A model-based method for 3D reconstruction of cerebellar parallel fibres from high-resolution electron microscope images

In order to understand how the brain works, we need to understand how its neural circuits process information. Electron microscopy remains the only imaging technique capable of providing sufficient resolution to reconstruct the dense connectivity between all neurons in a circuit. Automated electron microscopy techniques are approaching the point where usefully large circuits might be successfully imaged, but the development of automated reconstruction techniques lags far behind. No fully-automated reconstruction technique currently produces acceptably accurate reconstructions, and semi-automated approaches currently require an extreme amount of manual effort. This reconstruction bottleneck places severe limits on the size of neural circuits that can be reconstructed. Improved automated reconstruction techniques are therefore highly desired and under active development. The human brain contains ~86 billion neurons and ~80% of these are located in the cerebellum. Of these cerebellar neurons, the vast majority are granule cells. The axons of these granule cells are called parallel fibres and tend to be oriented in approximately the same direction, making 2+1D reconstruction approaches feasible. In this work we focus on the problem of reconstructing these parallel fibres and make four main contributions: (1) a model-based algorithm for reconstructing 2D parallel fibre cross-sections that achieves state of the art 2D reconstruction performance; (2) a fully-automated algorithm for reconstructing 3D parallel fibres that achieves state of the art 3D reconstruction performance; (3) a semi-automated approach for reconstructing 3D parallel fibres that significantly improves reconstruction accuracy compared to our fully-automated approach while requiring ~40 times less labelling effort than a purely manual reconstruction; (4) a "gold standard" ground truth data set for the molecular layer of the mouse cerebellum that will provide a valuable reference for the development and benchmarking of reconstruction algorithms

A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs

Recent developments in electron microscopy now permit the unambiguous reconstruction of even the smallest neural fibres by human experts. However, manual reconstruction of an interesting volume of neural tissue would take thousands of person-years. Techniques to automate such reconstruction are therefore highly desirable and currently under active development. Here we present a novel circle-based technique and assess its performance on classically stained electron micrographs of the molecular layer of mouse cerebellar cortex. We compare its performance to a recently published pixel-based classifier (ilastik), selected because a similar random forest classifier from the same group has shown promising results on images of neural tissue. The performance of our algorithm and that of ilastik are similar, achieving approximately 50% on an overlap-based f-measure

Direct and indirect effects of Johne's disease on farm and animal productivity in an Irish dairy herd

Johne's disease (JD) is caused by infection with the organism Mycobacterium avium spp. paratuberculosis, leading to chronic diarrhoea and ill thrift in adult cattle. JD is considered to adversely affect farm performance and profitability. This retrospective case study was undertaken on a single commercial dairy herd in the south west of Ireland. Animal production records were interrogated to assess the effect of JD on milk yield (total kg per lactation), somatic cell count (the geometric mean over the lactation), reasons for culling, cull price and changes in herd parity structure over time. JD groups were defined using clinical signs and test results. One control animal was matched to each case animal on parity number and year. Specific lactations (clinical, pre-clinical and test-positive only) from 1994 to 2004 were compared between JD case and control cows. A significantly lower milk yield (1259.3 kg/lactation) was noted from cows with clinical JD in comparison to their matched control group. Clinical animals had an average cull price of €516 less than animals culled without signs of clinical disease. In contrast, little effect was noted for sub-clinical infections. These direct effects of JD infections, in combination with increased culling for infertility and increasing replacement rates, had a negative impact on farm production. Results from this study provide preliminary information regarding the effects of JD status on both herd and animal-level performance in Ireland

Reduced ventral cingulum integrity and increased behavioral problems in children with isolated optic nerve hypoplasia and mild to moderate or no visual impairment.

To assess the prevalence of behavioral problems in children with isolated optic nerve hypoplasia, mild to moderate or no visual impairment, and no developmental delay. To identify white matter abnormalities that may provide neural correlates for any behavioral abnormalities identified

Shallow water methane-derived authigenic carbonate mounds at the Codling Fault Zone, western Irish Sea

Methane-derived authigenic carbonate (MDAC) mound features at the Codling Fault Zone (CFZ), located in shallow waters (50–120 m) of the western Irish Sea were investigated and provide a comparison to deep sea MDAC settings. Carbonates consisted of aragonite as the major mineral phase, with δ13C depletion to −50‰ and δ18O enrichment to ~ 2‰. These isotope signatures, together with the co-precipitation of framboidal pyrite confirm that anaerobic oxidation of methane (AOM) is an important process mediating methane release to thewater column and the atmosphere in this region. 18O-enrichment could be a result ofMDAC precipitation with seawater in colder than present day conditions, or precipitation with 18O-enriched water transported from deep petroleum sources. The 13C depletion of bulk carbonate and sampled gas(−70‰) suggests a biogenic source, but significant mixing of thermogenic gas and depletion of the original isotope signature cannot be ruled out. Active seepage was recorded from one mound and together with extensive areas of reduced sediment, confirms that seepage is ongoing. The mounds appear to be composed of stacked pavements that are largely covered by sand and extensively eroded. The CFZ mounds are colonized by abundant Sabellaria polychaetes and possible Nemertesia hydroids, which benefit indirectly from available hard substrate. In contrast to deep sea MDAC settings where seep-related macrofauna are commonly reported, seep-specialist fauna appear to be lacking at the CFZ. In addition, unlike MDAC in deep waters where organic carbon input from photosynthesis is limited, lipid biomarkers and isotope signatures related to marine planktonic production (e.g. sterols, alkanols) were most abundant. Evidence for microbes involved in AOM was limited from samples taken; possibly due to this dilution effect from organic matter derived from the photic zone, and will require further investigation

Deficient and null variants of SERPINA1 are proteotoxic in a Caenorhabditis elegans model of α1-antitrypsin deficiency

α1-antitrypsin deficiency (ATD) predisposes patients to both loss-of-function (emphysema) and gain-of-function (liver cirrhosis) phenotypes depending on the type of mutation. Although the Z mutation (ATZ) is the most prevalent cause of ATD, >120 mutant alleles have been identified. In general, these mutations are classified as deficient (<20% normal plasma levels) or null (<1% normal levels) alleles. The deficient alleles, like ATZ, misfold in the ER where they accumulate as toxic monomers, oligomers and aggregates. Thus, deficient alleles may predispose to both gain- and loss-of-function phenotypes. Null variants, if translated, typically yield truncated proteins that are efficiently degraded after being transiently retained in the ER. Clinically, null alleles are only associated with the loss-of-function phenotype. We recently developed a C. elegans model of ATD in order to further elucidate the mechanisms of proteotoxicity (gain-of-function phenotype) induced by the aggregationprone deficient allele, ATZ. The goal of this study was to use this C. elegans model to determine whether different types of deficient and null alleles, which differentially affect polymerization and secretion rates, correlated to any extent with proteotoxicity. Animals expressing the deficient alleles, Mmalton, Siiyama and S (ATS), showed overall toxicity comparable to that observed in patients. Interestingly, Siiyama expressing animals had smaller intracellular inclusions than ATZ yet appeared to have a greater negative effect on animal fitness. Surprisingly, the null mutants, although efficiently degraded, showed a relatively mild gainoffunction proteotoxic phenotype. However, since null variant proteins are degraded differently and do not appear to accumulate, their mechanism of proteotoxicity is likely to be different to that of polymerizing, deficient mutants. Taken together, these studies showed that C. elegans is an inexpensive tool to assess the proteotoxicity of different AT variants using a transgenic approach

Targeting tumour re-wiring by triple blockade of mTORC1, epidermal growth factor, and oestrogen receptor signalling pathways in endocrine-resistant breast cancer

Background Endocrine therapies are the mainstay of treatment for oestrogen receptor (ER)-positive (ER+) breast cancer (BC). However, resistance remains problematic largely due to enhanced cross-talk between ER and growth factor pathways, circumventing the need for steroid hormones. Previously, we reported the anti-proliferative effect of everolimus (RAD001-mTORC1 inhibitor) with endocrine therapy in resistance models; however, potential routes of escape from treatment via ERBB2/3 signalling were observed. We hypothesised that combined targeting of three cellular nodes (ER, ERBB, and mTORC1) may provide enhanced long-term clinical utility. Methods A panel of ER+ BC cell lines adapted to long-term oestrogen deprivation (LTED) and expressing ESR1wt or ESR1Y537S, modelling acquired resistance to an aromatase-inhibitor (AI), were treated in vitro with a combination of RAD001 and neratinib (pan-ERBB inhibitor) in the presence or absence of oestradiol (E2), tamoxifen (4-OHT), or fulvestrant (ICI182780). End points included proliferation, cell signalling, cell cycle, and effect on ER-mediated transactivation. An in-vivo model of AI resistance was treated with monotherapies and combinations to assess the efficacy in delaying tumour progression. RNA-seq analysis was performed to identify changes in global gene expression as a result of the indicated therapies. Results Here, we show RAD001 and neratinib (pan-ERBB inhibitor) caused a concentration-dependent decrease in proliferation, irrespective of the ESR1 mutation status. The combination of either agent with endocrine therapy further reduced proliferation but the maximum effect was observed with a triple combination of RAD001, neratinib, and endocrine therapy. In the absence of oestrogen, RAD001 caused a reduction in ER-mediated transcription in the majority of the cell lines, which associated with a decrease in recruitment of ER to an oestrogen-response element on the TFF1 promoter. Contrastingly, neratinib increased both ER-mediated transactivation and ER recruitment, an effect reduced by the addition of RAD001. In-vivo analysis of an LTED model showed the triple combination of RAD001, neratinib, and fulvestrant was most effective at reducing tumour volume. Gene set enrichment analysis revealed that the addition of neratinib negated the epidermal growth factor (EGF)/EGF receptor feedback loops associated with RAD001. Conclusions Our data support the combination of therapies targeting ERBB2/3 and mTORC1 signalling, together with fulvestrant, in patients who relapse on endocrine therapy and retain a functional ER

A cross sectional study of requests for knee radiographs from primary care

<p>Abstract</p> <p>Background</p> <p>Knee pain is the commonest pain complaint amongst older adults in general practice. General Practitioners (GPs) may use x rays when managing knee pain, but little information exists regarding this process. Our objectives, therefore, were to describe the information GPs provide when ordering knee radiographs in older people, to assess the association between a clinical diagnosis of osteoarthritis (OA) and the presence of radiographic knee OA, and to investigate the clinical content of the corresponding radiologists' report.</p> <p>Methods</p> <p>A cross sectional study of GP requests for knee radiographs and their matched radiologists' reports from a local radiology department. Cases, aged over 40, were identified during an 11-week period. The clinical content of the GPs' requests and radiologists' reports was analysed. Associations of radiologists' reporting of i) osteoarthritis, ii) degenerative disease and iii) individual radiographic features of OA, with patient characteristics and clinical details on the GPs' requests, were assessed.</p> <p>Results</p> <p>The study identified 136 cases with x ray requests from 79 GPs and 11 reporting radiologists. OA was identified clinically in 19 (14%) of the requests, and queried in another 31 (23%). The main clinical descriptor was pain in 119 cases (88%). Radiologists' reported OA in 22% of cases, and the features of OA were mentioned in 63%. Variation in reporting existed between radiologists. The commonest description was joint space narrowing in 52 reports (38%). There was an apparent although non significant increase in the reporting of knee OA when the GP had diagnosed or queried it (OR 1.95; 95% CI 0.76, 5.00).</p> <p>Conclusion</p> <p>The features of radiographic OA are commonly reported in those patients over 40 whom GPs send for x ray. If OA is clinically suspected, radiologists appear to be more likely to report its presence. Further research into alternative models of referral and reporting might identify a more appropriate imaging policy in knee disorders for primary care.</p

DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia

<p>Abstract</p> <p>Background</p> <p>The synapsin III (<it>SYN III</it>) gene on chromosome 22q is a candidate gene for schizophrenia susceptibility due to its chromosome location, neurological function, expression patterns and functional polymorphisms.</p> <p>Methods</p> <p>This research has established the mRNA expression of <it>SYN III </it>in 22 adult human brain regions as well as the methylation specificity in the closest CpG island of this gene. The methylation specificity studied in 31 brain regions (from a single individual) was also assessed in 51 human blood samples (representing 20 people affected with schizophrenia and 31 normal controls) including a pair of monozygotic twin discordant for schizophrenia and 2 non-human primates.</p> <p>Results</p> <p>The results show that the cytosine methylation in this genomic region is 1) restricted to cytosines in CpG dinucleotides 2) similar in brain regions and blood and 3) appears conserved in primate evolution. Two cytosines (cytosine 8 and 20) localized as the CpG dinucleotide are partially methylated in all brain regions studied. The methylation of these sites in schizophrenia and control blood samples was variable. While cytosine 8 was partially methylated in all samples, the distribution of partial to complete methylation at the cytosine 20 was 22:9 in controls as compared to 18:2 in schizophrenia (p = 0.82). Also, there is no difference in methylation between the affected and unaffected member of a monozygotic twin pair.</p> <p>Conclusion</p> <p>The variation in <it>SYN III </it>methylation studied is 1) not related to schizophrenia in the population sample or a monozygotic twin pair discordant for schizophrenia and 2) not related to the mRNA level of <it>SYN IIIa </it>in different human brain regions.</p