Imaging pancreas transplants

Pancreas transplants are performed in multiple centres across the UK with good graft survival rates. This places an increasing demand on radiology services, particularly as the complication rates are not insignificant. The imaging appearances of pancreas transplants and their complications can be difficult to interpret. This review provides an illustrative journey through the anatomical appearances of a graft and the imaging appearances of complications, as a reference tool for radiologists.

Synchrotron Reveals Early Triassic Odd Couple: Injured Amphibian and Aestivating Therapsid Share Burrow

Fossorialism is a beneficial adaptation for brooding, predator avoidance and protection from extreme climate. The abundance of fossilised burrow casts from the Early Triassic of southern Africa is viewed as a behavioural response by many tetrapods to the harsh conditions following the Permo-Triassic mass-extinction event. However, scarcity of vertebrate remains associated with these burrows leaves many ecological questions unanswered. Synchrotron scanning of a lithified burrow cast from the Early Triassic of the Karoo unveiled a unique mixed-species association: an injured temnospondyl amphibian (Broomistega) that sheltered in a burrow occupied by an aestivating therapsid (Thrinaxodon). The discovery of this rare rhinesuchid represents the first occurrence in the fossil record of a temnospondyl in a burrow. The amphibian skeleton shows signs of a crushing trauma with partially healed fractures on several consecutive ribs. The presence of a relatively large intruder in what is interpreted to be a Thrinaxodon burrow implies that the therapsid tolerated the amphibian’s presence. Among possible explanations for such unlikely cohabitation, Thrinaxodon aestivation is most plausible, an interpretation supported by the numerous Thrinaxodon specimens fossilised in curled-up postures. Recent advances in synchrotron imaging have enabled visualization of the contents of burrow casts, thus providing a novel tool to elucidate not only anatomy but also ecology and biology of ancient tetrapods.

Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells

Embryonic stem cell (ESC) self-renewal efficiency is determined by the level of Nanog expression. However, the mechanisms by which Nanog functions remain unclear, and in particular, direct Nanog target genes are uncharacterized. Here we investigate ESCs expressing different Nanog levels and Nanog^−/− cells with distinct functionally inducible Nanog proteins to identify Nanog-responsive genes. Surprisingly, these constitute a minor fraction of genes that Nanog binds. Prominent among Nanog-reponsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding of RNAPolII, and stimulates Esrrb transcription. Overexpression of Esrrb in ESCs maintains cytokine-independent self-renewal and pluripotency. Remarkably, this activity is retained in Nanog^−/− ESCs. Moreover, Esrrb can reprogram Nanog^−/− EpiSCs and can rescue stalled reprogramming in Nanog^−/− pre-iPSCs. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent ESC self-renewal. These findings are consistent with the functional placement of Esrrb downstream of Nanog.

Formation of artefacts while sampling emissions of PCDD/PCDF from open burning of biomass

Emission factors for PCDD/PCDF determined from open combustion are used to estimate national emission budgets; therefore, it is important to have confidence in their accuracy. It has been suspected that artefacts may form due to the presence of hot metal surfaces of sampling equipment, thus skewing emission factors. In this study, emissions of PCDD/PCDF from open burning of forest biomass over a brick hearth were sampled. Five experiments were carried out using a portable sampler. Experiments were designed where the key variable, sample hood and inlet temperatures were manipulated. Other variables such as fuel origin, type and density were consistent. The measured concentration of PCDD/PCDF in the smoke samples ranged from 0.01 μg TEQ (t fuel)(-1) at the lowest maximum hood temperature (185°C) to 15 μg TEQ (t fuel)(-1) at the highest maximum hood temperature (598°C). when hood inlet temperatures exceeded 400°C emission factors were significantly elevated and this is attributed to the formation of artefacts that can cause the over estimation of emission factors. The increase in hood temperature also resulted in a change in the PCDD/PCDF congener and homologue profile of the emissions. For example at the lowest temperature (Fire 1) the PCDD/PCDF ratio measured was 50:1, whereas at the highest temperature (Fire 5) this ratio was about 0.53:1. When the sampler hood and inlet temperatures were kept in the normal operating range of <200°C, emission factors were comparable to those observed in many previous studies in Australia with emissions dominated by PCDD.

An Oct4-centered protein interaction network in embryonic stem cells

Transcription factors, such as Oct4, are critical for establishing and maintaining pluripotent cell identity. Whereas the genomic locations of several pluripotency transcription factors have been reported, the spectrum of their interaction partners is underexplored. Here, we use an improved affinity protocol to purify Oct4-interacting proteins from mouse embryonic stem cells (ESCs). Subsequent purification of Oct4 partners Sall4, Tcfcp2l1, Dax1, and Esrrb resulted in an Oct4 interactome of 166 proteins, including transcription factors and chromatin-modifying complexes with documented roles in self-renewal, but also many factors not previously associated with the ESC network. We find that Esrrb associated with the basal transcription machinery and also detect interactions between transcription factors and components of the TGF-β, Notch, and Wnt signaling pathways. Acute depletion of Oct4 reduced binding of Tcfcp2l1, Dax1, and Esrrb to several target genes. In conclusion, our purification protocol allowed us to bring greater definition to the circuitry controlling pluripotent cell identity.

Ensembl Genomes: extending Ensembl across the taxonomic space

Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Is K-O Tab 1-2-3((R)) long lasting on non-polyester mosquito nets?

Many societies use locally sourced mosquito nets made from a variety of materials. For protecting against malaria these require regular re-treatment with insecticide. K-O Tab 1-2-3 is a 'dip-it-yourself' long-lasting formulation with time-limited interim recommendation from WHO for treatment of washed white and coloured polyester nets for up to 15 washes. To determine wash-resistance on different fabrics, nets made of polyester, polyethylene, cotton or nylon were treated with K-O Tab 1-2-3 and washed up to 20 times using standard WHO washing procedures. Efficacy was assessed using cone and cylinder bioassays and tunnel tests, and deltamethrin content using high-pressure liquid chromatography. Polyethylene and cotton nets treated with K-O Tab 1-2-3 and washed 20 times achieved the WHO threshold of >80% mortality in tunnel tests. Polyethylene matched the performance of polyester in all bioassays in contrast to cotton and nylon which produced low mortality and knock-down in cone and cylinder bioassays. After 20 washes 16.5% of the loading dose of deltamethrin remained on the polyester nets compared with 28.7% on polyethylene, 38.9% on cotton and 2.2% on nylon. Cotton nets retained a high concentration of insecticide but the relatively poor performance in terms of knock-down and mortality suggest most insecticide is bound within the cotton fibres rather than on the surface. K-O Tab 1-2-3 renders insecticide wash fast on polyethylene nets, less so on cotton and nylon. Nets made from polyethylene can be treated in the home to render the insecticide long lasting.

Unsupervised Methods for Determining Object and Relation Synonyms on the Web

The task of identifying synonymous relations and objects, or synonym resolution, is critical for high-quality information extraction. This paper investigates synonym resolution in the context of unsupervised information extraction, where neither hand-tagged training examples nor domain knowledge is available. The paper presents a scalable, fully-implemented system that runs in O(KN log N) time in the number of extractions, N, and the maximum number of synonyms per word, K. The system, called Resolver , introduces a probabilistic relational model for predicting whether two strings are co-referential based on the similarity of the assertions containing them. On a set of two million assertions extracted from the Web, Resolver resolves objects with 78% precision and 68% recall, and resolves relations with 90% precision and 35% recall. Several variations of resolver's probabilistic model are explored, and experiments demonstrate that under appropriate conditions these variations can improve F1 by 5%. An extension to the basic Resolver system allows it to handle polysemous names with 97% precision and 95% recall on a data set from the TREC corpus.

BioJava: an open-source framework for bioinformatics

Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher.

Contact:andreas.prlic@gmail.com. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes

The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples.

Chlorfenapyr: a pyrrole insecticide for the control of pyrethroid or DDT resistant Anopheles gambiae (Diptera: Culicidae) mosquitoes

Owing to the development and spread of pyrethroid resistance in Anopheles gambiae in Africa there is an urgent need to develop alternative insecticides to supplement the pyrethroids. Chlorfenapyr is a pyrrole insecticide first commercialized for the control of agricultural pests and termites. Performance against An. gambiae bearing kdr (pyrethroid and DDT resistance) or Ace-1(R) insensitive acetylcholinesterase (organophosphate and carbamate resistance) mechanisms was studied using a variety of adult bioassay tests including a simulated-experimental hut system (tunnel tests) that allows uninhibited mosquito behaviour/insecticide interactions. Strains resistant to pyrethroids and organophosphates showed no cross resistance to chlorfenapyr. In cone bioassays on treated netting the mortality of adult mosquitoes showed an unexpected curvilinear response, with highest mortality occurring at intermediate dosages. Adults expressed irritability to chlorfenapyr at higher dosages, which might explain the dosage-mortality trend. Toxic activity of chlorfenapyr was slow compared to conventional neurotoxic insecticides and additional mortality occurred between 24h and 72 h. In tunnel tests, the dosage-mortality trend showed a more typical sigmoid response and most mortality occurred during the first 24h. Mosquito penetration through the holed, treated netting showed only limited inhibition and blood-feeding was not inhibited. Mortality rates in the kdr strain exposed to chlorfenapyr treated netting in tunnel tests were much higher than with permethrin treated netting over the same 100-500 mg/m(2) dosage range. Chlorfenapyr has potential for malaria control in treated-net or residual spraying applications in areas where mosquitoes are pyrethroid resistant. For treated-net applications chlorfenapyr might be combined with pyrethroid as a mixture to provide personal protection as well as to give control of resistant mosquitoes.

Change in pancreatic B-cell function (HOMA-B) varies in different populations with similar genetic backgrounds but different environments

OBJECTIVE

To determine whether pancreatic B-cell function varies in different populations with similar genetic backgrounds but different environments.

RESEARCH DESIGN/METHODS

We compared a specific migrant Gujarati community in the UK (n = 205) with people still resident in the same villages of origin in Gujarat, India (n = 246). Pancreatic B-cell function (HOMA-B) was determined and the influence of age, migration and other factors was explored.

RESULTS

As anticipated, there was an age-related decline in log(HOMA-B) in both groups. However, the age-related fall in log(HOMA-B) was more pronounced in the UK than in Gujarat (normalized beta-0.29 vs. -0.14, P for difference = 0.03). The decline of HOMA-B with age persisted after adjustment for body mass index (UK beta = -0.31; Gujarat beta = -0.16, P = 0.015, P < 0.001). There was no significant change in insulin sensitivity (HOMA-S) with age at either site, although insulin sensitivity was lower in the UK. Fasting non-estrified fatty acid (NEFA) levels rose with age in the UK but not in Gujarat (P = 0.003 for difference in gradients). In multiple linear regression analysis, lower log(HOMA-B) was independently associated with higher fasting log(NEFA) levels; normalized beta = -0.24, P < 0.001, age; beta = -0.16, P = 0.005, higher log(insulin-like growth factor binding protein-1); beta = -0.19, P = 0.007 and lower body mass index; beta = 0.26, P = 0.001. This model accounted for 25% of the variability in HOMA-B.

CONCLUSIONS

HOMA-B as a measure of B-cell function declines more rapidly with age in the migrant UK group than in Gujarat. This may be a direct consequence of chronically higher NEFA exposure in the UK group.