MicroRNA-9 represses sirtuin 1 (SIRT1) in human keratinocytes

The protein deacetylase sirtuin 1 (SIRT1) is an established regulator of diverse physiological processes and one of several promising targets for pharmacologic modulation of ageing and longevity. In normal human keratinocytes, SIRT1 has been shown to inhibit proliferation and promote differentiation. MicroRNAs (miRNAs), small non-coding RNA molecules that negatively regulate gene expression, have been shown to regulate SIRT1 expression in several cell types. Using western blotting, we show that miR-9 represses SIRT1 expression in the HaCaT human keratinocytes. The attenuation of SIRT1 levels in response to ectopic miR-9 occurred in a dose-dependent manner. As miR-9 expression is known to be under epigenetic control, the effect of the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) was examined. Levels of mature miR-9 increased 8-fold following TSA treatment of HaCaT keratinocytes. Expression of the primary transcripts from which miR-9 is derived was also raised in HaCaT keratinocytes exposed to TSA, with a 7-fold elevation of pri-miR-9-1 and 4-fold increase of pri-miR-3. In contrast the DNA methyl transferase inhibitor 5-deoxy-azacytidine (DAC) had little effect on miR-9 or primary miR-9 expression. Together, our findings point to a role for chromatin remodelling in regulating miR-9 levels in human keratinocytes and in turn modulation of SIRT1 expression by miR-9

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. We benchmark this method against other SNP callers using our FDR method with three fungal genomes, finding that it was able achieve a high level of accuracy. These tools are available at http://cfdr.sourceforge.net/.R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study

Analysis of InAs/GaAs quantum dot solar cells using Suns-V<inf>oc</inf> measurements

This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S0927024814003833#.The performance of InAs/GaAs quantum dot solar cells was investigated up to an optical concentration of 500-suns. A high temperature spacer layer between successive layers of quantum dots was used to reduce the degradation in the open circuit voltage relative to a control device without quantum dots. This improvement is explained using optical data while structural imaging of quantum dot stacks confirm that the devices are not limited by strain. The evolution of the open circuit voltage as a function of number of suns concentration was observed to be nearly ideal when compared with a high performance single junction GaAs solar cell. Analysis of Suns-Voc measurements reveal diode ideality factors as low as 1.16 which is indicative of a low concentration of defects in the devices.The authors acknowledge financial support from the European Union under the Seventh Framework Programme under a contract for an Integrated Infrastructure Initiative. Reference 312483 – ESTEEM2

Analysis of InAs/GaAs quantum dot solar cells using Suns-Voc measurements

The performance of InAs/GaAs quantum dot solar cells was investigated up to an optical concentration of 500-suns. A high temperature spacer layer between successive layers of quantum dots was used to reduce the degradation in the open circuit voltage relative to a control device without quantum dots. This improvement is explained using optical data while structural imaging of quantum dot stacks confirm that the devices are not limited by strain. The evolution of the open circuit voltage as a function of number of suns concentration was observed to be nearly ideal when compared with a high performance single junction GaAs solar cell. Analysis of Suns-Voc measurements reveal diode ideality factors as low as 1.16 which is indicative of a low concentration of defects in the devices.The authors acknowledge financial support from the European Union under the Seventh Framework Programme under a contract for an Integrated Infrastructure Initiative. Reference 312483 – ESTEEM2.This is the final accepted version, the article was originally published in Solar Energy Materials & Solar Cells, Vol. 130, November 2014, Pages 241–245, doi:10.1016/j.solmat.2014.07.022

Temperature Dependence of Spin-Split Peaks in Transverse Electron Focusing

We present experimental results of transverse electron-focusing measurements performed using n-type GaAs. In the presence of a small transverse magnetic field (B⊥), electrons are focused from the injector to detector leading to focusing peaks periodic in B⊥. We show that the odd-focusing peaks exhibit a split, where each sub-peak represents a population of a particular spin branch emanating from the injector. The temperature dependence reveals that the peak splitting is well defined at low temperature whereas it smears out at high temperature indicating the exchange-driven spin polarisation in the injector is dominant at low temperatures

Performance of random forest when SNPs are in linkage disequilibrium

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change the tree-building algorithm by building each tree in an RF only with SNPs in LE, modify the importance measure (IM), and use haplotypes instead of SNPs to build a RF.</p> <p>Results</p> <p>We evaluated the performance of our alternative methods by simulation of a spectrum of complex genetics models. When a haplotype rather than an individual SNP is the risk factor, we find that the original Random Forest method performed on SNPs provides good performance. When individual, genotyped SNPs are the risk factors, we find that the stronger the genetic effect, the stronger the effect LD has on the performance of the original RF. A revised importance measure used with the original RF is relatively robust to LD among SNPs; this revised importance measure used with the revised RF is sometimes inflated. Overall, we find that the revised importance measure used with the original RF is the best choice when the genetic model and the number of SNPs in LD with risk SNPs are unknown. For the haplotype-based method, under a multiplicative heterogeneity model, we observed a decrease in the performance of RF with increasing LD among the SNPs in the haplotype.</p> <p>Conclusion</p> <p>Our results suggest that by strategically revising the Random Forest method tree-building or importance measure calculation, power can increase when LD exists between SNPs. We conclude that the revised Random Forest method performed on SNPs offers an advantage of not requiring genotype phase, making it a viable tool for use in the context of thousands of SNPs, such as candidate gene studies and follow-up of top candidates from genome wide association studies.</p

The role of the right temporoparietal junction in perceptual conflict: detection or resolution?

The right temporoparietal junction (rTPJ) is a polysensory cortical area that plays a key role in perception and awareness. Neuroimaging evidence shows activation of rTPJ in intersensory and sensorimotor conflict situations, but it remains unclear whether this activity reflects detection or resolution of such conflicts. To address this question, we manipulated the relationship between touch and vision using the so-called mirror-box illusion. Participants' hands lay on either side of a mirror, which occluded their left hand and reflected their right hand, but created the illusion that they were looking directly at their left hand. The experimenter simultaneously touched either the middle (D3) or the ring finger (D4) of each hand. Participants judged, which finger was touched on their occluded left hand. The visual stimulus corresponding to the touch on the right hand was therefore either congruent (same finger as touch) or incongruent (different finger from touch) with the task-relevant touch on the left hand. Single-pulse transcranial magnetic stimulation (TMS) was delivered to the rTPJ immediately after touch. Accuracy in localizing the left touch was worse for D4 than for D3, particularly when visual stimulation was incongruent. However, following TMS, accuracy improved selectively for D4 in incongruent trials, suggesting that the effects of the conflicting visual information were reduced. These findings suggest a role of rTPJ in detecting, rather than resolving, intersensory conflict

Tetrabenazine as anti-chorea therapy in Huntington Disease: an open-label continuation study. Huntington Study Group/TETRA-HD Investigators

<p>Abstract</p> <p>Background</p> <p>Tetrabenazine (TBZ) selectively depletes central monoamines by reversibly binding to the type-2 vesicular monoamine transporter. A previous double blind study in Huntington disease (HD) demonstrated that TBZ effectively suppressed chorea, with a favorable short-term safety profile (<it>Neurology </it>2006;66:366-372). The objective of this study was to assess the long-term safety and effectiveness of TBZ for chorea in HD.</p> <p>Methods</p> <p>Subjects who completed the 13-week, double blind protocol were invited to participate in this open label extension study for up to 80 weeks. Subjects were titrated to the best individual dose or a maximum of 200 mg/day. Chorea was assessed using the Total Maximal Chorea (TMC) score from the Unified Huntington Disease Rating Scale.</p> <p>Results</p> <p>Of the 75 participants, 45 subjects completed 80 weeks. Three participants terminated due to adverse events (AEs) including depression, delusions with associated previous suicidal behavior, and vocal tics. One subject died due to breast cancer. The other 26 subjects chose not to continue on with each ensuing extension for various reasons. When mild and unrelated AEs were excluded, the most commonly reported AEs (number of subjects) were sedation/somnolence (18), depressed mood (17), anxiety (13), insomnia (10), and akathisia (9). Parkinsonism and dysphagia scores were significantly increased at week 80 compared to baseline. At week 80, chorea had significantly improved from baseline with a mean reduction in the TMC score of 4.6 (SD 5.5) units. The mean dosage at week 80 was 63.4 mg (range 12.5-175 mg).</p> <p>Conclusions</p> <p>TBZ effectively suppresses HD-related chorea for up to 80 weeks. Patients treated chronically with TBZ should be monitored for parkinsonism, dysphagia and other side effects including sleep disturbance, depression, anxiety, and akathisia.</p> <p>Trial Registration</p> <p>Clinicaltrials.gov registration number (initial study): NCT00219804</p

Age differences in mental health literacy

BACKGROUND: The community's knowledge and beliefs about mental health problems, their risk factors, treatments and sources of help may vary as a function of age. METHODS: Data were taken from an epidemiological survey conducted during 2003-2004 with a national clustered sample of Australian adults aged 18 years and over. Following the presentation of a vignette describing depression (n = 1001) or schizophrenia (n = 997), respondents were asked a series of questions relating to their knowledge and recognition of the disorder, beliefs about the helpfulness of treating professionals and medical, psychological and lifestyle treatments, and likely causes. RESULTS: Participant age was coded into five categories and cross-tabulated with mental health literacy variables. Comparisons between age groups revealed that although older adults (70+ years) were poorer than younger age groups at correctly recognising depression and schizophrenia, young adults (18-24 years) were more likely to misidentify schizophrenia as depression. Differences were also observed between younger and older age groups in terms of beliefs about the helpfulness of certain treating professionals and medical and lifestyle treatments for depression and schizophrenia, and older respondents were more likely to believe that schizophrenia could be caused by character weakness. CONCLUSION: Differences in mental health literacy across the adult lifespan suggest that more specific, age appropriate messages about mental health are required for younger and older age groups. The tendency for young adults to 'over-identify' depression signals the need for awareness campaigns to focus on differentiation between mental disorders