New meanings from old buildings

The three modest house projects described here are by three fellow travellers — the two authors and David Lea — interested in the Organic side of Modernism. Conversational partners who have worked together in various capacities over many years, they share a common conviction about ‘working with the given

High-throughput sequencing of 16S rRNA gene amplicons : effects of extraction procedure, primer length and annealing temperature

The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers

Statistical modelling of transcript profiles of differentially regulated genes

Background: The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression. Results: Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Splitline" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t) = A + (B + Ct)Rt + ε. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data allowed 11% of the Escherichia coli features to be fitted by an exponential function, and 25% of the Rattus norvegicus features could be described by the critical exponential model, all with statistical significance of p < 0.05. Conclusion: The statistical non-linear regression approaches presented in this study provide detailed biologically oriented descriptions of individual gene expression profiles, using biologically variable data to generate a set of defining parameters. These approaches have application to the modelling and greater interpretation of profiles obtained across a wide range of platforms, such as microarrays. Through careful choice of appropriate model forms, such statistical regression approaches allow an improved comparison of gene expression profiles, and may provide an approach for the greater understanding of common regulatory mechanisms between genes

Response execution and inhibitionin children with AD/HD and other disruptive disorders: the role of behavioural activation.

Item does not contain fulltextThis study was aimed at (a) replicating findings of slow and variable response execution and slow response inhibition in Attention Deficit/Hyperactivity Disorder (AD/HD), (b) investigating whether these deficits are specifically related to AD/HD or may also be observed in Oppositional Defiant Disorder (ODD), and children comorbid for AD/HD+ODD, and (c) examining the role of activation level in task performance of children with AD/HD. To meet these aims, the stop paradigm was administered at three levels of activation, using a slow, medium, and fast presentation rate of stimuli, to 4 groups of children: 24 AD/HD children, 21 children with ODD, 27 children with comorbid AD/HD+ODD, and 41 normal controls. As hypothesized, children with AD/HD exhibited a slow response execution process with considerable variability in the speed of responding compared to normal controls. Slow response execution was also observed in the comorbid AD/HD+ODD group but not in the pure ODD group. Larger variability in the speed of responding was common to all disruptive groups compared with controls. In contrast to our hypothesis, no group differences emerged for inhibitory functioning. Finally, the slow event rate condition caused a further deterioration in the speed of the response execution process in both the AD/HD group and ODD group

Speed of inhibition predicts teacher-rated medication response in boys with attention deficit hyperactivity disorder

Item does not contain fulltextThis study aimed at investigating whether one of the key deficits in Attention Deficit Hyperactivity Disorder (ADHD), slow response inhibition, predicted the response to methylphenidate (MPH) treatment. In order to address this issue, we used Stop Signal Reaction Times (SSRTs) measured at baseline in 20 medication-nave boys with ADHD as predictor, and parent and teacher ratings that were collected during a double-blind, placebo-controlled titration trial of MPH in the same group as outcome measures. Parent and teacher ratings were collected on primary scales, measuring ADHD symptoms, and secondary scales, measuring oppositional and disruptive behaviour. Placebo response and ADHD/Oppositional Defiant Disorder symptom severity at baseline were controlled for in the analyses. The SSRT did not predict the MPH response as measured by parent ratings, but it did predict the MPH response as measured by teacher ratings. This effect was specific for the ADHD scales. The slower SSRTs were, the less children benefited from MPH. Moreover, children with longer SSRTs needed higher doses of MPH for optimal symptom relief than children with shorter SSRTs. These findings have implications for clinicians who face the decision of which MPH dose to prescribe.18 p

Response Inhibition in Children With DSM-IV Subtypes of AD/HD and Related Disruptive Disorders: The Role of Reward

Item does not contain fulltextThe current study had four aims: (a) to replicate previous findings of slow response inhibition in Attention Deficit/Hyperactivity Disorder (AD/HD), (b) to explore whether poor response inhibition in children with AD/HD is a core problem or rather a result of an underlying problem related to reward, (c) to investigate the specificity of poor response inhibition and the role of reward in relation to AD/HD, and (d) to study whether findings would be different for three subtypes of AD/HD. In order to address these issues, a stop paradigm was administered under a reward condition and under a nonreward condition to an AD/HD group (n = 24), an Oppositional Defiant Disorder (ODD)/Conduct Disorder (CD) group (n = 21), a comorbid AD/HD + ODD/CD group (n = 27), and a normal control (NC) group (n = 41). Firstly, contrary to prediction, none of the Disruptive Behavior Disorder (DBD) groups differed from the NC group with respect to the speed of the inhibition process. Secondly, it was shown that children with AD/HD and children with comorbid AD/HD + ODD/CD, but not children with ODD/CD alone, slowed down more dramatically in the reward condition than normal controls. This finding was interpreted as a strategy to increase the chance of being rewarded in children with AD/HD and children with comorbid AD/HD + ODD/CD, but not in children with pure ODD/CD. Finally, analysis of AD/HD subtypes did not change the main findings of this study

Recovery of a medieval Brucella melitensis genome using shotgun metagenomics

Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens

Substance use disorders in adolescents with attention deficit hyperactivity disorder: a 4-year follow-up study

Aim To examine the relationship between a childhood diagnosis of attention deficit hyperactivity disorder (ADHD) with or without oppositional defiant disorder (ODD)/conduct disorder (CD) and the development of later alcohol/drug use disorder [psychoactive substance use disorder (PSUD)] and nicotine dependence in a large European sample of ADHD probands, their siblings and healthy control subjects. Participants design and settingSubjects (n=1017) were participants in the Belgian, Dutch and German part of the International Multicenter ADHD Genetics (IMAGE) study. IMAGE families were identified through ADHD probands aged 5-17 years attending out-patient clinics, and control subjects from the same geographic areas. After a follow-up period (mean: 4.4 years) this subsample was re-assessed at a mean age of 16.4 years. Measurements PSUD and nicotine dependence were assessed using the Diagnostic Interview Schedule for Children, Alcohol Use Disorders Identification Test, Drug Abuse Screening Test and Fagerstrom test for Nicotine Dependence. Findings The ADHD sample was at higher risk of developing PSUD [hazard ratio (HR)=1.77, 95% confidence interval (CI)=1.05-3.00] and nicotine dependence (HR=8.61, 95% CI=2.44-30.34) than healthy controls. The rates of these disorders were highest for ADHD youth who also had CD, but could not be accounted for by this comorbidity. We did not find an increased risk of developing PSUD (HR=1.18, 95% CI=0.62-2.27) or nicotine dependence (HR=1.89, 95% CI=0.46-7.77) among unaffected siblings of ADHD youth. Conclusions A childhood diagnosis of attention deficit hyperactivity disorder is a risk factor for psychoactive substance use disorder and nicotine dependence in adolescence and comorbid conduct disorder, but not oppositional defiant disorder, further increases the risk of developing psychoactive substance use disorder and nicotine dependence

Executive functioning in adult ADHD: a meta-analytic review

. CONCLUSIONS: Neuropsychological difficulties in adult ADHD may not be confined to executive functioning. The field is in urgent need of better-designed executive functioning tests, methodological improvements, and direct comparisons with multiple clinical groups to answer questions of specificit

Aprotinin reduces cardiac troponin I release and inhibits apoptosis of polymorphonuclear cells during off-pump coronary artery bypass surgery

Objectives: In addition to blood-sparing effects, aprotinin may have cardioprotective and anti-inflammatory effects during cardiopulmonary bypass-assisted cardiac surgery. In this study, the authors examined whether aprotinin had cardioprotective and/or anti-inflammatory effects in patients undergoing off-pump coronary artery bypass grafting. Design: A prospective randomized clinical trial. Setting: University hospital. Participants: Fifty patients were randomized to control (n = 25) or aprotinin treatment (n = 25) groups. Interventions: Aprotinin was given as a loading dose (2 x 10(6) KIU) followed by a continuous infusion at 5 x 10(5) KIU/h until skin closure. Measurements and Main Results: Blood samples for cardiac troponin I; interleukin-6, interleukin-8, and interleukin-10; tumor necrosis factor a; and elastase were taken after anesthesia induction, completion of revascularization, and 6 hours, 12 hours, and 24 hours after revascularization. Blood samples were taken to assess for apoptosis in polymorphonuclear cells. Baseline plasma levels for cardiac troponin I did not differ between groups but were significantly lower in aprotinin-treated patients at the time of revascularization (P = 0.03) and 6 hours (p = 0.004) and 24 hours (p = 0.03) later. Aprotinin significantly reduced apoptosis in polymorphonuclear cells compared with control-treated patients (p = 0.04). There were no differences in plasma cytokine or elastase levels between groups. Conclusions: The authors conclude that aprotinin reduces perioperative cardiac troponin I release and attenuates apoptosis in polymorphonuclear cells but has no significant effects on plasma cytokine levels in patients undergoing off-pump coronary artery bypass graft surgery