The Bigger Picture: Why Oral Mucosa Heals Better Than Skin.
Ontology highlight
ABSTRACT:
SUBMITTER: Waasdorp M
PROVIDER: S-EPMC8394648 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description: Not available
| S-EPMC6560559 | biostudies-literature
Project description:A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.
| S-EPMC3020923 | biostudies-literature
Project description:This special issue intends to review and update our understanding of the antimicrobial defense mechanisms of the skin and oral cavity. These two environments are quite different in terms of water, pH, and nutrient availability, but have some common antimicrobial factors. The skin surface supports the growth of a limited range of microorganisms but provides a hostile environment for others. The growth of most microorganisms is prevented or limited by the low pH, scarcity of some nutrients such as phosphorus and the presence of antimicrobial peptides, including defensins and cathelicidins, and antimicrobial lipids, including certain fatty acids and long-chain bases. On the other hand, the oral cavity is a warm, moist, nutrient rich environment which supports the growth of diverse microflora. Saliva coating the oral soft and hard surfaces determines which microorganisms can adhere to these surfaces. Some salivary proteins bind to bacteria and prevent their attachment to surfaces. Other salivary peptides, including defensins, cathelicidins, and histatins are antimicrobial. Antimicrobial salivary proteins include lysozyme, lactoferrin, and lactoperoxidase. There are also antimicrobial fatty acids derived from salivary triglycerides and long-chain bases derived from oral epithelial sphingolipids. The various antimicrobial factors determine the microbiomes of the skin surface and the oral cavity. Alterations of these factors can result in colonization by opportunistic pathogens, and this may lead to infection. Neutrophils and lymphocytes in the connective tissue of skin and mucosa also contribute to innate immunity.
| S-EPMC7235825 | biostudies-literature
Project description:Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
| S-EPMC6431247 | biostudies-literature
Project description:Single nucleotide polymorphisms (SNPs) that cluster in the first intron of fat mass and obesity associated (FTO) gene are associated obesity traits in genome-wide association studies. The minor allele increases BMI by 0.39 kg/m(2) (or 1,130 g in body weight) and risk of obesity by 1.20-fold. This association has been confirmed across age groups and populations of diverse ancestry; the largest effect is seen in young adulthood. The effect of FTO SNPs on obesity traits in populations of African and Asian ancestry is similar or somewhat smaller than in European ancestry populations. However, the BMI-increasing allele in FTO is substantially less prevalent in populations with non-European ancestry. FTO SNPs do not influence physical activity levels; yet, in physically active individuals, FTO's effect on obesity susceptibility is attenuated by approximately 30%. Evidence from epidemiological and functional studies suggests that FTO confers an increased risk of obesity by subtly changing food intake and preference. Moreover, emerging data suggest a role for FTO in nutrient sensing, regulation of mRNA translation and general growth. In this Review, we discuss the genetic epidemiology of FTO and discuss how its complex biology might link to the regulation of body weight.
| S-EPMC4188449 | biostudies-literature
Project description:We enjoy the illusion that visual resolution is high across the entire field of vision. However, this illusion can be easily dispelled by trying to identify objects in a cluttered environment out of the corner of your eye. This reflects, in part, the well-known decline in visual resolution in peripheral vision; however, the main bottleneck for reading or object recognition in peripheral vision is crowding. Objects that can be easily identified in isolation seem indistinct and jumbled in clutter. Crowding is thought to reflect inappropriate integration of the target and flankers in peripheral vision [1, 2]. Here, we uncover and explain a paradox in peripheral crowding: under certain conditions, increasing the size or number of flanking rings results in a paradoxical decrease in the magnitude of crowding-i.e., the bigger or more numerous the flanks, the smaller the crowding. These surprising results are predicted by a model in which crowding is determined by the centroids of approximately 4-8 independent features within approximately 0.5x the target eccentricity. These features are then integrated into a texture beyond the stage of feature analysis. We speculate that this process may contribute to the illusion of high resolution across the field of vision.
| S-EPMC3045113 | biostudies-literature
Project description:If two to-be-identified targets are presented in close temporal succession, identification for the second target is typically impaired. This attentional blink (AB) phenomenon has long been considered as a robust, universal cognitive limitation. However, more recent studies have demonstrated that AB task performance greatly differs between individuals, with some individuals even showing no AB in certain paradigms. Several studies have focused on these individual differences in an attempt to reveal the mechanism underlying the AB, but an overview of this approach is currently missing. Here, by reviewing studies regarding individual differences in AB task performance, we investigate how individual differences have contributed to our understanding of the AB. We show that the individual differences AB literature provides reliable indications that the AB is a multifaceted phenomenon that presumably arises from a combination of factors; individuals with higher levels of executive working memory (WM) functioning and broad attentional focus perform better in the AB paradigm than individuals with lower executive functioning of WM and narrow attentional focus. As it turns out, seeing the bigger picture certainly seems helpful for AB task performance.
| S-EPMC5050248 | biostudies-literature
Project description:When compared to skin, oral mucosal wounds heal rapidly and with reduced scar formation. Recent studies suggest that intrinsic differences in inflammation, growth factor production, levels of stem cells, and cellular proliferation capacity may underlie the exceptional healing that occurs in oral mucosa. The current study was designed to compare the transcriptomes of oral mucosal and skin wounds in order to identify critical differences in the healing response at these two sites using an unbiased approach.Using microarray analysis, we explored the differences in gene expression in skin and oral mucosal wound healing in a murine model of paired equivalent sized wounds. Samples were examined from days 0 to 10 and spanned all stages of the wound healing process. Using unwounded matched tissue as a control, filtering identified 1,479 probe sets in skin wounds yet only 502 probe sets in mucosal wounds that were significantly differentially expressed over time. Clusters of genes that showed similar patterns of expression were also identified in each wound type. Analysis of functionally related gene expression demonstrated dramatically different reactions to injury between skin and mucosal wounds. To explore whether site-specific differences might be derived from intrinsic differences in cellular responses at each site, we compared the response of isolated epithelial cells from skin and oral mucosa to a defined in vitro stimulus. When cytokine levels were measured, epithelial cells from skin produced significantly higher amounts of proinflammatory cytokines than cells from oral mucosa.The results provide the first detailed molecular profile of the site-specific differences in the genetic response to injury in mucosa and skin, and suggest the divergent reactions to injury may derive from intrinsic differences in the cellular responses at each site.
| S-EPMC3091667 | biostudies-literature
Project description:The main functions of the kidney are to excrete metabolic waste products and actively reabsorb essential molecules such as amino acids, ions, glucose and water. In humans, a wide range of genetic disorders exist characterized by wasting of metabolically important compounds. At the cellular level, more than 20 highly specialized renal epithelial cell types located in different segments of the nephron contribute to the reabsorption process. In particular, proximal tubular cells play a crucial role and are uniquely adapted to maximize reabsorption efficiency. They accommodate high numbers of transporters and channels by increasing the apical surface area in contact with the primary filtrate by forming a brush border as well as undergoing hypertrophy and hyperplasia. This adaptation is evolutionarily conserved and is detected in the primitive pronephric kidney of fish and amphibians as well as the metanephric kidney of higher vertebrates. Surprisingly, signaling pathways regulating these three processes have remained largely unknown. Here we summarize recent studies that highlight the early phases of kidney development as a critical juncture in establishing proximal tubule size.
| S-EPMC3944135 | biostudies-literature
Project description:ObjectivesTo quantify and analyse the quality of evidence that is presented in national guidelines.SettingLevels of evidence used in all the current valid recommendations in the Scottish Intercollegiate Guideline Network (SIGN) guidelines were reviewed and statistically analysed.Outcome measuresThe proportion of level D evidence used in each guideline and a statistical analysis.MethodData were collected from published guidelines available online to the public. SIGN methodology entails a professional group selected by a national organisation to develop each of these guidelines. Statistical analysis of the relationship between the number of guideline recommendations and the quality of evidence used in its recommendations was performed.ResultThe proportion of level D evidence increases with the number of recommendations made. This correlation is significant with Kendall's τ=0.22 (approximate 95% CI 0.008 to 0.45), p = 0.04; and Spearman ρ=0.22 (approximate 95% CI 0.02 to 0.57), p=0.04.ConclusionsPractice guidelines should be brief and based on scientific evidence. Paradoxically the longest guidelines have the highest proportion of recommendations based on the lowest level of evidence. Guideline developers should be more aware of the need for brevity and a stricter application of evidence-based principles could achieve this. The findings support calls for a review of how evidence is used and presented in guidelines.
| S-EPMC3918980 | biostudies-literature