Livestock rearing is the main component of global food production systems and contributes to nearly half of global agricultural production. The emerging demand for animal products is considered a food revolution in developing countries. Although livestock farming is an essential component of the global economy but faces an immense challenge to meet out the increased demand of the exploding human population and other environmental factors. As a result, understanding animal health and production is becoming mandatory. Advances in genetic and genomic technologies have played a key role in improving animal welfare and productivity for decades. Genetic development in livestock, both in terms of productivity and other functional trait complexes associated with health and animal welfare, has been greatly aided by genomic selection, which is regarded as a success story. Genomic breeding programmes offer the potential to improve cattle productivity through the utilization of molecular genetics, the detection of markers and chromosomal areas that contain quantitative trait loci, and genome mapping technology. Present breeding strategies not only account for phenotypic variance in traits but also other factors like epigenetics. Epigenetic mechanisms  have been strongly found to influence livestock traits like growth, development, and other phenotypic effects. Technologies related to omics are developing more frequently in the area of animal production. Other omics topics like phosphoproteomics, peptidomics, or lipidomics are presently used in livestock production and disease management in addition to omics methodologies such as transcriptomics, genomics, proteomics, and metabolomics. Animal breeding systems already in place now have additional dimensions due to the introduction of revolutionary ideas like animal cloning and genetic engineering. It provides a faster way to increase the frequency of desirable alleles in an animal population using genetically modified animals than traditional breeding procedures. With this background, the aim of the current research topic was to collect research data on the role of omics technologies in livestock improvement from selection to breeding decisions.The special edition of Frontiers in Genetics i.e., “Omics Technologies in Livestock Improvement: From Selection to Breeding Decisions” published 26 original research articles, 2 review papers, and 01 methodology paper. All 29 articles were focused mainly on understanding the complex interplay of genes in mediating important traits, elucidating livestock genome/transcriptome, and improving livestock yield, nutrition values, and animal welfare.Chakraborty et al.).Omics technologies are effective tools, especially when used in conjunction with advanced molecular and breeding methods. Genomic research in particular has the potential to improve the precision and efficacy of traditional breeding and advanced breeding approaches by enhancing consistency and predictability. Indeed, the information provided by genomics and other omics-technologies like epigenomics and proteomics is crucial for understanding genes and their function. Additionally, summarized the role of omics technologies in improving livestock . The regulatory structure of circRNA in testis development and spermatogenesis in cattle bulls was evaluated using RNA sequencing by Khan et al., in immature and mature Wandong cattle bull testes. In calf and bull testes, 579 of the 17,013 circRNAs were elevated and 103 were downregulated. Bull spermatogenesis and the genes ATM, GSK3B, CCNA1, KMT2C, NSD2, KMT2E, QKI, SUCLG2, HOMER1, and SNAP91 were discovered to be strongly correlated. Through genetic selection, this information may aid in enhancing bulls’ reproductive productivity .Male infertility still poses a significant problem for animals, despite significant increases in reproductive efficiency brought about by artificial insemination procedures. Recent research indicates that the spermatozoa of fertile and infertile males have different populations of RNA. Studies have also shown that spermatozoal RNA (spRNA) is essential for spermatogenesis, fertilisation, and the early stages of embryonic development. Updated various spRNA species in livestock animals, including protein-coding and non-coding RNAs and their possible impact on quality of sperms, especially motility, freezability, and fertility . There were discovered to be 684 (464 SNPs and 220 INDELs) and 607 (442 SNPs and 169 INDELs) high-impact variations unique to Kashmir and Jersey cattle, respectively. The RNA sequencing-based SNP research revealed a considerable difference between Kashmiri and Jersey cattle in terms of milk production attributes. The high-impact SNP variations in Kashmiri cattle contributed to adaptive immunity and tolerance to infectious diseases of the mammary gland. Contrarily, in Jersey cattle, enhanced pathways were mostly implicated in production and lactation maintenance. These findings offer information on breed-specific genetic diversity that can be applied to the genomic selection of animals. There are many studies like RNA sequencing leads and high-throughput genomic DNA data, which have identified the genes related to lipid storage in broilers. Using RNA-Seq and microarray data techniques, Farzad Ghafouri et al. identified and categorised candidate genes and miRNAs involved in lipid metabolism. Based on the amount of abdominal fat present, two broiler groups were selected: high and low. In the analysis, 34 genes and 19 miRNAs were detected as common. A total of seven genes were revealed as common, three being most important viz., REBF1, SREBF2, SCD, and FASN. These have a significant impact on fat metabolism, storage, and signalling pathways of endocrine glands that are triggered by PPAR, AMPK, and adipokines. This method improved our comprehension of the biological mechanisms affecting adipose tissues . In animal food industry, the genetics and physiological mechanisms that govern skeletal muscle mass production are of prime importance to study. Satellite cells are crucial for skeletal muscle growth and regeneration. scRNA-seq was used by Lyu et al. to analyse the makeup of bovine satellite cells. According to the findings, bovine satellite cells may be divided into subpopulations with different transcriptional statuses, rates of proliferation, and myogenic potential. The current study by Lyu et al. also indicates the existence of FAP cells in bovine skeletal muscle, which may help researchers devise new methods for enhancing these features or find the DNA sequences and variants linked to them in cattle .Deep RNA sequencing was utilised to discover probable single nucleotide polymorphisms (SNP) in mammary epithelial cells from two different cow breeds (Jersey and Kashmiri) in order to study the alterations in coding regions that affect milk output differences. Ahmad et al., work seeks to find high-impact SNPs in Jersey and Kashmiri cows in order to uncover the main pathways controlling milk production features in each breed using RNA-Seq data . Lameness in an animal incurs financial burden on the animal owner, making it the third largest cause of culling an animal after mastitis and infertility. This condition is caused by foot lesions which can be either infectious or non-infectious in nature. Digital dermatitis (DD), WLD and SU are the most frequent causes. A study was performed by Lai et al. to find the loci influencing the association between the genetic causes of lameness and other prevalent health conditions. Estimates of the genetic connection between DD and SU, WLD and SU were all substantially different from zero (p < 0.05), whereas estimates of the genetic association between mastitis and DD, SU with metritis, and DD with milk fever were just suggestive (p < 0.1). These estimations of the five genetic correlations were all positive. Lai et al., observed that selection against disorders of foot may also reduce vulnerability to other health disorders because of the significant genetic association estimations between foot disorders and other illnesses .Lameness in cattle is frequently brought on by two non-infectious claw lesions: sole ulcers (SU) and white line disease (WLD). Sensitivity to SU and WLD is influenced by both hereditary and non-genetic variables, and protection can be accomplished by genetic methods and herd management. Genome-wide association studies (GWAS) were conducted using generalised linear mixed model (GLMM) regression, random forest (RF) and a chunk-based association testing (CBAT) technique to find susceptibility loci for WLD, SU, SU and/or WLD, and any sort of non-infectious claw damage. Potential genes for skeletal growth and mineralization, keratin, adipose tissue, wound healing and skin lesions were present in the linked areas on BTA8 and BTA13. The abundance of correlations found in this study conducted by Lai et al., as well as previous studies that showed the intricacy of the genetic background underlying non-infectious claw lesion vulnerability . Singh et al., conducted a GWAS to find substantially related SNPs between proteins in milk and minerals in cattle. Identifying potential genes connected to milk minerals and milk protein percentage in Vrindavani cattle was the goal of their study. Protein percentage Ca, Cu, Zn, P and Fe were found to have a strong association with BTA 7, 2, 3, 14, and 2, respectively . Further, consumers mostly judge the quality of meat based on its colour. In order to aid in pig breeding programs, Liu et al. conducted a study to identify the genes associated with meat colour in Suhuai pigs. Additionally, it calculates the genetic correlation and heredity of meat colour. . Using GWAS and FST testing on Suhuai pigs, six potential genes  and 39 possible SNPs associated to flesh colour were found. These findings pave the way for genetic modification of pig flesh colour since they have functional implications for muscle growth, lipid binding and phosphatidylinositol phosphorylation. For sheep breeding industry, ewe productivity is considered the most important economic trait. Genes influencing fertility and lamb growth following parturition in Iranian Baluchi sheep were discovered using GWAS methods and gene set enrichment analysis (GSEA). The notable SNPs within or close to the genes RDX, ARHGAP20, FDX1, THBS1, ZC3H12C, and EPG5 were linked to composite features at birth. The identified pathways and genes have roles relevant to pregnancy, such as autophagy in the placenta, calcium ion transport, placental development and progesterone release and maternal immunological response. Genes NR2C1, HSD17B4, RSU1, VEZT, CUBN, PRLR, VIM. and FTH were discovered to be associated with composite features at weaning. According to Esmaeili-Fard et al., the findings imply that calcium ion transport throughout pregnancy and milk feeding lambs following parturition had the greatest influence on weight gain in comparison to other maternal origin effects . Liao et al. analysed the selectively bred group of meat rabbits and used a non-linear mixed model to fit growth curves and measure the effects of SNPs throughout the entire genome. The genetic organization of growth parameters, which is useful for applying genome selection, was also disclosed in this study, which is the first report of GWAS based on single-step NMM for longitudinal traits in rabbits. The logistic model, comprised of 87,704 SNPs in rabbits, was ideally selected and subjected to GWAS using this approach. The two growth indices mature weight (A) and maturity rate (K) were shown to be simultaneously impacted by a total of 45 important SNPs spread across 5 chromosomes. Seven positional genes were proposed as potential candidates influencing meat rabbit growth, including GBA3, KCNIP4, LDB2, PPARGC1A, GNA13, SHISA3 and FGF10 .GWAS provide opportunities for comprehensive improvement of buffalo by finding genetic variants connected with lactation and reproductive features. The work conducted by Vohra et al., intends to find novel SNPs linked with milk output, lactation consistency, milk composition and fertility features at the genomic level in Murrah buffalo using the genotype-by-sequencing technique. To run GWAS on fat percentages and SNF percentages independently, more than 38,000 SNPs were employed. GWAS was also conducted on 305 days’ worth of milk output to test lactation consistency. SNPs were found to be substantially linked with the first principal component, which explained the greatest fraction of variability in milk output. Breeding effectiveness, post-partum breeding interval, and age at sexual maturity were all taken into account as fertility features. Additionally, certain putative genetic areas that may play a part in controlling milk production and fertility in Murrah were found (p > 0.05) between the prediction accuracies produced from these genomic approaches in each scenario, ssGBLUP and BayesC techniques often demonstrated the maximum predictive performance and unbiasedness, respectively .One of the most important economic traits in swine industry which determines its profitability is the meat quality and genetics has an important role in determining such traits. Ardestani et al., conducted a study to evaluate the accuracy of standard BLUP prediction with several prominent genetic assessment techniques such as GBLUP, ssGBLUP, and BayesC for back-fat thickness (BFT), average daily gain (ADG) and loin muscle depth (LMD) parameters in Canadian swine populations. Despite the absence of any significant differences .The milk cattle breed known as Sahiwal is indigenous to the Indian subcontinent. They are renowned for their high milk production, exceptional ability to adjust to the hot, humid conditions that prevails in their native territory, and resilience to parasites, ticks, and tropical diseases. This study uses a genotyping INDUS chip to investigate the signature of selection in the genome of Sahiwal cattle. The potential signs of selection in Sahiwal cattle were discovered in 14 important regions of the genome. The most prominent locations were mapped onto BTA 6, 20, and 23, and the Pollott et al.). The Pashmina goat genome published in the current edition by Bhat et al., may offers an opportunity to understand the biology of development of this pricy and luxurious fiber . This study is one of the first attempts at providing Pashmina genomics and transcriptomic information. Using the Illumina HiSeq 2500 sequencer, a total of 294.8 GB (>100X coverage) of the whole-genome sequence data was generated from a 26 months old male Changthangi Pashmina goat. Moreover, the genomes of a wild goat and a Pashmina goat were compared, and the results showed a total of 2,823 high impact single nucleotide variants as well as minor insertions and deletions that may be related to the evolution of Pashmina goats. The complex traits of the Pashmina goat, such as annual fibre cycling, defence mechanisms against hypoxia, a method of surviving in extremely cold temperatures, adjustment to a meagre diet, and distinctions of Pashmina fibre from other fibres to avoid marketing practises, can also be understood with the aid of this study.Bioinformatic techniques were used to streamline and accelerate the process into a single step in order to identify the causative variants of full penetrance recessive genetic diseases using only nine whole genome sequenced animals. A novel mutation causing prenatal mortality in Irish moiled calves was found utilising whole genome sequencing of only three situations and six carriers. The variant call format (VCF) data file of these 9 animals was examined using four different techniques: autozygosity-by-difference (ABD), genotyping criteria (GCR), variant prediction scoring, and enrolled SNP information. Only one site (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF 002263795.1)) out of around ten million variants in the VCF file was recognised by all these techniques. The glucokinase gene contained a splice acceptor variation at this location (GCK). This study by Pollott et al., showed that only a limited number of cases and controls are needed, and that controls should exceed cases by a ratio of 2:1 and should be less closely related to cases . Vaughn et al., used a mixed linear model in fixed effects and random effects to investigate the expression of Actinin-3 (ACTN3) gene, which encodes a muscle-specific structural protein, in correlation to the feeding efficiency phenotype in Bos taurus - Bos indicus crossbred steers . It was assumed that animals with a higher proportion of fast-twitch muscle fibres are comparatively feed inefficient because the ACTN3 is exclusive to fast-twitch muscle fibres and absent from slow-twitch muscle fibres.The majority of the effort in genomic selection has focused on computational efficiency and prediction accuracy, but computing restrictions are becoming an increasingly critical factor that must be considered. A Bayes-based genomic selection model named FMixFN was created in a study by Xu et al. It combines consistent prediction ability and computational effectiveness. The needs of large breeding enterprises or combined breeding programs could be satisfied by the reliable, big data-oriented genomic selection approach known as FMixFN. The FMixFN technique is publicly available at Tao et al.). Yak, a unique reservoir of genetic material that primarily lives on the Qinghai-Tibet Plateau. A clear heterosis in production performance may be shown in cattle-yak, the hybrid offspring of yak (Bos grunniens) and cattle (Bos taurus). Through RNA sequencing, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs that differ in expression between yaks and cattle-yaks in the longissimus dorsi muscle were discovered. The ncRNAs were discovered to be associated with the proliferation and differentiation of myoblast cells, skeletal development, and signalling pathway of muscle growth using bioinformatics techniques. Huang et al. claim that this study can be utilised as a benchmark to establish the molecular framework for understanding muscle growth . The blue egg is biologically interesting as well as economically significant for consumers, egg sellers, and scientists. Studies conducted in the past mostly focused on protein-coding genes to understand the genetic pathways behind pigment deposition. The underlying mechanism by which non-coding RNAs affect the pigment deposition in various eggshell colours is still unknown. Profiled the uterine gland transcriptome (lncRNA and mRNA) of 15 Changshun blue eggshell layers using RNA sequencing. 8 and 22 lncRNA-gene pairings were predicted by combining analyses of lncRNA and mRNA profiles. According to mRNA sequencing, the majority of pathways were mostly focused on lipid-related metabolisms. The found lncRNAs influence immunological and lipid-related metabolisms, as well as pigment disposition, to exert similar effects on colour creation . The integrated co-expressed transcriptomes, i.e., mRNA and miRNA, were investigated in primary bovine myoblasts following Resveratrol treatment. According to Hao et al., this study improved our knowledge of the functions of RSV in inducing miRNA, the features of DE miRNAs in the important co-expressed component that regulate mRNAs, and it discovered new potential transcription factors and miRNAs for traits associated with meat quality .The ovulation rate, a critical reproductive characteristic for goats, determines the top limit of the female’s litter size. The rate of ovulation in the ovary is influenced by follicle growth and development. To anticipate how lncRNAs and miRNAs would interact, Tao et al., sequenced and analysed the mRNA expression profiles of pre-ovulatory follicles from goats. Out of the 895 lncRNAs that were found, 88 displayed a clear difference in expression, suggesting important impacts on the ovarian follicles in goats. LncRNA XR_311113.2 might operate as a chi-miR-424-5p sponge. This research demonstrates that LncRNAs may be a valuable new area of investigation in the context of ovarian follicular development . Heat stress in cattle exhibit a direct impact on rumen health by affecting the processes of fermentation and metabolism of rumen papillae proliferating the rumen papillae. It may adversely affect the physical membrane of the rumen epithelium to a significant degree by increasing corneum loss. HS up-regulated biological processes such sister chromatid segregation while down-regulating MAPK and NF-kB cell signalling pathways, according to an examination of the rumen papillae’s transcriptome profile. These pathways were linked to DNA replication and repair, amino acid metabolism, and other pathways that were problematic. TLR4 or Tight junction protein signalling expression did not change specifically in response to heat stress, according to Guo et al., indicating that HS had a limited detrimental impact on the ruminal epithelium’s physical barrier but did not completely destroy it. The development of mitigation techniques as well as the productivity of lactation cows is both impacted by the increase in amino acid metabolism in rumen papillae .He et al., investigated the link between ACSF3 expression and cellular synthesis of triglycerides (TG) by silencing and over-expression of ACSF3. As a result of the discovery that ACSF3 regulates cytoplasmic triacylglycerol and long-chain PUFA levels, polymorphism may be used as a diagnostic biomarker for forthcoming marker-assisted selection in the production of elevated lipid accumulation traits in beef cattle . Khan et al. developed the first comprehensive buffalo user-friendly web genomic resource (BuffGR). It contained genetic research on five buffalo breeds with major commercial importance: the Mediterranean, Egyptian, Bangladeshi, Jaffrarabadi, and Murrah . The website’s database contains information on 4504691 SSR markers across all breeds, 1458 distinct circRNAs, 37712 lncRNAs, and 938 miRNAs from the genomic sequences of the Mediterranean breed of buffalo. This data could be utilised to research the genetic diversity of many buffalo breeds. It is also possible to research post-transcriptional regulation and its function in several bovine diseases. The BuffGR can be found at http://backlin.cabgrid.res.in/buffgr/.A basic description of the inheritance patterns of alternative splicing in broiler and layer chickens is provided by Qi et al. to best explain post-transcriptional regulation during hybridization. The White Leghorn and Cornish Game chicken breeds, which have markedly different body types and reproductive characteristics, were crossed in an experiment, and the muscle, brain, and liver tissues were then sequenced to determine the inheritance patterns. High tissue and strain specificity is suggested by alternative splicing profiles. The majority of the alternative splicing genes had patterns that were conserved across all three organs, according to a study between parental strains and hybrid crossings. This study gives an overview of the alternative splicing inheritance patterns in these chicken breeds . Variable selection ssGBLUP, especially XGBoost, has prediction accuracy that is higher than other ssGBLUP methods without the exaggerated bias and dispersion that come with weighted ssGBLUP. In this study, machine learning algorithms are used, which may provide a solution to the problem of genomic selection in small populations, such as the local cow population. The techniques described in his study may help preserve indigenous cow breeds, study them, and boost their economic competitiveness. For carcass evaluation in meat industry, rib eye area is an important index used. Since this indicator is inherited and possesses genetic diversity, it can be used to improve the genetic makeup of sheep. This study conducted KASPar genotyping on five SNPs, demonstrating that the rib eye region is highly linked with SNPs in LOC105611989, DPP6, and COL12A1. These SNPs could be used as genetic markers for rib eye area molecular breeding. The findings published by Zhao et al., offer genetic factors evaluated on the rib eye region and guidance for breeding Hu sheep based on carcass features .Precision when population size is small is a significant barrier to their genomic selection; during the past several years, variable selection approaches with diverse variance have been proposed to increase breeding value accuracy. While these models might be more accurate than conventional and genetic forecasts, they also carry a correspondingly higher breeding value bias and dispersion. Mancin et al., used a number of diverse techniques in his study to increase the precision of genomic selection in a small population. They were chosen using a variety of algorithms, including XGBoost, penalised regression, and recursive feature eliminations (


Cancer stem cells (CSC) are a subpopulation of cancer cells that exhibit properties of self-renewal and differentiation and have been implicated in metastasis and treatment failures. There is mounting evidence that carcinogen-initiated mucosal epithelial stem cells acquire the CSC phenotype following exposure to environmental or infectious mutagens and are responsible for promoting the malignant transformation of premalignant (dysplastic) epithelium. CSC further contribute to the progression of dysplasia by activating signaling pathways through crosstalk with various cell populations in the tumor microenvironment. Two cell types, tumor-associated macrophages (TAM) and vascular endothelial cells (EC) nurture CSC development, support CSC stemness, and contribute to tumor progression. Despite mounting evidence implicating CSC in the initiation and progression of dysplastic oral epithelium to squamous cell carcinoma (SCC), the molecular mechanisms underlying these synergistic biological processes remain unclear. This review will examine the mechanisms that underlie the transformation of normal epithelial stem cells into CSC and the mechanistic link between CSC, TAM, and EC in the growth and the malignant conversation of dysplastic oral epithelium. Oral SCC is one of the most common malignancies worldwide . While tWhile it is well known that dysplasia often precedes the development of oral SCC, the mechanism underlying the progression of epithelial dysplasias to SCC remains uncertain –8 CSC anThe term “premalignant” or “precancerous” is best defined as a lesion or condition that is at increased risk of developing into an SCC , 10. TheLocalized lesions and systemic conditions most commonly associated with an increased risk for progressing to SCC include leukoplakia (white patch), erythroplakia (red patch), proliferative verrucous leukoplakia, lichen planus, oral submucous fibrosis, chronic hyperplastic candidiasis, actinic cheilitis, reverse smoking, betel nut chewing, discoid lupus erythematosus, and the inherited disorders dyskeratosis congenita and Fanconi anemia , 19. FroOral leukoplakia is the most common precancerous lesion. It presents as a white patch on the surface of the oral mucosa , 20–22. It is generally agreed that adult stem cells are the targets of carcinogenic agents , 26. Thede facto preneoplastic. Lesions described as leukoplakia that microscopically exhibit severe dysplasia or carcinoma in situ have taken an irreversible step toward malignant transformation  comprise a small subpopulation of cancer cells with the unique capacity to sustain tumor growth and drive tumor progression. CSC are primarily responsible for the failure of conventional and precision therapies –48. The Recent studies have revealed the indispensable role of the IL-6 signaling in facilitating the acquisition of cancer stem cell functions in coordination with NF-kB-dependent inflammatory signals derived from tumor cells and host cells –65. IL-6in situ). This is further evidence in support of the idea that CSC play a role in the progression of dysplasia to invasive SCC  , 75, 76.sive SCC .CSC exist within a complex microenvironment. Bidirectional communication between CSC and host cells plays an essential role in augmenting the tumor-promoting functions of CSC. Recent studies suggest that bidirectional communication between vascular endothelial cells, macrophages, and CSC is central in orchestrating tumor progression , 84.Vascular endothelial cells and macrophages extend the tumor promoting effect of CSC in several ways –85. In aα, HIF2α. Many of these proangiogenic mediators ae also produced by cells within the tumor microenvironment that communicate with CSC to promote angiogenesis  are a heterogeneous population of cells. In addition to phagocytic and antigen-presenting functions, they play an essential role in inflammation, resolving infections, and tissue repair. In contrast, macrophages are also responsible for tissue damage, chronic inflammatory diseases, autoimmune disorders, and tumor growth and progression , 99. Thiand MAPK –105. On erferons . Additioerferons , 107–114The process of tumor progression is frequently associated with a phenotypic switch from M1 to M2 in tumor-associated macrophages . The polMacrophages and endothelial cells influence the CSC functions through a series of reciprocal interactions between CSC, endothelial cells, and TAM . NeovascThe tumor microenvironment is defined by the distribution of various stromal cells and their sequential and mutually beneficial cellular interactions. Recent studies of CSC and the tumor microenvironment have revealed novel insights into the complex mechanisms that drive tumor progression and underlie treatment failures. For example, the bidirectional flow of growth factors and cytokines between CSC and host cells  promotes TAM protumor functions, sustains angiogenesis, maintains the CSC phenotype, thereby facilitating tumor growth and progression . CSC, liIt is well established that cancer evolves from a series of random mutational events that lead to a complex series of aberrant cellular, genetic, and molecular processes. The ability of cancer cells to adapt to changes in their environment provides them with a selective growth and survival advantage. By co-opting the regenerative properties of the host, cancer cells can utilize the bidirectional flow of information between cancer cells and host cells to their advantage. It is this unique ability of cancer cells to thrive in an otherwise hostile host environment that characterizes the dynamic cancer ecosystem –127. Con


Collective cell migration on extracellular matrix (ECM) networks is a key biological process involved in development, tissue homeostasis and diseases such as metastatic cancer. During invasion of epithelial cancers, cell clusters migrate through the surrounding stroma, which is comprised primarily of networks of collagen-I fibers. There is growing evidence that the rheological and topological properties of collagen networks can impact cell behavior and cell migration dynamics. During migration, cells exert mechanical forces on their substrate, resulting in an active remodeling of ECM networks that depends not only on the forces produced, but also on the molecular mechanisms that dictate network rheology. One aspect of collagen network rheology whose role is emerging as a crucial parameter in dictating cell behavior is network viscoelasticity. Dynamic reorganization of ECM networks can induce local changes in network organization and mechanics, which can further feed back on cell migration dynamics and cell-cell rearrangement. A number of studies, including many recent publications, have investigated the mechanisms underlying structural changes to collagen networks in response to mechanical force as well as the role of collagen rheology and topology in regulating cell behavior. In this mini-review, we explore the cause-consequence relationship between collagen network viscoelasticity and cell rearrangements at various spatiotemporal scales. We focus on structural alterations of collagen-I networks during collective cell migration and discuss the main rheological parameters, and in particular the role of viscoelasticity, which can contribute to local matrix stiffening during cell movement and can elicit changes in cell dynamics. During cell migration and tissue rearrangement, cells exert mechanical forces on their substrate via the cytoskeleton, which is coupled to the substrate via adhesions. This mechanical force results in a local strain, or deformation, of the substrate. Collagen-I networks are a common biological substrate that can facilitate single-cell or collective modes of migration and that can be deformed by cell-generated stresses . CollageThe topological and rheological properties of collagen networks and local structural changes in the network can, in turn, feed back onto cellular activity. The impact of several factors such as fiber length and diameter , fiber aNumerous previous studies have developed theoretical models to predict collagen network behavior during mechanical stress . HoweverGroups of cells generate shear and volumetric strain on collagen networks during collective migration . The manCells and groups of cells can exert both puling and pushing forces on ECM networks . For celSeveral studies using different force measurement methods indicate that cells generate mechanical forces on 3D ECM networks on the order of ∼10–100 nN . SecondaCollagen-I networks behave in a viscoelastic manner. This means that when external strain is kept constant, the network will rearrange, relaxing the network stress over time . In geneViscoelastic behavior is often measured using two types of rheological experiments: 1) a creep test, where a material is placed under constant stress and the resulting deformation (strain) is measured over time or 2) a stress relaxation test, where a constant strain is applied and stress is measured over time . In streCollagen-I network strain stiffening and the associated structural changes to the network is a multi-scale phenomenon. Strain increases at short time-scales (regimes 1 and 2) induce entropic  and enthalpic (mostly filament stretching) effects in individual filaments, leading to overall network stiffening. However, strain stiffening is relatively short-lived in collagen gels, and even for high strain rates, the stiffness returns to basal levels within ∼5 min . This reLp) of ∼18 μm, similar to their typical contour length in cells (Lp≈ Lc), which classifies actin filaments as semi-flexible polymers (Lp<< Lc), classifying them as flexible polymers . The extensional modulus of collagen-I networks is several times larger than the compressional modulus under the same absolute strain , meaningCollagen networks can also be considered as poro-elastic, as fluid can flow within the network mesh in response to strain . NetworkExperimental evidence suggests that strain stiffening and stress accumulation also depend on the strain magnitude and the number of repeated stress relaxation cycles . At low in vitro polymerized collagen gels have demonstrated that varying polymerization conditions, for example by changing collagen monomer concentrations, polymerization temperature or pH, results in substantial changes in network organization. Increasing collagen monomer concentration, polymerization temperature or pH all lead to collagen networks with shorter filaments and smaller mesh sizes (i.e. higher density)  . Collagedensity) . Howeverdensity) . This indensity) . It is tdensity) .Just as cellular mechanical forces can induce changes in collagen-I network organization and mechanical properties, modifications in network topology and mechanics can influence cellular behavior. Collagen-I networks are complex materials, and it is difficult to independently tune elastic and viscoelastic properties. Previous studies using hydrogels such as poly-a-acrylamide have been widely used to test the effects of substrate elasticity. Cells and groups of cells typically develop more mature adhesions and exert higher forces on stiffer elastic substrates, leading to faster spreading and a biphasic change in migration speed . More reIn addition to the rheological properties of collagen-I networks caused by cell movement, local network topology can also regulate cell behavior. In particular, collagen fiber alignment has been shown to determine migration directionality. While cells embedded in isotropic collagen-I networks display overall random migration, when the networks are stretched to align filaments, cells preferentially migrate along the axis of collagen fiber alignment . Even inAsymmetries in network deformation can lead to the formation of gradients in ECM networks. It is well described that elastic stiffness gradients lead to a single- and collective migration in the direction of higher stiffness, termed “durotaxis” . EvidencECM network viscoelasticity can also impact invasive behavior from larger groups of cells, which is particularly important in the context of cancer dissemination. For cancer cell spheroids embedded in 3D collagen matrices, crosslinking collagen fibers, which leads to higher stiffness and reduced viscoelastic relaxation, leads to a reduction in cell invasion into the surrounding matrix. However, addition of the crosslinker after invasion has already begun further increases invasion, underlining the importance of the timing of network modification in affecting cellular behavior . SimilarViscoelastic behavior of the collagen-I networks during collective cell migration is determined by multi-scale molecular events occurring over serval different timescales. Cellular mechanical forces are sufficient to induce structural changes in collagen networks and can lead to rheological changes such as strain stiffening and residual stress accumulation, which depend on the magnitude and type of strain as well as the rate of strain change. In collagen networks, these effects are controlled primarily by changes in filament mobility within the network.In addition to cell-mediated changes to collagen networks, the rheological properties of collagen networks can also influence cell behavior, in particular during single-cell and collective migration. The experimental modification of network rheology offers new opportunities to study the interplay between cell-matrix interactions. Future studies probing the role of collagen network modification and the corresponding changes in cell behavior will have important implications for therapies targeting pathologies related to changes in cell and tissue dynamics, such as cancer metastasis.


Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs. Historically, crop domestication and improvement involving recurrent selection to increase the frequency of desirable yield traits led to a massive loss of genetic variation  than in the cultivated species, indicating that CWR can be used as a source for new variability in breeding programmes  transcription factor, the main repressor of flowering. However, the cold-induced epigenetic changes at AtFLC chromatin are reset during gametogenesis to guarantee that the cold exposure and vernalization response synchronize flowering to the optimal season in the following generation  for regulating adaptation to the environment  (Triticum turgidum subsp. dicoccoides), found in nature as a wild species, is considered as the primary progenitor of domesticated hexaploid bread wheat and tetraploid durum wheat. Since its rediscovery in Israel by Aharon Aaronsohn in 1906  locus on a naturally occurred variant. In the Cnr epimutant, normal fruit ripening was found to be inhibited because of the hypermethylation of a short region located 2.3–2.5 kb upstream of the LeSPL-CNR transcriptional start site , a gene encoding a 2-methyl-6-phytylquinol methyltransferase and influencing pigment accumulation and vitamin E biosynthesis in tomato. Differences in VTE3 transcriptional activity have been reported in introgression lines (ILs) obtained from crosses between the wild S. pennellii and S. lycopersicum (cv. M82). Variation in VTE3 activity was also detected in several Andean tomato landraces, commercial cultivars, and wild species differing in their capacity to accumulate vitamin E  gene was found to preside over this process. In the sldml2 mutant lines, fruit ripening was inhibited via hypermethylation with a negative consequence on the expression of well-known ripening-associated transcription factors and genes involved in carotenoid biosynthesis and ethylene biosynthesis and signalling  approach, Zhong et al.  found suRIPENING INHIBITOR (RIN), the fruit-specific ethylene biosynthetic ACS2 (1-aminocyclopropane-1-carboxylic acid synthase ACC 2), and ACO (ACC oxidase) genes, in non-ripening tissues, such as leaf and immature fruit. H3K27me3 was removed from these regions as the fruit matured, suggesting that its decline might be necessary for ripening induction mutant lines with characterized offspring.The unifying picture emerging is that phenotypic diversity in tomato is higher than expected based on the available genetic variation alone. However, although much has been learned so far, epialleles and epiQTLs associated with quality traits in tomato remain limited to a handful of examples. This emphasizes the need to explore further the epigenetic variation not only in Overall, identifying the key epialleles involved in plant development and adaptation to the environment, their mode of inheritance and heritability, and their effect on transcription are instrumental for CWR epigenetic variation exploitation. Next-generation sequencing (NGS) techniques are routinely used to analyse (epi)genomes and transcriptomes in many plant species. One clear advantage of NGS techniques for examining genomes is that they can be applied to both model  and non-model (without a genome sequenced or with no or limited annotation) plants. In addition, they allow data comparisons within and among populations and species and across environmental scales. The use of multiple NGS methods, such as genome sequencing and RNA sequencing , can be combined with proteomics and metabolomics and may ultimately make characterization of crop plant diversity possible at functional level. This is of course also fundamental to all steps of PGR conservation and particularly for the utilization of CWRs in plant breeding. In recent years, the most commonly used platforms for high throughput in non-model plant species include Illumina/Solexa, 454/Roche, ABI/SOLiD, and Helicos. Additionally, NGS can be used for studying DNA methylation, DNA–protein interactions, chromatin accessibility, and histone modifications genome wide.To analyse and interpret the data generated with next-generation sequencing (NGS), a plethora of bioinformatics tools and algorithms have been developed. For instance, more than 20,000 bioinformatics tools are listed in the bio.tools . DNA methylation is highly enriched in heterochromatic transposable elements (TEs) and repetitive DNA sequences, where it plays a prominent role in transcriptional silencing. Densely methylated gene regulatory regions are also associated with transcription repression. By contrast, cytosine methylation within transcribed regions  is found in constitutively transcribed genes. The function of this type of intragenic methylation is not well understood  coupled with NGS (BS-seq). Whole-genome bisulphite sequencing (WGBS) permits to distinguish any 5mC (5-methylcytosine) from C  have a role in almost all biological processes, and they are critical in heritable epigenetic variation. RNAs are functionally classified into two principal categories: microRNAs (miRNAs) and short interfering RNAs  genetic monitoring. (Epi)genetic monitoring, which is the quantification of temporal changes in population, genetics, and dynamics metrics, constitutes a method with a prognostic value and an important tool for the protection of biodiversity (Aravanopoulos In conclusion, there is a crucial need to improve food and fuel supply production efficiency for an ever-growing population in the modern world. Proper use of epigenetic variation from CWR and other gene pools may provide new opportunities for crop improvement and agrobiodiversity preservation. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers epiQTLs. Furthermore, the development of epigenome-editing tools paved the way for monitoring and manipulating crop epigenomes. For efficient use of epigenetic variation for crop improvement and agrobiodiversity preservation, it will be crucial to pursue research aimed at elucidating how to predict stability for epigenetic variants so that we can use epigenetics for the stable improvement in agronomically important traits.


Chest x-ray (CXR) is commonly used (when available) to support clinical management decisions for child pneumonia and provide a reference standard for diagnosis in research studies. However, its diagnostic and technical limitations for both purposes are well recognised. Recent evidence suggests that lung ultrasound (LUS) may have diagnostic utility in pneumonia. This systematic scoping review of research on the utility of CXR and LUS in the management of severe childhood pneumonia aims to inform pragmatic guidelines for low- and middle-income countries (LMICs) and identify gaps in knowledge.We included peer-reviewed studies published between 2000 and 2020 in infants and children aged from one month to nine years, presenting with severe pneumonia. CXR studies were limited to those from LMICs, while LUS studies included any geographic region. LUS and CXR articles were mapped into the following themes: indications, role in diagnosis, role in management, impact on outcomes, and practical considerations for LMIC settings.85 articles met all eligibility criteria, including 27 CXR studies and 58 LUS studies. CXR studies were primarily observational and examined associations between radiographic abnormalities and pneumonia aetiology or outcomes. The most consistent finding was an association between CXR consolidation and risk of mortality. Difficulty obtaining quality CXR images and inter-reader variability in interpretation were commonly reported challenges. Research evaluating indications for CXR, role in management, and impact on patient outcomes was very limited. LUS studies primarily focused on diagnostic accuracy. LUS had higher sensitivity for identification of consolidation than CXR. There are gaps in knowledge regarding diagnostic criteria, as well as the practical utility of LUS in the diagnosis and management of pneumonia. Most LUS studies were conducted in HIC settings with experienced operators; however, small feasibility studies indicate that good inter-operator reliability may be achieved by training of novice clinicians in LMIC settings.The available evidence does not support the routine use of CXR or LUS as essential tools in the diagnosis and initial management of severe pneumonia. Further evaluation is required to determine the clinical utility and feasibility of both imaging modalities in low-resource settings. Pneumonia is a leading cause of death in under-five children living in under-resourced settings . AccuratCurrently, chest x-ray (CXR) is the primary imaging modality for pneumonia and is commonly used as a reference standard for the diagnosis of pneumonia . HoweverLung ultrasound (LUS) has been used to recognise complications of pneumonia, such as pleural effusion , and is This scoping review aimed to systematically map and examine the literature on utility of CXR and LUS in children with severe pneumonia, to guide pragmatic recommendations for resource-limited settings.This study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement for Scoping Reviews (PRISMA-ScR).The search strategy was drafted by an experienced research librarian using Medical Subject Heading (MeSH) terms and keywords and refined through team discussion. We searched MEDLINE, Embase, PubMed, and Global Index Medicus for English-language studies published from January 1, 2000, to July 31, 2020. We reviewed reference lists of included papers for additional articles which may have been missed. We included studies of children (aged one month to nine years) with acute severe pneumonia which evaluated the role of either LUS or CXR in relation to one or more of our pre-defined themes: indications for the imaging, role of imaging in diagnosis (including diagnostic accuracy of LUS), role of imaging in management, impact of imaging on patient outcomes, feasibility, and practical considerations for low- and middle-income countries (LMIC). As the use of LUS for pneumonia is novel and not established globally, we included LUS studies from any geographic region, while CXR studies were limited to those from LMIC. The search strategy and details of the selection process are presented in Appendix S1 and Appendix S2 in the We used the Covidence electronic platform  for record management from screening to data extraction stages. Two reviewers independently assessed articles for relevance, and discrepancies were resolved by discussion, including a third reviewer where necessary. We used a pre-defined, custom-created data extraction template in Covidence to capture data on study design, aims, geographic setting, key findings, and limitations. Diagnostic accuracy of LUS has been explored in several recent systematic reviews and meta-analyses. Hence, we utilised the existing reviews to pool these results, so limited data were extracted from original studies evaluating LUS diagnostic accuracy. We classified research articles first by imaging modality, and then by theme. A single article could be classified into multiple thematic categories if it had more than one major focus. We utilised descriptive statistics to summarise characteristics of research papers and presented key results in a narrative format.Our search yielded 3540 individual studies; additional three studies were identified from references of other articles  included children with WHO severe or very severe pneumonia (as per the 2005 definition) while the remaining had a broader inclusion criterion for pneumonia and severity. No studies evaluated children based on the WHO 2014 definition of severe pneumonia. Most CXR studies  provided observational data about associations between CXR abnormality and clinical course, while one systematic review addressed predictors of pneumonia severity.Of the 58 articles examining the role of LUS in severe pneumonia, most original studies  and all systematic reviews (n = 8) primarily evaluated diagnostic accuracy. One-third  of LUS studies were conducted in LMICs, primarily addressing diagnostic accuracy  and feasibility .There were no studies evaluating indications for CXR or LUS. Included studies that did examine patient outcomes examined the association between imaging findings and patient outcomes rather than the impact of using the particular imaging modality. Further details of the nature and distribution of CXR and LUS studies can be found in Appendix S3 and S4 in the ). Most studies (80%) were conducted in LMICs. Only three studies were conducted solely in a low-income country (two in The Gambia and one in Ethiopia) and two were conducted over multiple sites which included low-income countries. Most CXR studies (92%) were based in emergency departments (EDs) or inpatient settings. One study was conducted in four peri-urban, primary health facility level study sites in Pakistan [The 26 original CXR studies had heterogenous study aims and designs  correlated poorly with radiographic pneumonia diagnosis ,18,27. IA normal CXR was commonly reported (24%-72%) in children with WHO-defined severe pneumonia ,30,32,36Streptococcus pneumoniae isolated on blood culture or PCR were unlikely to have a normal CXR  = 92%) [(P < .001). A study of 209 children in Brazil identified associations between a normal CXR and presumed viral pneumonia, as well as abnormal CXR and presumed bacterial pneumonia; however, assigning bacterial or viral aetiology on CXR alone would misclassify 30%-50% of cases [Two studies ,16, incl) = 92%) . AlveolaEighteen studies evaluated associations between CXR abnormalities and severity of pneumonia , while pooled specificity was slightly lower (range = 87%-96.1%). Compared with CXR, LUS had higher sensitivity in identifying lung consolidation and had a high negative predictive value for pneumonia ,43,44,48(P < .01), pleural effusion (P = 0.04), and consolidation (P = 0.26) in this patient population [Factors which may impact diagnostic accuracy of LUS include operator experience, presence of comorbidities, and patient age. LUS studies of diagnostic accuracy have primarily been conducted in children without significant comorbidities. A study from the USA evaluated children with suspected pneumonia and comorbidities such as malignancy, who required a CT chest as part of their clinical care . The accpulation . Three spulation ,42,44 pepulation  reportedAll systematic reviews reported heterogeneity between studies as a consistent limitation, including in operator experience, ultrasound technique, equipment utilised, and sonographic criteria for pneumonia.The characteristics, aims, and findings of the five studies evaluating LUS in diagnosis of severe pneumonia are presented in Four out of five studies evaluating LUS in diagnosis of severe pneumonia were conducted in LMICs ,80-82. TP = 0.68). Consolidation occurred in 33% of children with WHO-defined severe pneumonia (n = 12). A study conducted in Slovenia [LUS pneumonia correlated poorly with WHO-defined pneumonia ,80,83. INo study directly assessed the impact of the use of LUS on patient outcomes. Eight studies evaluated the association between LUS abnormalities and outcomes, one of which  was fromIn 364 children with suspected community-acquired pneumonia in Italy and Taiwan, LUS was used to identify surgical complications -91. LUS Nine studies ,62,92-97Although CXR is widely used for child pneumonia management, there is a lack of evidence to inform the optimal or pragmatic use of CXR for children presenting with possible pneumonia. Most existing research explored CXR as an independent tool in pneumonia diagnosis or evaluated association between CXR findings and patient outcomes, with significant limitations identified. Research evaluating LUS has focused mainly on diagnostic accuracy, and utility and feasibility are yet to be determined. Given the challenge of lack of a ‘gold standard’ for pneumonia diagnosis, ascertaining the precise diagnostic accuracy of CXR and LUS for pneumonia remains elusive.While CXR had suboptimal performance as an independent tool in severe pneumonia, there was little high-quality evidence to support, refute, or guide the use of CXR as it is conventionally interpreted – with consideration to clinical and contextual variables such as age, comorbidities, duration of illness, and prior antibiotic treatment. Besides for diagnostic clarification, CXR is often used to investigate treatment failure and identify complications, comorbidities, or alternate diagnoses. However, there were no studies evaluating these indications for CXR. The lack of clear evidence is reflected in the substantial variation in national and international guidelines for use of radiographs in severe pneumonia in HIC and LMIC settings .Despite many evidence gaps, there were a few consistent themes in the literature. Radiographic “dense” consolidation was associated with mortality in several studies from resource-limited settings. This has not been a convincing finding globally, and a recent systematic review including a large proportion of studies from HICs identified multi-lobar consolidation to be more predictive of adverse outcomes . The varLUS is superior to CXR in the detection of lung consolidation and pleural effusion, with high sensitivity consistently identified in several meta-analyses. Specificity was also high, but contingent upon the reference standard utilised for pneumonia, possibly making it lower in children with comorbidities. There is currently no consensus on the sonographic criteria for pneumonia or on an optimal scanning protocol. Small studies indicate LUS may have diagnostic capabilities in children with undifferentiated respiratory distress. Inter-operator reliability of LUS was influenced by operator experience, yet preliminary research on its feasibility in LMICs indicates that good diagnostic performance can be achieved following training of novice operators. Despite widespread availability of point of care ultrasound devices in HIC settings, LUS is not widely utilised as a first line investigation for pneumonia , particuOur scoping review was deliberately comprehensive in order to understand the range of relevant research. Therefore, we were able to obtain a clear picture of the strengths and limitations of the available research and identify significant gaps in knowledge. For both LUS and CXR studies, the lack of an optimal reference standard for pneumonia is a major limitation for evaluation. Moreover, both modalities lack a standardised radiological definition of pneumonia for clinical settings, hindering our ability to draw robust conclusions. By excluding CXR studies from HICs, we acknowledge there may have been data applicable to resource-limited settings which we could not include in our study. Similarly, we only evaluated recent literature from the last two decades, which may have excluded older studies relevant to informing and establishing the current practice of CXR. Any conclusions drawn regarding the practical utility of CXR and LUS is based on limited data as high-quality evidence was not available and for some outcomes there were no relevant studies.The limited diagnostic accuracy, combined with challenges of obtaining high quality images and need for expert interpretation do not support large scale programmatic use of CXR for pneumonia or specific recommendations for use in health facilities in resource-limited settings. CXR is unlikely to alter the initial case management of children with severe pneumonia. There is a paucity of research into the utility of CXR in specific contexts, such as exploring alternative diagnoses and investigating sudden deterioration or poor response to treatment. In such cases, CXR may identify complications such as pleural effusion, lung abscess, pneumothorax, pneumatoceles, or characteristic features of a specific aetiology such as tuberculosis. There is currently insufficient evidence to provide recommendations for the use of LUS in the case management of children with pneumonia. The use of LUS in the management of complicated pneumonia has already been established and may have a role in improving accuracy of a clinical diagnosis of pneumonia; further exploration of its utility and feasibility in low resource settings is needed.Pneumonia is a heterogenous entity, encompassing a range of aetiologies with a clinical course dependant on host factors, clinical context, and access to timely and appropriate treatment. There is significant discrepancy between the evidence for utility of CXR and its widespread and ongoing use for pneumonia. High-quality, pragmatic research is needed to understand its role and perceived benefits, including the identification of alternate diagnoses or comorbidities in children presenting with severe pneumonia, investigation of treatment failure, or identification of complications.LUS has the potential to improve diagnostic capabilities in low resource settings, with the benefit of greater sensitivity for pneumonia than CXR. However, there remain significant gaps in knowledge. High-quality, prospective studies are warranted in resource limited settings to explore LUS’s role in improving the accuracy of clinical diagnosis as well as predicting and managing complications of pneumonia, and on the benefits and risks of this imaging tool. Although LUS findings in pneumonia are well described, consensus is required regarding scanning protocols and diagnostic criteria. Future feasibility studies should evaluate barriers to implementation and uptake of LUS by clinicians, with longitudinal follow up to understand the maintenance needs for both equipment and technical skills over time.Children with co-morbidities which increase vulnerability to pneumonia-related mortality  should be included in research of imaging tools to promote early and accurate diagnosis in this high-risk population.


According to the current holistic concept of health, all patients require a thorough assessment of their physical, psychological, and emotional well-being, not merely a confirmation or classification of disease. Thus, in the context of oral health, the measurement of the impact of oral conditions on patients’ quality of life should be part of the routine evaluation of their oral health needs and dental treatments. The importance of measuring several patient-centered outcomes has been increasingly reported in the literature as a complementary tool for assessing dental interventions.Since caries and periodontal disease are the most common oral illnesses that, often preceded by a variety of surgical, periodontal, and restorative treatments, can lead to tooth loss, prosthetic needs are commonly associated with certain factors that affect daily living.The outcomes of the existing distinct prosthetic treatments are variable and cannot be reliably assessed using clinical measures alone. For example, improvement in masticatory function after replacing missing teeth with either fixed or removable dentures may be simultaneously assessed using subjective and objective methods to effectively quantify changes in mastication with both treatment alternatives. In this context, previous experiences have demonstrated that fixed prostheses are better options than removable partial dentures in terms of mastication, after both objective and subjective assessments ,2. ThoseIn this Special Issue, it was shown that new complete dentures resulted in significant improvements in chewing ability, patient satisfaction, and oral-health-related quality of life in comparison with baseline conditions, but the standard of care for mandibular edentulism is the implant-retained overdentures because they produce further and faster significant improvements in these afore-mentioned parameters . MoreoveIn this Special Issue, besides overdentures and fixed hybrid dentures, Yoo et al. demonstrated that implant-crown-retained removable partial dentures (IC-RPDs) could also be considered a viable treatment option for those edentulous patients who need few fixed abutments . The resOn the other hand, one of the longest cohort follow-up studies (6 years) regarding the biologically oriented preparation (BOPT) technique was published in this Special Issue . In thisThe current concept of evidence-based dentistry supplements the best clinical evidence with the experiences and preferences of patients to effectively address their oral health needs.


Using a multi-omic consensus representation,padma quantifies and characterizes individualizedpathway-specific multi-omic deviations and their underlying drivers, withrespect to the sampled population. We demonstrate the utility ofpadma to correlate patient outcomes with complex genetic,epigenetic, and transcriptomic perturbations in clinically actionable pathwaysin breast and lung cancer.Malignant progression of normal tissue is typically driven by complex networks ofsomatic changes, including genetic mutations, copy number aberrations,epigenetic changes, and transcriptional reprogramming. To delineate aberrantmulti-omic tumor features that correlate with clinical outcomes, we present anovel pathway-centric tool based on the multiple factor analysis frameworkcalled  With these goals in mind, many multivariate approaches havethe advantage of being unsupervised, using matched or partially matched omics dataacross genes, obviating the need for predefined groups for comparison as in theframework of standard differential analyses. A variety of such approaches has beenproposed in recent years. For example, Multi-omics Factor Analysis(MOFA) uses group factor analysis to infer sets of hidden factors that capturebiological and technical variability for downstream use in sample clustering, dataimputation, and sample outlier detection , to quantify individualized pathway deviation scores. In particular, wepropose an approach called padma  to characterize individuals with aberrantmulti-omic profiles for a given pathway of interest and to quantify this deviationwith respect to the sampled population using a multi-omic consensus representation.We further investigate the following succession of questions. In which pathways arehigh deviation scores strongly associated with measures of poor prognosis? For suchpathways, which specific individuals are characterized by the most highly aberrantmulti-omic profile? And for such individuals, which specific genes and omics drivelarge pathway deviation scores? By providing graphical and numerical outputs toaddress these questions, padma represents both an approach forgenerating hypotheses as well as an exploratory data analysis tool for identifyingindividuals and genes/omics of potential interest for a given pathway. There isalready some precedent for using MFA to integrate multi-omic data, although existingapproaches differ from that proposed here. For instance, padmashares some similarities with a recently proposed integrative multi-omicsunsupervised gene set analysis called mogsa, which is similarlybased on a MFA . Next, an individual PCA is performed using singular valuedecomposition for each gene table lculated B. Note tocument}C. Using mogsaapproach, supplementary binary variables representing gene membership in genesets are projected onto a transcriptome-wide multiple factor analysis tocalculate gene set scores  in the observation and variable space.Optionally, an independent set of supplementary individuals (or supplementaryvariables) can then be projected onto the original representation; this isperformed by centering and scaling variables for the supplementary individuals to the same scaleas for the reference individuals, and projecting these rescaled variables intothe reference PCA space. Note that in the related Biostatisticsonline.The MFA thus provides a consensus across-gene representation of the individualsfor a given pathway, and the global PCA performed on the weighted gene tablesdecomposes the consensus variance into orthogonal variables  that are ordered by the proportion of variance explained by each.The coordinates of each individual on these components, also referred to asfactor scores, can be used to produce factor maps to represent individuals inthis consensus space such that smaller distances reflect greater similaritiesamong individuals. In addition, partial factor scores, which represent theposition of individuals in the consensus for a given gene, can also berepresented in the consensus factor map; the average of partial factor scoresacross all dimensions and genes for a given individual corresponds to the factorscore D. A moreIn the consensus space obtained from the MFA, the origin represents the“average” pathway behavior across genes, omics, and individuals;individuals that are projected to increasingly distant points in the factor maprepresent those with increasingly aberrant values, with respect to this average,for one or more of the omics measures for one or more genes in the pathway. Toquantify these aberrant individuals, we propose an individualized pathwaydeviation score padma, there is no dimension reduction and thecalculation of the pathway deviation score (and the corresponding gene-levelcontributions) is equivalent to that calculated in the original space of theconcatenated set of weighted, standardized variables. However, if desired, theuser can calculate the pathway deviation score on a subset of components, forexample after removing one or more components that are correlated with batcheffects or those that explain little variability. Finally, to facilitatecomparisons of scores calculated for pathways of differing sizes , deviation scores with respect to the origin are normalized forthe pathway size by dividing them by the number of genes in the pathway.Note that the full set of components is used for this deviation calculation,rather than subsetting to an optimal number of components; we remark that due totheir small variance relative to lower components, higher components contributerelatively little to the overall pathway deviation scores. When all componentsare used in In order to quantify the role played by each gene for each individual, wedecompose the individualized pathway deviation scores into gene-levelcontributions. Recall that the average of partial factor scores across all MFAdimensions corresponds to each individual’s factor score. We define thegene-level deviation for a given individual as follows: Biostatistics online formore details.Interestingly, it is possible to quantify the contribution of any single variableof any arbitrary grouping of variables  to the individualized pathway deviation score; see theSupplementary Methods available at The richness of MFA outputs also includes various decompositions of the totalvariance  ofthe multi-omic data for a given pathway. Similarly to a standard PCA, thepercent contribution of each axis of the MFA can be calculated as the ratiobetween the variance of the corresponding MFA component and the total variance;by construction, the fraction of explained variance explained decreases as theMFA dimension increases. Similarly, the percent contribution to the inertia ofeach axis for a given omic, gene, or individual can be quantified as the ratiobetween the inertia of its respective partial projection in the consensus spaceand the inertia of the full data projection for that axis. These per-gene,per-omic, and per-individual contributions can be quantified for a subset ofcomponents  or for the entire set of components;here, as we calculate individualized pathway deviation scores using the full setof dimensions, we also calculated a weighted per-omic contribution, whichcorresponds to the average contribution across all dimensions, weighted by thecorresponding eigenvalue.padma, freely available athttps://bioconductor.org/packages/padma. Padmanotably makes use FactoMineR , which was chosen as individuals have previously beenclassified , and microRNA (miRNA) abundance forWe illustrate the utility of assified into onepadma approach integrates multi-omic data by mapping omicsmeasures to genes in a given pathway. Although this assignment of values togenes is straightforward for RNA-seq, CNA, and methylation data, a definitivemapping of miRNA-to-gene relationships does not exist, as miRNAs can eachpotentially target multiple genes. Many methods and databases based ontext-mining or bioinformatics-driven approaches exist to predict miRNA-targetpairs ; the number of MFA componentsneeded to explain 80% of the total variability was strongly associated with thetotal number of features in each pathway (Biostatistics online).The  instead . After rhttp://legacy.dx.ai/tcga_breast on March 7, 2019), which is anestablished cancer hallmark of cellular de-differentiation and poor prognosis(Biostatistics online).As a measure of patient prognosis, we focused on two different metrics. First, weused the standardized and curated clinical data included in the TCGA Pan-CancerClinical Resource . These multi-omic healthy tissue samples were subsequentlybatch-corrected in the same way as the tumor samples. Next, to create amulti-omic data set with a set of “true positives,” we randomlyselected five tumor samples to include with the 70 healthy samples; for eachpathway, this random sampling was repeated 20 independent times. Using theRNA-seq, miRNA-seq, and methylation data for the full set of 75 samples, we thenevaluated whether the padma pathway deviation scores were ableto successfully identify the five tumor samples by calculating the Area Underthe Curve (AUC) of the Receiver Operating Characteristic (ROC) curve for each ofthe 1136 pathways. Mean AUC values across the 20 repetitions were very high fornearly all pathways considered . As a whole, this suggests that the padma deviationscores indeed reflect true biological signal, as the tumor controls added tohealthy samples nearly always had the largest deviation scores acrosspathways.Before exploring in detail the results of padma pathway deviationscores can correctly identify aberrant individuals. We compared the AUC valuesof padma with those of pathway deviation scores calculatedusing two alternatives: a PCA on all concatenated data tables  and a padma single-omicsapproach. Full details of the simulation study may be found in the SupplementaryMethods available at Biostatistics online, and results areshown in Biostatisticsonline. Overall, we confirm the solid performance of padmaacross a wide range of settings, as well as an advantage in identifying aberrantindividuals for padma compared to a PCA-based alternative,particularly in cases with smaller sample sizes and fewer driver genes and omics. Finally, we also confirmed that the per-genecontributions to the individualized padma pathway deviationscores successfully recover the true gene drivers in all scenariosconsidered.In addition, we conducted a simulation study to investigate the conditions  under which n = 80; Stage II, n = 33; Stage III+,n = 31). Using the Benjamini–Hochberg ; for all of these, higher pathway scores corresponded to a worsesurvival outcome. Although overlaps in gene lists between pairs of pathwayscreate a positive dependency structure among the deviation scores (Biostatistics online), the BH correction methodhas been shown to control the FDR in such families of tests (Biostatistics online) have been univariatelyassociated with patient outcome  we consider only thosewith the most highly positively skewed distribution of deviation scores. Foreach of the top 5% of pathways ; further, after BHcorrection none of the 57 pathways were significantly associated with survival, as well as cell cycle and apoptosisrelated pathways, prompted us to consider whether these pathway deviation scoresare simply acting as proxies for the tumor mutational burden  for each individual. To investigate this, weestimated the mutational burden for each individual by counting the number ofsomatic nonsynonymous mutations in a set of cancer-specific driver genessignaling pathway. D4-GDI is a negative regulator of the ras-related Rho Familyof GTPases, and it has been suggested that it may promote breast cancer cellproliferation and invasiveness  for which large deviation scores were observed for the two highlyaberrant individuals (TCGA-78-7536 and TCGA-78-7155) in the D4-GDI signalingpathway. We plot boxplots of the Z-scores for each available omic for the threegenes across all 144 individuals with lung cancer .When examining the partial factor maps for this individual over the first threeMFA dimensions C,D, we npadma insuch a case, we focus on histological grade for breast cancer. To quantifywhether pathway deviation scores tend to be associated with histological gradein breast cancer, we performed a one-way ANOVA on the three measures thatcomprise histological grade for each of the 1136 pathways. Based on theBH-adjusted p-values from an F-test (FDR Biostatistics online). In allbut two cases, higher deviation pathway scores corresponded to the higher gradesfor these two measures, corresponding to more aggressive tumors; the twoexceptions were the presynaptic nicotinic acetylcholine receptor and highlycalcium permeable postsynaptic nicotinic acetylcholine receptor pathways (bothfrom Reactome), for which the largest pathway deviation scores were associatedwith grade II, rather than grade III, of the mitotic index.For some cancers, additional clinical phenotypes beyond survival information maybe of particular interest; to illustrate the use of Biostatistics online (see Table S5 of the Biostatistics online for the full gene lists ineach pathway). The Wnt signaling pathway, which is made up of 63 genes, had thehighest combined ranking for these two histological measures. Of this set ofgenes, all had RNA-seq, methylation, and CNA measures available, with theexception of FAM123B and PSMD10 (no CNA measures with nonzero variance) andPSMB1 to PSMB10, PSMC2, PSMC3, PSMC5, PSMC6, PSME1, and PSME2 (no promotermethylation measures). miRNA-seq data were included for only two predictedtarget pairs: hsa-mir-375 To prioritize pathways among this list, we calculated the rank product of theindividual rankings by p-value for mitosis and nuclear pleomorphism; the top 10pathways according to this joint ranking are shown in Table S2 of the Similarly to the distribution of D4-GDI pathway scores in lung adenocarcinomas, asmall number of breast cancer patients are characterized by highly aberrantscores in the Wnt signaling pathway, including TCGA-BH-A1FM, TCGA-E9-A22G, andTCGA-EW-A1PH, and the number of pathway-specific nonsynonymous somatic mutationsdoes not appear to be related to this score. The associated factor map on thefirst two dimensions of the MFA AclearlyBiostatistics online), miRNA expressioncontributed relatively little to the overall variation (1.2%). We do need to becautious in the interpretation of this phenomenon, as it may be due to realbiology or to the mapping uncertainty and much smaller number (with respect tothe other omics) of miRNA features (Biostatistics online). Because we have structured the datainto gene-tables (and not omics-tables) in padma, the MFAweighting leads to a balancing of contributions among genes (and not omics); assuch, the drastically smaller number of miRNA features is likely directly linkedto the overall smaller contributions to the variance explained.When examining the percent contribution of each omic to the axes of the MFA forthe Wnt signaling pathway B, werempadmaapproach, which is used in an unsupervised manner on multi-omic cancer data fora given pathway, is able to recapitulate known sample structure in the form ofintrinsic tumor subtypes as well as relevant prognostic factors such ashistological grade.Taken together, these results illustrate that the padma accommodates multipleomics-sources which, for some sample sets and pathways, account for more than 50% ofthe overall variation (Unsupervised dimension reduction approaches (such as PCA) have been widely used ingenetics and genomics for many years, both to identify sample structure and batcheffects  to identify any potential technical outliersbefore running padma. Here, we chose to remove known batch effectsprior to the padma analysis, but in principle the method could berun on uncorrected data and MFA components correlated with undesired batch effectscould be identified and removed prior to computing the pathway deviation score. Forlarge, multi-omic data such as TCGA, padma allows investigators tosummarize overall variation and assist in generating hypotheses for more targetedanalyses and follow-up studies. As a case in point, we identified two lung cancerpatients with aberrant multi-omic profiles at three CASP genes. With access to thetumor samples and more fine-grained clinical data, future molecular experimentscould help to clarify the role (if any) that these genes play in contributing tolung cancer mortality. Although the multi-omic TCGA data considered here were quitelarge  identify overall sources ofvariation (such as batch effects); (ii) prioritize high variance pathways defined byvariability across subjects; (iii) identify aberrant observations  within a given pathway; and (iv) identify the genes and omics sourcesthat drive these aberrant observations. As with any analysis of omic data wegenerally recommend that standard quality control analyses be performed  are of interest, the MFA can be based on one set of samples , and the other set of samples  can be projected onto this originalrepresentation. This is accomplished by centering and scaling supplementaryindividuals to the same scale as the reference individuals, and projecting theserescaled variables into the reference MFA space. In this setting, the interpretationof pathway deviation scores would no longer correspond to the identification of“aberrant” individuals compared to an overall average, but ratherindividuals that are most different from the reference set ; this strategy would besimilar in spirit to the individualized pathway aberrance score (iPAS) approach,which proposed using accumulated (unmatched) normal samples as a reference set(kxaa029_Supplementary_DataClick here for additional data file.


This Research Topic, led by Dr. Yingwang Ye, Dr. Stephen Forsythe, and Dr. Zhenbo Xu, has contained a total of six excellent manuscripts. As the background of this Research Topic was concerned, infant and young child food have received special attention from the government and society as a type of specialized food. In recent years, there have been numerous outbreaks of infections and poisons in infant food. As a result, quality control and government oversight are becoming more stringent over the world . Infant Since gut microbiota has been well-documented to be important for intestinal health, a large proportion of the published manuscripts in this Research Topic are relevant to gut microbiota.The gut microbiome of preterm infants treated with aminophylline is closely related to the occurrence of feeding intolerance and the weight gain” by Shen et al., has studied the gut microbiome of preterm infants treated with aminophylline. Via a cohort analysis on 118 preterm infants, the authors have found out gut microbiome in preterm infants treated with aminophylline was characterized by a decrease in Streptococcus and Rothia and increase in Staphylococcus, whereas Rothia positively correlated with the occurrence of feeding intolerance and Streptococcus but not Bifidobacter likely participated in the weight gain of preterm infants in early life. The second published manuscript, entitled “Intrahepatic cholestasis of pregnancy increases inflammatory susceptibility in neonatal offspring by modulating gut microbiota” by Lin et al., had investigated the effect of maternal cholestasis on neonatal offspring metabolism and immune function. In comparing neonates with Intrahepatic cholestasis of pregnancy (ICP) mothers (n = 71) and healthy mothers (n = 63), the authors had indicated that cholestatic pregnancy may increase the susceptibility of the offspring to inflammation by altering bile acid metabolism and gut microbiota at an early stage, and also supplementation with Lactobacillus rhamnosus LRX01 inhibits FXR expression in the ileum and thus may improve intestinal immunity in ICP offspring. Such finding has provided important knowledge on how ICP shapes the offspring's immunity and predisposition to inflammatory disorders at an early stage. The third published manuscript, entitled “Lactobacillus casei SYF-08 protects against Pb-induced injury in young mice by regulating bile acid metabolism and increasing Pb excretion” by Chen et al., had aimed at identifying a non-toxic treatment on Pb poisoning by studying the therapeutic effect of an infant feces-derived probiotic strain, Lactobacillus casei SYF-08 (SYF-08), on Pb poisoning in young mice. The authors had eventually provided valuable insights into the therapeutic role of SYF-08 in Pb poisoning and also suggested that its administration can significantly alleviate the Pb-induced damage. The fourth published manuscript in this Research Topic, entitled “Dietary supplementation of chitosan oligosaccharide–Clostridium butyricum synbiotic relieved early-weaned stress by improving intestinal health on pigeon squabs (Columba livia)” by Wen et al., was a follow-up study from previous finding whereas the authors had discovered early weaning causes harm to growth performance, intestinal morphology, activity of digestive enzymes, and antioxidant status in pigeon squabs (Columba livia). Consequently, in this study, the authors further explored whether dietary supplementation with COS-C. butyricum synbiotic could relieve early-weaned stress by evaluating its effects on growth performance and intestinal health in pigeon squabs. As found, dietary supplementation with synbiotic (150 mg/kg COS + 300–400 mg/kg C. butyricum) could relieve early-weaned stress by maintaining intestinal health in pigeon squabs. The fifth published manuscript in this Research Topic is a retrospective study, entitled “Effect of different feeding methods and gut microbiota on premature infants and clinical outcomes” by Liu et al., had investigated the effects of two routine feeding methods, breastfeeding and formula milk, on premature infants. Via statistical analysis on premature infants admitted to the neonatal intensive care unit between 2017 and 2018, the authors had obtained no significant differences between the two feeding methods, neither had significant effects on clinical indicators in premature infants. Gut microbiota has been well-studied in influencing many clinical indicators, this study suggests an important role of gut microbiota plays in the care of premature infants and further provides a basis for promoting the healthy development of this patient population. The sixth manuscript published in this Research Topic is a highlight study, entitled “Bacteroides fragilis ameliorates Cronobacter malonaticus lipopolysaccharide-induced pathological injury through modulation of the intestinal microbiota” by Ling et al. As well-studied, Cronobacter has been considered to be an important pathogen which is responsible for meningitis and necrotizing enterocolitis (NEC) in newborns, and lipopolysaccharide (LPS) has been identified to commonly facilitate bacterial translocation along with inflammatory responses as an endotoxin. Based on the unclear pathogenicity of Cronobacter LPS and the potential strategies to alleviate the toxicity, the authors had stimulated inflammatory responses in Sprague–Dawley young rats by intraperitoneal injection of Cronobacter malonaticus LPS, and fed with Bacteroides fragilis NCTC9343 continuously fed through gavage for 5 days before or after injection, to further evaluate the intervention effect of B. fragilis. As found, C. malonaticus LPS exacerbated intestinal infection by altering gut microbe profile, tight junction protein expression, and releasing inflammatory factors in a time- and dose-dependent manner, in which pathological injuries could be diminished by B. fragilis treatment. Shigella, Peptoclostridium, and Sutterella were found to be positively related to C. malonaticus LPS infection, with Prevotella negatively correlated. Collectively, the authors had concluded the intestinal microbiota is an important target for the prevention and treatment of pathogenic injuries induced by C. malonaticus LPS, which has provided a potential strategy to alleviate the toxicity.The first published manuscript in this Research Topic entitled “via studies on intestinal health, intestinal immunity, intestinal microflora, intestinal inflammation, which will further guide consumption of infant food and its production. As seen, gut microbiota modulation, probiotic and its application, as well as microbial pathogenicity based novel strategy for toxicity alleviation, are research hotspots in infant food and intestinal immunity. Up-to-date, this Research Topic has achieved 6,681 total views and 1,424 downloads.As concluded, the above manuscripts published in this Research Topic, had provided comprehensive knowledge and insight in understanding the relationship between infant food and intestinal immunity All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.