Generalized latent class modeling using gllamm

gllamm can estimate both conventional and unconventional latent class models. Models are specified using discrete latent variables whose values determine the conditional response distributions for the classes. A new feature of gllamm is that latent class probabilities can depend on covariates. We will first discuss the conventional exploratory latent class model. When a number of fallible diagnoses of some disease are available, this model can be used to estimate the prevalence of the disease as well as the sensitivities and specificities of the tests in the absence of a gold standard. After estimating the model in gllamm, gllapred can be used to diagnose individual subjects based on their posterior class probabilities. An advantage of using gllamm is that a wide range of response types can be accommodated. To illustrate this, we consider the analysis of rankings of political goals in the study of value orientations. We will also discuss confirmatory models such as latent class factor models and apply them to attitudes to abortion data, taking the survey design into account by using probability weighting and robust standard errors. Finally, we consider latent trajectory models for investigating distinct patterns of change in longitudinal data.

Metabolic studies on the transformation of trichodiene to trichothecene mycotoxins

Trichodiene and [14C]trichodiene have been produced in high yields by treatment of Fusarium culmorum CMI 14764 cultures with the furanocoumarin xanthotoxin. Smaller amounts of isotrichodermin (ITD) and the unsubstituted trichothecene 12,13-epoxytrichothec-9-ene (EPT) were obtained in the same way. EPT was also produced by semi-synthesis from ITD. Trichodiene (TDN) was shown to be a precursor of the trichothecene mycotoxins in F. culmorum, including EPT, ITD, calonectrin (CAL), 7a-hydroxycalonectrin (7-hydroxyCAL), 15-deacetylcalonectrin, 3-acetyldeoxynivalenol (3-AcDON) and 7,8-dihydroxycalonectrin (DHC). When large amounts of TDN were supplied, a new trichodiene metabolite was found to accumulate which was fully characterised as 12,13-epoxy-2a, 11 adihydroxytrichodiene, and given the trivial name isotrichodiol. A method for the production of 14C-labelled isotrichodiol (ITdiol) was developed, and the incorporation of ["C]ITdiol into 3-AcDON, DHC and 7-hydroxyCAL was demonstrated. Slow, acid-catalysed cyclisation of ITdiol to EPT and pre-sambucoin was demonstrated, and allylic isomerisation to both 9a- and 9p-trichodiol was also detected. Labelled pre-sambucoin was incorporated into sambucoin by F. culmorwn, and ITdiol is thus proposed as a precursor to both sambucoin and sambucinol, aswel as to the trichothecenes. A range of semi-synthetic derivatives of TDN were prepared and tested as possible inhibitors of the post-TDN biosynthesic pathway to trichothecenes in F. culmorum. In whole-cell systems all the derivatives inhibited the incorporation of labelled TDN into trichothecenes, and also initiated the production of ITdiol. One derivative, 9P, 10ß-epoxytrichodiene, was shown to be biotransformed by the fungus, undergoing 12,13-epoxidation with subsequent hydroxylation at C-3 producing 3a-hydroxy-9(3,10(3; 12,13-diepoxytrichodiene. 9ß-Trichodiol was isolated from Trichothecium roseum, and its slow, acidcatalysed cyclisation to EPT was demonstrated. 9a-Trichotriol, 9ß-trichotriol and isotrichotriol were isolated from F. culmorum for the first time, and literature assignments for the stereochemistry of the C-9 hydroxyl in trichodiol and trichotriol are reassessed. The incorporation of [`4C]ITdiol into trichothecenes in F. culmorum was found to be approximately 5 times greater than the incorporation of [14C]-913-trichotriol, and was shown to be inhibited by isotrichotriol but not by 9ß-trichodiol and 9ß-trichotriol. It is proposed that trichodiol and trichotriol are not biosynthetic intermediates in the pathway to the trichothecenes, and that they are non-enzymic metabolites produced from ITdiol and isotrichotriol, respectively, by acid-catalysed isomerisations. A new scheme for the biosynthesis of trichothecenes is proposed in which ITdiol and isotrichotriol are intermediates in the production of isotrichodermol from TDN. Two novel compounds, 15-deacetyl-7,8-dihydroxycalonectrin (15-deacetylDHC) and 8a-hydroxyisotrichodiol were isolated from F. culmorum, and 15-deacetylDHC and DHC were shown to be precursors to 3-AcDON. It is proposed that the post-cyclisation biosynthesis of 3-AcDON involves sequential oxygenation of isotrichodermol at C-15, C-7 and C-8 producing DHC, which then undergoes deacylation to 15-deacetylDHC followed by oxidation at C-8 to 3-AcDON

Avoiding Boundary Estimates in Linear Mixed Models Through Weakly Informative Priors

Variance parameters in mixed or multilevel models can be difficult to estimate, especially when the number of groups is small. We propose a maximum penalized likelihood approach which is equivalent to estimating variance parameters by their marginal posterior mode, given a weakly informative prior distribution. By choosing the prior from the gamma family with at least 1 degree of freedom, we ensure that the prior density is zero at the boundary and thus the marginal posterior mode of the group-level variance will be positive. The use of a weakly informative prior allows us to stabilize our estimates while remaining faithful to the data

The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)

The induction of ppGpp synthesis in Streptomyces coelicolor influenced the expression of several genomic elements characteristic of streptomycete biology, including antibiotic gene clusters, conservons, and morphogenetic proteins

Vitamins D3 and D2 have marked but different global effects on gene expression in a rat oligodendrocyte precursor cell line

Background: Vitamin D deficiency increases the risk of developing multiple sclerosis (MS) but it is unclear whether vitamin D supplementation improves the clinical course of MS, and there is uncertainty about the dose and form of vitamin D (D2 or D3) to be used. The mechanisms underlying the effects of vitamin D in MS are not clear. Vitamin D3 increases the rate of differentiation of primary oligodendrocyte precursor cells (OPCs), suggesting that it might help remyelination in addition to modulating the immune response. Here we analyzed the transcriptome of differentiating rat CG4 OPCs treated with vitamin D2 or with vitamin D3 at 24 h and 72 h following onset of differentiation. Methods: Gene expression in differentiating CG4 cells in response to vitamin D2 or D3 was quantified using Agilent DNA microarrays (n=4 replicates), and the transcriptome data were processed and analysed using the R software environment. Differential expression between the experimental conditions was determined using LIMMA, applying the Benjamini and Hochberg multiple testing correction to p-values, and significant genes were grouped into co-expression clusters by hierarchical clustering. The functional significance of gene groups was explored by pathway enrichment analysis using the clusterProfiler package. Results: Differentiation alone changed the expression of about 10% of the genes at 72 h compared to 24 h. Vitamin D2 and D3 exerted different effects on gene expression, with D3 influencing 1,272 genes and D2 574 at 24 h. The expression of the vast majority of these genes was either not changed in differentiating cells not exposed to vitamin D or followed the same trajectory as the latter. D3-repressed genes were enriched for Gene Ontology (GO) categories including transcription factors and the Notch pathway, while D3-induced genes were enriched for the Ras pathway. Conclusions: This study shows that vitamin D3, compared with D2, changes the expression of a larger number of genes in OLs. Identification of genes affected by D3 in OLs should help to identify mechanisms mediating its action in MS

The effects of physiological and injurious hydrostatic pressure on murine ex vivo articular and growth plate cartilage explants:an RNAseq study

Chondrocytes are continuously exposed to loads placed upon them. Physiological loads are pivotal to the maintenance of articular cartilage health, while abnormal loads contribute to pathological joint degradation. Similarly, the growth plate cartilage is subject to various loads during growth and development. Due to the high-water content of cartilage, hydrostatic pressure is considered one of the main biomechanical influencers on chondrocytes and has been shown to play an important role in the mechano-regulation of cartilage. Herein, we conducted RNAseq analysis of ex vivo hip cap (articular), and metatarsal (growth plate) cartilage cultures subjected to physiological (5 MPa) and injurious (50 MPa) hydrostatic pressure, using the Illumina platform (n = 4 replicates). Several hundreds of genes were shown to be differentially modulated by hydrostatic pressure, with the majority of these changes evidenced in hip cap cartilage cultures (375 significantly upregulated and 322 downregulated in 5 MPa versus control; 1022 upregulated and 724 downregulated in 50 MPa versus control). Conversely, fewer genes were differentially affected by hydrostatic pressure in the metatarsal cultures (5 significantly upregulated and 23 downregulated in 5 MPa versus control; 7 significantly upregulated and 19 downregulated in 50 MPa versus control). Using Gene Ontology annotations for Biological Processes, in the hip cap data we identified a number of pathways that were modulated by both physiological and injurious hydrostatic pressure. Pathways upregulated in response to 50 MPa versus control, included those involved in the generation of precursor metabolites and cellular respiration. Biological processes that were downregulated in this tissue included ossification, connective tissue development, and chondrocyte differentiation. Collectively our data highlights the divergent chondrocyte phenotypes in articular and growth plate cartilage. Further, we show that the magnitude of hydrostatic pressure application has distinct effects on gene expression and biological processes in hip cap cartilage explants. Finally, we identified differential expression of a number of genes that have previously been identified as osteoarthritis risk genes, including Ctsk, and Chadl. Together these data may provide potential genetic targets for future investigations in osteoarthritis research and novel therapeutics. [Abstract copyright: Copyright © 2023 Bourne, Hesketh, Sharma, Bucca, Bush and Staines.

Radiomics and circulating tumor cells: personalized care in hepatocellular carcinoma?

Personalized care in oncology is expected to significantly improve morbidity and mortality, facilitated by our increasing understanding of the molecular mechanisms driving tumors and the ability to target those drivers. Hepatocellular carcinoma has a very high mortality to incidence ratio despite localized disease being curable, emphasizing the importance of early diagnosis. Radiomics, the use of imaging technology to extrapolate molecular tumor data, and the detection of circulating tumor cells (CTCs) are two new technologies that could be incorporated into the clinical setting with relative ease. Here we discuss the molecular mechanisms leading to the development of hepatocellular carcinoma focusing on the latest developments in liver magnetic resonance imaging, CTC, and radiomic technology and their potential to improve diagnosis, staging, and therapy