No time for drifting: Comparing performance and applicability of signal detrending algorithms for real-time fMRI.

As a consequence of recent technological advances in the field of functional magnetic resonance imaging (fMRI), results can now be made available in real-time. This allows for novel applications such as online quality assurance of the acquisition, intra-operative fMRI, brain-computer-interfaces, and neurofeedback. To that aim, signal processing algorithms for real-time fMRI must reliably correct signal contaminations due to physiological noise, head motion, and scanner drift. The aim of this study was to compare performance of the commonly used online detrending algorithms exponential moving average (EMA), incremental general linear model (iGLM) and sliding window iGLM (iGLMwindow). For comparison, we also included offline detrending algorithms (i.e., MATLAB's and SPM8's native detrending functions). Additionally, we optimized the EMA control parameter, by assessing the algorithm's performance on a simulated data set with an exhaustive set of realistic experimental design parameters. First, we optimized the free parameters of the online and offline detrending algorithms. Next, using simulated data, we systematically compared the performance of the algorithms with respect to varying levels of Gaussian and colored noise, linear and non-linear drifts, spikes, and step function artifacts. Additionally, using in vivo data from an actual rt-fMRI experiment, we validated our results in a post hoc offline comparison of the different detrending algorithms. Quantitative measures show that all algorithms perform well, even though they are differently affected by the different artifact types. The iGLM approach outperforms the other online algorithms and achieves online detrending performance that is as good as that of offline procedures. These results may guide developers and users of real-time fMRI analyses tools to best account for the problem of signal drifts in real-time fMRI.

Reduced parahippocampal cortical thickness in subjects at ultra-high risk for psychosis.

BACKGROUND: Grey matter volume and cortical thickness represent two complementary aspects of brain structure. Several studies have described reductions in grey matter volume in people at ultra-high risk (UHR) of psychosis; however, little is known about cortical thickness in this group. The aim of the present study was to investigate cortical thickness alterations in UHR subjects and compare individuals who subsequently did and did not develop psychosis. METHOD: We examined magnetic resonance imaging data collected at four different scanning sites. The UHR subjects were followed up for at least 2 years. Subsequent to scanning, 50 UHR subjects developed psychosis and 117 did not. Cortical thickness was examined in regions previously identified as sites of neuroanatomical alterations in UHR subjects, using voxel-based cortical thickness. RESULTS: At baseline UHR subjects, compared with controls, showed reduced cortical thickness in the right parahippocampal gyrus (p < 0.05, familywise error corrected). There were no significant differences in cortical thickness between the UHR subjects who later developed psychosis and those who did not. CONCLUSIONS: These data suggest that UHR symptomatology is characterized by alterations in the thickness of the medial temporal cortex. We did not find evidence that the later progression to psychosis was linked to additional alterations in cortical thickness, although we cannot exclude the possibility that the study lacked sufficient power to detect such differences.

Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ).

Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18-85years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

The impact of physiological noise correction on fMRI at 7 T.

Cognitive neuroimaging studies typically require fast whole brain image acquisition with maximal sensitivity to small BOLD signal changes. To increase the sensitivity, higher field strengths are often employed, since they provide an increased image signal-to-noise ratio (SNR). However, as image SNR increases, the relative contribution of physiological noise to the total time series noise will be greater compared to that from thermal noise. At 7 T, we studied how the physiological noise contribution can be best reduced for EPI time series acquired at three different spatial resolutions (1.1 mm × 1.1 mm × 1.8 mm, 2 mm × 2 mm × 2 mm and 3 mm × 3 mm × 3 mm). Applying optimal physiological noise correction methods improved temporal SNR (tSNR) and increased the numbers of significantly activated voxels in fMRI visual activation studies for all sets of acquisition parameters. The most dramatic results were achieved for the lowest spatial resolution, an acquisition parameter combination commonly used in cognitive neuroimaging which requires high functional sensitivity and temporal resolution (i.e. 3mm isotropic resolution and whole brain image repetition time of 2s). For this data, physiological noise models based on cardio-respiratory information improved tSNR by approximately 25% in the visual cortex and 35% sub-cortically. When the time series were additionally corrected for the residual effects of head motion after retrospective realignment, the tSNR was increased by around 58% in the visual cortex and 71% sub-cortically, exceeding tSNR ~140. In conclusion, optimal physiological noise correction at 7 T increases tSNR significantly, resulting in the highest tSNR per unit time published so far. This tSNR improvement translates into a significant increase in BOLD sensitivity, facilitating the study of even subtle BOLD responses.

Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis.

Bacillus anthracis is a Gram-positive spore-forming bacterium that is the causative agent of anthrax disease. The use of anthrax as a bioweapon has increased pressure for the development of an effective treatment. Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the biosynthetic pathway yielding two essential bacterial metabolites, meso-diaminopimelate (DAP) and (S)-lysine. DHDPS is therefore a potential antibiotic target, as microbes require either lysine or DAP as a component of the cell wall. This paper is the first biochemical description of DHDPS from B. anthracis. Enzyme kinetic analyses, isothermal titration calorimetry (ITC), mass spectrometry and differential scanning fluorimetry (DSF) were used to characterise B. anthracis DHDPS and compare it with the well characterised Escherichia coli enzyme. B. anthracis DHDPS exhibited different kinetic behaviour compared with E. coli DHDPS, in particular, substrate inhibition by (S)-aspartate semi-aldehyde was observed for the B. anthracis enzyme (K(si(ASA))=5.4+/-0.5 mM), but not for the E. coli enzyme. As predicted from a comparison of the X-ray crystal structures, the B. anthracis enzyme was not inhibited by lysine. The B. anthracis enzyme was thermally stabilised by the first substrate, pyruvate, to a greater extent than its E. coli counterpart, but has a weaker affinity for pyruvate based on enzyme kinetics and ITC studies. This characterisation will provide useful information for the design of inhibitors as new antibiotics targeting B. anthracis.

Spotlight on measles 2010: ongoing measles outbreak in Northern Ireland following an imported case, September-October 2010.

We report an ongoing outbreak of measles with five laboratory-confirmed and four epidemiologically linked cases in Northern Ireland as at 26 October 2010. The index case was an unvaccinated non-Northern Ireland resident with subsequent genotyping suggesting that infection originated in the usual country of residence of this case. Confirmed cases include one patient with a history of two measles-mumps-rubella vaccine doses.

Water quality modelling of the Mekong River basin: Climate change and socioeconomics drive flow and nutrient flux changes to the Mekong Delta.

The Mekong delta is recognised as one of the world's most vulnerable mega-deltas, being subject to a range of environmental pressures including sea level rise, increasing population, and changes in flows and nutrients from its upland catchment. With changing climate and socioeconomics there is a need to assess how the Mekong catchment will be affected in terms of the delivery of water and nutrients into the delta system. Here we apply the Integrated Catchment model (INCA) to the whole Mekong River Basin to simulate flow and water quality, including nitrate, ammonia, total phosphorus and soluble reactive phosphorus. The impacts of climate change on all these variables have been assessed across 24 river reaches ranging from the Himalayas down to the delta in Vietnam. We used the UK Met Office PRECIS regionally coupled climate model to downscale precipitation and temperature to the Mekong catchment. This was accomplished using the Global Circulation Model GFDL-CM to provide the boundary conditions under two carbon control strategies, namely representative concentration pathways (RCP) 4.5 and a RCP 8.5 scenario. The RCP 4.5 scenario represents the carbon strategy required to meet the Paris Accord, which aims to limit peak global temperatures to below a 2 °C rise whilst seeking to pursue options that limit temperature rise to 1.5 °C. The RCP 8.5 scenario is associated with a larger 3-4 °C rise. In addition, we also constructed a range of socio-economic scenarios to investigate the potential impacts of changing population, atmospheric pollution, economic growth and land use change up to the 2050s. Results of INCA simulations indicate increases in mean flows of up to 24%, with flood flows in the monsoon period increasing by up to 27%, but with increasing periods of drought up to 2050. A shift in the timing of the monsoon is also simulated, with a 4 week advance in the onset of monsoon flows on average. Decreases in nitrogen and phosphorus concentrations occur primarily due to flow dilution, but fluxes of these nutrients also increase by 5%, which reflects the changing flow, land use change and population changes.

Inhibiting protein-protein interactions as an emerging paradigm for drug discovery.

Association of proteins into homo- and hetero-oligomers plays an important role in a plethora of biological phenomena. Inhibition of these interactions is increasingly recognized as a valuable new direction in drug design. In this mini-review we consider inhibition of protein misfolding and aggregation, molecules that disrupt enzyme quaternary structure, and signaling inhibitors, as emerging drugs.

Older age is an adverse prognostic factor in stage I, favorable histology Wilms' tumor treated with vincristine monochemotherapy: a study by the United Kingdom Children's Cancer Study Group, Wilm's Tumor Working Group.

PURPOSE: To identify clinical prognostic factors in children with stage I, favorable histology (FH) Wilms' tumor treated with vincristine monochemotherapy after immediate nephrectomy to define subgroups for consideration of further reduction in treatment intensity. PATIENTS AND METHODS: During two consecutive trials of the United Kingdom Children's Cancer Study Group (UKW2 and UKW3, 1986 to 2001), 242 children with stage I FH Wilms' tumor were treated with immediate nephrectomy followed by 10 weekly injections of vincristine 1.5 mg/m2. Event-free survival (EFS) and overall survival (OS) were compared by age group. RESULTS: The 4-year EFS rate was 93.2%, 87.2%, and 71.3% for children less than 2 years old, 2 to 4 years old, and 4 years old or older at diagnosis, respectively (log-rank, P =.001); the corresponding 4-year OS rate was 98.1%, 95.0%, and 87.2% (log-rank, P =.01). There were no toxicity- or procedure-related deaths. In multivariate analysis, specimen weight was not of independent prognostic value (P =.66). Among the 186 children younger than 4 years at diagnosis, there were 17 relapses and five deaths, compared with 16 relapses and eight deaths among the 56 children at least 4 years old at diagnosis. OS after relapse was surprisingly poor (61.6% at 4 years). CONCLUSION: Treatment for stage I FH Wilms' tumor is generally successful using vincristine monotherapy after immediate nephrectomy, and therefore, the risks of dactinomycin hepatopathy can be avoided. However, age at least 4 years is a significant adverse prognostic factor. This treatment schedule should be considered in any trial of treatment reduction in very young children with stage I FH Wilms' tumor, regardless of tumor size, and we suggest that the upper age limit for the reduced therapy be set at 4 years.

Trends in biomass and metal sequestration associated with reeds and algae at Wheal Jane Biorem pilot passive treatment plant.

An assessment of the rate of biomass production both of the reeds in the aerobic cells and the algae in the rock filters, which form the final stage in the series of treatment cells, has been undertaken. The biomass production for the reeds was found to be highest for the lime-dosed anoxic limestone drain system, but even this was very low in comparison to values reported for natural and constructed wetlands. The algal coverage of each lagoon was relatively homogeneous, with no significant difference between the three systems studied. However, too many unknown factors suggest that further study is required. The metal uptake was higher in the roots than the stems, although no variation between cells of systems was detectable, and the difference was not as marked as reported by other workers. The metal concentrations in the debris samples were markedly higher than the roots of the reeds. The values for Fe, Al and As were several orders of magnitude larger than the influent minewater. Further study is required here, but this appears to be a key component in the function of the reeds. The lime-dosed system rock filter showed the highest Fe removal rate but the lowest Mn removal rate. Some possible mechanisms are discussed in the paper, but further investigation would be required to test these hypotheses.

Trends in biomass and metal sequestration associated with reeds and algae at Wheal Jane Biorem pilot passive treatment plant.

An assessment of the rate of biomass production both of the reeds in the aerobic cells and the algae in the rock filters, which form the final stage in the series of treatment cells, has been undertaken. The biomass production for the reeds was found to be highest for the lime-dosed anoxic limestone drain system, but even this was very low in comparison to values reported for natural and constructed wetlands. The algal coverage of each lagoon was relatively homogeneous, with no significant difference between the three systems studied. However, too many unknown factors suggest that further study is required. The metal uptake was higher in the roots than the stems, although no variation between cells of systems was detectable, and the difference was not as marked as reported by other workers. The metal concentrations in the debris samples were markedly higher than the roots of the reeds. The values for Fe, Al and As were several orders of magnitude larger than the influent minewater. Further study is required here, but this appears to be a key component in the function of the reeds. The lime-dosed system rock filter showed the highest Fe removal rate but the lowest Mn removal rate. Some possible mechanisms are discussed in the paper, but further investigation would be required to test these hypotheses.

Synergistic effects of diet and exercise on hippocampal function in chronically stressed mice.

Severe chronic stress can have a profoundly negative impact on the brain, affecting plasticity, neurogenesis, memory and mood. On the other hand, there are factors that upregulate neurogenesis, which include dietary antioxidants and physical activity. These factors are associated with biochemical processes that are also altered in age-related cognitive decline and dementia, such as neurotrophin expression, oxidative stress and inflammation. We exposed mice to an unpredictable series of stressors or left them undisturbed (controls). Subsets of stressed and control mice were concurrently given (1) no additional treatment, (2) a complex dietary supplement (CDS) designed to ameliorate inflammation, oxidative stress, mitochondrial dysfunction, insulin resistance and membrane integrity, (3) a running wheel in each of their home cages that permitted them to exercise, or (4) both the CDS and the running wheel for exercise. Four weeks of unpredictable stress reduced the animals' preference for saccharin, increased their adrenal weights and abolished the exercise-induced upregulation of neurogenesis that was observed in non-stressed animals. Unexpectedly, stress did not reduce hippocampal size, brain-derived neurotrophic factor (BDNF), or neurogenesis. The combination of dietary supplementation and exercise had multiple beneficial effects, as reflected in the number of doublecortin (DCX)-positive immature neurons in the dentate gyrus (DG), the sectional area of the DG and hippocampal CA1, as well as increased hippocampal BDNF messenger ribonucleic acid (mRNA) and serum vascular endothelial growth factor (VEGF) levels. In contrast, these benefits were not observed in chronically stressed animals exposed to either dietary supplementation or exercise alone. These findings could have important clinical implications for those suffering from chronic stress-related disorders such as major depression.

Dynamic modeling of the Ganga river system: impacts of future climate and socio-economic change on flows and nitrogen fluxes in India and Bangladesh.

This study investigates the potential impacts of future climate and socio-economic change on the flow and nitrogen fluxes of the Ganga river system. This is the first basin scale water quality study for the Ganga considering climate change at 25 km resolution together with socio-economic scenarios. The revised dynamic, process-based INCA model was used to simulate hydrology and water quality within the complex multi-branched river basins. All climate realizations utilized in the study predict increases in temperature and rainfall by the 2050s with significant increase by the 2090s. These changes generate associated increases in monsoon flows and increased availability of water for groundwater recharge and irrigation, but also more frequent flooding. Decreased concentrations of nitrate and ammonia are expected due to increased dilution. Different future socio-economic scenarios were found to have a significant impact on water quality at the downstream end of the Ganga. A less sustainable future resulted in a deterioration of water quality due to the pressures from higher population growth, land use change, increased sewage treatment discharges, enhanced atmospheric nitrogen deposition, and water abstraction. However, water quality was found to improve under a more sustainable strategy as envisaged in the Ganga clean-up plan.

A simple and rapid method for the selection of oligodeoxynucleotide-directed mutants.

We describe an in vitro selection procedure for oligodeoxynucleotide-directed mutagenesis, which produces mutants at frequencies of greater than 90%, facilitating the identification of mutants directly by nucleotide sequencing. The method is based on the selective methylation of the mutant strand by the incorporation of 5-methyl-dCTP. Restriction endonuclease digestion of the resulting hemimethylated DNA with MspI results in the nicking of only the nonmethylated-parental strand. The parental strand is removed by treatment with exonuclease III. The mutants are recovered by transformation of a mcrAB strain of Escherichia coli with the nascent strand.

Synthesis of beta-hydroxy-beta-(fluoronitrophenyl)alanines: vital components in the assembly of biologically active cyclic peptides.

[formula: see text] Numerous biologically active cyclic peptides, such as the antibiotic vancomycin, contain amino acid residues connected through side-chain biaryl or aryl-alkyl ether linkages. Nucleophilic aromatic substitution reactions have recently been shown to provide a general method for the formation of such ether linkages, and consequently the synthesis of functionalized fluoronitro-substituted aromatic amino acids is of great interest. Herein, a method for the stereospecific synthesis of 3-fluoro-4-nitro- and 4-fluoro-3-nitro-threo-beta-hydroxyphenylalanine is described.

Total synthesis of (-)-reveromycin B.

[structure: see text] The total synthesis of the epidermal growth factor inhibitor reveromycin B (2) is described. A novel, convergent, and stereoselective reaction sequence was utilized to construct the 5,6-spiroketal system 10 which was converted into the natural product 2 by a 16-step sequence.

Relationship between serum cholinesterase and low density lipoproteins in children with nephrotic syndrome.

1. A significant increase in the activity of serum cholinesterase and concentration of dextran sulphate precipitable lipoproteins, cholesterol and triglycerides was observed in sixteen children with a diagnosis of nephrotic syndrome when compared with the values obtained in 22 other normal children of comparable ages. 2. In 7 children with nephrotic syndrome serum concentrations of beta-lipoprotein and cholinesterase were markedly higher in the acute stage compared to the convalescent stage. A working hypothesis is proposed to explain the hyperlipoproteinemia in nephrotic syndrome.

Serum beta -- lipoproteins: studies in a patient and in guinea pigs after the ingestion of organophosphorus compounds.

A patient admitted to this hospital with Parathion poisoning had a marked reduction in serum cholinesterase activity and concentration of low density lipoprotein. The enzyme and the lipoprotein levels returned to normal with clinical recovery. Guinea pigs treated with phospholine iodide showed depressed levels of serum cholinesterase and beta-lipoprotein. It is suggested that the decrease in beta-lipoproteins is due to the decrease in cholinesterase activity.

Assessment of the zinc nutritional status of selected elderly subjects.

Elderly participants (with a mean age range of 71 to 75 years) residing in two housing complexes in Tuscaloosa, Alabama, can generally be characterized as predominantly women with a low socioeconomic status living alone. A majority of the participants consumed less than the RDA for food energy. The protein intake was nearly equal to or exceeded the RDA; however, the mean intake of zinc was only half of the RDA. The mean hair zinc concentration of the participants corresponded with the levels reported for this age group by other researchers. Their mean taste thresholds were higher (lower taste acuity) than those reported for young adults. Detection thresholds decreased as the ages of the participants increased. The taste acuity of the participants resembled that of groups of elderly studied by other investigators. A precise definition of low zinc status measurements among the elderly is not available at this time. However, the low hair zinc concentrations and taste acuity, compounded with the low zinc intake, indicate that this population is at risk for zinc deficiency.

Preschool vegetarian children. Dietary and anthropometric data.

Three-day dietary intakes were obtained on forty-eight preschool children between two and five years old, who had followed a vegetarian diet since birth. Intakes were calculated for food energy and selected nutrients. In addition, the children were measured for height, weight, triceps and subscapular skinfolds, and arm circumference. Average dietary intakes of the children compared favorably with the Recommended Dietary Allowances. Calcium was the only nutrient consumed in less than optimal amounts. Average intakes of the calculated amino acids were adequate when compared with available information. In general, anthropometric data were below the standards established by HANES findings, the National Center for Health Statistics, and available arm circumference data.