The “Noah’s Ark” project, afoot at M.V. Lomonosov MoscowState University since 2015 and aimed at studying biodiversity, is the largestongoing Russian project in life sciences. During its implementation, severalhundred new species have been described; a comprehensive genetic andbiochemical characterization of these species, as well as that of thepre-existing specimens in Moscow University’s collections, has beenperformed. A consolidated IT system intended to house the knowledge generatedby the project has been developed. Here, we summarize the investigations aroundthe Moscow University classical biocollections which have taken place withinthe framework of the project and discuss future promise and the outlook forthese collections. There is little doubt that, in the near future, our existence will be largelygoverned by so-called “big data”: huge arrays of information whoseeffective use is already revolutionizing many aspects of human life. In thefield of life sciences, the term “big data” is traditionallyassociated with genomic information; i.e., the results of sequencing of manygenomes. However, genomic data is just one example of real “bigdata” generated by life sciences; namely, by profound studies ofbiological collections. A biological collection is defined as an organizedrepository of biological specimens of any kind – from dried plants toliving human cells, and even sequenced genomes.It is becoming increasingly clear that the potential of biological collectionsis significantly higher than has been commonly accepted. However, to harnessthis potential, one must treat biological collections as sources of “bigdata” – vast amounts of information about living systems. Combiningthis information with the modern techniques of life sciences would allow us toobtain invaluable insights into the origin and evolution of life on Earth. Thisis expected to arise from comparative studies of numerous biological samples.The resulting knowledge could be implemented in practice for the preservationof the biodiversity of our planet.This was the guiding principle behind Noah’s Ark, a project dedicated tothe conservation, investigation, and profitable use of biological diversity.The most important prerequisite for successful implementation of the projectwas the creation of a unified virtual space for biocollections with thepotential to harvest diverse data on a virtually unlimited number of biologicalsamples. Such a space has already been created, so far on the scale of MoscowState University, but there are plans to make it nationwide. It is alreadyobvious that a global approach to the study of biodiversity significantlyincreases the quality of scientific results, allowing us to identify moregeneral, and more complex, patterns in the organization of life on our planet.Here, we review the interim results of Noah’s Ark project for classicalbiological  collections.The purpose of a biobank is to accumulate collections that adequately reflectthe multidimensional structure of biodiversity (BD), making it possible toexplore its various manifestations. An analysis of the scientific status ofzoological collections was carried out , and it The studies in the “Animals” section are aimed at analyzing keyaspects of BD on the basis of an integrated approach combining phylogenomic andphylomorphological analyses of data resulted from electron microscopic and 3Dreconstructions data.The macrotaxonomic analysis of the main Animalia groups included taxa rangingfrom order to phylum. One fundamentally new finding is the reliablesubstantiation of the monophiletic status of the Lophophorata clade includingPhoronida, Brachiopoda, and Bryozoa: it is supported by the architecture of thecoelomic system and innervation of lophophore tentacles -9. This The microtaxonomic analysis of species and subspecies was carried out on thebasis of the concept of integrative taxonomy: species were identified usinggenetic material, then the results were clarified using morphological andepiphenotypic (including acoustic) characters.New species and subspecies of animals were identified (their number isindicated in brackets) in Cercozoa (4) , 24, CniCOI gene analysis in revealing the diversityof phylogenetic lineages in a number of Amphibia genera has beendemonstrated [The combination of genomic phylogeography and genetic barcoding provided newdata on the structure of species diversity in a number of animal groups. In theNothybidae (Insecta) family ,severalnstrated .Darevskia (Reptilia)[Salvelinus (Osteichthies) suggests their sympatric speciation[Hypomesus olidus and Salvelinus malma (Osteichthies)are being formed as independent units in isolation on the Commander Islands[A preliminary study of the molecular genetic and morphological diversity ofrepresentatives of the Megophryidae, Dicroglossidae, Microhylidae,Rhacophoridae (Amphibia), and Gekkonidae (Reptilia) families revealed a highlevel of “hidden” species diversity, which requires a more detailedstudy. Comparative analysis of the geographic variability of some modelPalaearctic bird species indicates a group-specific nature of their intraspecific differentiation.. Active eptilia). Revealieciation, 82.It  Islands, 100.OnVulpeslagopus on the Commander Islands were shown to result from selection,rather than genetic drift [Within the results of a study of the meronomic diversity of animals, the mostimpressive is the demonstration that the miniaturization of insects of theColeoptera (fam. Ptiliidae), Psocoptera (fam. Liposcelididae), and Thysanopteraorders, which are comparable in size to unicellulars (about 1 mm), has almostno effect on the anatomy of the most important organs of the head section, 102.Thic drift .In the studies of the biochorological section, the faunistic complexes ofinvertebrates and vertebrates of the seas of the Arctic Basin, the Russian FarEast, the North Atlantic, the Australasian tropical seas, and the Red Sea wereexamined. An analysis of the diversity of representatives of five Nematodagroups of hydrothermal sites of the Mid-Atlantic Ridge at depths of 1,200–1,500 m, 106wasThe development of an integrated approach to long-term monitoring of thespatial dynamics of species and faunistic diversity based on the regularcollection and analysis of monitoring collections in the focal regions ofnorthern Eurasia is of fundamental importance.It alloThe study of the ecological aspect of BD mainly centers on the analysis of thespatial dynamics of the energetics of birds inhabiting different environments.A significant specificity of the energy of Old World tropical birds wasconfirmed. In particular, it was demonstrated that the absence of aphylogenetic signal in basal metabolism is independent of body weight.Reconstruction of the origin, spread, and kinship of various groups of plantsin the project is achieved through a wide use of molecular methods in classicalscience.Lotus genus, but also the key pointsof the historical biogeography of the group [Hammatolobium, Tripodion, andCytisopsis was also demonstrated [Lagochilus genusfrom the Lamiaceae family was also reconstructed [Prangos genus has been revised based on a DNA analysis anda new Koelzella subgenus has been established [Prangos akymatodes [Alococarpumgenus was transferred to the Prangos genus [In the Fabaceae family, the results of a long-term molecular-genetic andmorphological analysis of wild bird-foots made it possible to reconstruct notonly the evolution of the he group . The indnstrated . The hisstructed . It was ablished . In turnymatodes  was restos genus .Mollugo genus was provided, which made it possible to drawimportant conclusions for the classification and taxonomy of groups [Minuartia genus [The integrative molecular-morphological approach allows not only to establishthe origin and relationship of taxa, but also to restore the most probablecourse of evolution of individual features. For example, the presence ofsingle-seeded fruits from a common ancestor of the Caryophyllales order,numbering 12,000 species, has been established . A detaif groups . A consiia genus .Molecular phylogenetic analysis was used to demonstrate the need to revise manygroups of moss. The most illustrative example is the polyphilia of theDitrichaceae family: a detailed analysis convincingly demonstrated thatcharacteristics that were considered to be taxonomically significant appearedindependently in different groups . Based oBryoerythrophyllum duellii, using molecular data not only forthis genus, but also for its immediate relatives, made it possible tocompletely revise the scope of the Bryoerythrophyllum genus[Attempts to solve the particular problem of describing a new species ofum genus.Dryopteris,Adianthum hispidulum [Seselimontanum [Schistidium genus was studied in detail[An in-depth study of the genomes of flowering plants and mosses has beenperformed. The full plastomas of three types of spidulum , Seselimontanum ,and somn detail.Allium saxatilegroup [An example of a monographic study that combines both the classicalmorphological approach and the latest molecular methods is the processing ofherbarium specimens of wild onions from the legroup . Of the legroup  andanotlegroup  were desParamollugo(Molluginaceae) genus, which, as expected, consists of only threespecies, has doubled the number of known species[Paramollugo simulans and P.elliotii), and another “forgotten” species was foundin collections from New Caledonia.A monographic revision of the recently described  species. Two newCorbichonia (Lophiocarpaceae) genus, which includedonly two species [C. exellii, which is spread over several countries ofSouthern Africa at once, has been discovered and certified.Another successful example of monographic processing is the revision of theAfrican  species . A thirdRhabdosciadium genus fromthe Apiaceae family have been published, which includes seven speciesdistributed in the mountainous areas of Turkey and Iran. It was possible toanalyze the DNA of all members of the genus, including several narrow-localendemics. The monophyletism of this genus has been demonstrated, and a newspecies, R. anatolyi, common in Turkish Kurdistan[Xyloselinumlaoticum [The results of the revision of the urdistan, has beelaoticum .Dysphaniageoffreyi, has been described for areas hard-to-reach for Europeanresearchers, such as Lhasa and Bhutan[Atriplexcongolensis orach from the Democratic Republic of the Congo[Arthrocnemum franzii saltwaterfrom the Cape Verde Islands [The traditional study of the systemic structure and taxonomy of theChenopodiaceae family has been extended. A new species, d Bhutan. Subsequhe Congo and the  Islands have beeAtraphaxis, several new taxa of the Polygonaceae family haveemerged: Atraphaxis kamelinii species from Mongloia[Bactria genus withB. lazkoviispecies from Kygryzstan [Persepolium genus [According to the results of an extensive revision of the genusMongloia, Bactriagryzstan ,and theum genus .Calciphilopteris wallichii, a newspecies of fern from the Philippines, had to be re-described[Schistidium relictum[For reasons of nomenclature, escribed. We woulrelictum, widesprRefining of our knowledge of the geographical distribution of organisms followstwo paths: studying existing collections that had not previously been describedaccurately and field studies. As a result of this work, a whole layer of newdata has been acquired, which is referred to as “floristic finds”.Scapania asperaearwort. It was possible to find in nature, correctly recognize, andsubsequently perform a DNA analysis of the plant found on the Anabarskyplateau, 3,000 km from the nearest known habitats of this earwort in Europe[One of the most remarkable discoveries is that of n Europe.Floristic finds are merely at the top of a huge reservoir of information thataccumulates as a result of a floristic survey of any territory. The results ofsuch work are reflected in the “Floras” and checklists. Forexample, the results of studying the flora of Sevastopol were summarized. Ithas been shown that the western extremity of Mountainous Crimea is one of themost floristically rich corners of Russia, with 1,859 species of vascularplants recorded in an area of about 600 km2 .Important results were obtained in the field of palelinology during the courseof the project. Mass pollination of plants can be considered not only as abiological process, but also as a special natural phenomenon that can bestudied from the standpoint of botany, meteorology, paleogeography, andallergology.A group of palynologists analyzed long-term data on birch pollination in theMoscow region and identified the main meteorological factors affecting theconcentration of pollen during its season . A compaMyosotis scorpioides and their development were described indetail [Traditional studies of the morphology and anatomy of pollen and spores wereextended: heterosulcate pollen grains of the swamp forget-me-notndetail , as wellndetail .Herbarium samples are an important and easily accessible source for theselection of DNA samples, but DNA molecules are gradually destroyed duringstorage. Therefore, the method developed for extracting DNA from old herbariumspecimens deserves special attention .Translating these collections into electronic form or, in other words,virtualization of the collection space was conceived as a mainstreamdevelopment in the study of plants. The large project on the digitization ofthe Herbarium of Moscow State University was used as the basis for this work.Phoma, Thelebolus,Penicillium, Rhodotorula, in “cobblestone pavement”,Cadophora, Cladosporium, Cladophialophora, in aquatichabitats, Antarctomyces, Hyphozyma, Goffeauzyma, Phoma, Thelebolus, andGeotrichum.Within the “Microorganisms and fungi” section, a comprehensivedepository of bacteria, fungi, fungi-like organisms (myxomycetes andoomycetes), and algae has been created. A unique array of information about themicroorganisms has been compiled, along with extensive collections importantfor scientific research as well as for practice. The uniqueness of thebiomaterial collections and knowledge accumulated within the framework of theProject rests in its complexity and the scope of the biodiversity captured inthe collections and in the diversity of the habitats screened. Microbialcommunities of soils of different natural zones, urbanized biotopes, habitatswith extreme conditions have been characterized . An impoHeracleum sosnowskyi) [Another group of fungi, macromycetes, was the focus of research on diversity,ecology, and potential practical use. This group encompasses major decomposersclosing the nutrient loop in ecosystems. Rare species were found , and a nnowskyi) -176, soinowskyi) , 178, annowskyi) . OverallFungi and fungi-like organisms (myxomycetes and oomycetes) are extremelyimportant both for the functioning of ecosystems and for human practice. Theirubiquity obviates the need for collections encompassing many different regionsfor studying these organisms. It is important to cover both reference habitatsin natural reserves and anthropogenically impacted areas. The Project made itpossible to carry out unprecedentedly broad studies of the diversity of soilmicroscopic fungi and myxomycetes of nature reserves  .ExtensiPhytophthora infestans [Alternaria [The collections created within the framework of the Project became a uniquedatabase for studies of practically important microorganisms.Strains–producers of broad-spectrum antibiotics from the peptaibol family, the antnfestans  and Alteternaria . Their pternaria ,188. Amternaria .Identification of the most resilient microorganisms in the extreme naturalhabitats of the Earth is among the most important tasks of microbiology,largely unsolvable without the study of ancient rock sediments. Gamma-rayresistance of the microbial communities from permafrost sedimentary rocks ofthe Arctic was studied by exposure to gamma radiation (100 kGy) in lowtemperature (–50 °C) and low pressure (1 mmHg) conditions. Theseresults can be considered as terrestrial models of the conditions encounteredby microorganisms in the regolith habitats on Mars. Microbial communities ofpermafrost showed high resistance to the simulated harsh extraterrestrialconditions, retaining ample cultured, metabolically active prokaryotes . The resThe abovementioned studies convincingly demonstrate the scientific potential inapproaching biocollection studies globally. Such an approach presumes, forexample,, comprehensive analyses of large numbers of samples regardless oftheir  nature. Moreover, the depth ofthe insight from comparative studies seems to linearly or even exponentiallydepend on the number of specimens involved. Therefore, the number of biologicalspecimens available should be maximized by every means for further progress incomprehensive biological studies. We believe that the natural way to achievethis is to embrace as many biological collections as possible in a consolidateddata environment. The prototype of such an environment has already been createdin the form of the IT-system of the Noah’s Ark project(https://depo.msu.ru/). As of March 2018, the IT -system contained informationon more than a million biological specimens. Making this system nationwide willprovide a powerful impetus to the development of life sciences in Russia and tothe translation of the fundamental research results into practice. We envisionthe extension of the IT-system of the Noah’s Ark project towards the maindirections of its development.The success of the Noah’s Ark project is largely due to itsinterdisciplinary character. Implementation of the project was the main driverbehind fulfilling the long-held dream of classical biocollection owners atMSU–creating genetic and biochemical service labs focused on maintenanceof these collections. Of course, specimens of these collections had beenstudied before, but that activity was of secondary importance to otherlaboratories in the project, naturally affecting their efficiency. At present,any specimen newly deposited in a MSU collection is subjected to thoroughgenetic and, in many cases, biochemical characterization. It also becamepossible to analyze DNA extracted from museum samples. Of special importance isthe possibility of comprehensive microscopic studies. It is clear that such anintegrated approach will be much more insightful. There is also little doubtthat the synthesis of the classical and modern research methods implemented inthe project must be fully endorsed and further developed in other researchareas.Collectively, we envision (i) the extension of the project IT nationwide and,later, internationally as well as (ii) the elaboration of new advanced genetic,biochemical, and physico-chemical tools that would be used to analyze specimensfrom biocollections as the main avenues for further development of theNoah’s Ark project.


The prevalence of obesity in women of childbearing age around the globe has dramatically increased in the last decades. Obesity is characterized by a low-state chronic inflammation, metabolism impairment and oxidative stress, among other pathological changes. Getting pregnant in this situation involves that gestation will occur in an unhealthy environment, that can potentially jeopardize both maternal and fetal health. In this review, we analyze the role of maternal obesity-induced oxidative stress as a risk factor to develop adverse outcomes during gestation, including reduced fertility, spontaneous abortion, teratogenesis, preeclampsia, and intrauterine growth restriction. Evidences of macromolecule oxidation increase in reactive oxygen species generation and antioxidant defense alterations are commonly described in maternal and fetal tissues. Thus, antioxidant supplementation become an interesting prophylactic and therapeutic tool, that yields positive results in cellular, and animal models. However, the results from most meta-analysis studying the effect of these therapies in complicated gestations in humans are not really encouraging. It is still to be analyzed whether these therapies could work if applied to cohorts of patients at a high risk, such as those with low concentration of antioxidants or obese pregnant women. Prevalence of obesity in both developed and developing countries has increased among women over the last decades , includiThe available epidemiological data in Latin-American countries are dispersed, obtained from periodic national surveys in some cases, or from low-scale, punctual regional studies in others. As it is shown in the Figure The trend in the prevalence of obesity has become a matter of concern to preconception healthcare programs because pre-pregnancy obesity and excessive GWG is associated with an increased risk of adverse reproductive health outcomes . ObesityObesity is associated with a dysregulation in the metabolic balance comprising lipid metabolism, inflammatory or hormonal processes in addition to insulin resistance . The patOS has been traditionally recognized as a key factor in the pathophysiology of numerous conditions, including cardiovascular and neurodegenerative diseases, cancer, diabetes, and obesity.OS has been classically defined as an imbalance between ROS generation and its detoxification by antioxidant systems, in favor of the former. ROS are partially reduced, oxygen-containing metabolites  that are generated because of normal cellular metabolism and environmental factors. They are extremely reactive and have the potential to oxidize lipids, proteins and DNA. On the other side, enzymatic  and non-enzymatic  antioxidants neutralize the effect of highly reactive ROS by transforming them into less reactive species and eliminating oxidation by-products, protecting cells from oxidative damage.However, ROS, at a physiological concentration, behave as second messengers in several signaling pathways that are critical for the normal cellular function. Several studies in the last 10 years have described how ROS can modify the redox state of key residues of proteins  regulatiAdipose tissue has been proposed as the origin of obesity-induced OS, that is later transmitted to other tissues and may account for obesity-associated diseases such as hypertension, cardiovascular disease, or even cancer . HyperglIn addition, oxidative stress has also been observed in healthy gestation. In the second trimester, there is a spike in oxygen supply and metabolic rate in placenta. If ROS levels are maintained under control, they regulate trophoblast proliferation, invasion and angiogenesis, required for a healthy pregnancy .Thus, both obesity and gestation are characterized by an increased OS. When combined, OS is one of the proposed mechanisms involved in many reproductive and pregnancy disorders that may lead to adverse pregnancy outcomes .Pre-existing obesity is an independent risk factor for anovulation, subfertility and infertility in women . SeveralThe deleterious effect of obesity on reproduction is mainly driven by endocrine and metabolic alterations, which may interfere with the neuroendocrine and ovarian function through a disruption in the hypothalamus-hypophysis-ovarian axis. The mechanisms underlying the defective endocrine program in obese women include metabolic alterations due to hyperinsulinemia, the effect of pro-inflammatory cytokines, endoplasmic reticulum stress, alterations in the mitochondria and OS .In rodents, oocytes from dams fed on high fat diet showed abnormal mitochondrial morphology and increased activity, resulting in increased ROS production and GSH reduction  leading The use of antioxidants to improve fertility in obese patients is still a matter of debate. A recent meta-analysis concludes that there is low-quality evidence of a beneficial effect of antioxidants to increase fertility . HoweverOverweight and obese pregnant women present a higher risk of pregnancy loss and recurrent miscarriage compared to normal weight gestations (OR vary from 1.31 to 1.67) . There iRecent results suggest a reduced regenerative capacity and plasticity of the endometrium in obese pregnant women , factors2 when the maternal blood enters the placenta. This signal triggers the transcription of antioxidant genes  to overcome the prooxidant environment  prior to pregnancy or during the early stages of pregnancy . Given t2 almost double the risk of suffering major congenital malformations in the nervous system compared to the offspring of normal weight mothers  concomitant with a reduced antioxidant capacity . These pPreclinical experiments in cellular and animal models reported beneficial effects of antioxidants reducing maternal blood pressure and improving endothelial function . However2 and nutrients in the mother-placenta-fetus circuit is mandatory for the normal development of gestation. An excess in the nutrient supply from obese mothers  has been found in placenta, maternal and chord plasma  of IUGR-To our knowledge, there is not any published clinical trial in humans to determine the potential effect of antioxidants (vitamins or GSH-precursors) on the intrauterine growth from obese mothers. Retrospective, food intake survey-based studies, showed conflicting results. For example, in Spain no relation was found between the consumption of antioxidant vitamins and SGA frequency  and a mePregestational obesity affects approximately to 1 out of 3 women of childbearing age in the world. The excessive fat mass accumulation correlates with OS, caused by an overactivation of the ROS-generating systems (mainly NOS and NADPH oxidases) and a depleted antioxidant defense. Obesity-induced OS arises as a central factor that increases the risk of adverse outcomes in gestation, as it has been summarized in the Figure Despite the multiple evidence of the oxidative disbalance along normal pregnancies, the use of antioxidants to prevent these outcomes is conflicting. While they have proven to be effective in preclinical studies in cellular and animal models, the reports of its application in large-scale clinical trials is often discouraging. However, the analyzed clinical trials in this mini-review do not specifically analyze a cohort of women with pregestational obesity. The design of specific clinical trials for this population, with a basal situation of increased OS, could potentially generate more promising results. Besides clinical recommendations to obese women, such as weight loss before conception and controlling GWG, specific studies on antioxidant therapies focused on this population could help clarifying the adequacy of targeting OS to prevent complications.MA and MV participated in the conception of the work and in the preparation of the manuscript. SG-V, EC, EG-G, and MR-Á participated in the preparation of the manuscript and critically reviewed the final draft.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.


The gut barrier consists of several components, including the mucus layer, made of mucins and anti-bacterial molecule, the epithelial cells, connected by tight junction proteins, and a mixed population of cells involved in the interplay with microbes, such as M cells, elongations of “antigen presenting cells” dwelling the lamina propria, intraepithelial lymphocytes and Paneth cells secreting anti-bacterial peptides. Recently, the influence of intestinal permeability (IP) changes on organs far from gut has been investigated, and IP changes in multiple sclerosis (MS) have been described. A related topic is the microbiota dysfunction that underpins the development of neuroinflammation in animal models and human diseases, including MS. It becomes now of interest to better understand the mechanisms through which IP changes contribute to pathophysiology of neuroinflammation. The following aspects seem of relevance: studies on other biomarkers of IP alterations; the relationship with known risk factors for MS development, such as vitamin D deficiency; the link between blood brain barrier and gut barrier breakdown; the effects of IP increase on microbial translocation and microglial activation; the parallel patterns of IP and neuroimmune changes in MS and neuropsychiatric disorders, that afflict a sizable proportion of patients with MS. We will also discuss the therapeutic implications of IP changes, considering the impact of MS-modifying therapies on gut barrier, as well as potential approaches to enhance or protect IP homeostasis. The requirement for different functions is reflected by the structural complexity of the intestinal surface. Its role as a barrier relies on three components. The layer of mucus contributes to separate the microbiota from the upper part of the epithelium. The epithelial cells, with tight junction (TJ), regulate the paracellular permeability. A third component with immunological functions includes M cells and elongations of “antigen presenting cells” dwelling the lamina propria, that scan the luminal antigens, intraepithelial lymphocytes, and Paneth cells secreting anti-bacterial peptides. The passage of substances through this physical barrier is possible thanks to trans-cellular or para-cellular transport mechanisms. The first is closely related to the presence of selective transporters, the second is under the control of the proteins that make up the TJ, especially occludin and claudins. The TJ can be assembled or disassembled according to the different signals coming from the intra- and extra-cellular environment. Dietary factors, microbiota composition, cytokines, enzymes and growth factors can all contribute to modulate TJ .The enteric nervous system, consisting of the ganglia of enteric neurons and glial cells able to release important mediators in repair, cell proliferation, epithelial differentiation and TJ changes , regulatThe IP changes (IPC) and the dysbiosis appear as virtually co-occurring events, that trigger a vicious circle leading to pathogenic cascades in gut and far-from-gut tissues. In fact, recent evidences coming from children with beta cell autoimmunity, at risk for type 1 diabetes, showed that both increased intestinal permeability and differences in microbiota composition are contemporarily associated with the pre-pathological condition, being thus early events in the development of autoimmunity . HoweverStreptococcus and decreased Prevotella strains in patients with active disease  by gut prokaryotes have been reported to correlate with indicators of mental health, by surveying a large microbiome population cohort, with validation in independent data sets . These dAmong the translational implication of IPC, two points should be emphasized: the possible effects of disease-modifying therapies (DMT) on gut barrier and the potential therapeutic approaches aimed at antagonizing the IPC through stabilizers or enhancers of intestinal integrity. A recent review reported that DMTs, currently used in clinical practice for MS, would be able to act at different levels on IPC, modulating the gut barrier, the gut microbiota and the interaction between the two. However, these actions, though plausible, seem indirect, and whether they actually play a meaningful role in the clinical response remains to be established. Among these drugs, dimethyl-fumarate and fingolimod seem to have an antimicrobial action and a positive direct effect on TJ . On the Besides being of pathophysiological interest, the brain-gut axis abnormalities  could also open new avenues for therapeutic targets. The probiotics use and the successful modification of the microbiome could be one strategy to modulate and improve intestinal barrier function. However, probiotics do not modify the host microbiome in a satisfying and lasting manner . Fecal microbiota transplantation would constitute the optimal strategy and isolated cases were described with beneficial effects on disease course. Also supplementation of bile acids might have several beneficial effects, modulating the intestinal barrier function, shaping the gut microbiota toward homeostatic profiles, and also regulating inflammatory signaling in the central nervous system . At leasEscherichia coli strain Nissle 1917 (ECN), but not with another strain, repaired intestinal permeability dysfunction and induced a general modulation of immune effectors, with a beneficial effect on the disease progression , underlying many conditions of chronic inflammation in gut and far-from-gut organs. Many drugs come from studies conducted in chronic gastro-enteric inflammation: an interesting example is larazotide (a 8-mer peptide with activity as TJ regulator), that was tested in a model of celiac disease and was shown to inhibit gliadin-induced macrophage accumulation in the intestine and to preserve the TJ structure . Larazotgression . Vitamingression . Finallygression .All these findings provide several hints to try therapeutic approaches in MS: repurposing compounds that have been studied especially for IPC in chronic gastro-intestinal inflammation, and/or reworking the increasingly growing data coming from microbiota studies in EAE and MS will plausibly yield fruitful lines of attack against neuroinflammation.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.


At present, living cells are widely used in cell transplantation and tissue engineering. Many efforts have been made aiming towards the use of a large number of living cells with high activity and integrated functionality. Currently, cryopreservation has become well-established and is effective for the long-term storage of cells. However, it is still a major challenge to inhibit cell damage, such as from solution injury, ice injury, recrystallization and osmotic injury during the thawing process, and the cytotoxicity of cryoprotectants. Hence, this review focused on different novel gel cryopreservation systems. Natural polymer hydrogel cryopreservation, the synthetic polymer hydrogel cryopreservation system and the supramolecular hydrogel cryopreservation system were presented, respectively. Due to the unique three-dimensional network structure of the hydrogel, these hydrogel cryopreservation systems have the advantages of excellent biocompatibility for natural polymer hydrogel cryopreservation systems, designability for synthetic polymer hydrogel cryopreservation systems, and versatility for supramolecular hydrogel cryopreservation systems. To some extent, the different hydrogel cryopreservation methods can confine ice crystal growth and decrease the change rates of osmotic shock in cell encapsulation systems. It is notable that the cryopreservation of complex cells and tissues is demanded in future clinical research and therapy, and depends on the linkage of different methods. At present, various living cells such as embryonic stem cells ,2,3, ger2), and also obtained higher normal primordial follicles than the group without sucrose. Thus, the CPAs could significantly influence the cell cryopreservation in the slow freezing method. Vitrification is a modern cryopreservation technique based on an extremely rapid cooling rate of cells along with the process of the extreme concentration of CPAs in cell suspension , an, an39], In clinical and industrial applications, the production of human embryonic stem cells (hESCs) with the feature of cell integrality and their long-term storage is a major challenge. An integrated expansion and cryopreservation strategy for hESCs was reported by Serra and co-workers . Single l-lysine . Th. Th56]. For the freeze–thaw process, the state transition of a cell cryopreservation system such as the crystallization of water produced polymer–solvent phase separation, which offered an opportunity for non-covalent bond hydrogel formation. Vrana et al. encapsulated bovine arterial smooth muscle cells within PVA )–gelatin hydrogels . The effl-lysine and azide groups in dextran, and the carboxylation of partial amino groups. The dextran-based polyampholytes showed good cryoprotective properties, which could form in situ hydrogels with desired amounts of dibenzylcyclooctyne dextran (DBCO-Dex) via Cu-free click chemistry. The cryoprotective properties depended on the polymer concentration, the number of amino groups introduced into the dextran, the ratio of carboxylation, and the osmolarity of the solution. The survival rate of L929 cells encapsulated in the dextran-based polyampholyte hydrogels without any additional cryoprotectants was over 90% after thawing, and the result indicated that these hydrogels served as a CPA, and also have the ability to protect cells from freezing damage but without high cytotoxicity. Thus, these hydrogels appear appropriate to serve as scaffolds for the field of tissue engineering due to their excellent cryoprotective properties and high biocompatibility.Minkle Jain and colleagues synthesized a dextran-based polyampholyte hydrogel which was suitable for the encapsulation cryopreservation of murine fibroblasts . The strSupramolecular gel is a physically crosslinked gel which is self-assembled by gelators via a non-covalent bond reaction in water and organic solvent medium . The gelO-dodecyl-l-tyrosine cultured supramolecular gel system) for neural cell cryopreservation . Th. Th72]. Different hydrogel cryopreservation systems are listed in The cell cryopreservation is the main method for the long-term storage of living cells in cell-based applications. For the natural polymer hydrogel cryopreservation system, alginate or chitosan hydrogel encapsulated the initial cell via a permeable protective mechanism, which was cryopreserved at different conditions; thus, the ice formation was confined in the porous three-dimensional network structure, which minimized the cell damage. The efficiency of this cryopreservation technique depended on the shape, morphology, and size of microcapsules and the intrinsic properties of the microcapsule membrane. The synthetic polymer hydrogel has a good flexibility in its structure and properties for cell cryopreservation. However, the hydrogel membrane material with a strong chemical bond reaction could be difficult to remove after cell thawing, which could have an impact on the viability and function of thawed cells. For the supramolecular hydrogel, its weak reaction was suitable for encapsulation and cryopreservation and being removed after cell thawing. However, the different category of the supramolecular hydrogel is yet to be developed and the cell types which are cryopreserved should also be extended. The association of other technologies, such as multicomponent CPA cryopreservation and the microchannel method, may be the subject of future research in hydrogel cryopreservation systems.


Background: Kawasaki disease (KD) is a childhood acute febrile vasculitis of unknown aetiology. The diagnosis is based on clinical criteria, including unilateral cervical lymphadenopathy, which is the only presenting symptom associated with fever in 12% of cases. A prompt differential diagnosis distinguishing KD from infective lymphadenitis is therefore necessary to avoid incorrect and delayed diagnosis and the risk of cardiovascular sequelae. Case presentation: We describe the case of a 4 years old boy presenting with febrile right cervical lymphadenopathy, in which the unresponsiveness to broad-spectrum antibiotics, the following onset of other characteristic clinical features and the evidence on the magnetic resonance imaging (MRI) of retropharyngeal inflammation led to the diagnosis of incomplete and atypical KD. On day 8 of hospitalisation , one dose of intravenous immunoglobulins  was administered with rapid defervescence, and acetylsalicylic acid (4 mg/kg/day) was started and continued at home for a total of 8 weeks. Laboratory examinations revealed a reduction in the white blood cell count and the levels of inflammatory markers, thrombocytosis, and persistently negative echocardiography. Clinically, we observed a gradual reduction of the right-side neck swelling. Fifteen days after discharge, the MRI of the neck showed a regression of the laterocervical lymphadenopathy and a resolution of the infiltration of the parapharyngeal and retropharyngeal spaces. Conclusion: Head and neck manifestations can be early presentations of KD, which is frequently misdiagnosed as suppurative lymphadenitis or retropharyngeal infection. A growing awareness of the several possible presentations of KD is therefore necessary. Computed tomography (CT) or MRI can be utilised to facilitate the diagnosis. Kawasaki disease (KD) is an acute self-limiting vasculitis that occurs in childhood, also known as acute febrile mucocutaneous lymph node syndrome, described for the first time by Dr. Tomikasu Kawasaki in 1967. The disease involves small and medium-sized blood vessels and leads to coronary artery aneurysms in approximately 25% of untreated cases, with increased risks of cardiovascular complications and mortality . KD typiThe pathogenesis of KD is related to an abnormal immune response to environmental and infectious triggers ,9,10. ThLymphadenopathy occurs in 50–70% of patients with KD, which is less frequent than the prevalence of the other diagnostic criteria that are present in approximately 90% of cases . CervicaA 4 year old boy presented to our paediatric unit with a 5 day history of right laterocervical swelling and neck pain without restriction of movement, dysphagia or dyspnoea, and a 3 day history of fever. Antibiotic therapy with amoxicillin-clavulanate was started and continued for 72 h without clinical improvement. Physical examination showed right-side, painful, tender, tense–elastic laterocervical lymphadenopathy with no inflammation of the overlying skin and non-suppurative pharyngotonsillitis. The remaining superficial lymph nodes were not affected and the liver and spleen were palpable at the costal margin. The initial laboratory tests showed neutrophilic leucocytosis, an increase in the levels of inflammatory markers  and ferritin in the normal range . The neck ultrasound highlighted multiple hypoechoic lymph nodes in the right anterolateral compartment, with a tendency towards confluence and a maximum diameter of 34 mm that displaced muscular and vascular bundles. Toxoplasma gondii, Bartonella henselae, Mycoplasma pneumoniae and Adenovirus, were negative. Abdominal ultrasounds and chest radiography were normal. On the first day of hospitalisation, intravenous antibiotic therapy was started with ceftriaxone, vancomycin and clarithromycin based on the suspicion of suppurative lymphadenitis. The blood peripheral smear, blood culture and infectious serology, including Epstein-Barr, cytomegalovirus, On day 6 of hospitalisation, due to the persistence of daily fever, the elevation of the level of C reactive protein (8 mg/dL) and the lack of clinical or ultrasound improvements in the neck lymphadenopathy, antibiotic therapy was implemented with the replacement of ceftriaxone with meropenem . MagnetiBased on this clinical presentation  and on the lack of response to different broad-spectrum antibiotics, incomplete KD was hypothesised. The echocardiography performed on the sixth day did not show coronary artery abnormalities. No evidence of uveitis was found on the eye exam. On day 8 of hospitalisation , one dose of intravenous immunoglobulins  was administered with rapid defervescence , meropenFifteen days after discharge, the MRI of the neck showed a regression of the laterocervical lymphadenopathy and a resolution of the infiltration of the parapharyngeal and retropharyngeal spaces.The management of this patient was approved by the Ethics Committee of Umbria Region (PED-2019-08), and both parents provided written informed consent for the evaluation of the child. The Ethics Committee of Umbria Region approved the publication of this case, and both parents provided written informed consent for the publication of this manuscript, including MRI imagingphotos.The prompt diagnosis of KD remains a challenge for clinicians who have to be alert to identifying head and neck manifestations with a poor response to broad-spectrum intravenous antibiotic therapy as possible early presentations of KD. This case report shows that retropharyngeal involvement with oedema, cellulitis and abscess-like lesions is a rare but possible manifestation of KD. Computed tomography (CT) or MRI can be utilised to facilitate the diagnosis.Cervical lymphadenopathy is a frequent pathological condition in children. A careful differential diagnosis, especially among infectious diseases, KD and lymphoproliferative disorders, is fundamental to avoid incorrect and delayed diagnosis ,12. In KRegarding ultrasound for cervical lymphadenopathy, recent studies suggest that there are no sensitive or specific findings in patients with KD to differentiate this disease from bacterial lymphadenitis, even if the more commonly detected characteristics are multiple hypoechoic enlarged nodes with normal echogenic hilum and well-defined contour forming a mass known as a “cluster of grapes” ,16. PuruThe associations of cervical lymphadenopathy, retropharyngeal oedema, cellulitis or abscess-like lesions in KD have been increasingly described ,17. DeepThe retropharyngeal abnormalities in KD are presumably linked to the vasculitis of microvessels that cause oedema and inflammation . In the In our case, an initial erroneous diagnosis of cervical bacterial lymphadenopathy delayed the correct identification of incomplete and atypical KD when other characteristic features appeared sequentially. The MRI images showed the presence of retropharyngeal involvement without clinical response to antibiotic therapy, but a rapid response to IVIG treatment.Our case showed that persistent febrile cervical lymphadenopathy with unresponsiveness to broad-spectrum antibiotics, and the evidence on the MRI of retropharyngeal inflammation should lead to consideration of incomplete and atypical KD. A growing awareness of the several possible presentations of KD is therefore necessary. CT or MRI can be utilised to facilitate the diagnosis. This report is very valuable for practitioners, because cervical lymphadenopathy and fever are usually common in bacterial infections, and antibiotics are prescribed as first-line treatment. If no effect is observed, KD must be considered if the fever lasts, other symptoms occur and inflammatory markers increase.


Advances in nanotechnology and nanomaterials have enabled the development of functional biomaterials with surface properties that reduce the rate of the device rejection in injectable and implantable biomaterials. In addition, the surface of biomaterials can be functionalized with macromolecules for stimuli-responsive purposes to improve the efficacy and effectiveness in drug release applications. Furthermore, macromolecule-grafted surfaces exhibit a hierarchical nanostructure that mimics nanotextured surfaces for the promotion of cellular responses in tissue engineering. Owing to these unique properties, this review focuses on the grafting of macromolecules on the surfaces of various biomaterials  to create nanostructure-enabled and macromolecule-grafted surfaces for biomedical applications, such as thrombosis prevention and wound healing. The macromolecule-modified surfaces can be treated as a functional device that either passively inhibits adverse effects from injectable and implantable devices or actively delivers biological agents that are locally based on proper stimulation. In this review, several methods are discussed to enable the surface of biomaterials to be used for further grafting of macromolecules. In addition, we review surface-modified films (coatings) and fibers with respect to several biomedical applications. Our review provides a scientific update on the current achievements and future trends of nanostructure-enabled and macromolecule-grafted surfaces in biomedical applications. The development of biocompatible and biodegradable polymers has enabled the use of injectable and implantable biomaterials for various diseases. To successfully utilize the advantages of their functions for disease treatment, the key component of the strategy relies on the surface properties of the materials. From a materials science (or polymer science) point of view, previous efforts have been focused on the development of polymeric drug carriers and/or tissue scaffolds with bulk properties that match the surrounding tissues for a particular application. However, adverse side effects in device rejection were noticeable as a result of inflammation, abnormal tissue growth, and cytotoxicity. In addition, the conventional polymer surfaces exhibited poor biocompatibility, resulting in critical obstacles, such as undesirable protein adsorption and cell adhesion, for biomedical applications. Based on these observations, the focus of the injectable and implantable biomaterials has translated into the understanding and the design of desirable surfaces properties for the materials. Since most of the injectable and implantable biomaterials are based on polymers, the effects of surface hydrophobicity, polarity, roughness, and texture will play important roles in cellular responses. To solve these problems, numerous basic and applied works have been explored on the surface modifications of polymeric materials for biomedical applications ,2,3.The importance of surface properties in injectable and implantable biomaterials was addressed through surface modifications in various fields with different innovative techniques, including chemical and physical processes. Physical processes utilize techniques to induce surface segregation. For example, polymeric surfaces may be radiated by electromagnetic waves or oxidized by gases in order to create the surface features. In contrast, chemical modifications involve the use of wet-treatment, blending, coating, and etching. In this review, we provide several methods for the surface modifications of materials, in which macromolecules can be grafted onto the surface of the materials providing improved surface properties. Grafting is a process to attach molecules onto the surface of an object, and its advantages include the easy introduction, controllable density, and exact localization of graft chains at the surface, without changing the bulk properties of the materials. In some cases, graft chains via covalent bonding onto polymer surfaces are necessary to avoid molecule delamination with long-term chemical stability, which has a superior advantage over physical grafting methods.The primary function of the injectable and implantable biomaterials is to provide therapeutic performance locally. Surface grafting of macromolecules not only enhances the compatibility of the materials with surrounding tissues, but it also can be utilized as the module for drug delivery . In the Surface functionalization of polymers by grafting (“graft polymerization”) is of utmost importance in biomedical, environmental, and industrial applications ,5,6. WheGrafting by chemical means can be distinguished into three major pathways: free radical, ionic, and living polymerization ,11,12. IPlasma treatment is an efficient way to add functional groups to biomaterial surfaces, create closer pore membranes, and alter nanostructure membranes symmetrically . In thisUltraviolet radiation is an inexpensive, clean, and straightforward method for surface grafting of polymers ,30. ThisPolymeric structures and other macromolecules can also be changed by high energy γ-radiation, which causes the induction of radicals, ions, and free electrons. These created reactive sites on a polymer backbone can react with a monomer producing a grafted polymer ,35,36. IIn the first method, the irradiation of macromolecules can cause homolytic fission; thus, resulting in the formation of free radicals on the polymer . AlthougFinally, ionic grafting is based upon the irradiation of the polymer to generate the polymeric ion (cationic or anionic), and subsequently, it is reacted with the monomer to produce the grafted polymer ,36. IoniIn this grafting method, radicals are generated by enzymes. Enzymatic grafting is environmentally clean and has a high specificity; thus, allows for the synthesis of almost pure modified products without homopolymers ,43,44,45The use of nanoparticles to modify the polymer surface is an effective way to enable cell adhesion . There iLaser-induced periodic surface structures (LIPSS) can be formed under specific conditions when solid substrates are treated with laser irradiation . These LThe biocompatibility of a polymer substrate can also be modified using ion implantation. This method has the capability of increasing both the adhesion and the resulting proliferation of cells . It is bContaminations from various proteins and microbicides on the surface of implantable and injectable devices, which are known as biofouling, were responsible for 26% of device failure in 2011, according to the Centers for Disease Control and Prevention in the United States (U.S.) . To prevN-vinylformamide (NVF), N-vinylacetamide (NVA), or N-methyl-N-vinylacetamide (MVA) for comparison in antifouling behaviors . T. T101]. Graft stenosis and occlusion are a result of neointimal hyperplasia that is caused by smooth muscle cells (SMCs). Even though SMCs are necessary for the structure and the function of the neovessel, its abnormal proliferation can damage the vascular graft ,103. Trad,l-lactide-co-glycolide) and polycaprolactone with nanopores for drug-eluting stents to increase biodegradability . T. T147]. The immobilization of proteins and peptides on the surface of electrospun fibers promotes cell growth in tissue engineering. In a study, peptide sequence E7 was immobilized on electrospun PCL fibers to promote the formation of mesenchymal stem cells (MSCs) . The in Staphylococcus aureus and a three-fold reduction of Escherichia coli over 4 h of incubation as compared to the control -lactide-co-glycolide (PLGA) and vancomycin were electrospun into fibers and were further attached to commercial and endovascular aortic stent grafts . R. Rl-lactOverall, fiber scaffolds have been widely used in cell cultures for various tissue engineering applications. The abilities to promote cell proliferation while maintaining cell phenotypic expression are beneficial in cell therapy and regenerative medicine.In light of the advances in nanotechnology, grafting of macromolecules onto the surface of polymeric coatings can create a nanostructure-enabled and/or nanotextured surface that is capable of acting as a functional device to perform the specific biomedical functions. While the various combinations of attachment methods and the types of macromolecules that are used are seemingly endless, the next breakthrough is likely on the long-term performance of these macromolecule-grafted biomaterials, which also depends on the types of diseases or pathologies they target. For example, vascular stents are required to be implanted in the body for several years and must be able to resist inflammation and thrombosis during this time period to prevent rejection, whereas foot ulcers may need weeks to months of treatment . As suchAs a result, a potential solution for future direction is to research the long-term efficacy and the effectiveness of injectable and implantable biomaterials by utilizing various "regeneration" methods for macromolecules that are attached to the surface of biomaterials. For example, macromolecules grafted onto a surface coating on vascular stents may be designed for later controlled release  from the surface along with their clotting factors or enzyme targets to be carried away by the circulation. These combined molecules circulate in the body and they may be eliminated or separated by a secondary redox reaction. Therefore, the macromolecules are activated again for further re-attachment at specific sites on the stent while the proteins and/or enzymes are carried away by our body’s own metabolism system . This paIn summary, surface modifications of the injectable and implantable biomaterials improve their biocompatibility and enable biomedical functions in thrombosis prevention and wound healing. In this review, we discussed various grafting methods to functionalize the surfaces of biomaterials for further attachment of macromolecules. Current research showed that nanostructure-enabled coating surfaces exhibited a particular nanotexture that acts as an active device to prevent thrombosis formation that is caused by traditional bare-metal stents. In addition, the grafting of macromolecules on fiber surfaces showed ability in the controlled release of drugs to promote wound healing. The improvement of surface functionalization enables the long-term use of injectable and implantable biomaterials with low device rejection rate. Finally, we illustrate our vision in future directions of surface modifications in biomedical devices where we emphasize the concept of ”re-activation” of these macromolecule-grafted surfaces. Our review provides an in-depth discussion of current technologies and future trends in nanostructure—enabled and macromolecule-grafted surfaces for biomedical applications.


Glioma constitutes the most common type of primary brain tumor with a dismal survival, often measured in terms of months or years. The thin line between treatment effectiveness and patient harm underpins the importance of tailoring clinical management to the individual patient. Randomized trials have laid the foundation for many neuro-oncological guidelines. Despite this, their findings focus on group-level estimates. Given our current tools, we are limited in our ability to guide patients on what therapy is best for them as individuals, or even how long they should expect to survive. Machine learning, however, promises to provide the analytical support for personalizing treatment decisions, and deep learning allows clinicians to unlock insight from the vast amount of unstructured data that is collected on glioma patients. Although these novel techniques have achieved astonishing results across a variety of clinical applications, significant hurdles remain associated with the implementation of them in clinical practice. Future challenges include the assembly of well-curated cross-institutional datasets, improvement of the interpretability of machine learning models, and balancing novel evidence-based decision-making with the associated liability of automated inference. Although artificial intelligence already exceeds clinical expertise in a variety of applications, clinicians remain responsible for interpreting the implications of, and acting upon, each prediction. Glioma constitutes the most common type of primary malignant brain tumor with an incidence of over 20,000 new cases a year in the United States. TreatmeFor much of the history of scientific inquiry, classical frequentist statistics have formed the basis of data analysis, with randomized clinical trial (RCT) design forming the pinnacle of evidence-based medicine . There aFigure 1) [Classical statistical methods were developed to evaluate the strength of association or effect of covariates  and a single dependent variable  within a sample population, with the aim of generalizing these conclusions to the larger population (igure 1) . In thatigure 1) .The use of machine learning provides clinicians with the analytical support for personalizing treatment decisions. Machine learning is the branch of artificial intelligence that gives computer algorithms the ability to learn through experience rather than the explicit programming of a set of rules. Statistical models typically describe the relationship between clinical factors and the outcome, whereas machine learning models typically seek to predict the outcome using these factors as input features. In the context of glioma patients, statistical approaches are particularly well suited for identifying treatment strategies and other factors associated with survival, whereas machine learning uses these factors to predict survival. Although similar mathematical models are used in both fields, modern machine learning algorithms prioritize prediction over inference, even if it is achieved at the cost of its interpretability . This alThe application of traditional machine learning is limited, however, to structured data. Typically, unstructured data from diagnostic modalities is summarized in tabular format to make the data more suitable for analysis. In the context of imaging analysis in glioma patients, this means that a neuroradiologist has to manually score predetermined variables, such as tumor location, size, extension, and contrast-enhancement pattern. However, this simplification reduces the amount of information that is contained in the raw data, places a significant time burden on the clinician or researcher, introduces human subjectivity with regard to the generation and selection of input features, and limits this selection to features that can only be measured by humans. As we are entering an era of Big Data, more and more patient-generated health data on glioma patients is heterogeneous in format, such as imaging scans, pathology slices, monitoring devices, and free text clinical communications .Deep learning has emerged as a family of techniques to maximize our use of all of these data streams and has demonstrated new and astonishing results in a variety of fields . Today, The wide use of complex diagnostic and therapeutic modalities in neuro-oncology calls for automated methods to analyze this data, but it also provides an opportune framework for the development of machine learning models. The utility of machine learning in neuro-oncology has, therefore, been explored extensively and showed excellent results, at times even beyond the performance of clinical experts . TraditiDeep learning is particularly well suited to enhance the analysis of medical imaging data because the subtle but relevant patterns within the digital information are not always detectable by clinical experts . InformiDeep learning models trained on medical imaging data achieve high accuracy with regard to histopathological diagnosis , geneticGiven the unprecedented variety and accuracy of machine learning algorithms in answering specific types of clinical questions, the use of these methods in healthcare will transform clinical care . MachineDespite their significant promise, some hurdles remain associated with the implementation of machine learning in clinical practice. Unlike the data sources used in most commercial applications of machine learning, health information including diagnostic imaging, genetic testing, and pathology specimens is protected under the law. In the United States, this is regulated by the Health Insurance Portability and Accountability Act of 1996 (HIPAA) . ResearcThe volume and complexity of the unstructured data, such as MRI, genomics, and free text clinical notes, hamper the assembly of multicenter, or even nationwide data sets. These types of datasets are still in their infancy and will require a more rigorous organizational backing, such as systematizing the inclusion criteria of studies and providing quality assurance of both image quality and veracity of associated clinical data . VariatiMachine learning algorithms are typically left unequipped with explanations that accompany their predictions, which conflicts with the fundamental inquisitive human nature that drives scientific inquiry . HoweverAs machine learning algorithms are trained on retrospective data, these algorithms may also mirror human biases in clinical decision-making . For exaCurrently, there is a growing interest in developing healthcare indicators for quality assessment and reimbursement, such as length of stay, thirty-day complication rate, non-routine discharge rate, unplanned readmissions, and patient reported outcome measures. Although these metrics are highly suitable as outcome measures in machine learning models, these algorithms do not have an understanding of good clinical practice, let alone a moral compass. They just aim to optimize the performance according to the metric that is used for analysis, regardless of any other clinical or ethical considerations. It is important, however, to understand that most of these indicators are constructs to measure, objectify, and perhaps quantify clinical care, but do not reflect good practice in itself. For example, improving overall survival is not necessarily desirable if it drastically reduces health related quality of life, and reducing the length of stay is not effective if it comes at a cost of increased thirty-day complication or readmission rate. Besides this unintentional divergence between quality indicators and good clinical practice, models can also be trained for this purpose intentionally. A decision-support tool can be programmed to increase profits for stake holders while ensuring to meet the minimum quality standards. It is therefore imperative that the potential power of such tools is monitored and regulated to ensure they are used for improving patient care above all else. While it is not possible to regulate the internal mechanisms and calculations derived by the algorithm, it will still be possible to monitor the input data, output results, the training datasets used, and the way these models are used to guide clinical care.To facilitate a safe and effective implementation of machine learning in the clinical care of glioma patients, we recommend several solutions. As large-scale, high-quality data is the cornerstone of model performance, future research should focus on harmonizing data acquisition parameters, such as the MRI machine settings, pathology specimen preparation protocols, and reporting standards for free text clinical notes. Furthermore, cross-institutional collaboration should be encouraged to gain sufficient training data but also improve external generalizability.To ensure transparency with regard to the intent and construction of each model, we support the concept of open-source coding as a requirement for the acceptance of manuscripts submitted to journals or for models that are eligible for implementation in clinical care. Making the code available on data repositories, such as GitHub, allows for reproducible research, external validation, and a timely detection and resolution of coding errors.A better understanding of the promises and pitfalls among clinicians can facilitate a safe and effective deployment of machine learning in clinical practice. By improving the interpretability of constructed models but also the computational knowledge among clinicians, a dependency on “black-box” algorithms can be reduced, and a doctor-versus-machine paradigm can be shifted to a doctor-and-machine paradigm. Several studies that evaluated the combined performance of clinical experts and machine learning models demonstrated a better performance compared to clinicians or models on their own . FurtherAlthough machine learning can produce highly accurate models, clinicians remain responsible for interpreting the clinical and personal implications of these predictions. After all, personalized medicine is not a concatenation of decisions that follow directly from series of accurate predictions. Machine learning-informed decision-making can be very different in two patients even if their predicted outcomes are the same. Machine learning should, therefore, not be considered as a substitute for clinical decision-making, but as a very powerful tool to unlock insight from untapped data sources and an adjunct to clinical decision-making.The thin line between treatment effectiveness and patient harms underpins the importance of tailoring clinical management to the individual glioma patient. The use of machine learning provides clinicians with the analytical support for personalizing important treatment decisions. Machine learning, and deep learning in particular, is capable of detecting patterns in large and complex data sets that might not even be detectable or understandable by clinical experts, thereby allowing clinicians to analyze the increasing amount of imaging, genomic, pathology, and free text data that is generated in glioma patients. The astonishing performance, as well as the lack of interpretability, raises ethical concerns in the way clinical decision-making is balanced between man and machines. Future challenges include the assembly of well-curated cross-institutional datasets, improvement of the interpretability of machine learning models, and balancing novel evidence-based decision-making with its associated liability of automated inference. Although artificial intelligence already exceeds clinical expertise in a variety of applications, clinicians remain responsible for interpreting the implications of, and acting upon, each prediction.


Aristolochia plants. These plants were widely used to prepare herbal remedies until AAs were observed to be highly nephrotoxic and carcinogenic to humans. Although the use of AA-containing Aristolochia plants in herbal medicine is prohibited in countries worldwide, emerging evidence nevertheless has indicated that AAs are the causative agents of Balkan endemic nephropathy (BEN), an environmentally derived disease threatening numerous residents of rural farming villages along the Danube River in countries of the Balkan Peninsula. This perspective updates recent findings on the identification of AAs in food as a result of the root uptake of free AAs released from the decayed seeds of Aristolochia clematitis L., in combination with their presence and fate in the environment. The potential link between AAs and the high prevalence of chronic kidney diseases in China is also discussed.Aristolochic acids (AAs) are nitrophenanthrene carboxylic acids naturally produced by  Aristolochia species (spp.) , Bragantia spp. or Asarum spp. plants that have been widely used as herbal medicines .,14.13,14the food . HoweverEnvironmental exposure to AAs has been proposed to be the main cause of BEN. Only recently, through a collaborative effort led by research groups from Hong Kong and Serbia, scientists have further supported and strengthened the hypothesis that BEN is an environmentally derived disease, by analyzing wheat and corn grains cultivated in endemic villages in Serbia . Both AAAristolochia, Bragantia, and Asarum usually grow in valley ditches, on roadsides and on hillsides as bushes at 200–1,500 meters above sea level. They can be widely found as weeds in tropical and subtropical areas, including continental Southeast Asia, Malaysia, China, tropical Africa, and South America. For instance, in China, AA-containing plants are known to grow in the south near the Yangtze River to the Yellow River Basin in Shandong and Henan provinces . Th. ThN-hyd adducts ,38. 7- [Another category of biomarkers is the biomarkers of effect. Li et al. discovered that oxidative stress participates in the development of AAN due to the significant decrease in the level of the antioxidant glutathione (GSH) . For insne (CML) . The genne (CML) . In the ne (CML) . AA-I isne (CML) . Cysteinne (CML) ,52; GSH ne (CML) . TherefoOne fundamental clinical feature of AAN is progressive kidney tubulointerstitial fibrosis, which is common in CKD and ultimately leads to end-stage renal disease . AAs havMost of the AA-intoxicated rodent models pointed to a significant role of the overexpression of transforming growth factor-β (TGF-β), an essential cytokine in fibrogenesis and stimulator of myofibroblast activation, in the development of interstitial fibrosis, although the underlying molecular events remained poorly understood in past decades ,59,60,61Recent studies also have shown that BMP-7 inhibited epithelial to mesenchymal transition (EMT) through reducing the production of TGF-β and myofibroblast activation in HK-2 cells initiated by AAs . EMT is u presents an array of challenges. There are official and sound medical records of BEN and UTUC in the Balkan regions but no data or records about AA-contaminated crops, soil, or water, presenting difficulties in analyzing and defining their geographical distribution. If there were proper records and statistics on the geographical distribution of BEN patients and AA contamination in addition to the medical records, we could target those areas with high BEN incidences and launch large-scale projects to discover the root cause of the diseases. This strategy could also be extended to countries that are suffering from CKDu.The study of AAs in the pathophysiology of BEN and other related CKDAAN does not endanger only a single country or region, since cases have been reported in many countries worldwide in the past decades . Due to With significant evidence demonstrating that AAs are strong human carcinogens and potent nephrotoxins , consideAristolochia spp. in the preparation of traditional herbal remedies, Grollman has speculated on an unrecognized linkage between AAs and global diseases [Aristolochia spp. are still allowed to be used according to the 2015 Chinese Pharmacopoeia [Owing to the widespread use of diseases . He and diseases . Such andiseases . Given tacopoeia  and the u? To answer this question, at the first stage, large-scale TCM and herbal medicine analyses are needed to differentiate AA-containing and non-AA-containing TCM and quantitate the concentration of AAs in these remedies. Furthermore, to uncover the true cause of the diseases, the clinical features of CKDu could be compared to those of AAN and BEN, and the analysis of a robust and sensitive biomarker, DNA-AA adducts, should be performed in patients with CKD, given their high persistence in target organs and unique mutation patterns. Other biomarkers, such as covalent blood protein adducts, should also be developed to obtain simple and routine clinical tests and screening for human exposure to AAs.Could AAs, therefore, be responsible for the prevalence of CKD in China or of other CKDAristolochia plants grow all over the earth in different geographic environments, worldwide surveillance for the existence of AAs in cultivation fields and in food and drug products is urgently needed. To safeguard public health, methods for remediating AA-contaminated farmland should be developed and implemented in a timely and appropriate manner in contaminated areas. The residents in the endemic areas should be immediately informed of the existence of AAs in their cultivated fields, food, and drug ingredients in order to stop the dietary intake of AAs through AA-contaminated food and to help prevent them from acquiring end-stage kidney disease and carcinoma of the upper urinary tract. Last but not least, we should investigate the molecular events involved in the carcinogenesis and fibrogenesis of AAN and CKD more vigorously to discover new therapeutic agents for appropriate disease prevention and treatment. Since


The brain is the most complex of human organs, and the pathophysiology underlying abnormal brain function in psychiatric disorders is largely unknown. Despite the rapid development of diagnostic tools and treatments in most areas of medicine, our understanding of mental disorders and their treatment has made limited progress during the last decades. While recent advances in genetics and neuroscience have a large potential, the complexity and multidimensionality of the brain processes hinder the discovery of disease mechanisms that would link genetic findings to clinical symptoms and behavior. This applies also to schizophrenia, for which genome-wide association studies have identified a large number of genetic risk loci, spanning hundreds of genes with diverse functionalities. Importantly, the multitude of the associated variants and their prevalence in the healthy population limit the potential of a reductionist functional genetics approach as a stand-alone solution to discover the disease pathology. In this review, we outline the key concepts of a “biophysical psychiatry,” an approach that employs large-scale mechanistic, biophysics-founded computational modelling to increase transdisciplinary understanding of the pathophysiology and strive toward robust predictions. We discuss recent scientific advances that allow a synthesis of previously disparate fields of psychiatry, neurophysiology, functional genomics, and computational modelling to tackle open questions regarding the pathophysiology of heritable mental disorders. We argue that the complexity of the increasing amount of genetic data exceeds the capabilities of classical experimental assays and requires computational approaches. Biophysical psychiatry, based on modelling diseased brain networks using existing and future knowledge of basic genetic, biochemical, and functional properties on a single neuron to a microcircuit level, may allow a leap forward in deriving interpretable biomarkers and move the field toward novel treatment options. Mental In other fields of biomedicine, significant progress has been made during the last decades. There has been a continuous reduction in the mortality rate of heart disease since the 1970s, and the mortality rate for several types of cancer has also started to decline , 9. A kede novo mutations) mental disorders  of the subject and, apart from cancerous tissue, generalizable to any cell type in the human body . First,http://channelpedia.epfl.ch/) and ICGenealogy (https://icg.neurotheory.ox.ac.uk/) are examples of sources for such information , each of which expresses a different set of ion channels and other proteins that change with the developmental stage of the cell and its involvement in neuronal network dynamics  , 59. ConUnlike simpler models such as integrate-and-fire models or the basic two-channel Hodgkin–Huxley model , the bioRather than simple genetic channelopathies, heritable mental disorders are typically hypothesized to be complex diseases affected by genetic variants in a variety of gene ontologies as well as by environmental factors. To this end, many types of genetic perturbations, other than variants of neuronally expressed voltage-gated ion channel-encoding genes as outlined above, can be flexibly included in computational studies of heritable mental disorders. The premise is that neuronal signalling is the common pathway for all brain biology generating thoughts, emotions, and behavior, and therefore, dysfunctional or lacking neuron firing in one form or another is a common abnormality in all mental diseases. A typical solution for modelling mental diseases other than channelopathies is to use less biophysically detailed modelling approaches, where a disease-related condition observed at a cellular or network level (instead of at the level of proteins) is implemented, and the effects of the condition on the network dynamics or circuit functions are predicted. To name a few examples, in the modelling study of Vattikuti and Chow , the autAnother new promising subfield of computational psychiatry is the biochemically detailed modelling of brain disorders. For example, computational modelling has clarified the effects of Alzheimer’s disease-related genetic variants on β-amyloid plaque formation and tau-protein phosphorylation, which are among the main hypothesized causes for Alzheimer’s disease ; ERA-NET NEURON project “SYNSCHIZ” ; Research Council of Norway ; South East Norway Health Authority ; KG Jebsen Stiftelsen, and a research grant from Mrs. Throne-Holst.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.


Endotoxin has been one of the topical chemical contaminants of major concern to researchers, especially in the field of bioprocessing. This major concern of researchers stems from the fact that the presence of Gram-negative bacterial endotoxin in intracellular products is unavoidable and requires complex downstream purification steps. For instance, endotoxin interacts with recombinant proteins, peptides, antibodies and aptamers and these interactions have formed the foundation for most biosensors for endotoxin detection. It has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove endotoxin, without compromising the quality and quantity of the end-product. However, the underlying mechanism involved during endotoxin-biomolecule interaction is still a gray area. The use of quantitative molecular microscopy that provides high resolution of biomolecules is highly promising, hence, may lead to the development of improved endotoxin detection strategies in biomolecule preparation. Förster resonance energy transfer (FRET) spectroscopy is one of the emerging most powerful tools compatible with most super-resolution techniques for the analysis of molecular interactions. However, the scope of FRET has not been well-exploited in the analysis of endotoxin-biomolecule interaction. This article reviews endotoxin, its pathophysiological consequences and the interaction with biomolecules. Herein, we outline the common potential ways of using FRET to extend the current understanding of endotoxin-biomolecule interaction with the inference that a detailed understanding of the interaction is a prerequisite for the design of strategies for endotoxin identification and removal from protein milieus. In the production of recombinant biomolecules (using Gram-negative bacteria) for pharmaceutical and biomedical purposes, a significant level endotoxin remains with the bioproduct, even after purification. Sometimes, further stringent purification results in a compromise on product quality and quantity. This brings to fore the belief that there may be some localization and time-dependent interactions holding lipopolysaccharide (LPS) and these molecules together in forms that make them difficult to separate. Some of the relevant sectors facing endotoxin associated challenges are commonly the pharmaceutical and therapeutic products manufacturing industries, the food industries, and the potable water manufacturing industries. By virtue of the dangers, it has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove undesirable traces of endotoxin from aqueous solutions, without compromising the quality and quantity of the end-product.Cell culture contamination has been a prevalent issue in most bioproduct manufacturing processes, especially in companies producing cell culture-based product such as vaccines and injectable drugs. One of the topical chemical contaminants of major concern to researchers, especially in applications involving Gram-negative bacteria bioprocessing, is endotoxin. In biotechnology, endotoxin detection and removal from recombinant proteins are critical and challenging steps in the preparation of bioproducts such as vaccines, injectable therapeutics, and useful food supplements. The reason is that endotoxin is a natural component of the bacterial expression systems widely used in manufacturing therapeutic proteins . HoweverTable 1). However, Förster resonance energy transfer (FRET) has the potential to bridge the gap, owing to its notable achievements in protein and other biomolecular studies. Herein, the article introduces the structure of endotoxin and some associated mechanistic consequences and accentuates the prospects of FRET as a promising complementary technique for the identification and analysis of endotoxin-biomolecule interaction. Also, the article presents some of the limitations of the existing detection methods for endotoxin in protein milieu and suggests how FRET could help improve the drawbacks. In no way does this article claim itself as a complete review of endotoxin and FRET; however, the essential concepts necessary for prefacing the main idea—the need to extend the frontiers of endotoxin-biomolecule interactions with FRET—have been addressed. Due to space constraints, the reader’s attention would be drawn to relevant literature with regards to principles, protocols, and technical details.Several attempts such as the study of endotoxin-biomolecule interactions ,5 and enEndotoxin is a saccharolipid which constitutes the most abundant component of the outer membrane of most Gram-negative bacteria ,10. It fFig. 1). Both names, endotoxin and LPS, are considered synonymous even though LPS is only the component in the endotoxin that stimulates the toxicity effect  or absence [−]) and quantitative demands [Interestingly, ratiometric FRET and other FRET techniques are equally capable of yielding the same results and even giving extra details such as the binding dynamics, conformational specificities, localization and the intermolecular distances between the LPS and the relevant molecule. These spatial and temporal details obtainable  demands .et al. [e.g., proteins, vaccine, therapeutic drugs, etc.) even in the presence of cell-lysing chemicals and extraction sorbents are woefully deficient in the literature. Most of the endotoxin removal strategies currently existing employ the use of detergents, chelating agents, chaotropic agents, or bile salt. However, the underlying mechanism behind these procedures is less understood; thus, explaining the incessant challenge. Fortunately, such an interaction could be highly captured under the nanometer resolution of FRET with appreciable insights.Correspondingly, Voss et al.  demonstret al. . In spitin vivo interaction with the relevant biomolecule  becomes traceable. In a similar fashion, fluorescent dyes could be used for in vitro investigation. The ensuing information is what will be of relevance in the planning of better ways of detecting, quantifying and reducing endotoxin contamination in biomanufacturing. The preliminary information regarding the unique behavior of endotoxin at different manufacturing conditions  could help engineers develop a process that best minimizes endotoxin-bioproducts interaction hence the ease of product purification.It is evident, from the scope of published literature on endotoxin investigation, that the understanding of endotoxin-biomolecule interplay based on high-resolution imaging techniques is suffering a dearth. Although some researchers have demonstrated the use of Fourier transform infrared (FTIR) microscopy , UV/visiFig. 5) may not be much different from that of the most practiced protein-protein interaction analysis. Moreover, the fundamental conditions that need to be satisfied before FRET occurs will remain unchanged since FRET is a condition bound mechanism. However, the application of FRET in endotoxin-biomolecule investigations may, perhaps, necessitate simple algorithmic modifications based on the fundamental principles of FRET; thus, an area requiring investigation.In principle, the application of FRET in endotoxin-protein interaction analysis  the binding kinetics between molecules of endotoxin and the biomolecule of interest; (2) the localization and spatial distribution of endotoxins and biomolecules in complexes; (3) the relative proximity of the molecules; (4) the endotoxin-biomolecule physiological responses and conformational changes; and (5) the endotoxin-biomolecule high-resolution FRET images.et al. [via FRET [These outlines are generally the stronghold of FRET; however, the existing body of literature is in paucity of such information. Cho et al.  has presvia FRET . Such inThe main challenge in FRET studies is in association with materials and instrumentation selection. In terms of the materials, one possible challenge would be in association with the stability differences between the endotoxin and the biomolecule of interest. The thermal and chemical stabilities of endotoxin are significantly superior to that of most biomolecules ,8,46 theThe deficiencies in the existing knowledge on endotoxin-biomolecule interactions are significant contributors to the persistent challenges in downstream separation and purification of cell culture-based bio-products, especially regarding Gram-negative bacteria. FRET spectroscopy could complement and consolidate existing knowledge on endotoxins and biomolecules, as well as their interplay. Such results are prerequisite for the development of efficient biomolecule purification strategies. The promising advantages of FRET should echo resonating ideas in the minds of researchers to explore its possible use for endotoxin-biomolecule studies and subsequent development of endotoxin identification and quantification tool.