Real-time functional magnetic resonance imaging: methods and applications

Functional magnetic resonance imaging (fMRI) has been limited by time-consuming data analysis and a low signal-to-noise ratio, impeding online analysis. Recent advances in acquisition techniques, computational power and algorithms increased the sensitivity and speed of fMRI significantly, making real-time analysis and display of fMRI data feasible. So far, most reports have focused on the technical aspects of real-time fMRI (rtfMRI). Here, we provide an overview of the different major areas of applications that became possible with rtfMRI: online analysis of single-subject data provides immediate quality assurance and functional localizers guiding the main fMRI experiment or surgical interventions. In teaching, rtfMRI naturally combines all essential parts of a neuroimaging experiment, such as experimental design, data acquisition and analysis, while adding a high level of interactivity. Thus, the learning of essential knowledge required to conduct functional imaging experiments is facilitated. rtfMRI allows for brain-computer interfaces (BCI) with a high spatial and temporal resolution and whole-brain coverage. Recent studies have shown that such BCI can be used to provide online feedback of the blood-oxygen-level-dependent signal and to learn the self-regulation of local brain activity. Preliminary evidence suggests that this local self-regulation can be used as a new paradigm in cognitive neuroscience to study brain plasticity and the functional relevance of brain areas, even being potentially applicable for psychophysiological treatment.     

Cardiovascular and respiratory dynamics during normal and pathological sleep

Sleep is an active and regulated process with restorative functions for physical and mental conditions. Based on recordings of brain waves and the analysis of characteristic patterns and waveforms it is possible to distinguish wakefulness and five sleep stages. Sleep and the sleep stages modulate autonomous nervous system functions such as body temperature, respiration, blood pressure, and heart rate. These functions consist of a sympathetic tone usually related to activation and to parasympathetic (or vagal) tone usually related to inhibition. Methods of statistical physics are used to analyze heart rate and respiration to detect changes of the autonomous nervous system during sleep. Detrended fluctuation analysis and synchronization analysis and their applications to heart rate and respiration during sleep in healthy subjects and patients with sleep disorders are presented. The observed changes can be used to distinguish sleep stages in healthy subjects as well as to differentiate normal and disturbed sleep on the basis of heart rate and respiration recordings without direct recording of brain waves. Of special interest are the cardiovascular consequences of disturbed sleep because they present a risk factor for cardiovascular disorders such as arterial hypertension, cardiac ischemia, sudden cardiac death, and stroke. New derived variables can help to find indicators for these health risks.     

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.     

Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue

Extensive collections of formalin-fixed paraffin-embedded (FFPE) tissues exist that could be exploited for genetic analyses in order to provide important insights into the genetic basis of disease or host/pathogen cointeractions. We report here an evaluation of a 44 SNP multiplex genotyping method, multiplex PCR with minisequencing (MPMS), on 92 DNA extractions performed on six archival FFPE samples of variable DNA quality, which date between 9 and 25 years old. On the three extracts with highest quality, we found the assay efficiency to be near 100%. However, the efficiency of the lowest quality extracts varied significantly. In this study, we demonstrate that although direct measures of DNA concentration in the extracts provide no useful information with regard to subsequent MPMS success, the success of the assay can be determined to some degree a priori, through initial screening of the DNA quality using a simple quantitative real-time PCR (qPCR) assay for nuclear DNA, and/or an assay of the maximum PCR amplifiable size of nuclear DNA. MPMS promises to be of significant use in future genetic studies on FFPE material. It provides a streamlined approach for retrieving a large amount of genetic information using simple, single reactions and minute amounts of archival tissue/DNA. In the light of this evidence, we suggest that the systematic screening of FFPE collections may in the future provide valuable insights into the past.     

New methods for the direct determination of dissolved inorganic, organic and total carbon in natural waters by Reagent-Free Ion Chromatography and inductively coupled plasma atomic emission spectrometry

New methods have been developed and applied successfully for the determination of dissolved inorganic, organic and total carbon in water samples. The new methods utilize two instrumental setups, Reagent-Free™ Ion Chromatography (RF™-IC) and inductively coupled plasma atomic emission spectrometry (ICP-AES). Dissolved inorganic carbon (DIC) was measured in untreated samples along with Cl⁻, F⁻ and SO₄²⁻ using RF™-IC and by in-line mixing with 0.1 M HNO₃ to enhance CO₂ removal in the nebulizer, followed by ICP-AES analysis. Total dissolved carbon (TDC) was measured by in-line mixing with 0.1 M NaOH following ICP-AES analysis. Dissolved organic carbon (DOC) was obtained as the difference between DIC and TDC. Only non-volatile organic carbon could be detected by the present method. The workable limits of detection obtained in the present study were 0.5 mM (RF™-IC) and 0.1 mM (ICP-AES) for dissolved inorganic and organic carbon, respectively. The power of the new methods lies in routine analysis of DIC and DOC in samples of natural waters of variable composition and salinity using analytical techniques and facilities available in most laboratories doing water sample analysis. The techniques are sensitive and precise, can be automated using gas-tight sample vials and auto-samplers, and are independent of most elemental interferences with the exception of chloride overload by saline samples when using RF™-IC. The new methods were successfully applied for analysis of DIC and DOC in selected samples of natural and synthetic waters.     

Fully-Dynamic Min-Cut*

We show that we can maintain up to polylogarithmic edge connectivity for a fully-dynamic graph in worst-case time per edge insertion or deletion. Within logarithmic factors, this matches the best time bound for 1-edge connectivity. Previously, no o(n) bound was known for edge connectivity above 3, and even for 3-edge connectivity, the best update time was O(n^2/3), dating back to FOCS'92. Our algorithm maintains a concrete min-cut in terms of a pointer to a tree spanning one side of the cut plus ability to list the cut edges in O(log n) time per edge. By dealing with polylogarithmic edge connectivity, we immediately get a sampling based expected factor (1+o(1)) approximation to general edge connectivity in time per edge insertion or deletion. This algorithm also maintains a pointer to one side of a near-minimal cut, but if we want to list the cut edges in O(log n) time per edge, the update time increases to . * A preliminary version of this work was presented at the The 33rd ACM Symposium on Theory of Computing( STOC) [22], Crete, Greece, July 2001.     

Continuous analysis of δ¹⁸O and δD values of water by diffusion sampling cavity ring-down spectrometry: a novel sampling device for unattended field monitoring of precipitation, ground and surface waters

A novel sampling device suitable for continuous, unattended field monitoring of rapid isotopic changes in environmental waters is described. The device utilises diffusion through porous PTFE tubing to deliver water vapour continuously from a liquid water source for analysis of δ1?O and δD values by Cavity Ring-Down Spectrometry (CRDS). Separation of the analysed water vapour from non-volatile dissolved and particulate contaminants in the liquid sample minimises spectral interferences associated with CRDS analyses of many aqueous samples. Comparison of isotopic data for a range of water samples analysed by Diffusion Sampling-CRDS (DS-CRDS) and Isotope Ratio Mass Spectrometry (IRMS) shows significant linear correlations between the two methods allowing for accurate standardisation of DS-CRDS data. The internal precision for an integration period of 3 min (standard deviation (SD) = 0.1‰ and 0.3‰ for δ1?O and δD values, respectively) is similar to analysis of water by CRDS using an autosampler to inject and evaporate discrete water samples. The isotopic effects of variable air temperature, water vapour concentration, water pumping rate and dissolved organic content were found to be either negligible or correctable by analysis of water standards. The DS-CRDS system was used to analyse the O and H isotope composition in short-lived rain events. Other applications where finely time resolved water isotope data may be of benefit include recharge/discharge in groundwater/river systems and infiltration-related changes in cave drip water.     

Injection molded nanofluidic chips: fabrication method and functional tests using single-molecule DNA experiments

We demonstrate that fabrication of well-defined nanofluidic systems can be greatly simplified by injection molding of thermoplastic polymers. Chips featuring nanochannel arrays, microchannels and integrated interconnects are produced in a single processing step by injection molding. The resulting open channel structures are subsequently sealed by facile plasma-enhanced thermal bonding of a polymer film. This fast, inexpensive and industry-compatible method thus provides a single-use all-polymer platform for nanofluidic lab-on-a-chip applications. Its applicability for nanofluidics is demonstrated by DNA stretching experiments performed on individual double-stranded DNA molecules confined in the injection molded nanochannels. The obtained results are consistent with measurements performed in costly state-of-the-art silica nanochannels, for both straight and tapered channel geometries.     

SCS-pincer palladium-catalyzed auto-tandem catalysis using dendritic catalysts in semi-permeable compartments

Novel monometallic and dendritic SCS-pincer palladium complexes 2, 3 and 4 have been synthesized in good yields (60-89%) and high purity (palladium loading >97%). These complexes were successfully used as catalysts in the stannylation of cinnamyl chloride with hexamethylditin and in the catalytic auto-tandem reaction consisting of this stannylation followed by an electrophilic addition with 4-nitrobenzaldehyde, showing similar reaction rates and selectivities for all complexes. Dendritic complex 4 has furthermore been used in the compartmentalized catalysis of single and auto-tandem reactions, allowing catalyst reuse for four consecutive runs.     

Phase diagrams of colloidal spheres with a constant zeta-potential

We study suspensions of colloidal spheres with a constant zeta-potential within Poisson-Boltzmann theory, quantifying the discharging of the spheres with increasing colloid density and decreasing salt concentration. We use the calculated renormalized charge of the colloids to determine their pairwise effective screened-Coulomb repulsions. Bulk phase diagrams in the colloid concentration-salt concentration representation follow, for various zeta-potentials, by a mapping onto published fits of phase boundaries of point-Yukawa systems. Although the resulting phase diagrams do feature face-centered cubic and body-centered cubic phases, they are dominated by the (re-entrant) fluid phase due to the colloidal discharging with increasing colloid concentration and decreasing salt concentration.