A Boolean Network Approach to Study the Mechanism Associated with Inflammatory Response Induced by Porphyromonas gingivalis.

Anaerobic Porphyromonas gingivalis is a rod-shaped bacterium and is a primary agent of periodontal inflammation and thus periodontitis. This bacterium disturbs the normal flora of the oral cavity and causes dysbiosis. Databases including Google Scholar Scopus and PubMed were employed to find the evidence by using keywords like 'Porphyromonas gingivalis,' 'Boolean network,' 'inflammatory response and Porphyromonas gingivalis,' 'inflammation and Porphyromonas gingivalis. Only articles that reviewed the role of Porphyromonas gingivalis in oral inflammation were selected. Porphyromonas gingivalis promotes and reorganizes host immune systems against normal host flora, which causes a dysbiotic state. A reorganized immune system induces dysbiosis and periodontitis. Specifically, the role of the C5a receptor in the complement system is vital in this mechanism. P. gingivalis can change the metabolic pathways of phagocytic cells without impeding inflammation. Toll-like receptor and complement signaling are inverted by Porphyromonas gingivalis, which aids them in overcoming immunological responses. However, they sustain the inflammation process, which promotes dysbiosis. Instead of a subjective approach, a systems perspective is required to comprehend this intricate process. A Boolean network is a system approach that seems to be a better approach to understanding this complicated interaction process of Porphyromonas gingivalis with the immune system and inflammation. In short, attempts to understand the complex process using the Boolean network will ultimately help in the early detection of periodontitis, and immediate treatment can prevent soft tissue destruction and dentition loss.

Toxic Metal -Mediated Neurodegradation: A Focus on Glutathione and GST Gene Variants.

Increasing pieces of evidence have supported those chemicals from industrial, agricultural wastes and organoleptic activities play important role in the development of neurological disorders. The frequency of neurological disorders is increased to a much extent in recent years with the advancements in science and technology. Google Scholar, PubMed, and Scopus databases were selected to search the relevant information by using keywords including "Heavy metals", "Neurotoxicity", "Glutathione", "Glutathione AND Neurodegenerative disorders" etc. Heavy metals are particularly recognized as a major resource of toxicities during the stage of early pregnancy where a fetus gets exposed to them from maternal activities and circulation. As infants have a weak immune system and cannot respond to the specific challenge as faced by the body during mercury, zinc, iron, and cadmium exposure. Daily diet and drinking habits in addition to industrial activities also form a major field of study under investigation. This study aims to investigate the role of these metals in the accumulation of pollutants in the brain, liver, and kidneys hence leading to serious consequences. Moreover, their prevalence in teenagers that are under the age of ten years is being observed that leads them to learn, writing, and intellectual abilities. Males are more affected due to their hormonal differences. The role of the GST gene in the development of cognitive conditions and its phenotypes has been discussed thoroughly in this review. The mutations of GST lead to the accumulation of peroxides and superoxides which exacerbate oxidative damage to cells. Binding of toxic metals to GSH genes and the role of glutathione transferase genes is was demonstrated in this review.

Extremal states and coupling properties in electroelasticity.

Electroelastic materials possess properties most attractive for the design of smart devices and systems such as actuators and sensors. Typical polymers show changes in shape under the action of an electric field, and vice versa, together with fast actuation times, high strain levels and low elastic moduli. This paper deals with an Ogden model inspired framework for large deformation electroelasticity which, as a special case, can also be reduced to the modelling of transversely isotropic elasticity. Extremal (local) states are elaborated based on a coaxiality analysis, i.e. extremal states of energy are considered at fixed deformation and changing direction of electric field, respectively, fixed electric field and changing principal directions of deformation. This analysis results in extremal states when stresses and strain commutate, respectively, dielectric displacements and electric field are aligned. In order to further elaborate electromechanical coupling properties, the sensitivity of stresses with respect to electric field is analysed. This sensitivity is represented by a third-order tensor which, in general, depends on deformation and electric field. To illustrate this third-order tensor, a decomposition into deviators is adopted. Related norms of these deviators, together with the electromechanical coupling contribution to the augmented energy, are investigated for different states under homogeneous deformation and changing electric field direction. The analysis is considered to contribute to a better understanding of electromechanical coupling properties and extremal states in large deformation electroelasticity and by that, as a long-term goal, may contribute to the improved design of related smart devices and systems. This article is part of the theme issue 'The Ogden model of rubber mechanics: Fifty years of impact on nonlinear elasticity'.

Toxic Metals Exposure and APOE4 Gene Variant in Cognitive Decline Disorders.

Neurodegenerative disorders are those which affect cognitive functions. Misfolding of proteins especially apolipoprotein E is a key genetic factor involved in several cognitive impairments. Increasing evidence also described the toxic effects of metals, generated by both nature and humans, on the development of neurological disorders. Understanding of interaction between toxic metals and apolipoprotein E protein in cognitive decline diosrders would provide alternative treatment options. Google Scholar and PubMed database were used to search the articles using different search terms like 'toxic metals', 'cognitive decline', 'Apolipoprotein E', "neurodegenerative disorders" and "metals neurotoxicity". Only those papers were included that discussed the metal exposure-apolipoprotein association in the development of cognitive decline disorders. Heavy metals are particularly recognized as a major source of neurotoxicity. These toxic metals can interact with genetic factors and play important role in disease etiology. Understanding the underlying mechanism of this interaction could provide tremendous benefits to treat cognitive decline disorders. In this study, the role of the apolipoprotein E4 gene in the development of cognitive disease conditions and their phenotypes has been discussed thoroughly which leads to the accumulation of amyloid-beta fibrils. This exploratory study revealed novel hypothetical findings which might contribute to the understanding of the neurotoxic effects of chronic toxic metals exposure and possibly improve our knowledge on the molecular mechanisms linking metal exposure to cognitive decline disorder risk.

Mediated interactions between rigid inclusions in two-dimensional elastic or fluid films.

Interactions between rigid inclusions in continuous three-dimensional linearly elastic solids and low-Reynolds-number viscous fluids have largely been quantified in the past. Prime example systems are given by functionalized elastic composite materials or fluid colloidal suspensions. Here, we address the significantly less frequently studied situation of rigid inclusions in two-dimensional elastic or low-Reynolds-number fluid films. We concentrate on the situation in which disklike inclusions remain well separated from each other and do not get into contact. Specifically, we demonstrate and explain that the logarithmic divergence of the associated Green's function is removed in the absence of net external forces on the inclusions, in line with physical intuition. For instance, this situation applies when only pairwise mutual interactions between the inclusions prevail. Our results will support, for example, investigations on membranes functionalized by appropriate inclusions, both of technical or biological origin, or the dynamics of active microswimmers in appropriately prepared thin films.

Increasing Efficacy of Covid-19 Vaccines by Lifestyle Interventions.

COVID-19 caused a serious threat to the world population as it spread worldwide rapidly. Existing medicines and vaccines could not cure and control this deadly disease. In this regard, several vaccines have been proposed and designed to control this infection's spread effectively. Along with these vaccines, the general population should adopt specific lifestyle interventions to strengthen their immune system and combat deadly viruses. We used Google Scholar and PubMed databases to find the related information using key terms such as 'COVID-19', 'COVID-19 AND Vaccine efficacy', 'Lifestyle intervention AND COVID-19', and "Lifestyle intervention AND Vaccines," etc. Only articles that discussed the interactions between lifestyle intervention and the efficacy of COVID-19 vaccines were selected for this study. Several previous clinical trials and scientific observations with influenza, polio, and other viral vaccines have demonstrated that vaccine response varies across individuals for antibody titer, independent of vaccine antigenicity. This different vaccine response observed among individuals is attributed to several factors such as dietary and nutritional habits, physical activity, stress and sleep deprivation, deficiency of micronutrients (minerals, vitamins), gut microbiota composition, immunosenescence, smoking, and drinking habits. Although there is not much information about COVID-19 vaccine efficacy and lifestyle interventions, experience with other vaccines can undoubtedly be used to suggest lifestyle interventions to improve COVID-19 vaccine efficacy. These lifestyle interventions may boost antibody responses against COVID-19 vaccines, leading to higher protection from the disease, especially among elderly and immunocompromised people. In conclusion, the present review attempts to understand the role of various nutritional and psychological factors that lead to poor vaccine response and suggests specific nutritional and psychological interventions that can enhance vaccine efficacy and improve immune response against COVID-19 vaccines.

A Review on Metabolic Paradoxes and their Impact on Metabolism.

The current review paper portrays the important link of different nutrients like trace elements, proteins, fatty acids, vitamins, and amino acids with the immune system as well as information related to metabolic paradoxes. Optimum working of the metabolic system is essential because it gives various types of supplements to the human body and aid in chemical pathways. Here related data have been retrieved from two databases i.e., PubMed and Google scholar to grasp detailed knowledge about micronutrients and nutrients as well as their association in the metabolic system. Like protein play important role in the normal development of different immune components, amino acids including alanine, Arginine, and glutamic acid properly control the movement of neutrophils, macrophages, and cytokines. While fatty acids act as an anti-inflammatory agent because they possess the ability to inhibit the expression of the MHC class. Apart from these, many essential molecules like uric acid, proteins, calcium, lanolin are also obtained as end products after catabolic and anabolic reactions, and it was found that the uric acid paradox has a cancer inhibitory role. Additionally, TGF and IL-6 paradoxes have a role in the development of tumors, the onset of diabetes, and low-grade inflammatory disorders respectively. However, the entire functioning of metabolic processes depends upon daily diet because humans get the important nutrient from the diet which further vital role in the immune system. Moreover, it was also observed that calcium paradox is related to heart disorders because high calcium accumulation leads to cardiac disorders. Thus, the complete knowledge about these essential components as well as metabolic paradoxes is very important due to their antagonistic role to plan better and improved therapeutic strategies for various diseases.

Lifestyle Genetics-Based Reports in the Treatment of Obesity.

Obesity becomes a chronic disease due to the increasing number of mortality and morbidity cases around the world. In most regions, chronic illnesses, such as obesity, are important sources of morbidity and mortality. Due to a lack of effective strategies for prevention and management, the adverse effects of obesity and related diseases on health continue to be a serious problem. Relevant information was searched from Google Scholar, Scopus, and PubMed using such different terms as "Obesity", "Obesity Management", "Obesity AND Physical activity", "Obesity AND Genetics", "Obesity AND Diet", and "Obesity AND Nutrigenomics". Obesity is characterized by a complex interaction of hereditary and lifestyle factors, which includes food. Diet is an environmental element that plays an important and considerable role in the management of health and reduces the risk of obesity and its comorbidities. Changes in lifestyle patterns not only help burn extra calories but also prevent the development of obesity via its modulating effect on genetic factors. Different people respond differently to an obesogenic environment. The notion of nutrigenetics emerged as a result of various genetic variations that may explain this heterogeneity. Nutritional genomics, also known as nutrigenetics, is the study that investigates and analyses gene variations linked to varied responses to certain foods; moreover, it links this variation to diseases, such as obesity. As a result, tailored nutrition advice based on a person's genetic profile may improve the outcomes of a specific dietary strategy and offer a novel dietary strategy to improve life quality and preventing obesity. This study concluded that physical activity and dietary interventions play an effective role in the management of obesity. Moreover, understanding of the function of the most prominent obesity-related genes, as well as the interaction between nutrition and gene expression, will help researchers design personalized treatment strategies for humans.

Oral Aphthous: Pathophysiology, Clinical Aspects and Medical Treatment.

Oral aphthosis is a painful inflammatory process of the oral mucosa. Oral aphthous can appear alone or secondary to numerous distinct disease processes. If recurrence occurs frequently, it is called recurrent aphthous stomatitis. The pathophysiology of oral aphthous ulcers remains unclear but various bacteria are part of its microbiology. Three morphological types hold great importance in literature because these types help manage the illness properly. Google Scholar and PubMed databases were used to retrieve the relevant data and information. Different keywords including "Aphthous", "Aphthosis", "Canker sores", "Aphthous stomatitis", "Aphthous ulcer causes", "Aphthous ulcer AND Microbiota" and "Aphthous ulcer AND treatment". The causes for oral aphthous ulcerations are widespread and ranges from localized trauma to rare syndromes, underlying intestinal disease, or even malignant disease processes. A detailed history and thorough examination of systems can assist the physician or dermatologist in defining whether it is related to a systemic disease process or truly idiopathic. Management of oral aphthous ulcers is challenging. For oral aphthous or recurrent aphthous ulcers from an underlying disease, topical medications are preferred due to their minimum side effects. Systemic medications are necessary if the disease progresses. Within the limitation of research and literature provided, it is safe to say that topical corticosteroids are the first line of treatment. Herein, the author discusses the pathophysiology, types, causes, diagnosis, and appropriate treatment ladder of oral aphthous stomatitis as described in the literature.

Predicting the start, peak and end of the Betula pollen season in Bavaria, Germany.

Betula pollen is frequently found in the atmosphere of central and northern Europe. Betula pollen are health relevant as they cause severe allergic reactions in the population. We developed models of thermal requirements to predict start, peak and end dates of the Betula main pollen season for Bavaria (Germany). Betula pollen data of one season from 19 locations were used to train the models. Estimated dates were compared with observed dates, and the errors were spatially represented. External validation was carried out with time series datasets of 3 different locations (36years in total). RESULTS: The temperature requirements to detonate the main pollen season proved non-linear. For the start date model (error of 8,75days during external validation), daily mean temperatures above a threshold of 10°C from 28th of February onwards were the most relevant. The peak model (error of 3.58days) takes into account mean daily temperatures accumulated since the first date of the main pollen season in which the daily average temperature exceeded 11°C. The end model (error of 3.75days) takes into account all temperatures accumulated since the start of the main pollen season. CONCLUSION: These models perform predictions that enable the allergic population to better manage their disease. With the established relationship between temperatures and pollen season dates, changes in the phenological behaviour of Betula species due to climate change can be also estimated in future studies by taking into account the different climate scenarios proposed by previous climate change studies.

Functional xylem anatomy of aspen exhibits greater change due to insect defoliation than to drought.

The study of tree rings can reveal long-term records of a tree's response to the environment. This dendroecological approach, when supplemented with finer-scale observations of the xylem anatomy, can provide novel information about a tree's year-to-year anatomical and hydraulic adjustments. Here we use this method in aspen (Populus tremuloides Michx.) to identify xylem response to drought and insect defoliation. Surprisingly, we found that precipitation influenced vessel diameter mostly in the trees' youth, while this correlation was less pronounced at maturity. This is likely due to a reduction in stress the stand experiences as it ages, and reflects an ability to mediate drought stress as trees mature. Defoliation events caused consistent and profound changes in fiber anatomy likely leading to reduced structural support to vessels. We therefore expect that in years of defoliation trees may be vulnerable to drought-induced cavitation when leaf area recovers. This study highlights how the inclusion of cellular level measurements in tree ring studies provides additional information on how stress events may alter tree functioning through alterations in structure.

Model-free classification of X-ray scattering signals applied to image segmentation.

In most cases, the analysis of small-angle and wide-angle X-ray scattering (SAXS and WAXS, respectively) requires a theoretical model to describe the sample's scattering, complicating the interpretation of the scattering resulting from complex heterogeneous samples. This is the reason why, in general, the analysis of a large number of scattering patterns, such as are generated by time-resolved and scanning methods, remains challenging. Here, a model-free classification method to separate SAXS/WAXS signals on the basis of their inflection points is introduced and demonstrated. This article focuses on the segmentation of scanning SAXS/WAXS maps for which each pixel corresponds to an azimuthally integrated scattering curve. In such a way, the sample composition distribution can be segmented through signal classification without applying a model or previous sample knowledge. Dimensionality reduction and clustering algorithms are employed to classify SAXS/WAXS signals according to their similarity. The number of clusters, i.e. the main sample regions detected by SAXS/WAXS signal similarity, is automatically estimated. From each cluster, a main representative SAXS/WAXS signal is extracted to uncover the spatial distribution of the mixtures of phases that form the sample. As examples of applications, a mudrock sample and two breast tissue lesions are segmented.

Quantitative region-of-interest tomography using variable field of view.

In X-ray computed tomography, the task of imaging only a local region of interest (ROI) inside a larger sample is very important. However, without a priori information, this ROI cannot be exactly reconstructed using only the image data limited to the ROI. We propose here an approach of region-of-interest tomography, which reconstructs a ROI within an object from projections of different fields of view acquired on a specific angular sampling scheme in the same tomographic experiment. We present a stable procedure that not only yields high-quality images of the ROI but keeps as well the quantitative contrast on the reconstructed images. In addition, we analyze the minimum number of projections required for ROI tomography from the point of view of the band region of the Radon transform, which confirms this number must be estimated based on the size of the entire object and not only on the size of the ROI.

OMNY-A tOMography Nano crYo stage.

For many scientific questions gaining three-dimensional insight into a specimen can provide valuable information. We here present an instrument called "tOMography Nano crYo (OMNY)," dedicated to high resolution 3D scanning x-ray microscopy at cryogenic conditions via hard X-ray ptychography. Ptychography is a lens-less imaging method requiring accurate sample positioning. In OMNY, this in achieved via dedicated laser interferometry and closed-loop position control reaching sub-10 nm positioning accuracy. Cryogenic sample conditions are maintained via conductive cooling. 90 K can be reached when using liquid nitrogen as coolant, and 10 K is possible with liquid helium. A cryogenic sample-change mechanism permits measurements of cryogenically fixed specimens. We compare images obtained with OMNY with older measurements performed using a nitrogen gas cryo-jet of stained, epoxy-embedded retina tissue and of frozen-hydrated Chlamydomonas cells.

A three-dimensional view of structural changes caused by deactivation of fluid catalytic cracking catalysts.

Since its commercial introduction three-quarters of a century ago, fluid catalytic cracking has been one of the most important conversion processes in the petroleum industry. In this process, porous composites composed of zeolite and clay crack the heavy fractions in crude oil into transportation fuel and petrochemical feedstocks. Yet, over time the catalytic activity of these composite particles decreases. Here, we report on ptychographic tomography, diffraction, and fluorescence tomography, as well as electron microscopy measurements, which elucidate the structural changes that lead to catalyst deactivation. In combination, these measurements reveal zeolite amorphization and distinct structural changes on the particle exterior as the driving forces behind catalyst deactivation. Amorphization of zeolites, in particular, close to the particle exterior, results in a reduction of catalytic capacity. A concretion of the outermost particle layer into a dense amorphous silica-alumina shell further reduces the mass transport to the active sites within the composite.Catalyst deactivation in fluid catalytic cracking processes is unavoidably associated with structural changes. Here, the authors visualize the deactivation of zeolite catalysts by ptychography and other imaging techniques, showing pronounced amorphization of the outer layer of the catalyst particles.

Climate threats on growth of rear-edge European beech peripheral populations in Spain.

European beech (Fagus sylvatica L.) forests in the Iberian Peninsula are a clear example of a temperate forest tree species at the rear edge of its large distribution area in Europe. The expected drier and warmer climate may alter tree growth and species distribution. Consequently, the peripheral populations will most likely be the most threatened ones. Four peripheral beech forests in the Iberian Peninsula were studied in order to assess the climate factors influencing tree growth for the last six decades. The analyses included an individual tree approach in order to detect not only the changes in the sensitivity to climate but also the potential size-mediated sensitivity to climate. Our results revealed a dominant influence of previous and current year summer on tree growth during the last six decades, although the analysis in two equally long periods unveiled changes and shifts in tree sensitivity to climate. The individual tree approach showed that those changes in tree response to climate are not size dependent in most of the cases. We observed a reduced negative effect of warmer winter temperatures at some sites and a generalized increased influence of previous year climatic conditions on current year tree growth. These results highlight the crucial role played by carryover effects and stored carbohydrates for future tree growth and species persistence.

A density functional approach to ferrogels.

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a 'pairwise pseudopotential'. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an 'external pseudopotential' when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

Model-independent particle species disentanglement by X-ray cross-correlation scattering.

Mixtures of different particle species are often investigated using the angular averages of the scattered X-ray intensity. The number of species is deduced by singular value decomposition methods. The full disentanglement of the data into per-species contributions requires additional knowledge about the system under investigation. We propose to exploit higher-order angular X-ray intensity correlations with a new computational protocol, which we apply to synchrotron data from two-species mixtures of two-dimensional static test nanoparticles. Without any other information besides the correlations, we demonstrate the assessment of particle species concentrations in the measured data sets, as well as the full ab initio reconstruction of both particle structures. The concept extends straightforwardly to more species and to the three-dimensional case, whereby the practical application will require the measurements to be performed at an X-ray free electron laser.

Phase behavior of binary and polydisperse suspensions of compressible microgels controlled by selective particle deswelling.

We investigate the phase behavior of suspensions of poly(N-isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions. We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest microgels, which are the softest, changing the size distribution of the suspension and enabling crystal formation in conditions where incompressible particles would not crystallize.