Physical map and cosmid contig encompassing a new interstitial deletion of the X-linked lymphoproliferative syndrome region

The X-linked lymphoproliferative syndrome (XLP) is an inherited immuno-deficiency to Epstein-Barr virus infection that has been mapped to chromosome Xq25. Molecular analysis of XLP patients from ten different families identified a small interstitial constitutional deletion in 1 patient (XLP-D). This deletion, initially defined by a single marker, DF83, known to map to interval Xq24-q26.1, is nested within a previously reported and much larger deletion in another XLP patient (XLP-739). A cosmid minilibrary was constructed from a single mega-YAC and used to establish a contig encompassing the whole XLP-D deletion and a portion of the XLP-739 deletion. Based on this contig, the size of the XLP-D deletion can be estimated at 130 kb. The identification of this minimal deletion, within which at least a portion of the XLP gene is likely to reside, should greatly facilitate efforts in isolating the gene.

An Investigation of Compressor Map Width Enhancement and the Inducer Flow Field Using Various Configurations of Shroud Bleed Slot

This paper describes an investigation of various shroud bleed slot configurations of a centrifugal compressor using CFD with a manual multi-block structured grid generation method. The compressor under investigation is used in a turbocharger application for a heavy duty diesel engine of approximately 400hp. The baseline numerical model has been developed and validated against experimental performance measurements. The influence of the bleed slot flow field on a range of operating conditions between surge and choke has been analysed in detail. The impact of the returning bleed flow on the incidence at the impeller blade leading edge due to its mixing with the main through-flow has also been studied. From the baseline geometry, a number of modifications to the bleed slot width have been proposed, and a detailed comparison of the flow characteristics performed. The impact of slot variations on the inlet incidence angle has been investigated, highlighting the improvement in surge and choked flow capability. Along with this, the influence of the bleed slot on stabilizing the blade passage flow by the suction of the tip and over-tip vortex flow by the slot has been considered near surge.

A Case Study of OpenMP applied to Map/Reduce-style Computations

As data analytics are growing in importance they are also quickly becoming one of the dominant application domains that require parallel processing. This paper investigates the applicability of OpenMP, the dominant shared-memory parallel programming model in high-performance computing, to the domain of data analytics. We contrast the performance and programmability of key data analytics benchmarks against Phoenix++, a state-of-the-art shared memory map/reduce programming system. Our study shows that OpenMP outperforms the Phoenix++ system by a large margin for several benchmarks. In other cases, however, the programming model is lacking support for this application domain.

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers. © 2012 Biek et al.

Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp

The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m3. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM) is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected-24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012-2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported.

The single component geochemical map: Fact or fiction?

Single component geochemical maps are the most basic representation of spatial elemental distributions and commonly used in environmental and exploration geochemistry. However, the compositional nature of geochemical data imposes several limitations on how the data should be presented. The problems relate to the constant sum problem (closure), and the inherently multivariate relative information conveyed by compositional data. Well known is, for instance, the tendency of all heavy metals to show lower values in soils with significant contributions of diluting elements (e.g., the quartz dilution effect); or the contrary effect, apparent enrichment in many elements due to removal of potassium during weathering. The validity of classical single component maps is thus investigated, and reasonable alternatives that honour the compositional character of geochemical concentrations are presented. The first recommended such method relies on knowledge-driven log-ratios, chosen to highlight certain geochemical relations or to filter known artefacts (e.g. dilution with SiO2 or volatiles). This is similar to the classical normalisation approach to a single element. The second approach uses the (so called) log-contrasts, that employ suitable statistical methods (such as classification techniques, regression analysis, principal component analysis, clustering of variables, etc.) to extract potentially interesting geochemical summaries. The caution from this work is that if a compositional approach is not used, it becomes difficult to guarantee that any identified pattern, trend or anomaly is not an artefact of the constant sum constraint. In summary the authors recommend a chain of enquiry that involves searching for the appropriate statistical method that can answer the required geological or geochemical question whilst maintaining the integrity of the compositional nature of the data. The required log-ratio transformations should be applied followed by the chosen statistical method. Interpreting the results may require a closer working relationship between statisticians, data analysts and geochemists.

What defines a geochemical map? Implications for environmental assessment.

The environmental quality of land is often assessed by the calculation of threshold values which aim to differentiate between concentrations of elements based on whether the soils are in residential or industrial sites. In Europe, for example, soil guideline values exist for agricultural and grazing land. A threshold is often set to differentiate between concentrations of the element that naturally occur in the soil and concentrations that result from diffuse anthropogenic sources. Regional geochemistry and, in particular, single component geochemical maps are increasingly being used to determine these baseline environmental assessments. The key question raised in this paper is whether the geochemical map can provide an accurate interpretation on its own. Implicit is the thought that single component geochemical maps represent absolute abundances. However,because of the compositional (closed) nature of the data univariate geochemical maps cannot be compared directly with one another.. As a result, any interpretation based on them is vulnerable to spurious correlation problems. What does this mean for soil geochemistry mapping, baseline quality documentation, soil resource assessment or risk evaluation? Despite the limitation of relative abundances, individual raw geochemical maps are deemed fundamental to several applications of geochemical maps including environmental assessments. However, element toxicity is related to its bioavailable concentration, which is lowered if its source is mixed with another source. Elements interact, for example under reducing conditions with iron oxides, its solid state is lost and arsenic becomes soluble and mobile. Both of these matters may be more adequately dealt with if a single component map is not interpreted in isolation to determine baseline and threshold assessments. A range of alternative compositionally compliant representations based on log-ratio and log-contrast approaches are explored to supplement the classical single component maps for environmental assessment. Case study examples are shown based on the Tellus soil geochemical dataset, covering Northern Ireland and the results of in vitro oral bioaccessibility testing carried out on a sub-set of archived Tellus Survey shallow soils following the Unified BARGE (Bioaccessibility Research Group of Europe).

The Complexity of MAP Inference in Bayesian Networks Specified Through Logical Languages

We study the computational complexity of finding maximum a posteriori configurations in Bayesian networks whose probabilities are specified by logical formulas. This approach leads to a fine grained study in which local information such as context-sensitive independence and determinism can be considered. It also allows us to characterize more precisely the jump from tractability to NP-hardness and beyond, and to consider the complexity introduced by evidence alone.

Praying for Salvation: A Map of Relatedness

This article attempts to push Mauss’ work on the sociality of prayer (1909) to its fullest conclusion by arguing that prayer can be viewed anthropologically as providing a map for social and emotional relatedness. Based on fieldwork among deep-sea fisher families living in Gamrie, North-East Scotland (home to 700 people and six Protestant churches), the author takes as his primary ethnographic departure the ritual of the ‘mid-week prayer meeting’. Among the self-proclaimed ‘fundamentalists’ of Gamrie’s Brethren and Presbyterian churches, attending the prayer meeting means praying for salvation. Yet, contrary to the stereotype of Protestant soteriology as highly individualist, in the context of Gamrie, salvation is not principally focused upon the self, but is instead sought on behalf of the ‘unconverted’ other. Locally, this ‘other’ is made sense of with reference to three different categories of relatedness: the family, the village and the nation. The author’s argument is that each category of relatedness carries with it a different affective quality: anguish for one’s family, resentment toward one’s village, and resignation towards one’s nation. As such, prayers for salvation establish and maintain not only vertical – human-divine – relatedness, but also horizontal relatedness between persons, while also giving them their emotional tenor. In ‘fundamentalist’ Gamrie, these human relationships, and crucially their affective asymmetries, may be mapped, therefore, by treating prayers as social phenomena that seek to engage with a world dichotomised into vice and virtue, rebellion and submission, and, ultimately, damnation and salvation.