Analysing covariates with spike at zero: A modified FP procedure and conceptual issues

In epidemiology and in clinical research, risk factors often have special distributions. A common situation is that a proportion of individuals have exposure zero, and among those exposed, we have some continuous distribution. We call this a ‘spike at zero’. Examples for this are smoking, duration of breastfeeding, or alcohol consumption. Furthermore, the empirical distribution of laboratory values and other measurements may have a semi‐continuous distribution as a result of the lower detection limit of the measurement. To model the dose–response function, an extension of the fractional polynomial approach was recently proposed. In this paper, we suggest a modification of the previously suggested FP procedure. We first give the theoretical justification of this modified procedure by investigating relevant distribution classes. Here, we systematically derive the theoretical shapes of dose–response curves under given distributional assumptions (normal, log normal, gamma) in the framework of a logistic regression model. Further, we check the performance of the procedure in a simulation study and compare it to the previously suggested method, and finally we illustrate the procedures with data from a case–control study on breast cancer.     

Molecular genetic study of human arginase deficiency

We have explored the molecular pathology in 28 individuals homozygous or heterozygous for liver arginase deficiency (hyperargininemia) by a combination of Southern analysis, western blotting, DNA sequencing, and PCR. This cohort represents the majority of arginase-deficient individuals worldwide. Only 2 of 15 homozygous patients on whom red blood cells were available had antigenically cross-reacting material as ascertained by western blot analysis using anti-liver arginase antibody. Southern blots of patient genomic DNAs, cut with a variety of restriction enzymes and probed with a near-full-length (1,450-bp) human liver arginase cDNA clone, detected no gross gene deletions. Loss of a TaqI cleavage site was identified in three individuals: in a homozygous state in a Saudi Arabian patient at one site, at a different site in homozygosity in a German patient, and in heterozygosity in a patient from Australia. The changes in the latter two were localized to exon 8, through amplification of this region by PCR and electrophoretic analysis of the amplified fragment after treatment with TaqI; the precise base changes (Arg291X and Thr290Ser) were confirmed by sequencing. It is interesting that the latter nucleotide variant (Thr290Ser) was found to lie adjacent to the TaqI site rather than within it, though whether such a conservative amino acid substitution represents a true pathologic mutation remains to be determined. We conclude that arginase deficiency, though rare, is a heterogeneous disorder at the genotypic level, generally encompassing a variety of point mutations rather than substantial structural gene deletions.     

Loss of complexity from larval towards adult nervous systems in Chaetopteridae (Chaetopteriformia,Annelida) unveils evolutionary patterns in Annelida

Organisms Diversity & Evolution - Chaetopteridae — the parchment worms — comprise a group of early branching annelids with a scarcely investigated neuroanatomy and neurogenesis. Due...     

Synthesis of novel steroidal agonists,partial agonists,and antagonists for the glucocorticoid receptor

Adverse effects of glucocorticoids could be limited by developing new compounds that selectively modulate anti-inflammatory activity of the glucocorticoid receptor (GR). We have synthesized a novel series of steroidal GR ligands, including potent agonists, partial agonists and antagonists with a wide range of effects on inhibiting secretion of interleukin-6. Some of these new ligands were designed to directly impact conformational stability of helix-12, in the GR ligand-binding domain (LBD). These compounds modulated GR activity and glucocorticoid-induced gene expression in a manner that was inversely correlated to the degree of inflammatory response. In contrast, compounds designed to directly modulate LBD epitopes outside helix-12, led to dissociated levels of GR-mediated gene expression and inflammatory response. Therefore, these new series of compounds and their derivatives will be useful to dissect the ligand-dependent features of GR signaling specificity.     

A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures

MicroRNAs (miRNAs) are important components of cellular signaling pathways, acting either as pathway regulators or pathway targets. Currently, only a limited number of miRNAs have been functionally linked to specific signaling pathways. Here, we explored if gene expression signatures could be used to represent miRNA activities and integrated with genomic signatures of oncogenic pathway activity to identify connections between miRNAs and oncogenic pathways on a high-throughput, genome-wide scale. Mapping >300 gene expression signatures to >700 primary tumor profiles, we constructed a genome-wide miRNA-pathway network predicting the associations of 276 human miRNAs to 26 oncogenic pathways. The miRNA-pathway network confirmed a host of previously reported miRNA/pathway associations and uncovered several novel associations that were subsequently experimentally validated. Globally, the miRNA-pathway network demonstrates a small-world, but not scale-free, organization characterized by multiple distinct, tightly knit modules each exhibiting a high density of connections. However, unlike genetic or metabolic networks typified by only a few highly connected nodes ("hubs"), most nodes in the miRNA-pathway network are highly connected. Sequence-based computational analysis confirmed that highly-interconnected miRNAs are likely to be regulated by common pathways to target similar sets of downstream genes, suggesting a pervasive and high level of functional redundancy among coexpressed miRNAs. We conclude that gene expression signatures can be used as surrogates of miRNA activity. Our strategy facilitates the task of discovering novel miRNA-pathway connections, since gene expression data for multiple normal and disease conditions are abundantly available.     

Plasma Membrane Tetraspanin CD81 Complexes with Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) and Low Density Lipoprotein Receptor (LDLR), and Its Levels Are Reduced by PCSK9

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is an important factor in plasma cholesterol regulation through modulation of low density lipoprotein receptor (LDLR) levels. Naturally occurring mutations can lead to hyper- or hypocholesterolemia in human. Recently, we reported that PCSK9 was also able to modulate CD81 in Huh7 cells. In the present study, several gain-of-function and loss-of-function mutants as well as engineered mutants of PCSK9 were compared for their ability to modulate the cell surface expression of LDLR and CD81. Although PCSK9 gain-of-function D374Y enhanced the degradation both receptors, D374H and D129N seemed to only reduce LDLR levels. In contrast, mutations in the C-terminal hinge-cysteine-histidine-rich domain segment primarily affected the PCSK9-induced CD81 degradation. Furthermore, when C-terminally fused to an ACE2 transmembrane anchor, the secretory N-terminal catalytic or hinge-cysteine-histidine-rich domain domains of PCSK9 were able to reduce CD81 and LDLR levels. These data confirm that PCSK9 reduces CD81 levels via an intracellular pathway as reported for LDLR. Using immunocytochemistry, a proximity ligation assay, and co-immunoprecipitation, we found that the cell surface level of PCSK9 was enhanced upon overexpression of CD81 and that both PCSK9 and LDLR interact with this tetraspanin protein. Interestingly, using CHO-A7 cells lacking LDLR expression, we revealed that LDLR was not required for the degradation of CD81 by PCSK9, but its presence strengthened the PCSK9 effect.     

Consumption of benthic invertebrates by waterbirds in the Oosterschelde estuary,SW Netherlands

The number of waders in the Oosterschelde, S.W. Netherlands, declined after a reduction in intertidal area due to the construction of a storm surge barrier and secondary dams, suggesting that the carrying capacity had been reached (Schekkerman et al., 1993). In this paper we present data on consumption and predation pressure by birds to explore whether the reduction in their numbers is due to prey depletion or to other factors.The total annual consumption of benthic invertebrates by birds in the Oosterschelde amounted to 1573 × 10³ g ADW y^–1 in the period before the coastal engineering works (pre-barrier) and 1500 × 10³ kg ADW y^–1 in the post-barrier period. More than half of the total amount of biomass is eaten by the Oystercatcher, and only seven (pre-barrier) or even six (post-barrier) bird species together take 90% of the total.Although the consumption by individual species may vary considerably among years, the total consumption was remarkably stable, with a CV of only 3–4% of the mean, especially compared to the variability of the prey populations. In the pre-barrier period, consumption was lowest in mid summer, increased sharply from August onwards until a peak was reached in January. A sharp decrease took place in March. In the post-barrier period, consumption peaked in October.The total consumption per unit area per year does not differ much between different sectors of the Oosterschelde, apart from a distinctly lower value in the eastern part. Of the total amount of food taken by birds, only 0.1–0.4% is taken in the subtidal compartment. In several study plots on an individual tidal flat, there was a clear relation between consumption and benthic biomass.The predation pressure was 13 and 23% of the standing stock, in the post- and pre-barrier period respectively. When cockles, mussels and their main predator, the Oystercatcher, are excluded from the calculations, the predation pressure of the other species was 30 and 37% of the biomass, respectively.Predation pressure of Oystercatchers in individual study plots varied from less than 10% to more than 70% of the standing stock. On cockle beds the predation pressure was positively related to the average length of the cockles present.Based on these results and a comparison with the literature we conclude that, at least for several species that feed intertidally, carrying capacity could be limited by the stocks of food. This does not mean that birds face food shortage each season. As the variability of the benthos populations is much higher than that of the bird densities it is likely that at some times food is not limiting, at other times it is. On the other hand, consumption is very low in the subtidal compartment and species feeding here could potentially increase substantially in numbers in the Oosterschelde.