180 urine samples and compared the results with those of urine flow cytometry (UFC). Using standard evaluation metrics for our screening test, we found similar performance for DHM and UFC, indicating DHM as a suitable and fast screening technique retaining several advantages. As a benefit of DHM, the technique is label-free and does not require sample preparation. Moreover, the phase and amplitude images of the cells and other particles present in urine are digitally recorded and can serve for further investigation afterwards.
ARTICLE | doi:10.20944/preprints202306.0676.v1
Subject: Physical Sciences, Biophysics Keywords: Trastuzumab; Pertuzumab; HER2; Binding Free Energy; PRODIGY; Size Exclusion Chromatography
Online: 9 June 2023 (07:01:32 CEST)
The binding affinity of trastuzumab and pertuzumab to HER2 has been studied using both experimental and in-silico methods. The experiments were conducted using the antibodies in their complete IgG form, as used in clinical therapy, and the extracellular domain of the HER2 protein in solution. This approach provides a precise, reproducible, and reliable view of the interaction between them in physiological conditions. Dynamic light scattering and size exclusion chromatography coupled with tetra detection were utilized to characterize the protein complexes, measure their concentrations, and calculate the equilibrium free binding energy, ΔGbind. In addition, PRODIGY, a QSAR-like model with excellent predictive ability, was employed to obtain in-silico ΔGbind estimations. The results obtained indicate that pertuzumab exhibits a slightly higher binding affinity to HER2 than trastuzumab. The difference in binding affinity was explained based on the contribution of the different interfacial contact (IC) descriptors to the ΔGbind value estimated by the PRODIGY model. Furthermore, experiments revealed that the pertuzumab IgG antibody binds preferentially to two HER2 proteins, one per Fab fragment, while trastuzumab mainly forms a monovalent complex. This finding was interpreted based on a geometrical model that identified steric crowding in the trastuzumab-HER2 complex as compared to the pertuzumab-HER2 complex.
ARTICLE | doi:10.20944/preprints202305.1176.v1
Subject: Physical Sciences, Biophysics Keywords: origin of life; evolution; disspative structuring; prebiotic chemistry; abiogenisis; adenine; biosphere; natural selection
Online: 17 May 2023 (03:47:07 CEST)
Evolutionary theory suggests that the origin, persistence, and evolution of biology is driven by the “natural selection” of characteristics improving the differential reproductive success of the organism in the given environment. The theory, however, lacks physical foundation, and, therefore, at best, can only be considered a heuristic narrative, of some utility for assimilating the biological and paleontological data at the level of the organism. On deeper analysis, it becomes apparent that this narrative is plagued with problems and paradoxes. Alternatively, non-equilibrium thermodynamic theory, derived from physical law, provides a physical foundation for describing material interaction with its environment at all scales. Here we describe a “natural thermodynamic selection” of characteristics of structures (or processes), based stochastically on increases in the global rate of dissipation of the prevailing solar spectrum. The different mechanisms of thermodynamic selection are delineated for the different biotic-abiotic levels, from the molecular level at the origin of life, up to the level of the present biosphere with non-linear coupling of biotic and abiotic processes. At the levels of the organism and the biosphere, the non-equilibrium thermodynamic description of evolution resembles, respectively, Darwinian and Gaia descriptions, although the underlying mechanisms and the objective function of selection are fundamentally very different.
REVIEW | doi:10.20944/preprints202305.0232.v1
Subject: Physical Sciences, Biophysics Keywords: Non-Ionizing Radiation; Electromagnetic Radiation; Health; UV Solar radiation; Nigeria
Online: 4 May 2023 (08:20:47 CEST)
The emergence of Non-Ionizing Radiation (NIR) has stimulated the growth and advancement of technological civilization. NIR is ubiquitous; it has helped improve all fields and even deepened democratic processes through the transfer of data and electronic transmission of results etc. A breathtaking part of NIR is its recent application in the treatment of adverse health effects through radiofrequency ablation, phototherapy, etc. as summarized in Table 1. The benefits of NIR are enormous, however, technological civilization has not come without a cost; some of the adverse health effects associated with NIR include skin cancers, sleep disorders, photo-aging, etc. as summarized in Table 2. Therefore, with the rapid and sporadic increase in the sources of NIR from Natural and Artificial sources including fossil fuel burning, Starlink technology, mobile phones, mobile base antennas, etc., background radiation is expected to rise beyond the exposure limit leading to health illnesses. Intrinsically, there is a dare need to marry concerns that evolve with this growth. Hence, this review article aims to congregate the health hazards associated with NIR and the state-of-the-art applications of NIR in medicine and the health sector in Nigeria being a developing country. Part of our recommendations is that the government at all levels should set up enforcement agencies and policies to drive strict adherence to NIR as provided by ICNIRP; frequent-periodic assessments of background radiation in public places should be carried out due to the increasing sources. In addition, further research is needed to ascertain the health hazard from emerging sources of NIR like Starlink technology and to substantiate findings of non-thermal effects.
ARTICLE | doi:10.20944/preprints202304.0938.v1
Subject: Physical Sciences, Biophysics Keywords: light-harvesting antenna; phycobilisomes; time-resolved spectroscopy; energy transfer
Online: 26 April 2023 (03:23:40 CEST)
The phycobilisomes (PBS) of cyanobacteria and red algae are the primary light-harvesting an-tennas, absorbing solar energy and transporting it to photosynthetic reaction centres with ex-traordinary efficiency and rate. The mechanism of energy transfer in PBS should be investigated in conjunction with biological structural information, as the functions of proteins result from structures. Here, we report the energy transfer study in PBS from a thermophilic cyanobacte-rium Thermosynechococcus vulcanus NIES 2134 (T. 2134), with the Cryo-EM model resolved at near-atomic-resolution recently. The time-resolved fluorescence spectroscopy of PBS with the sub-picosecond resolution was discovered at 77K. Deconvolution of the fluorescence decay curve was then used to reveal the energy transfer channels and the associated transfer rates. Expert for the fluorescence lifetimes of terminal emitters, four time-components, i.e., 9 ps, 13 ps, 23 ps, and 55 ps, were recognised in the energy transfer in PBS. The energy transfer dynamics in PBS were further analysed by combining the cryo-EM structure and the spectral property. The findings aid our understanding of the energy transfer mechanisms in PBS.
ARTICLE | doi:10.20944/preprints202301.0208.v1
Subject: Physical Sciences, Biophysics Keywords: Deep belief network; Diabetes; Prediction; Risk Factors; Deep Learning
Online: 12 January 2023 (03:54:15 CET)
Diabetes mellitus is a popular life-threatening disease and patients may gradually have started suffering from other diabetes-causing diseases such as heart attacks, stroke, hypertension, blurry vision, blindness, foot ulcer, amputation, kidney damage and other organ failures before diagnosis. Early detection can help reduce the fatality of this disease. Deep learning models have proven very useful in disease detection and computer-aided diagnosis. In this work, we proposed a deep unsupervised machine learning model for early detection of diabetes using voting ensemble feature selection and deep belief neural networks (DBN). Dataset was obtained from an online repository containing responses of prediagnosed patients to direct questionnaires administered in Sylhet Diabetes Hospital in Sylhet, Bangladesh. The dataset was preprocessed and preprocessed. Features were reduced using the ensemble feature selector. The DBN model was pretrained and tuned to obtain optimal performance. The model was also compared with other models with no multiple hidden layers. The DBN performed at its relative best with F1-measure, precision and recall of 1.00, 0.92 and 1.00 respectively. We conclude that DBN is a useful tool for an unsupervised early prediction of Type II diabetes mellitus.
ARTICLE | doi:10.20944/preprints202301.0158.v1
Subject: Physical Sciences, Biophysics Keywords: subtalar joint instability; chronic ankle instability; footprint osteoarthritis
Online: 9 January 2023 (09:22:22 CET)
This study aimed to clarify the relationship between the joint and ligament structures of the subtalar joint and degeneration of the subtalar articular facet. We examined 50 feet from 25 Japanese cadavers. The number of articular facets, joint congruence, and intersecting angle were measured for the joint structure of the subtalar joint, and the footprint areas of the ligament attachments of the cervical ligament, interosseous talocalcaneal ligament (ITCL), and anterior capsular ligament were measured for the ligament structure. Also, subtalar joint facets were classified into Degeneration (+) and (-) groups according to degeneration of the talus and calcaneus. No significant relationship was identified between the joint structure of the subtalar joint and degeneration of the subtalar articular facet. In contrast, footprint area of the ITCL was significantly higher in the Degeneration (+) group than in the Degeneration (-) group for the subtalar joint facet. These results suggest that the joint structure of the subtalar joint may not affect degeneration of the subtalar articular facet. Degeneration of the subtalar articular facet may be related to the size of the ITCL.
ARTICLE | doi:10.20944/preprints202301.0146.v1
Subject: Physical Sciences, Biophysics Keywords: menstrual cycle; mechanical properties; stiffness; estradiol; musculotendon complex
Online: 9 January 2023 (06:50:28 CET)
The purpose of this study was to determine changes in the mechanical properties of the thigh and lower leg musculature during the early follicular and ovulatory phases. Subjects were 15 female university students with normal menstrual cycles. The early follicular and ovulatory phases were estimated by the basal body temperature method, ovulation kits, and salivary estradiol concentration measurement. The MyotonPRO digital palpation device (Myoton AS, Tallinn, Estonia) was used to measure muscle and tendon stiffness in the early follicular and ovulatory phases. Measurement sites were the rectus femoris (RF), vastus medialis (VM), patellar tendon (PT), medial head of gastrocnemius, soleus, and Achilles tendon. No significant differences in stiffness of all muscle tendons were identified between the early follicular and ovulatory phases. In the ovulatory phase, a significant positive correlation was seen between stiffness of RF and PT, and between stiffness of VM and PT. These results suggest that the stiffness of muscles and tendons of anterior sites of the thigh and posterior sites of the lower leg may not change between the early follicular and ovulatory phases. During the ovulatory phase, tendons may also be stiffer in individuals with stiffer anterior thigh muscles.
ARTICLE | doi:10.20944/preprints202210.0344.v1
Subject: Physical Sciences, Biophysics Keywords: X-ray scattering; DNA; RNA; X-ray diffraction; ultrashort pulse; trinucleotides; CCG; CGG; CAG; CUG
Online: 24 October 2022 (03:08:05 CEST)
X-ray diffraction (XRD) analysis of complex poly-atomic systems, especially of biomolecules, using ultra-short laser pulses (USP), is currently one of the most important fields of modern physics. The basis for interpreting and "deciphering" experimental data is the well-known theory of X-ray scattering, where the main parameter of USPs - its duration - is not taken into account. In the present work it is shown that for scattering of attosecond USPs on DNA and RNA trinucleotides the pulse length is the most important scattering parameter. In this case the diffraction pattern significantly changes with respect to the previously known scattering theory. The results obtained are extremely important in XRD when using attosecond pulses to study trinucleotides of DNA and RNA because using the previously known scattering theory which does not take into account the duration of USPs one can not correctly interpret and therefore "decode" DNA and RNA structures.
ARTICLE | doi:10.20944/preprints202210.0285.v1
Subject: Physical Sciences, Biophysics Keywords: Botulinum toxin; bladder hypertrophy; spinal cord injury
Online: 19 October 2022 (11:08:17 CEST)
Following spinal cord injury (SCI), pathological reflexes develop that result in altered bladder function and sphincter dis-coordination, with accompanying changes in the detrusor. Bladder chemodenervation is known to ablate the pathological reflexes, but the resultant effects on the bladder tissue are poorly defined. In a rodent model of contusion SCI, we examined the effect of early bladder chemodenervation with botulinum toxin A (BoNT-A) on bladder histopathology and collagen deposition. Adult female Long Evans rats were given a severe contusion SCI at spi-nal level T9. The SCI rats immediately underwent open laparotomy and received detrusor injec-tions of either BoNT-A (10 U/animal) or saline. At 8 weeks post injury, the bladders were col-lected, weighed, and examined histologically. BoNT-A injected bladders of SCI rats (SCI-BoNT-A) weighed significantly less than saline injected bladders of SCI rats (SCI-saline) (241 ± 25 mg vs. 183 ± 42 mg; p<0.05). Histological analyses showed that SCI resulted in significantly thicker bladder walls due to detrusor hypertrophy and fibrosis compared to bladders from uninjured animals (339 ± 89.0 m vs. 193 ± 47.9 m; p<0.0001). SCI-BoNT-A animals had significantly thinner bladder walls compared to SCI-saline animals (202 ± 55.4 m vs. 339 ± 89.0 m; p<0.0001). SCI-BoNT-A animals had collagen organization in the bladder walls similar to that of uninjured animals. Detrusor chemodenervation soon after SCI appears to preserve bladder tissue integrity, by reducing the development of detrusor fibrosis and hypertrophy associated with SCI.
REVIEW | doi:10.20944/preprints202208.0366.v1
Subject: Physical Sciences, Biophysics Keywords: Curvature proteins; Membrane Remodelling; Protein-protein interactions; Mesoscopic Modeling; Backmapping and molecular reconstruction
Online: 22 August 2022 (03:20:01 CEST)
Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles membrane morphology. Due to the various ex- perimental constraints, including the resolution limits of imaging techniques, it is non-trivial to accurately elucidate interactions among the various components involved in membrane deformation. The spatial and temporal scales of the systems also make it formidable to investigate them using simulations with molecular details. Interestingly, mechanics-based mesoscopic models have been used with great success in recapitulating the membrane defor- mations observed in experiments. In this review, we collate together and discuss the various mechanics based mesoscopic models for protein-mediated membrane deformation studies. In particular, we provide an elaborate description of a mesoscopic model where the membrane is modeled as a triangulated sheet and proteins are represented as either nematics or fila- ments. This representation allows us to explore the various aspects of protein-protein and protein-membrane interactions as well as examine the underlying mechanistic pathways for emergent behavior such as curvature-mediated protein localization and membrane deforma- tion. We also put forward current efforts in the field towards back-mapping these mesoscopic models to finer-grained particle based models - a framework that could be used to explore how molecular interactions propagate to physical scales and vice-versa. We end the review with an integrative-modeling based road map where experimental imaging micrograph and biochemical data are combined with mesoscopic and molecular simulations methods in a theoretically consistent manner to faithfully recapitulate the multiple length and time scales in the membrane remodeling processes.
ARTICLE | doi:10.20944/preprints202208.0107.v1
Subject: Physical Sciences, Biophysics Keywords: biology; symmetry; asymmetry; periodic ordering; aperiodic ordering; Curie principle; information; Landauer principle; continuous measure of symmetry; Shannon measure of symmetry.
Online: 4 August 2022 (08:54:04 CEST)
Physical roots, exemplifications and consequences of periodic and aperiodic ordering (represented by Fibonacci series) in biological systems are discussed. The role and physical and biological roots of symmetry and asymmetry appearing in biological patterns is addressed. Generalization of the Curie-Neumann Principle as applied to biological objects is presented, briefly summarized as: “asymmetry is what creates a biological phenomenon”. The “up-bottom approach” and “bottom up” approaches to the explanation of symmetry in organisms are presented in detail. The “up-bottom approach”, implies that the symmetry of the biological structure follows the symmetry of media in which this structure is functioning; the “bottom-up” approach, in turn, adopt that the symmetry of biological structures emerges from the symmetry of molecules constituting the structure. A diversity of mathematical measures applicable for quantification of ordering in biological patterns is introduced. The continuous, Shannon and Voronoi measures of symmetry/ordering and their application to biology objects are addressed. The fine structure of the notion of “ordering” is discussed. Informational/algorithmic roots of ordering inherent for the biological systems are considered. Ordered/symmetrical patterns provide economy of biological information, necessary for algorithmic description of a biological entity. Application of the Landauer principle bridging physics and theory of information to the biological systems is discussed.
ARTICLE | doi:10.20944/preprints202205.0040.v1
Subject: Physical Sciences, Biophysics Keywords: jump header shooting; soccer, trunk muscle activity; stabilization exercise
Online: 5 May 2022 (12:38:08 CEST)
Background: This study aimed to clarify trunk muscle activity during jump header shooting and examine the immediate effects of trunk stabilization exercises on trunk muscle activity. Methods: Nineteen male college students who had played soccer in junior high and high school clubs and youth sports teams for over 5 years were assigned to either the trunk stabilization exercise group (n = 10) or the control group (n = 9). Muscle activity during jump header shooting was measured before and after intervention. The intervention in the trunk stabilization exercise group was trunk muscle training, whereas that in the control group was sitting. The phases of jump header shooting and the effects of the interventions were compared. Results: The internal oblique activity during the push-off phase and early floating phase was significantly greater than that during the late floating phase. The muscle activity of the internal oblique increased from the push-off phase, prior to the increase in muscle activity of the rectus abdominis and external oblique, whereas the muscle activity of all abdominal muscles increased immediately after take-off. The trunk stabilization exercise intervention decreased the muscle activity of the erector spinae during jump header shooting. Conclusions: These results provide useful coaching-related insights for jump header shooting.
REVIEW | doi:10.20944/preprints202204.0258.v1
Subject: Physical Sciences, Biophysics Keywords: prostate cancer; androgen deprivation therapy; exercise; adherence
Online: 27 April 2022 (10:43:52 CEST)
Androgen deprivation therapy (ADT) for prostate cancer treatment is associated with adverse physiological changes, however exercise can improve outcomes. This systematic review and meta-analysis aimed to determine exercise intervention adherence, and its effects on physiological outcomes in men diagnosed with prostate cancer undergoing ADT. Uniquely, this review incorporates a meta-aggregation of qualitative data, providing perspectives from the men’s experiences. A systematic review and meta-analysis were completed following PRISMA Guidelines. Databases (CINAHL, Cochrane, PubMed) were searched for studies using “prostate cancer”, “exercise intervention”, and “androgen deprivation therapy”. Quantitative randomised controlled trials describing adherence to exercise interventions were selected, with qualitative articles selected based on descriptions of experiences around participation. Subgroup meta-analyses of adherence, exercise mode, and intervention duration were completed for quality of life, aerobic fitness, fatigue, and strength. Articles (n=64) articles were identified, with 29 (n=23 quantitative; n=6 qualitative) articles from 25 studies included. Exercise had no effects (p<0.05) on quality of life and fatigue. Significant effects (all p<0.05) were observed for aerobic fitness, and upper- and lower-body strength. Adherence to exercise-based interventions was 80.38%, with improvements observed in aerobic fitness and strength. Subgroup analysis revealed exercise adherence impacted fatigue and strength, with greater improvements observed in programs >12-weeks.
ARTICLE | doi:10.20944/preprints202204.0179.v1
Subject: Physical Sciences, Biophysics Keywords: anterior knee laxity; stiffness; general joint laxity; genu recurvatum
Online: 19 April 2022 (10:28:50 CEST)
The purpose of this study was to investigate the changes in anterior knee laxity (AKL), stiffness, general joint laxity (GJL), and genu recurvatum (GR) during the menstrual cycle in female non-athletes and female athletes with normal and irregular menstrual cycles. Participants were 19 female non-athletes (eumenorrhea, n=11; oligomenorrhea, n=8) and 15 female athletes (eumenorrhea, n=8; oligomenorrhea, n=7). AKL was measured as the amount of anterior tibial displacement at 67 N - 133 N. Stiffness was calculated as change in (Δ)force/Δ anterior displacement. The Beighton method was used to evaluate the GJL. The GR was measured as the maximum angle of passive knee joint extension. AKL, stiffness, GJL, and GR were measured twice in four phases during the menstrual cycle. Stiffness was significantly higher in oligomenorrhea groups than in eumenorrhea groups, although no significant differences between menstrual cycle phases were evident in female non-athletes. GR was significantly higher in the late follicular, ovulation, and luteal phases than in the early follicular phase, although no significant differences between groups were seen in female athletes. Estradiol may affect the stiffness of the periarticular muscles in the knee, suggesting that GR in female athletes may change during the menstrual cycle.
ARTICLE | doi:10.20944/preprints202108.0444.v1
Subject: Physical Sciences, Biophysics Keywords: actin cytoskeleton; super-resolution microscopy; embryonic stem cells; primed embryonic stem cells; micro-rheology; cell culturing; optical tweezers
Online: 23 August 2021 (13:31:33 CEST)
The cellular cytoskeleton provides the cell with a mechanical rigidity which allows mechanical interaction between cells and the extracellular environment. The actin structure plays a key role in mechanical events like motility, or establishment of cell polarity. From the earliest stages of development, as represented by ex vivo expansion of naïve embryonic stem cells (ESCs), the critical mechanical role of the actin structure is becoming recognized as a vital cue for correct segregation and lineage control of cells and as a regulatory structure that controls several transcription factors. Naïve ESCs have a characteristic morphology and the ultrastructure that underlies this condition remains to be further investigated. Here, we investigate the 3D actin cytoskeleton of naïve mouse ESCs using super resolution optical reconstruction microscopy (STORM). We investigate the morphological, cytoskeletal and mechanical changes in cells cultured in 2i or Serum/LIF media reflecting a homogenous preimplantation cell state and a state that is closer to embarking on differentiation. STORM imaging showed that the peripheral actin structure undergoes a dramatic change between the two media conditions. We also detected micro-rheological differences in the cell periphery between the cells cultured in these two media correlating well with the observed nano-architecture of the ESCs in the two different culture conditions. These results pave the way for linking physical properties and cytoskeletal architecture to cell morphology during early development.
ARTICLE | doi:10.20944/preprints202105.0091.v1
Subject: Physical Sciences, Biophysics Keywords: Sports injury, health-seeking behaviour, junior school footballers, Bangladesh
Online: 6 May 2021 (14:52:41 CEST)
Globally, football as a sport has recorded the highest rate of injury morbidity compared with other sports due to the high degree of contact between the players. Coaches play an important role in reducing injuries among the players. The objective of this study was to explore the pattern of football-related sports injuries among junior high school footballers in Dhaka, Bangladesh. A descriptive cross-sectional study was conducted between January 2019 to March 2019 in 20 junior high schools in Dhaka Metropolitan city. We observed 368 boys in the age range of 10 to 18 years old. A pre-structured questionnaire was provided to six trained junior physiotherapists to conduct the face-to-face interview with the boys in the school setting. Most students were from middle-income families. The injury prevalence of defenders was the most (157, 42.7%) followed by mid-fielders (132, 35.94%), forwards (63, 17.1%), and goalkeepers (16, 4.3%). Tackling was the main cause of injury in 21.1% of cases followed by foul play in 19.1% of the cases. In July, there were more injuries (69.0%) and associated muscle strain. Injured footballers did not visit sports physiotherapists as much as they did other health profession and the association was significant. When considering scientific knowledge, students were aware of fitness, flexibility & endurance (25.5%), sports massage (24.5%), the relation of body structure with sports Injury (21.2%), warm-up and/or cool down (19.6%). Based on the study, it was seen that students had no scientific knowledge of sports. As sports is a key activity for school-going children, comprehensive sports injury preventive knowledge is needed for students and sports teachers and coaches. Access to sports physiotherapists is also needed to prevent and manage sports injury at the field level and for rehabilitation.
ARTICLE | doi:10.20944/preprints202103.0016.v1
Subject: Physical Sciences, Biophysics Keywords: keyword 1; Hapkido 2; Service Quality 3; Quality on Exercise Continuation 4; Recommendation Intentions
Online: 1 March 2021 (13:37:51 CET)
This research analyzed the impact of quality of service as perceived by Hapkido students on their exercise continuation and recommendation intentions. It also identified the measures to reduce the rate of student dropout, strengthen competitiveness, and create more efficient marketing strategies for consumer patterns that are rapidly diversifying Hapkido. A questionnaire survey method was conducted with 300 middle and high school students aged 14–19 years having Hapkido training of three months to two years in Incheon and Bucheon during March–April 2019. Frequency, factor, reliability, correlation, and standard multiple regression analyses were conducted on the surveyed data. The conclusions are as follows. First, considering the impact of service quality on exercise continuation intention, service quality positively affects reliability, personification, and perceptual openness; in terms of possibility, it positively affects typicality, personification, and perceptual openness; and in terms of reinforcement, it positively affects reliability and perceptual openness. Second, examining the impact of service quality on recommendation intention positively affects reliability, personification, and perceptual openness. Third, exercise continuation intention positively affects recommendation intention.
HYPOTHESIS | doi:10.20944/preprints202011.0544.v2
Subject: Physical Sciences, Biophysics Keywords: atoms; nucleus, electrons; energy; spectral shift; polymers
Online: 23 November 2020 (09:46:17 CET)
A long standing problem in paleontology is the presence of giant arthropods during the so-called carboniferous era. The same difficulty occurs for the size of plants at the same period. We devise a possible answer to this question entirely different from the theories developed until now, based on the hypothesis that the size of atoms is decaying for very large times and the dimensions of polymers such as chitin and cellulose, containing expansible holes, are decreasing more slowly than rigid materials such as metals, alloys, composite materials and stone. Incidentally, this hypothesis might also give an alternative statement to the expansion of space.
Subject: Physical Sciences, Biophysics Keywords: aerobic dance; electromyostimulation; percent fat; cytokine
Online: 16 February 2020 (14:06:49 CET)
Electromyostimulation (EMS) has been shown to improve body composition, but what biomarkers it affects has not been investigated. The purpose of this study was to compare the EMS-effect of aerobic dance on fatness and biomarkers’ levels in obese elderly women. Methods: Twenty-five women with obesity were randomly classified into a control group (CON; n = 12) and EMS group (EMSG; n = 13). EMS suits used in this study enabled the simultaneous activation of eight muscles with selectable intensities. Program sessions of EMS were combined with aerobic dance three times a week for 8 weeks. Although both groups received the same program, CON did not receive electrical stimuli. Results: Compared with CON, a significant effect of the EMS intervention concerning decreased fatness, as well as an increased skeletal muscle mass and basal metabolic rate, were evident. Compared with CON, aerobic dancing with an EMS suit also improved biomarkers in EMSG. Cytokines, including interleukin-6, tumor necrosis factor, C-reactive protein, resistin, and carcinoembryonic antigen were significantly changed in EMSG, whereas those of CON did not change from the baseline to the end of the experiment. These results showed significant differences between groups. Similarly, the changes caused by EMS were represented in high-density lipoprotein-cholesterol and low-density lipoprotein-cholesterol. Conclusions: The results indicate that a significant effect due to the EMS intervention was found concerning body composition and biomarkers in obese elderly women.
ARTICLE | doi:10.20944/preprints202001.0122.v1
Subject: Physical Sciences, Biophysics Keywords: cervical adenocarcinoma; immune-checkpoint inhibitor; programmed cell death-1(PD-1); programmed cell death-ligand 1(PD-L1); CD8 expression; lymphocyte; survival analysis
Online: 12 January 2020 (15:01:23 CET)
The effectiveness of immunotherapy for cervical adenocarcinoma (CA) has not been demonstrated yet. It may be possible for us to use programmed cell death 1 (PD-1), programmed cell death-ligand 1 (PD-L1), and CD8 as biomarkers of response to immune therapy in CA patients. In the present study, we aimed to investigate whether the expression levels of PD-1, PD-L1, and CD8 can predict the prognosis of CA patients and their response to ICI therapy. The levels of the PD-1, PD-L1, and CD8 proteins were analyzed by immunohistochemical analysis from formalin-fixed, paraffin-embedded tumor samples. The correlation between the expression levels and patient prognosis was analyzed by the Kaplan–Meier method and univariate and multivariate Cox proportional hazard regression model. We observed a significant inverse-correlation between the PD-1 and CD8 expression (p=0.001, chi square test). We also found a significant inverse-correlation between the PD-L1 and CD8 expression (p=0.027). The overall survival was significantly worse in patients with positive PD-1 expression (p=0.027). Similarly, the progression-free survival was also worse (p=0.087). Our results demonstrate that a high level of PD-1 expression is associated with a poor prognosis in CA patients. Further research is necessary to identify the molecular mechanisms that mediate this association.
Subject: Physical Sciences, Biophysics Keywords: rumen-protected l-tryptophan; growth performance; metabolites; glucose; gene expression
Online: 29 September 2019 (09:02:27 CEST)
We assessed the growth performance, physiological traits, and gene expressions in steers fed with dietary rumen-protected L-tryptophan (RPT) under cold environment. Eight Korean native steers were assigned to two dietary groups, no RPT (Control) and RPT (0.1% RPT supplementation on a dry matter basis), 6 wks. Maximum and minimum temperatures throughout the experiment were 6.7°C and -7.0°C, respectively. Supplementation of 0.1% RPT to a total mixed ration did not increase body weight but had positive effects of elevating average daily gain (ADG) and reducing the feed conversion ratio (FCR) at day 27 and 48. Metabolic parameter showed higher glucose level (at day 27) in the 0.1% RPT group compared to the control group. Real-time PCR analysis showed no significant differences in the expression of muscle (MYF6, MyoD, and Desmin) metabolism genes between the two groups, whereas the expression of fat (PPARγ, C/EBPα, and FABP4) metabolism genes was lower in the 0.1% RPT group than in the control group. Thus, we demonstrate that long-term (6 wks) dietary supplementation of 0.1% RPT was beneficial owing to enhanced growth performance by increasing ADG and glucose level, decreasing FCR, and maintaining homeostasis in immune responses in beef steers during cold environment.
Subject: Physical Sciences, Biophysics Keywords: conformation of protein; albumin protein; non-gaussian chain
Online: 7 August 2019 (09:59:10 CEST)
We study a conformation of an albumin protein in the temperature range of 300K-315K, i.e. in the physiological range of temperature. Using simulations we calculate values of two backbone angles, that carry most of information about positioning of the protein chain in a conformational space. Given these, we calculate energy components of such protein. Further, using the Flory theory we determine the temperature in which investigated albumin chain model is closest to the free joined chain model. Near the Flory temperature, we study energy components and the conformational entropy, both derived from two angles that reflect most of the chain dynamics in a conformational space. We show that the conformational entropy is an oscillating function of time in considered range of temperature. Our finding is that, the only regular oscillation pattern appears near the Flory temperature.
ARTICLE | doi:10.20944/preprints201907.0041.v1
Subject: Physical Sciences, Biophysics Keywords: biomechanics, finite element modelling, pelvis, bone adaptation, musculoskeletal modelling
Online: 2 July 2019 (11:34:08 CEST)
This study presents the development of a number of finite element (FE) models of the pelvis using different continuum and structural modelling approaches. Four FE models were developed using different modelling approaches: continuum isotropic, continuum orthotropic, hybrid isotropic and hybrid orthotropic. The models were subjected to an iterative adaptation process based on the Mechanostat principle. Each model was adapted to a number of common daily living activities (walking, stair ascent, stair descent, sit-to-stand and stand-to-sit) by applying onto it joint and muscle loads derived using a musculoskeletal modelling framework. The resulting models, along with a structural model previously developed by the authors, were compared visually in terms of bone architecture, and their response to a single load case was compared to a continuum FE model derived from CT imaging data. The main findings of this study were that the continuum orthotropic model was the closest to the CT derived model in terms of load response albeit having less total bone volume, suggesting that the role of material directionality in influencing the maximum orthotropic Young's modulus should be included in continuum bone adaptation models. In addition, the hybrid models, where trabecular and cortical bone were distinguished, had similar outcomes, suggesting that the approach to modelling trabecular bone is less influential when the cortex is modelled separately.
ARTICLE | doi:10.20944/preprints201905.0167.v1
Subject: Physical Sciences, Biophysics Keywords: Morus alba L.; Salinity; Alkalinity; Proteomics; Photosynthesis; Photoprotective mechanism
Online: 14 May 2019 (10:19:19 CEST)
Photosynthetic function, photoprotection, and the response of related proteomics of mulberry (Morus alba L.) seedling leaves under NaCl and NaHCO3 stress with the same Na+ concentration (100 mmol•L-1) were studied by using photosynthetic gas exchange and chlorophyll fluorescence techniques combined with TMT proteomics. The results showed that NaCl stress had no significant effect on photosystem II (PSII) activity in mulberry seedling leaves, and the expressions of the related proteins, OEE3-1 and PPD4, of the PSII oxygen-evolving complex (OEC) and the antenna proteins, CP24 10A, CP26, and CP29, of LHCII in the leaves also increased to varying degrees. The photosystem I (PSI) activity in the leaves of mulberry seedling also increased, and the expressions of some proteins, PsaF, PsaG, PsaH, PsaL, PsaN, and Ycf4, in PSI increased significantly under NaCl stress. Under NaHCO3 stress, the activity of PSII and PSI and the expression of their protein complexes and the electron transfer-related proteins significantly decreased. NaCl stress had little effect on RuBP regeneration during dark reaction in the leaves and the expressions of glucose synthesis related proteins and net photosynthetic rate (Pn) did not decrease significantly. The leaves could adapt to NaCl stress by reducing stomatal conductance (Gs) to increase water use efficiency (WUE). Under NaHCO3 stress, the expression of dark reaction-related proteins was mostly down-regulated, and Gs was significantly reduced, which indicated that non-stomatal factors were important reasons for the significant inhibition of carbon assimilation. In the photoprotective mechanism under NaCl stress, the expression of cyclic electron flow (CEF) related proteins, ndhH, ndhI, ndhK, and ndhM, involved in NAD(P)H dehydrogenase (NDH) and the key enzyme of the xanthophyll cycle, violaxanthin de-epoxidase (VDE) were up-regulated. In addition, the ratio of xanthophyll cycle components (A+Z)/(V+A+Z) was increased. The expressions of proteins FTR and Fd-NiR, which are related to Fd-dependent ROS metabolism and nitrogen metabolism, were also significant up-regulated under NaCl stress, which can effectively reduce the electronic pressure on Fd. Under NaHCO3 stress, the expressions of CEF-related proteins, VDE, ZE, FTR, Fd-NiR, Fd-GOGAT, SGAT, and GGAT, were significant down-regulated, and the photoprotective mechanism, like the xanthophyll cycle, CEF, and photorespiration, might be damaged, resulting in the inhibition of PSII activity and carbon assimilation in leaves of mulberry seedling under NaHCO3 stress.
ARTICLE | doi:10.20944/preprints201810.0458.v2
Subject: Physical Sciences, Biophysics Keywords: biophoton emission; age; temporal variation; asymmetry; analytical model; photon diffusion; steady-state
Online: 14 January 2019 (11:26:03 CET)
Biophoton emission has been experimented for decades. The photo-genic origin of biophoton has also been attributed to the oxidative stress or free radical production. However, there are considerable gaps in quantitative understanding of biophoton emission. In this work, I propose an analytical hypothesis for interpreting a few patterns of steady-state biophoton emission of human, including the dependency on age, the diurnal variation, and the geometric asymmetry associated with serious asymmetrical pathological conditions. The hypothesis is based on an alternative form of energy state, termed vivo-nergy, which is associated with only metabolically active organisms that are also under neuronal control. The hypothesis projects a decrease of the vivo-nergy in human during growth beyond puberty. The hypothesis also proposes a modification of the vivo-nergy by the phases of systematic or homeostatic physiology. The hypothesis further postulates that the deviation of the physiology-modified vivo-nergy from the pre-puberty level is deteriorated by acquired organ-specific pathological conditions. A temporal differential change of vivo-nergy is hypothesized to proportionally modulate oxidative stress that functions as the physical source of biophoton emission. The resulted steady-state diffusion of the photon emitted from a photo-genic source in a human geometry simplified as a homogeneous spherical domain is modeled by photon diffusion principles incorporating an extrapolated zero-boundary condition. The age and systematic physiology combined determines the intensity of the centered physiological steady-state photo-genic source. An acquired pathology sets both the intensity and the off-center position of the pathological steady-state photo-genic source. When the age-commemorated, physiology-commanded, and pathology-controlled modifications of the steady-state photo-genetic sources are implemented in the photon diffusion model, the photon fluence rate at the surface of the human-representing spherical domain reveals the patterns on age, the temporal variation corresponding to systematic physiology, and the geometric asymmetry associated with significant asymmetric pathological condition as reported for spontaneous biophoton emission. The hypothesis, as it provides conveniences for quantitative estimation of biophoton emission patterns, will be extended in future works towards interpreting the temporal characteristics of biophoton emission under stimulation.
ARTICLE | doi:10.20944/preprints201812.0365.v1
Online: 31 December 2018 (10:17:25 CET)
Since matter, energy and information are the three major components of the world, is there an interaction between information and matter? In the present work, the coevolution of human language and brain is taken as a case of interaction between information and brain. Some evidence that may show interactions between human language and brain revealed by previous researches is summarized in this paper, such as the language areas in the cerebral cortex of the modern human brain, the evolution of human language and brain in human history, and the genetic basis for the evolution of language. Based on the evidence, a dynamic model is developed to investigate the possible mechanism of coevolution of human language and brain. In the model, human language development and brain development reinforce each other: the developmental level of language can be promoted by advances in brain function due to language-related gene mutations, in turn, whether such mutations are selected positively can be influenced by the current developmental level of language. The coevolution of human language and brain can be taken as a case of interaction between information and matter.
ARTICLE | doi:10.20944/preprints201810.0489.v1
Subject: Physical Sciences, Biophysics Keywords: diabetes mellitus; blood glucose; kidney; diabetic neuropathy; pancreas
Online: 22 October 2018 (10:45:08 CEST)
This present study was designed to find out whether the acankoreagenin showed the antidiabetic and renoprotective effects in streptozotocin (STZ)-induced diabetic nephropathy (DN) rats. Type I diabetes was induced by a single intraperitoneal injection of STZ (70 mg/kg). At the end of the experiment, rats were euthanized and serum/plasma was separated for the determination of glucose, insulin, glycated hemoglobin A1c (HbA1c), C-peptide, biochemical parameters, and kidney function. One kidney was used for determining glutathione, superoxide dismutas, malondialdehyde, and tumor necrosis factor-alpha levels. The other kidney and pancreas were used for histopathological studies and immunohistochemical measurement of transforming growth factor beta (TGF-β) or NF-κB. Acankoreagenin (2 mg/kg) treatments led to a significant reduction in blood glucose assessed via oral glucose tolerance test (OGTT) in diabetic rats at 2 h. The treatment also resulted in improved body weight, decreased HbA1c, restored lipid profile, and renal oxidative stress. By inhibiting NF-κB, the release of proinflammatory cytokines was suppressed and by inhibiting TGF-β, the renal fibrosis was suppressed in STZ-induced diabetic rat model. Histopathological injury was also observed in pancreatic and renal tissues. These findings support the beneficial effect of acankoreagenin treatment in DN, which could be attributed to its antidiabetic and renoprotective effects.
REVIEW | doi:10.20944/preprints201809.0059.v1
Subject: Physical Sciences, Biophysics Keywords: landuse change; climate change; garden city model; green vegetation; Landsat; urban heat island
Online: 4 September 2018 (06:28:33 CEST)
The key anthropogenic effects on climate include the changes in land use and emission of greenhouse gases into the atmosphere. Depletion of vegetation poses serious threat that speeds the process of climate change and reduces carbon sequestration by the environment. Thus, the preservation of natural environment in urban areas is an essential component of the garden city model, proposed by Sir Ebenezer Howard in 1898, to ensure ecological balance. Recent Landsat images showed that Kumasi does not have the required percentage of green vegetation as was stipulated in the garden city model on which the city was built. It was observed that most parts of Kumasi's green vegetation have been lost to built environments. This study was conducted to assess the impact of urbanization on the garden city status and its effect on the micro-climate of the city. Significant changes in the vegetation cover of the city was evaluated from Landsat-TM imagery and analysis of a long term climatic data of Kumasi carried out over a 55-year period (1960 to 2015). It was observed that, climatic conditions have slightly changed, as mean surface temperature of has increased by 1.2 °C/ 55 years, due to the significant landuse changes from development of non-transpiring, reduced evaporative urban surfaces. However, the impact is not greatly felt due to the geographical location of the city on the globe despite the evidence of a considerable temperature change. Green vegetation conservation for the city is recommended as a top priority in future for city authorities and planners.
REVIEW | doi:10.20944/preprints201807.0492.v1
Subject: Physical Sciences, Biophysics Keywords: membranes; vesicles; lipids; proteins; mesophase separation; domains; lipid rafts; clusters
Online: 25 July 2018 (15:50:38 CEST)
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this Review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we show that the mechanisms generically dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e. due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.
ARTICLE | doi:10.20944/preprints201807.0356.v1
Subject: Physical Sciences, Biophysics Keywords: Anomalous diffusion; FRAP; Numerical Simulations; PH -domain, Membrane Binding
Online: 19 July 2018 (11:17:03 CEST)
FRAP technique have been used for decades to measure movements of molecules in 2D. Data obtained by FRAP experiments in cell plasma membranes are assumed to be described through means of two parameters, a diffusion coefficient D (as defined in a pure Brownian model) and a mobile fraction M. Nevertheless, it has also been shown that recoveries can be nicely fit using anomalous sub-diffusion. FRAP at variable radii has been developed using the Brownian diffusion model to access geometrical characteristics of the surrounding landscape of the molecule. Here we performed numerical simulations of continuous time random walk (CTRW) anomalous subdiffusion and interpreted them in the context of variable radii FRAP. These simulations were compared to experimental data obtained at variable radii on living cells using the PH domain of the membrane binding protein EFA6 (exchange factor for ARF6, a small G protein). This protein domain is an excellent candidate to explore the structure of the interface between cytosol and plasma membrane in cells. By direct comparison of our numerical simulations to the experiments, we show that this protein does not exhibit anomalous diffusion in BHK cells. The non Brownian PH-EFA6 dynamics observed here is more related to spatial heterogeneities such as cytoskeleton fences effects.
ARTICLE | doi:10.20944/preprints201803.0203.v1
Subject: Physical Sciences, Biophysics Keywords: DNA; DNA nanotechnology; patchy particles; Wertheim theory; thermodynamic integration; phase coexistence
Online: 25 March 2018 (16:14:27 CEST)
We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest order virial expansion and a nearest-neighbor DNA model, can provide, in an undemanding way, a thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of such scheme are as accurate as the ones obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.
ARTICLE | doi:10.20944/preprints201608.0082.v1
Subject: Physical Sciences, Biophysics Keywords: hitting; ultrasonography; lateral dominance; abdominal muscle; back muscle
Online: 8 August 2016 (14:36:41 CEST)
The purpose of the present study was to examine the relationships between bat swing speed (BSS) and muscle thickness and lateral asymmetry of the trunk and limbs in collegiate baseball players. Twenty-four collegiate baseball players participated in this study. The maximum BSS in hitting a teed ball was measured using a motion capture system. The muscle thicknesses of the trunk (upper abdominal rectus, central abdominal rectus, lower abdominal rectus, abdominal wall, and multifidus lumborum), upper limb, and lower limb were measured using a B-mode ultrasonography. Lateral asymmetry between each pair of muscles was determined as the ratio of the thickness of the dominant side to that of the non-dominant side. Significant positive correlations were observed between BSS and muscle thicknesses of the abdominal wall and multifidus lumborum on the dominant side (r = 0.426 and 0.431, respectively; p < 0.05), while nearly significant positive correlations were observed between BSS and muscle thicknesses on the non-dominant side. No significant correlations were found between BSS and lateral asymmetry of all muscles. These findings indicate the importance of the trunk muscles for bat swing, and the lack of association between BSS and lateral asymmetry of muscle size.