Comment on "Including Systematic Uncertainties in Confidence Interval Construction for Poisson Statistics"

The incorporation of systematic uncertainties into confidence interval calculations has been addressed recently in a paper by Conrad et al. (Physical Review D 67 (2003) 012002). In their work, systematic uncertainities in detector efficiencies and background flux predictions were incorporated following the hybrid frequentist-Bayesian prescription of Cousins and Highland, but using the likelihood ratio ordering of Feldman and Cousins in order to produce "unified" confidence intervals. In general, the resulting intervals behaved as one would intuitively expect, i.e. increased with increasing uncertainties. However, it was noted that for numbers of observed events less than or of order of the expected background, the intervals could sometimes behave in a completely counter-intuitive fashion -- being seen to initially decrease in the face of increasing uncertainties, but only for the case of increasing signal efficiency uncertainty. In this comment, we show that the problematic behaviour is due to integration over the signal efficiency uncertainty while maximising the best fit alternative hypothesis likelihood. If the alternative hypothesis likelihood is determined by unconditionally maximising with respect to both the unknown signal and signal efficiency uncertainty, the limits display the correct intuitive behaviour.Comment: Submitted to Physical Review

Graded potential of neural crest to form cornea, sensory neurons and cartilage along the rostrocaudal axis

Neural crest cells arising from different rostrocaudal axial levels form different sets of derivatives as diverse as ganglia, cartilage and cornea. These variations may be due to intrinsic properties of the cell populations, different environmental factors encountered during migration or some combination thereof. We test the relative roles of intrinsic versus extrinsic factors by challenging the developmental potential of cardiac and trunk neural crest cells via transplantation into an ectopic midbrain environment. We then assess long-term survival and differentiation into diverse derivatives, including cornea, trigeminal ganglion and branchial arch cartilage. Despite their ability to migrate to the periocular region, neither cardiac nor trunk neural crest contribute appropriately to the cornea, with cardiac crest cells often forming ectopic masses on the corneal surface. Similarly, the potential of trunk and cardiac neural crest to form somatosensory neurons in the trigeminal ganglion was significantly reduced compared with control midbrain grafts. Cardiac neural crest exhibited a reduced capacity to form cartilage, contributing only nominally to Meckle's cartilage, whereas trunk neural crest formed no cartilage after transplantation, even when grafted directly into the first branchial arch. These results suggest that neural crest cells along the rostrocaudal axis display a graded loss in developmental potential to form somatosensory neurons and cartilage even after transplantation to a permissive environment. Hox gene expression was transiently maintained in the cardiac neural tube and neural crest at 12 hours post-transplantation to the midbrain, but was subsequently downregulated. This suggests that long-term differences in Hox gene expression cannot account for rostrocaudal differences in developmental potential of neural crest populations in this case

Lexical organization in deaf children who use British Sign Language: Evidence from a semantic fluency task

We adapted the semantic fluency task into British Sign Language (BSL). In Study 1, we present data from twenty-two deaf signers aged four to fifteen. We show that the same ‘cognitive signatures’ that characterize this task in spoken languages are also present in deaf children, for example, the semantic clustering of responses. In Study 2, we present data from thirteen deaf children with Specific Language Impairment (SLI) in BSL, in comparison to a subset of children from Study 1 matched for age and BSL exposure. The two groups' results were comparable in most respects. However, the group with SLI made occasional word-finding errors and gave fewer responses in the first 15 seconds. We conclude that deaf children with SLI do not differ from their controls in terms of the semantic organization of the BSL lexicon, but that they access signs less efficiently

Resistance of corneal RFUVA-cross-linked collagens and small leucine-rich proteoglycans to degradation by matrix metalloproteinases

Purpose. Extracellular matrix metalloproteinases (MMPs) are thought to play a crucial role in corneal degradation associated with the pathological progression of keratoconus. Currently, corneal cross-linking by riboflavin and ultraviolet A (RFUVA) has received significant attention for treatment of keratoconus. However, the extent to which MMPs digest cross-linked collagen and small leucine-rich proteoglycans (SLRPs) remains unknown. In this study, the resistance of RFUVA–cross-linked collagens and SLRPs to MMPs has been investigated. Methods. To investigate the ability of MMPs to digest cross-linked collagen and SLRPs, a model reaction system using purified collagen type I, type IV, and nonglycosylated, commercially available recombinant SLRPs, keratocan, lumican, mimecan, decorin, and biglycan in solution in vitro has been compared using reactions inside an intact bovine cornea, ex vivo. Results. Our data demonstrate that corneal cross-linked collagen type I and type IV are resistant to cleavage by MMP-1, MMP-2, MMP-9, and MMP-13, whereas non–cross–linked collagen I, IV, and natively glycosylated SLRPs are susceptible to degradation by MMPs. In addition, both cross-linked SLRPs themselves and cross-linked polymers of SLRPs and collagen appear able to resist degradation. These results suggest that the interactions between SLRPs and collagen caused by RFUVA protect both SLRPs and collagen fibrils from cleavage by MMPs. Conclusions. A novel approach for understanding the biochemical mechanism whereby RFUVA cross-linking stops keratoconus progression has been achieved

Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment.

Microbial sulfate reduction is a primary cause of oil reservoir souring. Here we show that amendment with chlorate or perchlorate [collectively (per)chlorate] potentially resolves this issue. Triplicate packed columns inoculated with marine sediment were flushed with coastal water amended with yeast extract and one of nitrate, chlorate, or perchlorate. Results showed that although sulfide production was dramatically reduced by all treatments, effluent sulfide was observed in the nitrate (10 mM) treatment after an initial inhibition period. In contrast, no effluent sulfide was observed with (per)chlorate (10 mM). Microbial community analyses indicated temporal community shifts and phylogenetic clustering by treatment. Nitrate addition stimulated Xanthomonadaceae and Rhizobiaceae growth, supporting their role in nitrate metabolism. (Per)chlorate showed distinct effects on microbial community structure compared with nitrate and resulted in a general suppression of the community relative to the untreated control combined with a significant decrease in sulfate reducing species abundance indicating specific toxicity. Furthermore, chlorate stimulated Pseudomonadaceae and Pseudoalteromonadaceae, members of which are known chlorate respirers, suggesting that chlorate may also control sulfidogenesis by biocompetitive exclusion of sulfate-reduction. Perchlorate addition stimulated Desulfobulbaceae and Desulfomonadaceae, which contain sulfide oxidizing and elemental sulfur-reducing species respectively, suggesting that effluent sulfide concentrations may be controlled through sulfur redox cycling in addition to toxicity and biocompetitive exclusion. Sulfur isotope analyses further support sulfur cycling in the columns, even when sulfide is not detected. This study indicates that (per)chlorate show great promise as inhibitors of sulfidogenesis in natural communities and provides insight into which organisms and respiratory processes are involved

Modular Connector Keying Concept

For panel-mount-type connectors, keying is usually "built-in" to the connector body, necessitating different part numbers for each key arrangement. This is costly for jobs that require small quantities. This invention was driven to provide a cost savings and to reduce documentation of individual parts. The keys are removable and configurable in up to 16 combinations. Since the key parts are separate from the connector body, a common design can be used for the plug, receptacle, and key parts. The keying can then be set at the next higher assembly

Galaxy Integrated Omics:Web-based standards-compliant workflows for proteomics informed by transcriptomics

With the recent advent of RNA-seq technology the proteomics community has begun to generate sample-specific protein databases for peptide and protein identification, an approach we call proteomics informed by transcriptomics (PIT). This approach has gained a lot of interest, particularly among researchers who work with nonmodel organisms or with particularly dynamic proteomes such as those observed in developmental biology and host-pathogen studies. PIT has been shown to improve coverage of known proteins, and to reveal potential novel gene products. However, many groups are impeded in their use of PIT by the complexity of the required data analysis. Necessarily, this analysis requires complex integration of a number of different software tools from at least two different communities, and because PIT has a range of biological applications a single software pipeline is not suitable for all use cases. To overcome these problems, we have created GIO, a software system that uses the well-established Galaxy platform to make PIT analysis available to the typical bench scientist via a simple web interface. Within GIO we provide workflows for four common use cases: a standard search against a reference proteome; PIT protein identification without a reference genome; PIT protein identification using a genome guide; and PIT genome annotation. These workflows comprise individual tools that can be reconfigured and rearranged within the web interface to create new workflows to support additional use cases