Arabidopsis thaliana, and applied the traditional PWM, and two alternative motif models BaMM and SiteGA, proposing the dependencies of the positions. The variation in the stringency of the recognition thresholds for the models proposed that the hits of PWM, BaMM, and SiteGA models are associated with the sites of high/medium, any, and low affinity, respectively. At the medium recognition threshold, about 60% of ChIP-seq peaks contain PWM hits consisting of conserved core consensuses, while BaMM and SiteGA provide hits for an additional 15% of peaks in which a weaker core consensus is compensated through intra-motif dependencies. The presence/absence of these dependencies in the motifs of alternative/traditional models was confirmed by the dependency logo DepLogo visualizing the position-wise partitioning of the alignments of predicted sites. We exemplify the detailed analysis of ChIP-seq profiles for plant TFs CCA1, MYC2, and SEP3. Gene ontology (GO) enrichment analysis revealed that among the three motif models, the SiteGA had the highest portions of genes with the significantly enriched GO terms among all predicted genes. We showed that both alternative motif models provide for traditional PWM greater extensions in predicted sites for TFs MYC2/SEP3 with condition/tissue specific functions, compared to those for TF CCA1 with housekeeping functions. Overall, the combined application of standard and alternative motif models is beneficial to detect various modes of the direct TF-DNA interactions in the maximal portion of ChIP-seq loci.Position weight matrix (PWM) is the traditional motif model representing the transcription factor (TF) binding sites. It proposes that the positions contribute independently to TFs binding affinity, although this hypothesis does not fit the data perfectly. This explains why PWM hits are missing in a substantial fraction of ChIP-seq peaks. To study various modes of the direct binding of plant TFs, we compiled the benchmark collection of 111 ChIP-seq datasets for  Transcription factors (TFs) read out the gene regulatory nucleotide context  in a genome and subsequently initiate RNA synthesis  an indirect TF binding or (b) the disadvantage of PWM models in ignoring the dependencies of nucleotides occurrences in different site positions  from the Myb-like family is a key component of the circadian clock regulation. CCA1 is able to initiate and set the phase of clock-controlled rhythms  nucleotides in the background sequences respect those in peaks with 1% precision; the foreground and background sequences possess the same distribution of lengths. We ensured that any background sequence did not possess even a partial perfect overlap with any sequence from the foreground dataset. We included the background generation program in the SiteGA package (see above). We used the following values of parameters in this program: (a) the maximal number of background sequences per one peak, the values 5 (PWM/BaMM) and 10 (SiteGA); in separate tests for three motif models, we changed this parameter from 1 to 10 and we confirmed that the performance estimates have remained almost the same; (b) the total number of attempts to get the background sequences from the genome per one foreground sequence, the value 500 . Hence, the exact size of the background dataset several times exceeded the foreground dataset.In A. thaliana protein coding genes. The recognition scores for a model were transformed to the uniform scale of ERRs, i.e., we compared the recognition scores of two distinct models that respected the same range of ERRs. We estimated each recognition threshold by a respective value of ERR and applied in analysis the stringent, medium, and mild thresholds corresponding to ERRs 1E-4, 2.5E-4, and 5E-4. We used the cross-validation procedure to select parameters of models and to estimate the recognition performance of models. We selected model parameters within the following ranges: the motif lengths 8, 12, 16, and 20 bp for all models; the orders of the Markov model 1, 2, and 3 for BaMM; and the numbers of locally positioned dinucleotides (LPDs) 40, 60, 80, and 100 for SiteGA. For all other parameters of PWM STREME, BaMM, and SiteGA models, we applied their default recommended by developers values. We applied the 2-fold bootstrap cross-validation procedure, alternately using odd/even ranked peaks for the model training or estimating its accuracy. For each true positive rate , we calculated a false positive rate  and drew the receiver operating characteristic (ROC) curve. To estimate the recognition performance of a model, we applied the measure partial area under ROC curve (pAUC). pAUC is defined as the sum of FPRs values below a certain threshold McClish, . We emplde novo Analysis (MultiDeNA) pipeline . For each GO term, we computed the fold enrichment  to the known motifs for the target TFs from the CIS-BP database . We ensured that predicted sites for these three ChIP-seq datasets for models PWM, BaMM, and SiteGA are significantly similar . However, the traditional sequence logo is unable to represent dependencies between various positions of predicted BSs. We performed the visualization of these dependencies with the alternative sequence logo DepLogo that was recently proposed . For each combination of two models, we compiled the list of hits supported by these two models; the term “hit” implies the overlapping of BSs predicted by two distinct models. We have demonstrated above that the motifs predicted by PWM, BaMM, and SiteGA models possess a distinct structure in terms of traditional and alternative logos, we can expect that the fractions of recognized peaks for various models are overlapped only partially. In this section, we test whether the combined application of three models respects higher portions of recognized peaks, compared to the application of individual models.Regardless of the threshold selection, the combined application of three models adds about 15% to a model with the maximal fraction of recognized peaks . Thereafter, we detected the lists of GO terms for biological processes enriched in the gene lists for all peaks, and for their TFBS predicted by PWM, BaMM, or SiteGA models  and the fold enrichment  to model in this search TFBS by a PWM  to use ChIP-seq peaks for consequent de novo motif models for ChIP-seq data analysis  on particular TFs still were not complete to describe in vivo DNA affinity  TF in vitro. However, the different cores could act as SEP3 binding sites, preferred AT-rich flanking motifs were almost always the same.Our results on visualization of TFBS with estimated high, medium, and low affinities with the traditional and alternative logos indicate that PWM, BaMM, and SiteGA models provide distinct structures of TFBS. While the popular PWM model reveals only the context pattern of the canonical consensus, and, respectively, the predicted BSs show strict consensuses at the stringent threshold, and this pattern is gradually blurred at the mild threshold . The depPairwise comparison of recognition scores of PWM, BaMM, and SiteGA models revealed the moderately similar estimated affinity for PWM/BaMM, while the scores for PWM/SiteGA and BaMM/SiteGA pairs show more diverse estimated affinities . We propNext, we enquired whether PWM, BaMM, and SiteGA models provide almost complete verification of TFBS in peaks. A comparison of the application of individual models and their combinations for the benchmark collection of ChIP-seq datasets confirmed that almost half of ChIP-seq data contain the conserved consensuses . For theFinally, the GO enrichment analysis for CCA1, MYC2, and SEP3 datasets  confirmsA. thaliana TFs. The analysis of enrichment of the known motifs for target TFs confirmed the consistency of this collection. To recognize motifs of target TFs, we applied three methodologically distinct motif models: the traditional PWM neglecting dependencies between nucleotide occurrences in various positions, and its alternatives BaMM, and SiteGA permitting dependencies within the close and arbitrary positions, respectively. Noteworthy, the BaMM extended the PWM approach, while SiteGA was developed independently from the PWM approach. We performed the bootstrap cross-validation procedure that selected the parameters of models and compared their recognition performance. We assessed that PWM and BaMM models showed the superior performance for the stringent and medium threshold, while SiteGA and BaMM models reached the superior performance for the mild and extra mild thresholds. We selected for further detailed analysis three ChIP-seq datasets for CCA1, MYC2, and SEP3 TFs. The visualization of BSs respecting various predicted affinities for three models with the traditional logos suggested that the transition from stringent to mild thresholds led to the gradual destruction of a PWM consensus approximately equal in all positions, while the alternative BaMM and SiteGA models distinguished more and less conserved positions within a consensus. We believe that these less conserved positions reflect their dependencies with other positions. The visualization by the dependency logo provided direct evidence that BaMM and SiteGA models deduced the specific patterns of mutually dependent nucleotide occurrences almost completely invisible with a traditional sequence logo. Notably, the dependency logo also proved that such dependencies were substantially weaker or they were found at a much lower frequency in potential BSs of the PWMs. The analysis of the changes in the fractions of peaks with predicted BSs depending on the recognition threshold for the whole benchmark collection proposed that PWM BSs were clearly detected already for the stringent and medium thresholds; the transition from them to milder ones showed greater impacts of alternative models compared to those of PWMs. Hence, the traditional PWM model deduces a canonical motif of high affinity for a target TF. More advanced BaMM/SiteGA models further specify this motif, and this specification is clearer for BSs of low affinity. Finally, GO enrichment analysis confirmed that alternative models may notably extend predictions of PWM in the genes possessing the inherent significant GO terms of the target TFs. For CCA1 and MYC2/SEP3 TFs, which have predominant housekeeping and condition/tissue specific biological functions, we found a lower and higher abundance of predicted binding sites specific for alternative motif models, both in peaks and in genes supported by the significantly enriched GO terms. Overall, the combined application of the traditional PWM and the alternative methodologically diverse BaMM and SiteGA models respect various TF-DNA interaction options in vivo, therefore, our approach notably extends a pool of context-specific TFBS in ChIP-seq data.We considered the benchmark collection of 111 ChIP-seq datasets for https://gtrd.biouml.org.Publicly available datasets were analyzed in this study. This data can be found at: AT developed the implemented algorithms, analyzed data, performed the statistical analysis, and drafted the manuscript. VM developed the study and contributed to the writing of the manuscript. VL developed the implemented algorithms, analyzed and interpreted data, developed the study, supervised the project, and drafted and wrote the manuscript. All authors contributed to the article and approved the submitted version.The development and implementation of motif search tools and statistical analysis were supported by Russian Science Foundation Project 21-14-00240.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


As the first barrier of the human body, the skin has been of great concern for its wound healing and regeneration. The healing of large, refractory wounds is difficult to be repaired by cell proliferation at the wound edges and usually requires manual intervention for treatment. Therefore, therapeutic tools such as stem cells, biomaterials, and cytokines have been applied to the treatment of skin wounds. Skin microenvironment modulation is a key technology to promote wound repair and skin regeneration. In recent years, a series of novel bioactive materials that modulate the microenvironment and cell behavior have been developed, showing the ability to efficiently facilitate wound repair and skin attachment regeneration. Meanwhile, our lab found that the fascial layer has an indispensable role in wound healing and repair, and this review summarizes the research progress of related bioactive materials and their role in wound healing. The skin is the largest organ in the body and has multiple functions; its main function is to serve as a protective barrier. It protects the body from harmful chemicals, UV radiation, and pathogenic microorganisms. Among its diverse functions, the skin also synthesizes vitamin D, regulates body temperature, and prevents water loss. With over millions of burn victims, bedsores, venous stasis, and chronic skin ulcers such as diabetic foot reported each year in the United States and tens of millions of burn victims reported in China each year, skin wound healing has piqued the interest of researchers worldwide. The cost of skin wound treatment varies depending on the strategy, and the annual medical cost of chronic wound treatment in the United States is approximately $6 to $15 billion. Therefore, the development of some new biomaterials targeted for application in the right position of the skin to accelerate wound healing and achieve scar-free healing is a problem that the research community is trying to solve today.The skin is composed of three layers: the upper epidermis, the dermis, and the hypodermis , each with its own unique structure and function. Refer to The epidermis is the first layer of the skin. Most epidermal cells are keratin-forming cells, but skin also contains melanocytes, Merkel cells, Langerhans cells, and inflammatory cells . The outThe dermis is the second layer of the skin, a thick layer of dense fibrous and elastic connective tissue that gives the skin its elasticity and strength. The dermis is divided into two layers; the superficial layer adjacent to the epidermis is called the papillary dermis, whereas the deeper, thicker region is called the reticular dermis . DiffereThis is the lowermost tissue layer of the skin, which consists mainly of loose connective tissue and contains larger blood vessels and nerves than in the dermis ,12. The Skin wound healing progresses by peri-wound resident cells, and can be divided into three key phases: inflammatory phase, proliferation phase, and scar formation and remodeling phase . Refer tThe inflammatory phase begins after wound formation. First, cells in the injured tissue release vasoactive substances to cause vasoconstriction to prevent further bleeding, fibrinogen forms an insoluble fibrin network, platelets, lymphocytes, and granulocytes form a blood clot to close broken blood vessels and form a protective film at the wound to prevent further contamination by pathogens. Immune cells around the wound secrete various inflammatory mediators such as tumor necrosis factor (TNF), interleukin (IL), and several other cytokines and growth factors, which together with regulatory signals promote the progression of wound healing .During the proliferative phase, endothelial cells of the vessel wall break through the basement membrane and migrate to the peri-wound area, dividing to form vascular buds and interconnecting to form new vascular pathways, which further form vascular networks and capillary rings to form granulation tissue. The transition of wound healing from the inflammatory phase to the vascularized granulation phase is achieved with the joint participation of various growth factors and cytokines such as fibroblast growth factor (FGF) to promote angiogenesis and fibroblast division , epidermThe third phase of wound healing involves remodeling of wounded tissue and the eventual growth of new skin after a long period of repair. The conversion of granulation tissue production to wound re-epithelialization marks the beginning of dermal tissue remodeling. During this process, the disorganized extracellular matrix (ECM), originally composed of type III collagen and elastin, is replaced by an ordered ECM composed of type I collagen and elastin fibers, remodeling the strength and elasticity of the dermis . PlateleThe traditional theory of wound healing suggests that the wound ECM is mainly derived from fibroblasts migrating to the wound bed, where they proliferate and differentiate into myofibroblasts, and then myofibroblasts produce collagen to deposit the ECM de novo ,24,25,26Biomedical materials are materials used to diagnose, treat, repair, or replace diseased tissues or organs of living organisms or enhance their functions. There are many kinds of trauma repair materials, among which there are hundreds of biological scaffold materials and more than 1800 different kinds of products. The existing scaffolds can be divided into three categories according to the materials used for their production: natural biological scaffolds, synthetic organic scaffolds, and inorganic scaffolds, each with its own advantages and disadvantages. Therefore, the form and function of prosthetic materials should also be diverse. The existing biological scaffolds are summarized as follows, see The process of wound repair is closely related to the inflammatory response because immune cells not only play the role of phagocytosis of pathogens and clearance of necrotic tissues , but alsThese biomaterials can modulate neutrophils in addition to macrophage polarization. For example, chitosan scaffolds increased the number of neutrophils in aged wounds and accelerated wound closure in pressure ulcers of aged mice . In situMast cell has a non-negligible role in all phases of wound healing. During the hemostatic phase, MC enhances the expression of factor XIIIa in dermal dendritic cells through the release of TNF-α ,44 and iAlthough immune cells are essential for wound healing, the role of non-immune cells cannot be ignored. The use of bioactive materials can modulate non-immune cells on the wound surface, which can achieve faster wound healing and smaller scar formation. During the process of wound repair, fibroblasts in deep wounds are overactive, proliferating and differentiating into myofibroblasts, synthesizing collagen and other matrix molecules in large numbers, and keratin-forming cells are also proliferating and differentiating, migrating toward the wound center, continuously covering the wound surface and eventually forming scar tissue . Therefo® and PELNAC® that have been marketed can inhibit the formation of scars. They regulate the adhesion behavior of myofibroblasts through the GFOGER and GLOGER polypeptides in the scaffold, inhibit the aggregation of myofibroblasts, and reduce the contraction of the wound [® did not inhibit myofibroblast differentiation, whereas some decellularized matrix materials showed an impediment to myofibroblast differentiation in wounds [Collagen-based dermal substitutes such as Integrahe wound . Howevern wounds ,63. The n wounds . In addin wounds . Three-dn wounds . Collagen wounds . Engineen wounds . In addin wounds ,69,70,71n wounds , and AgNn wounds . Collagen wounds .In addition, bioactive materials show high potential for application in skin attachment regenerative medicine techniques, which can complete skin regeneration by promoting the regeneration of hair follicles, sebaceous glands, sweat glands, and skin vessels and nerves.Lee et al. found that raising epidermal and dermal cells from neonatal rats in integral dermal substitutes made from type 1 collagen resulted in visible hairs 11–15 days after transplantation . Qi et aLi et al. found that matrigel promotes the differentiation of human epithelial cells of exocrine sweat gland tissue origin into exocrine sweat gland tissue . MatrigeThe development of different biological scaffolds to enhance vascular regeneration of wounds is also one of the effective methods to accelerate wound healing. Keratin-forming cells cultured on bladder matrix scaffolds can increase angiogenesis and aid in rapid wound healing . FunctioThe study of fasciology is not yet fully researched, and there is even a lot of potential to study. Fascia is a layer of fibrous connective tissue that runs throughout the body, lining the skin and encasing muscles, muscle groups, blood vessels, nerves, and internal organs . There aAs the fascia layer plays a crucial role in the process of skin wound repair, the contraction of the fascia leads to the closure of the wound. Moreover, the fascia layer is a layer of loose connective tissue under the skin, rich in blood vessels and nerves. Targeted regulation of fascia can intervene in wound healing and guide the clinical treatment of chronic wounds and diabetic wounds. At present, biomaterials mainly act on the epidermis and dermis, so it is a new direction to develop biomaterials to target the fascia layer.


Neurodegenerative diseases (NDs) are expected by 2050 to rise to 300% worldwide. Patients affected by Alzheimer's Disease (AD), Parkinson's Disease (PD), Huntington Disease (HD), and Amyotrophic Lateral Sclerosis (ALS) experience gradual and progressive neurons loss and neuronal function deterioration, which frequently result in cognitive dysfunctions and severe impairment of activities of daily living. Due to the unknown etiology of these neurological disorders and the difficulty of an early diagnosis, we are currently experiencing a lack of effective and disease-modifying treatments  belong to a class of growth factors which regulate survival, development and function of neurons through the Trk-p75 NTR receptors system  and chronic social stress .The progressive deficient activity of neurotrophic factors like nerve growth factor (NGF), brain derived neurotrophic factor (BDNF) and glial cell-derived neurotrophic factor (GDNF) in different neurodegenerative diseases has prompted intensive research to identify neurotrophic-based disease modifying therapies .NTs and their pro-forms, namely the proneurotrophins (ProNTs), exert opposite effects on adult neurons, with the former generally being neuroprotective and the latter promoting a degenerative pattern .NGF plays a major role in the maintenance of cholinergic baso-cortical and baso-hippocampal circuits involved in memory and higher cognition, and is considered a critical molecule for integrity and function of cholinergic neurons during development and adulthood. Numerous studies have also shown that NGF contributes to the survival and regeneration of neurons during aging and in age-related diseases such as AD .A mutated form of NGF has been proposed as a valuable neurotrophic substitute of the wild-type molecule without its pain-related side effects .Nonetheless, NGF- and BDNF-based clinical trials for AD and ALS, respectively, have failed probably due to poor brain penetration and insufficient target engagement. So far, the poor pharmacokinetic properties of neurotrophins render their use for the treatment of CNS disorders limited. To overcome this issue, in the last 15 years, the nasal route of administration for neurotrophins and peptidomimetics has been widely attempted in animal and human settings with promising preliminary results .Several small neurotrophic agents that efficiently cross the blood-brain barrier (BBB) have been designed and tested in preclinical and clinical research. Recently, a European consortium, the first of its kind, has been intended to foster the study of neurotrophin mimetics in neuroinflammation and neurodegenerative diseases . Among these molecules, the most promising are specific blockers of the p75NTR receptors. Additional compounds designed to activate Trk receptors signaling have been demonstrated to improve synaptic loss and memory deficits .In the last decade, neuroscientists resorted to the nose-to-brain route of drugs delivery as non-invasive approach to bypass the BBB. Different forms of nanocarriers, including liposomes, nanopolymers, and emulsions have been attempted to transport drugs directly into the brain. However, and despite the potential of nasal delivery, optimal pharmacokinetics and target engagement are still waiting for significant optimization  is a ground-breaking technology for ablative surgery. FUS technology has been approved by FDA for the treatment of essential tremors and Parkinson's disease-related tremors. At lower intensity, FUS can stimulate or inhibit neural activity with potential applications in clinical practice for epileptic seizures and psychiatric disorders, as well as for chronic pain management by temporarily blocking nerves. Recently, preclinical studies demonstrated how low intensity FUS can transiently and finely regulate the BBB opening, thereby facilitating the brain penetrance of drugs especially when combined with intranasal drug delivery (Compelling evidence accumulated over the last two decades strongly pinpoint neurotrophins as neuroprotective and possibly disease-modifying treatments for the treatment of neurodegenerative diseases. Despite this growing hope, neurotrophins-based therapies are still suffering from major biological limitations including poor pharmacokinetic properties and very low penetration rates through the BBB. The exploitation of a new and adaptable technology like FUS, which allows non-invasive, efficient, and focused drug delivery to the brain, would possibly open a new era in the treatment of developmental and age-related deadly illnesses of the CNS.There is promise for brain therapy. It will be up to the scientific community and drug developers to take a chance on it.All authors equally contributed to the editorial conceptualization and writing, approved the submitted version.BI is an employee at Chiesi Farmaceutici. He is listed among the inventors of a number of Chiesi Farmaceutici's patents of anti-Alzheimer drugs. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Neurological disorders represent one of the leading causes of disability and mortality in the world. Parkinson's Disease (PD), for example, affecting millions of people worldwide is often manifested as impaired posture and gait. These impairments have been used as a clinical sign for the early detection of PD, as well as an objective index for pervasive monitoring of the PD patients in daily life. This review presents the evidence that demonstrates the relationship between human gait and PD, and illustrates the role of different gait analysis systems based on vision or wearable sensors. It also provides a comprehensive overview of the available automatic recognition systems for the detection and management of PD. The intervening measures for improving gait performance are summarized, in which the smart devices for gait intervention are emphasized. Finally, this review highlights some of the new opportunities in detecting, monitoring, and treating of PD based on gait, which could facilitate the development of objective gait-based biomarkers for personalized support and treatment of PD. Parkinson's Disease (PD) is a chronic and progressive neuro-disorder that affects movement  are frequently used , is an episodic yet obvious sign that occurs in most PD patients, which brings a severe burden on patients in daily life  or time . These parameters can be calculated based on the extracted gait cycles, such as gait speed, step/stride length, cadence, progression line, walking base width, stance/swing duration, and so on Deligianni et al.  and ZanaSpatiotemporal parameters are typically be extracted by using vision-based systems and inertial sensors, which have been extensively used for clinical gait analysis as the indication of intrinsic information of the gait patterns  is the most common marker-based system, which requires patients to attach reflective markers to their bodies , then collects the infrared light reflected from the markers passively or actively, and further determines the 3D positions of corresponding markers. Meanwhile, the pre-built model of the human body is constructed maturely to fit the extracted related marker positions. Nowadays, Mocap systems have become the golden standard in clinical gait analysis owing to the high tracking accuracy and sampling frequency  can be directly inferred from either color or depth images , measuring GRF or plantar pressure distribution of the feet when contacting the ground  is one of the most important wearable sensors in gait analysis, which consists of accelerometer, gyroscope, and sometimes magnetometer. By attaching IMUs on the human body, the linear and angular velocity, acceleration, as well as heading reference during gait can be derived, which can be further used for gait event detection and gait stability evaluation  sensors attached to the skin measure the electrical signals introduced by muscle activities, which can be contaminated by noise originating from cross-talk and motion artifacts  during human walking  Gait data capture: Human gait can be captured via different vision-based and/or wearable sensor-based gait analysis systems as mentioned in Section 3. Meanwhile, clinical scales for assessing the movement and posture stability of PD patients are simultaneously recorded. 2) Data preprocessing: Given the raw gait data, various preprocessing steps can be first taken. For instance, smoothing and denoising are standard steps to improve the quality of data containing noises and drifts. Another important step is segmenting the time sequence into small fractions, which involves either the gait cycle extraction or the sliding window techniques. Meanwhile, min-max and z-score normalization methods are frequently utilized to remove the bias across segments or trials. 3) Feature extraction: In order to improve the performance in automatic PD recognition, informative features are additionally extracted from raw gait data. As introduced in Section 3.2, spatiotemporal, kinematic, and kinetic gait parameters are significant features for characterizing walking patterns. To apply these parameters with machine learning models, statistical features and frequency domain features are commonly calculated. Specifically, for the visual input, a number of image-based  and skeleton-based  feature extraction strategies were developed for clinical gait analysis and gait recognition. Recently, advanced deep learning algorithms have gained increasing popularity in gait-based PD detection, providing a unified framework for automatic feature extraction and recognition. 4) Automatic recognition: Subsequently, the extracted gait features are fed into the dedicated classification models to either recognize PD patients or the occurrence of FOG events (detection) or predict the severity level of PD patients (staging). Intuitively, the detection problem can be treated as a binary classification , while the staging is modeled by regression or multi-class classification. Some early studies designed dedicated rules  for classification. However, these rule-based methods are with low generalization capability to new trials and subjects. Lately, extensive Machine Learning (ML) classifiers have been utilized in previous PD detection and staging studies  Evaluation: In terms of the evaluation of classification/recognition algorithms, the reported results are validated under either K-fold cross-validation or leave-one-subject-out (LOSO) validation protocols, and the reported metrics include accuracy, precision, recall, F1-score, sensitivity, specificity, and Area Under Curve (AUC).An overview of the pipeline of the automatic recognition based on gait data is demonstrated in 1) quantitative gait parameters used in clinical gait analysis, 2) feature extraction from visual inputs, 3) as well as common features related to wearable sensors.With the development of wearable sensors and vision-based systems, we have witnessed the flourish of gait analysis in both clinical and healthcare scenarios. However, automatically identifying and staging PD could be more challenging due to the blossom of data modality and capacity  as well as spatiotemporal gait parameters  can be derived with high precision. Similar to Mocap systems, recent advanced human pose estimation algorithms enable the markerless estimation of 2D/3D key joints of the human body from either RGB or depth images, then the informative gait parameters can be calculated subsequently , Discrete Wavelet Transformation (DWT), and Continuous Wavelet Transformation (CWT). For instance, the main frequencies and the wavelet coefficients can be regarded as the features . Previous works investigated the effectiveness and accuracy of different gait analysis systems and classification algorithms in gait-based PD detection. In addition to this binary detection task, the capability of classifying multiple neurodegenerative diseases was also explored in Wang et al.  and ZhaoFor vision-based systems, Guayacán and Mart́ınez  recentlyInertial sensors were also extensively studied for PD detection. Zhang et al.  construcFor force sensors, the PhysioNet dataset is one of the most popular datasets for PD detection and staging  of the target PD patient is first extracted from videos  visual cues, such as the indication of steps, can shift patients' attention to lower limbs, thus compensating the proprioceptive deficit to some extent  can contribute to the improvement of gait and mobility in PD by evoking the brain regions involved in the control of walking  received wide attention for helping patients recover from gait impairments induced by stroke, spinal cord injury, cerebral palsy, PD, and Alzheimer's disease  and Augmented Reality (AR) technologies are promising tools that can provide immersive/augmented visual feedback to patients. By modulating the visual perception under specific protocols, the underlying mechanisms of gait rehabilitation and intervention of PD patients can be investigated  will also have an immediate impact on gait performance , the Interdisciplinary Program of Shanghai Jiao Tong University under Grant YG2021QN117, the National Natural Science Foundation of China under Grant 61922075, and the USTC Research Funds of the Double First-Class Initiative under Grant KY2100000123.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


The filling of the root canal system (RCS) is an important step in endodontic treatment and aims to obtain a three-dimensional sealing of the root canal spaces to prevent bacterial contamination. For this, the selection of an appropriate sealer must be performed synchronously with the choice of the root canal filling technique. This study aims, through an integrative review, to evaluate the quality of root canal filling by comparing thermoplastic and single-cone (SC) techniques. The Medline/PubMed, Scopus, Web of Science and Virtual Health Library (VHL) databases were used to find articles published until November 2021. The eligibility criteria comprised articles that evaluating the quality of root canal filling comparing thermoplastic techniques with the SC technique using tricalcium silicate-based sealer. Studies that evaluated primary teeth, endodontic retreatment or perforations, different outcomes, and studies that considered artificial teeth or different sealer and material for obturation of different techniques were excluded. For articles that were not available for access, an additional contact with authors were considered. A total of 1699 articles were found. After duplicate removal, the title and abstract of 828 articles were screened. Sixteen articles were considered for full-text analysis, but only ten articles met the eligibility criteria. Data extracted from the studies were discussed and tabulated to allow the comparison of desired factors. Concerning the formation of gaps/voids, the thermoplastic techniques showed better results than the SC technique in 3 articles. On the other hand, 2 articles reported no statistical difference between the tested techniques. In addition, about the penetration of tricalcium silicate-based sealer in the dentinal tubules, of the 5 articles selected, in 4 there was no significant difference between the tested techniques and only one study showed better penetration of the sealer when using thermoplastic techniques. The thermoplastic technique was better in most selected studies regarding gaps and voids, but regarding the penetration of the sealer into the tubules, both techniques were effective. Key words:Root canal filling, thermoplastic techniques, tricalcium silicate. The aim of root canal filling is to achieve the three-dimensional sealing of the root canal spaces to obtain a fluid-tight barrier, stable over time, for preventing bacterial contamination or recontamination, enabling conditions for the repair of periradicular tissues -3. For tCold lateral compaction is the most commonly filling technique worldwide and is regarded as the standard against which other filling techniques. Despite being predicTable and relatively simple to execute in regularly tapered canals, root canal filling using a lateral using a lateral compaction technique might lack homogeneity and thus result in a great amount of sealer .Thermoplastic techniques (continuous wave of condensation (CWC), Tagger’s hybrid technique (THT), carrier-based (Thermafill system) have been developed to incorporate the use of thermal or frictional heat to obtain gutta-percha thermoplastic molding -6 to allSimilarly, the single-cone technique (SC) has become used because it is easier to implement, consequently it is less sensitive to operator variations, has low cost, and short operation time. This technique uses a gutta-percha cone with a diameter similar to the last instrument used to shape the root canal. However, this technique demands a greater amount of sealer and thus, the flowability and other physicochemical properties of the sealer play an essential role in the success of the endodontic treatment ,7.Thereby, tricalcium silicate-based sealers have attracted considerable attention because of their high biocompatibility, slight expansion while setting. Moreover, this sealerhas high bioactivity and canpromotes chemical adhesion between the dentin walls and the filling material, through the formation of a structure similar to the biological hydroxyapatite -11.To date, there is no consensus in the literature on which root canal filling technique should be chosen when using the tricalcium silicate-based sealer, to improve the quality of the root canal filling. Furthermore, due to the growing amount and complexity of information in the health area, it has become essential to develop devices, in the context of scientifically based research, capable of delimiting more concise methodological steps and providing professionals with better use of the elucidated evidence in numerous studies. In this scenario, the integrative review emerges as a methodology that provides the synthesis of knowledge and the incorporation of the applicability of results of significant studies in practice.In order to synthesize the results obtained in research on this topic comprehensively, the integrative literature review provides broader information on the subject/problem . TherefoThis study selected the integrative review method to achieve the proposed objective of comparing two or more root canal filling techniques, one of which was the thermoplastic technique and another which was a SC technique when associated with tricalcium silicate-based sealer in the filling quality of the RCS. The question that supported the scientific evidence collection was: “Which root canal filling technique (SC or thermoplastic techniques) promotes better filling quality when combined with tricalcium silicate-based sealer?”. An electronic search was performed in the online databases MEDLINE/PubMed , Scopus, Web of Science, and Virtual Health Library- VHL (Lilacs and BBO). The same units were considered, however, due to the particularities of the databases, as the searches were performed according to To carry out the selection, the Rayyan QCRI reference manager was used in order to determine the eligible potential for this integrative review. At first, studies dealing with duplication of residues between databases were identified and excluded.Thus, the selection was performed after reading the title, abstract, and keywords. This was done independently by two reviewers (C.F.M.G and M.R.A). After resolution of any ambiguity by a discussion with a third reviewer (M.F.L.S.L), the studies identified during the initial search were independently evaluated by both reviewers with full-text reading. In addition, a manual search was performed in the reference lists of eligible studies, as well as a cross-search in the authors’ database, checking the possibility of selecting new relevant articles. For articles that were not available for access, an additional contact with authors of the published studies were considered.The eligibility criteria were: articles published until November 2021, and that their content addressed the following criteria for evaluating the quality of root canal filling , comparing thermoplastic techniques with the SC technique when associated with tricalcium silicate-based sealer.On the other hand, the exclusion criteria comprised studies performed on primary teeth, which addressed the use of tricalcium silicate-based sealer in endodontic retreatment or perforations. Studies that evaluated apical leakage using the dye extraction leakage method, and when the bond strength of the root canal filling materials was evaluated by the push-out test or sealer penetration in simulated lateral canals were also excluded. In addition, studies that considered artificial teeth or different sealer and material for obturation of different techniques were excluded.Data extracted from the studies included, author/year, the tricalcium silicate-based sealer used, thermoplastic technique used, compared technique, measurement method, evaluation method, and the results. The data were extracted by two reviewers independently, discussed, and tabulated. The details were tabulated to allow comparison between the studies regarding the completeness of obturation .Reviewers assessed the studies based on the same criteria. For each selected study, sample numbers, tabulated root canal filling methods, and efficacy of the established protocol. The combination of these factors provided a new set of articles that were used in the present review.An initial search of databases using the search terms revealed a total of 1699 articles in the databases. After the removal of duplicates, 828 articles were screened using the titles and abstracts. After reading the full texts, a total of 16 articles were selected for. Out of these articles, 6 articles did not satisfy the inclusion criteria, because three articles evaluated different endodontic sealers for both evaluated techniques ,14, two Of the selected articles, all were published in dental journals, between 2015 and 2021. Analyzing the void/gap formation, of the 5 articles selected, the thermoplastic technique showed better results than SC technique in three articles and no statistical difference between the techniques tested in two selected articles. Regarding the penetration of tricalcium silicate-based sealer in the dentinal tubules, of the 5 selected articles, 4 there was no significant difference between the tested techniques, and only one article showed better penetration of the sealer in the dentinal tubules with the use of the thermoplastic technique.A successful filling of the RCS is directly related to the absence of empty spaces between the filling material and the dentin walls (gaps), as well as inside the filling mass (voids) ,18,19. NThe present study compared the thermoplastic techniques and SC technique associated with tricalcium silicate-based sealer, concerning the root canal, filling quality, through an integrative review. For this purpose, the volume of voids/gaps was used as a method of assessing root canal filling quality.The continuous wave of condensation (CWC) has the least means of gaps at all sections of the root when compared with SC technique . In addiThe continuous wave of condensation (CWC) has fewer gaps at all sections of the root when compared with SC technique ,20. In aOn the other hand, it was also possible to identify the absence of a significant difference in the percentage of empty spaces between CWC and SC techniques in other studies ,21. ThisTo achieve tubule penetration, the particle size of the material must be smaller than the tubule diameter; the larger the tubule, the deeper a particle can penetrate. The penetration of the endodontic sealer forms a physical barrier with the dentin, improves filling retention and confine residual bacteria . HoweverThus, tricalcium silicate–based sealers penetrated into the dentinal tubules without applying intracanal compaction pressure that is usually used in thermoplastics techniques. This finding would be clinically significant because it would eliminate the application of excessive forces that could cause root fractures, especially in thin roots. Regarding the relationship between the penetration of the tricalcium silicate-based sealer in the dentinal tubule and sealability, it is only possible to infer that there is a chemical bond at the sealer and dentin wall, but further studies need to be carried out to know whether it could prevent or minimize bacterial recontamination.Regarding the methods for evaluating the quality of fillings, micro-CT proved to be a favorable option to calculate empty spaces in both techniques for root canal fillings. This non-destructive and highly accurate method provides 2D scans and 3D reconstructions at different grayscale levels allowing to distinguish all the different components of root canal filling, such as gutta-percha, sealer, gaps, and voids ,18. HoweThe integrative review has some limitations, such as the fact that it includes studies with different methodologies, which can difficult the synthesis of the results and and possible bias . Thus, tBased on the results of this integrative review, it is not possible to accurately conclude which technique is better, given the variation between the tricalcium silicate-based sealers used and the various thermoplasticizing techniques, which may interfere with the quality of root canal filling. However, based on the above, it was possible to observe that thermoplastic technique showed best results in most selected studies regarding gaps and voids, but regarding the penetration of the sealer into the tubules, both techniques were effective.


Microorganisms are stupendous source of secondary metabolites, having significant pharmaceutical and industrial importance. Genome mining has led to the detection of several cryptic metabolic pathways in the natural producer of secondary metabolites (SMs) such as actinobacteria and fungi. Production of these bioactive compounds in considerable amount is, however, somewhat challenging. This led to the search of using epigenetics as a key mechanism to alter the expression of genes that encode the SMs toward higher production in microorganisms. Epigenetics is defined as any heritable change without involving the changes in the underlying DNA sequences. Epigenetic modifications include chromatin remodeling by histone posttranslational modifications, DNA methylation, and RNA interference. Biosynthetic gene cluster for SMs remains in heterochromatin state in which the transcription of constitutive gene is regulated by epigenetic modification. Therefore, small-molecule epigenetic modifiers, which promote changes in the structure of chromatin, could control the expression of silent genes and may be rationally employed for discovery of novel bioactive compounds. This review article focuses on the types of epigenetic modifications and their impact on gene expression for enhancement of SM production in microorganisms. Streptomyces is an efficient producer of 7,600 SMs identified until 2005 (Secondary metabolites (SMs) are low-molecular-weight compounds not directly involved in cell growth, development, or reproduction and produced when the active growth (cell expansion and cell division) stops. Transition from primary to secondary metabolism is achieved due to depletion of nutrients, absence of light, and change in the ambient pH . Microbetil 2005 . These stil 2005 . Howevertil 2005 . The preS. coelicolor and S. avermitilis, which led to the discovery of 22 , terpene cyclase (TC), non-ribosomal peptide synthetase (NRPS), and dimethylallyl tryptophan synthetase (DMATS) are involved in the biosynthesis of huge number of secondary metabolites. However, few secondary metabolites are formed with other pathways; for example, oxylipins are derived from fatty acids. Biosynthetic genes of SMs are co-expressed and remain co-localized in gene cluster. Due to tight transcriptional regulation, most of these SM gene clusters remain silent under laboratory conditions. Activation of gene clusters has the potential for production of new natural products with high therapeutic leads. Various strategies were applied for activation of silent SM gene cluster including changes in the culture conditions  or co-cuAspergillus is a large group of filamentous fungi with high capacity to produce secondary metabolites like penicillin, sterigmatocystin, aflatoxin, etc. Studies on penicillin and sterigmatocystin gene in A. nidulans by A. flavus, A. parasiticus, Fusarium graminearum, and Penicillium chrysogenum  is responsible for methylation of cytosine 5′-carbon atom . In geneNeurospora, Ascobolus, and in other filamentous fungi. Tuber melanospermum (truffle), having a methyl group attached to the 5’-carbon of cytosine ring (5 mC) at transposable element, accounts for 58% of genomic DNA. Decitabine (5-aza-20-deoxycytidine) and 5-azacytidine are frequently used as inhibitors of DNMTIn fungi, the presence and importance of DNA methylation are still not clear. The absence of DNA methylation in some fungi has been observed using some highly sensitive techniques . DNA metTorrubiella luteorostrata  in the presence of 5-AZA produced seven new diethylene glycol phthalate ester monomers and oligomers, with four known analogs (Aspergillus sp. (SCIOW2 strain) produced three new eremophilane-type sesquiterpenes  and a new dihydrobipolaroxin analog. The addition of nicotinamide or sodium butyrate (NaBut) in the culture medium of Penicillium brevicompactum resulted in a 2–10-fold increase in the phenolic compound production, some of which possessed cytotoxicity against liver carcinoma cells  mutation during the sexual phase  in A. fumigatus increased the production of fumitremorgin B and pseurotin and decreased the gliotoxin production. In A. fumigatus strain AF293, transcription of NRPS gene cluster increased after deletion of homolog of hdaA  are functional RNA transcribed from DNA but not translated into protein and play an important role in the regulation of gene expression at transcriptional and posttranscriptional level. Non-coding RNA are divided into two categories, short ncRNAs and long ncRNAs. Short ncRNAs comprise microRNA (miRNA), short interfering RNAs (siRNA), and Piwi interacting RNAs (piRNA). miRNAs and siRNAs inhibit the translation by binding to the target messenger mRNA with complementary sequences leading to their degradation. All eukaryotic cells, including fungi, comprise long ncRNA . Some loabolites . In anot patulin .The importance of microbial secondary metabolites in various industries aroused the interest in regulation of these metabolites by manipulating their pathway of synthesis. The richness of silent and cryptic pathways in genomes of microbes provides excellent opportunities for production of new natural compounds with high therapeutic properties. These regulatory pathways could be manipulated toward increased production of secondary metabolites. To achieve this, there is a challenge of activating the many silent gene clusters. Besides, it is also important to learn about how secondary metabolism is regulated and how gene clusters are activated or silenced. This review summarizes the different types of epigenetic regulation for increased production of SMs in microbes. Nowadays, epigenetics is an emerging tool increasingly gaining importance in microbial biotechnology for production of new bioactive compounds and their enhanced concentration in microorganisms. The soaring demand for novel drugs increased the requirement of alternative epigenetic modifiers on one hand and smart methods for high-throughput natural product discovery on the other. Epigenetic modifiers play a key role in the activation of silent gene cluster of SMs that has the ability to increase the production of various bioactive compounds. Epigenetic modification is quite challenging, yet it is one of the highly efficient tools used for the synthesis of industrial secondary metabolites having pharmaceutical and nutraceutical values. It is, however, very important to advance our knowledge about the effect of epigenetic modifiers on chromatin structure and their efficiency in activation of silent biosynthetic gene cluster in order to enhance the SM production.Epigenetic modification is a key tool for gene expression and SM production. Despite the advance research, tools, and techniques in the field of molecular biology and biotechnology, there are some questions that are still unsolved with regard to epigenetic modification. Research is needed to focus on understanding the molecular mechanism of various factors involved in epigenetic modification so as to make the process more convenient and feasible at industrial scale. This will eventually revolutionize the research in microbial world for metabolite production.All authors listed have made a substantial, direct, and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Nanotechnology has great potential to significantly advance the biomedical field for the benefit of human health. However, the limited understanding of nano–bio interactions leading to unknowns about the potential adverse health effects of engineered nanomaterials and to the poor efficacy of nanomedicines has hindered their use and commercialization. This is well evidenced considering gold nanoparticles, one of the most promising nanomaterials for biomedical applications. Thus, a fundamental understanding of nano–bio interactions is of interest to nanotoxicology and nanomedicine, enabling the development of safe-by-design nanomaterials and improving the efficacy of nanomedicines. In this review, we introduce the advanced approaches currently applied in nano–bio interaction studies—omics and systems toxicology—to provide insights into the biological effects of nanomaterials at the molecular level. We highlight the use of omics and systems toxicology studies focusing on the assessment of the mechanisms underlying the in vitro biological responses to gold nanoparticles. First, the great potential of gold-based nanoplatforms to improve healthcare along with the main challenges for their clinical translation are presented. We then discuss the current limitations in the translation of omics data to support risk assessment of engineered nanomaterials. First introduced in 1959 by the Nobel Prize Laureate physicist Richard Feynman, the concept of nanotechnology has been considered by many as the most significant technological breakthrough of the 21st century. Engineered nanomaterials (ENMs), defined by the International Organization for Standardization (ISO) as materials with at least one dimension between 1 and 100 nm . Due to However, in parallel to the societal benefits, the widespread use of ENMs along with the exponential growth in the global nanotechnology market, which is expected to reach 2314.81 kilotons by 2028 in terms of volume , has raiThe novel and variable properties of ENMs pose unique challenges in predicting their impact on living systems . The bioIn recent years, advanced approaches have been proposed to provide insights into the mechanisms underlying the biological responses to ENMs to ultimately support risk assessment ,22. ThesIn life sciences, the suffix “omics” means “a study of the totality of something”. Omics are comprehensive approaches for the analysis of complete molecular profiles of cells and tissues and include genomics, transcriptomics, proteomics, metabolomics, epigenomics, epitranscriptomics, etc. Omics allow studying how complex interactions between genes and molecules influence a phenotype, providing a comprehensive understanding of the biological system of interest. In the context of nanosafety, omics-based approaches have been used to investigate the mechanisms underlying the biological responses to ENMs at the molecular level, providing clues about the associations between ENM characteristics and biological features ,26,27. OSystems toxicology focuses on the understanding of complex interactions within biological systems and uses the “big data” derived from omics measurements combined with computational tools (modeling and bioinformatics) to describe the resilience of biological systems to perturbation by toxicants ,30. SincIn this review, we provide an overview of the literature available that best illustrates the application of omics and systems toxicology approaches in studies aiming to understand the biological effects of ENMs at the molecular level, focusing on gold nanoparticles. Since the number of reports on in vitro omics is much higher than that of in vivo experiments, only studies applying human and mouse cells as model systems for assessing the molecular changes and biological pathways perturbed by nanoparticles were considered. The great potential of gold nanoparticles to improve diagnosis and therapeutics, the clinical trials involving gold-based nanoplatforms, as well as the main challenges for their clinical translation are presented. Then, the current limitations to translate the omics data to support risk assessment of ENMs are discussed.Among the nanoparticles of interest for nanomedical applications, gold nanoparticles (AuNPs) are some of the most investigated. The reason behind such great interest is mostly linked to their fascinating tunable physicochemical properties resulting from surface plasmon resonance (SRP) ,32,33, dhttps://clinicaltrials.gov/ (accessed on 1 December 2022)  , which ihttps://clinicaltrials.gov/ (accessed on 1 December 2022). Another gold-based nanoplatform, NU-0129, is composed of spherical gold nanoparticles loaded with RNA interference (siRNA) specific for the oncogene Bcl2Like12 (Bcl2L12) and OEG (oligo(ethylene glycol)), and has been showing good potential for the systemic treatment of glioblastoma (NCT03020017). Besides cancer therapy, gold nanoplatforms have also been evaluated in clinical trials for applications in other human diseases or conditions. For instance, CNM-Au8, 13 nm gold nanocrystals in a drinkable bicarbonate solution, has been investigated as therapeutics for neurodegenerative diseases such as Parkinson’s disease (NCT03815916), relapsing multiple sclerosis (NCT03993171); and amyotrophic lateral sclerosis (NCT04098406). This formulation has showed significant positive results regarding the diseases’ progression [Aurimune, a 7 nm PEGylated (poly(ethylene glycol)) colloidal gold particle loaded with TNF-α , was developed to treat patients with advanced and metastatic solid tumors, and has successfully completed Phase I (NCT00356980 and NCT00436410). AuroLase, gold-silica nanoshells coated with PEG , was designed to maximally absorb near-infrared light and convert it to heat, and has been investigated for photothermal cancer therapy against lung (NCT01679470), head and neck (NCT00848042), and prostate tumors (NCT02680535) . Despitegression . Anothergression . RecentlDespite the exciting results observed in the early-phase clinical trials aforementioned, the approval of gold nanoformulations to the clinic is still a challenge.In drug development, including nanomedicines, the major causes of failure in clinical trials are related to the lack of effectiveness and poor safety profiles that were not predicted in preclinical studies. A survey of clinical translation of cancer nanomedicines pointed out that around 94% of new nanomedicines are successful in Phase I of the clinical trial, but the success rate drops to about 48% and 14% in Phases II and III, respectively. This phenomenon is associated with the poor/lack of efficacy and toxicity of the nanomedicines, which highlights our limited understanding of the behavior of ENMs in biological systems .Regarding AuNPs, their life cycle in the organism has not been fully understood. Once inside the body, nanoparticles are covered by biomolecules  that are adsorbed in their surface forming a corona that “hides” the surface ligand in targeted nanoplatforms. The composition of this biocorona is influenced by the composition of the biological matrices and by the physicochemical properties of ENMs, such as surface coating, size, shape, etc. ,49. It iIn addition to life cycle, little is known about the fate of AuNPs after their cellular internalization. Gold is widely considered “biologically inert” and then, supposed to be stable in biological environments. However, Balfourier et al.  recentlyMoreover, toxicity is a subject of major concern for the clinical translation of gold, as well as other inorganic nanoparticles. Undoubtedly, the path to clinical implementation is more difficult for inorganic nanoplatforms due to their complex formulations and uncertainties with long-term side effects as well ,55. The Here, we present an overview of the studies exploring the mechanisms underlying the biological responses to AuNPs based on omics changes  using human and mouse cells.Transcriptomics allows the analysis of the changes in the expression of thousands of genes in a cell or organism through the detection of mRNA levels. Transcriptomics has been extensively applied to describe the effects and mechanisms of a potential toxicant ,65. MicrTranscriptomic changes in human cells  were determined by microarray after short-term exposure to different types of surface-modified nanospheres . SignifiThe increased amount of data regarding the transcriptional-based mechanism of action of ENMs (tMOA) prompted the development of INSIdE NANO, a computational tool that provides a systemic biology framework to contextualize the tMOA signatures of ENMs with respect to human diseases, drug treatments, and chemical exposures . By usin2, suggesting that the four gene signatures could be potentially used as biomarkers for early AuNPs exposure [Transcriptomics data have also been used to identify the biomarkers of ENMs’ exposure and effect. Gene signatures for AuNPs exposure were explored by microarray analysis of several human cell lines representing the primary routes of ENMs’ exposure such as inhalation (A549 cells) and ingestion  . After aexposure . Biomarkexposure ,74. ThusThe proteome is the complete set of proteins produced by a cell, tissue, or organism. Proteome-wide studies provide a close link to cell phenotypes under a particular environmental condition. However, proteomics approaches have been mainly applied in nano–bio interaction studies to qualitatively characterize the layer of proteins adsorbed to the surface ENMs, the protein corona, which is critical for ENMs’ uptake by cells, intracellular localization, and toxicity ,76,77. Qhttps://www.metaboanalyst.ca)the metabolic pathways affected by the exposure of HDF cells to AuNPs were mainly related to the glutathione metabolism. Indeed, glutathione, which plays an important role in protecting cells from an oxidative environment, was identified as the key metabolite induced by AuNPs, reflecting a protective response in HDFs to reduce AuNPs-mediated oxidative damage [11 AuNPs/kg) to rats, an increase in the glutathione levels was also observed in the liver, where both types of AuNPs were preferentially accumulated [Metabolites are typically defined as small molecules (mass < 1500 Da) that are required for metabolic reactions that drive cellular/organism growth and functions ,85 Metabe damage . Interesumulated . The metumulated . Xu et aumulated  also repumulated . Recentlumulated . Since mumulated . The metThe epigenome covers heritable changes in gene expression without direct alteration in the DNA sequence. DNA methylation, histone modifications, and noncoding RNAs are included in the panel of epigenetic mechanisms. The epigenome is deeply responsive to the environment and may be altered by a myriad of factors, such as stress, chemicals, etc. Since substantial evidence suggests that epigenetic mechanisms have a critical role in determining adverse health outcomes, regulatory agencies, such as EPA, have been discussing the incorporation of epigenetic data to identify chemicals with the potential to cause adverse effects and support human health risk assessment ,95,96. SDNA methylation is one of the main epigenetic mechanisms for gene regulation and represents the most investigated epigenetic parameter in studies focused on the impact of ENMs in biological systems. DNA methylation is a post-replication modification that predominantly involves the covalent addition of a methyl (CH3) group, almost exclusively found in the 5′ positions of cytosines (5mC), present in the dinucleotide sequence CpG in mammal cells. The methylation of cytosines within CpG sequences, and their subsequent interaction with methyl-CpG-binding proteins (MBDs), may induce chromatin conformational modifications and inhibit the access of the transcriptional machinery to gene promoter regions, thus altering gene expression levels . In the Histone modifications are posttranslational covalent modifications of histone protein tails also involved in the epigenetic regulatory mechanism since these chemical modifications determine the interaction between histones and other proteins and regulate the chromatin structure as well . ModificMicroRNAs (miRNAs), the most studied family of noncoding RNAs, are short (18–25 nucleotides), single-stranded molecules that mediate the regulation of gene expression by inducing translation repression and/or degradation of mRNA targets . The humMicroarray analysis of miRNA isolated from the blood of rats at 1 week and 2 months after 20 nm AuNPs injection revealed short- and long-term changes in miRNA expression levels . TransplAs in DNA, reversible chemical modifications are also known now to occur in RNAs. These posttranslational RNA modifications are referred to as epitranscriptomics modifications . The epiAn integrative analysis of multi-omics data is emerging to further elucidate the underlying molecular pathways affected by ENMs in living systems ,135,136.Based on the omics results presented in this review, the cellular exposure to AuNPs provokes molecular perturbations represented by changes in the profile of transcripts, proteins, metabolites, and epigenetics/epitranscriptomics markers. Coupled with bioinformatics analysis, omics studies identified multiple biological pathways perturbed by AuNPs mostly in sub-cytotoxic concentrations, anticipating effects not captured by conventional cellular assays. Overall, perturbations in pathways related to cell proliferation, adhesion, death (apoptosis), and metabolism were reported at multiple molecular levels, even when low doses of AuNPs were applied. The increased levels of ROS and the generation of an oxidative environment in cells seem to play an important role in the molecular changes and dysregulation of biological pathways induced by AuNPs. This is exemplified by the overexpression of antioxidant genes and proteins ,68,80,81The reader can notice that citrate spheres were the preferred type of AuNP used in the in vitro omics studies. Citrate is considered a relatively “safe” surface chemistry to cells. However, citrate-capped AuNPs with different sizes evoked short- and long-term changes in the molecular profile of different cell types, leading to the disruption of cell homeostasis, even at a very low dose (0.1 nM) ,124,137.Novel and more specific biological responses induced by AuNPs, such as metabolic reprogramming and inflammatory effects, were mostly related to the intrinsic properties of the AuNPs tested, particularly shape and surface chemistry. These results emphasize the importance of “as-made”, as well as the biotransformed ENMs’ characterization in the understanding of nano–bio interactions.Despite the enormous potential to improve healthcare, from the diagnosis to the treatment and prevention of diseases, the full benefits of nanotechnology in the biomedical field have not yet been achieved. The safety of ENMs has been a global concern , particuEfforts have been made to fulfill the knowledge gaps for the safe adoption of nanotechnology. Understanding the impact of ENMs on biological networks and their potential adverse outcomes is required to predict the potential health risks associated with exposure to ENMs. Thus, omics approaches and systems toxicology have been progressively applied in nanotoxicology studies to potentially characterize the mechanism of action of ENMs, even at low doses, and identify adverse outcomes beyond phenotypes alteration. These approaches open new possibilities for the safety assessment of ENMs . CurrentIn summary, by integrating data from omics and systems toxicology with the physiochemical properties of ENMs, it is possible to contextualize ENMs’ mechanisms of action with respect to human diseases, enabling the development of safe-by-design nanomaterials, and boosting ENM-driven innovations. Additionally, the knowledge of the interactions of ENMs with biological systems at multiple levels of the molecular organization can be used to improve the efficacy of nanomedicines and open new avenues for nanotechnology applications in the biomedical field.


The pathophysiological mechanisms involved in chronic disorders such as complex regional pain syndrome, fibromyalgia, chronic fatigue syndrome, silicone breast implant–related symptoms, and post-COVID syndrome have not been clearly defined. The course of the pain in some of the syndromes, the absence of evident tissue damage, and the predominance of alterations in the autonomic nervous system are shared similarities between them. The production of autoantibodies following a trigger in the syndromes was previously described, for instance, trauma in complex regional pain syndrome, infectious agents in fibromyalgia, chronic fatigue syndrome, and post-COVID syndrome, and the immune stimulation by silicone in women with breast implants. In fact, the autoantibodies produced were shown to be directed against the autonomic nervous system receptors, leading to the amplification of the perception of pain alongside various clinical symptoms seen during the clinical course of the syndromes. Therefore, we viewed autoantibodies targeting the autonomic nervous system resulting in autonomic dysfunction as likely the most comprehensive explanation of the pathophysiology of the disorders mentioned. Based on this, we aimed to introduce a new concept uniting complex regional pain syndrome, fibromyalgia, chronic fatigue syndrome, silicone breast implant–related symptoms, and post-COVID syndrome, namely “autoimmune autonomic dysfunction syndromes”. Due to its etiological, pathophysiological, and clinical implications, the suggested term would be more precise in classifying the syndromes under one title. The new title would doubtlessly facilitate both laboratory and clinical studies aimed to improve diagnosis and make treatment options more directed and precise. The interplay between pain processing and the autonomic nervous system has long been described . DefinedCorrespondingly, based on previous studies addressing autoimmune aspects of the syndromes, we introduce in this review a new concept in regard to the pathophysiological mechanism of the aforementioned chronic syndromes, called “autoimmune autonomic dysfunction syndromes” . In our CRPS is a chronic pain disorder of undefined etiology characterized by persistent pain confined to one region of the body, more commonly affecting the lower extremities . In addiDue to the unanswered questions regarding the etiology and pathophysiology of the disease, CRPS has been widely investigated in the last decades . For insFurthermore, the role of the autonomic nervous system in the manifestation of CRPS has been widely documented yet not fully established. Birklein and colleagues  thoroughA generalized and chronic pain is a central component in the definition of fibromyalgia, in addition to fatigue as well as cognitive and sleep disorders . The etiFatigue is a subjective feeling of tiredness leading to the inability to conduct regular activities . In turnTherefore, the correlation and similarities between CFS, fibromyalgia, and post-COVID syndrome are numerous and may share a common mechanism. The involvement and disturbances of the autonomic nervous system in CFS has been described. Freeman and colleagues  reportedThe correlation between silicone breast implants and autoimmunity in terms of the production of autoantibodies and the clinical presentation is not a new finding. High titers of antinuclear antibodies (ANA) were found in 10 out of 11 symptomatic women with SBIs . The chaIn regard to the function of the autonomic nervous system in women with SBIs, alterations in the autonomic nervous system and its dysfunction were termed “autoimmune dysautonomia” by Halpert et al. . The autPost-COVID and long COVID have been used interchangeably to address a variety of symptoms in the period of time following the clinical recovery from acute SARS-CoV-2 infection . Among oIn fact, the role the immune system plays in the manifestations and complications of COVID-19 induced by hyperstimulation, hyperferritinemia with its pathological consequences, and the cytokine storm ,61 cannoPapers and studies addressing autoimmune mechanisms in the syndromes investigated are summarized in We view autoimmunity, in the form of autoimmune autonomic dysfunction as a potential pathophysiological mechanism of complex regional pain syndrome, fibromyalgia, chronic fatigue syndrome, silicone breast implant–related symptoms, and post-COVID syndrome, as revolutionary. As the pathophysiology of the syndromes addressed is unclear, the presence of autoantibodies directed against the autonomic nervous system receptors and the subsequent clinical presentations offer a comprehensive pathophysiological explanation. The term “autoimmune autonomic dysfunction syndromes” could serve as a base for directed research, initially through detailed animal model–based experiments, followed by appropriately designed clinical studies. The results will doubtlessly improve the diagnosis of the syndromes and provide targeted treatment options.


Conductive gels are a special class of soft materials. They harness the 3D micro/nanostructures of gels with the electrical and optical properties of semiconductors, producing excellent novel attributes, like the formation of an intricate network of conducting micro/nanostructures that facilitates the easy movement of charge carriers. Conductive gels encompass interesting properties, like adhesion, porosity, swelling, and good mechanical properties compared to those of bulk conducting polymers. The porous structure of the gels allows the easy diffusion of ions and molecules and the swelling nature provides an effective interface between molecular chains and solution phases, whereas good mechanical properties enable their practical applications. Due to these excellent assets, conductive gels are promising candidates for applications like energy conversion and storage, sensors, medical and biodevices, actuators, superhydrophobic coatings, etc. Conductive gels offer promising applications, e.g., as soft sensors, energy storage, and wearable electronics. Hydrogels with ionic species have some potential in this area. However, they suffer from dehydration due to evaporation when exposed to the air which limits their applications and lifespan. In addition to conductive polymers and organic charge transfer complexes, there is another class of organic matter called “conductive gels” that are used in the organic nanoelectronics industry. The main features of this family of organic materials include controllable photoluminescence, use in photon upconversion technology, and storage of optical energy and its conversion into electricity. Various parameters change the electronic and optical behaviors of these materials, which can be changed by controlling some of the structural and chemical parameters of conductive gels, their electronic and optical behaviors depending on the applications. If the conjugated molecules with π bonds come together spontaneously, in a relative order, to form non-covalent bonds, they form a gel-like structure that has photoluminescence properties. The reason for this is the possibility of excitation of highest occupied molecular orbital level electrons of these molecules due to the collision of landing photons and their transfer to the lowest unoccupied molecular orbital level. This property can be used in various nanoelectronic applications such as field-effect organic transistors, organic solar cells, and sensors to detect explosives. In this paper, the general introduction of conductive or conjugated gels with π bonds is discussed and some of the physical issues surrounding electron excitation due to incident radiation and the mobility of charge carriers, the position, and role of conductive gels in each of these applications are discussed. A new solution to increase the conductivity of these materials is to bind gold nanoparticles to the ligands of TTF molecules. This is shown in Fig. The organs of some marine animals have structures rich in water and organic matter. For example, mermaid tissues are composed of 1% organic matter in 96% water and are a good example of functional hydrogels. Chemists and materials engineers have long sought to mimic nature and make materials with the function of natural hydrogels. “Gels” are examples of these materials that can trap very large volumes of solutions in their three-dimensional lattice-like structure. These semisolid viscoelastic materials are used today in various parts of human life, including food and cosmetics. The process of gelation or synthesis of hydrogels is accelerated by the formation of non-covalent bonds  . “ConjugConductive polymers have been researched over the past few decades owing to their unique ability to provide tunable electrical conductivity and flexibility during processing –48. The Conductive polymers with various nanostructures including 0D nanoparticles,  1D nanofInspired by the chemical/structural features and synthetic approaches of natural gels , conductConductive hydrogels have drawn significant attention in the field of stretchable/wearable sensors due to their intrinsic stretchability, tunable conductivity, biocompatibility, multi-stimuli sensitivity, and self-healing ability. Recent advancements in hydrogel- and organohydrogel-based sensors, including a novel sensing mechanism, outstanding performance, and broad application scenarios, suggest the great potential of hydrogels for stretchable electronics. However, a systematic summary of hydrogel- and organohydrogel-based sensors in terms of their working principles, unique properties, and promising applications is still lacking. In this spotlight, we present recent advances in hydrogel- and organohydrogel-based stretchable sensors with four main sections: improved stability of hydrogels, fabrication and characterization of organohydrogel, working principles, and performance of different types of sensors. We particularly highlight our recent work on ultrastretchable and high-performance strain, temperature, humidity, and gas sensors based on polyacrylamide/carrageenan double-network hydrogel and ethylene glycol/glycerol modified organohydrogels obtained via a facile solvent displacement strategy. The organohydrogels display higher stability (drying and freezing tolerances) and sensing performances than corresponding hydrogels. The sensing mechanisms, key factors influencing the performance, and application prospects of these sensors are revealed. Particularly, we find that the hindering effect of polymer networks on the ionic transport is one of the key mechanisms applicable for all four of these kinds of sensors .Chromophore is the part of a molecule that causes color in it. Chromaticity occurs when matter can absorb a certain wavelength of visible light and pass or reflect the rest. A chromophore is a region of a molecule where the energy balance difference between two molecular orbitals is within the energy range of part of the incident beam spectrum . A certaIn addition to controllable photoluminescence behavior, one of the main approaches to the development of conjugated gels with π bonds is the conversion of optical energy into electrical energy by electron excitation. In other words, scientists are looking for conductive gels to emit their excited electrons through an electronic circuit, instead of emitting light or exhibiting photon upconversion due to electron stimulation after exposure to the incoming beam. Collected and stored. Observations show that conductive gels are a good option for converting solar energy into electric current, because the electron donor and receiver centers in the three-dimensional structure of these materials are arranged independently and in a controllable arrangement, and the possibility of electron transfer at macroscopic distances , 72. TheN,N-bis-3,4,9,10-perylenedicarboximide (PDI) is used in these gel structures, the mobility of the electrons will increase  are exposed to electron-deficient analyses, the gel-stimulated electrons are rapidly transferred to the analytic band structure and photoluminescence properties of these materials they destroy , 75. ThiRecently, conductive gels have been used in the manufacture of many nanoelectronic devices due to their controllable conductivity. The most important of these applications are organic field-effect transistors (OFETs), organic solar cells, and organic sensors. In the following, the role of these materials in the mentioned applications is described. It should be noted that one of the main applications of conductive gels is the production of hydrogen using water splitting, but since the present article deals with the nanoelectronic applications of conductive gels, this issue will not be discussed , 77.Organic semiconductors are preferred over silicon-based semiconductors in many applications, including integrated circuits, sensors, and electronic chips, due to their low weight and flexibility. The relatively regular arrangement of the large molecules in these materials due to the processing of the solution phase can provide continuous conduction paths for the electrons and cavities (percolation network) and increase the efficiency and electrical efficiency of the devices. Since conductive gels are prepared from solution phase and in which large molecule chromophores have the ability of molecular self-assembly, these materials are a very good option for making active materials in field-effect organic transistors (OFETs) , 79. BefEase of processing, coating, production of thin films, and production of nanometer fibers.The possibility of making heterogeneous connections from chromophores giving or receiving large molecules in mesa- or nanodimensions.Possibility of easy self-assembly of large molecules and engineering of three-dimensional arrangement of electron donor and receiver chromophores to achieve high energy conversion efficiency.Organic solar cells (OSCs) have relatively low efficiencies in converting solar energy into electrical energy, but very low weight, low cost, and flexibility of organic matter relative to inorganic semiconductors are the focus of energy industries. Has attracted. Has attracted Conductive gels, on the other hand, have been considered in comparison with other semiconductor or non-conductive organic materials for several important reasons for making OSCs , 84:EaseOrganic monolayer solar cellsThese solar cells are the simplest type of photovoltaic device in terms of energy storage conversion mechanism. In the structure of these devices, an organic semiconductor is placed between two thin layers of conductive metal. One of these metal layers, such as indium tin oxide (ITO), has a very high working function, and the other layer, such as aluminum or magnesium, has a relatively lower working function  are used as the two points of contact for the external circuit. Also, conductive gels are often used as the organic layer between these two conductive metal layers. This layer is also called the active layer. Recently, some researchers have used organic gels based on conductive polymers as the active layer in organic solar cells [In this section, a sample of organic solar cells based on conductive gels is reviewed. But before entering into this discussion, it is better to introduce the general structure of organic solar cells. Figure ion Fig. a. The mear cells . Figure In the organic nanoelectronics industry, in addition to organic charge transfer complexes and conductive polymers, conjugated gels with π bonds are also used. These materials are large molecules that, similar to organic charge transfer complexes, have electron donor and receptor centers and, like conductive polymers, are composed of conjugated molecules with π bonds. These large molecular units in gel structures are placed next to each other with non-covalent bonds, increasing the viscosity of the system. One of the main features of conductive gels is the ability to change the optical behavior of these materials by controlling chromophores, viscosity, arrangement of molecular arrays, and doping with other molecules. These materials can also be used in photon upconversion technology. Conductive gels are now used in the manufacture of solar cells to convert solar energy into electricity.In the present paper, the nanoelectronic applications of conductive gels were reviewed. The most important of these applications are sensors for detecting explosives, thin-film organic solar cells, and field-effect nanotransistors. As mentioned, conductive gels can be used as non-intrinsic semiconductors due to the self-arrangement of large molecules and can be used as the active layer in organic solar cells or the main body of semiconductors in field-effect transistors. The basis of these materials is the excitation of HOMO level electrons and their transfer to the LUMO level. The efficiency and performance of this group of materials are strongly related to the kinetics of the process of excitation and transfer of charge carriers due to the collision of landing photons. Conductivity can significantly increase the conductivity of conductive gels. The most important method is to dope or add a specific functional group to the molecular arrays of these materials. More details of the mentioned applications are discussed in the present article.