Optimizing Stimulation and Analysis Protocols for Neonatal fMRI

The development of brain function in young infants is poorly understood. The core challenge is that infants have a limited behavioral repertoire through which brain function can be expressed. Neuroimaging with fMRI has great potential as a way of characterizing typical development, and detecting abnormal development early. But, a number of methodological challenges must first be tackled to improve the robustness and sensitivity of neonatal fMRI. A critical one of these, addressed here, is that the hemodynamic response function (HRF) in pre-term and term neonates differs from that in adults, which has a number of implications for fMRI. We created a realistic model of noise in fMRI data, using resting-state fMRI data from infants and adults, and then conducted simulations to assess the effect of HRF of the power of different stimulation protocols and analysis assumptions (HRF modeling). We found that neonatal fMRI is most powerful if block-durations are kept at the lower range of those typically used in adults (full on/off cycle duration 25-30s). Furthermore, we show that it is important to use the age-appropriate HRF during analysis, as mismatches can lead to reduced power or even inverted signal. Where the appropriate HRF is not known (for example due to potential developmental delay), a flexible basis set performs well, and allows accurate post-hoc estimation of the HRF

Formal Verification of Real-Time Function Blocks Using PVS

A critical step towards certifying safety-critical systems is to check their conformance to hard real-time requirements. A promising way to achieve this is by building the systems from pre-verified components and verifying their correctness in a compositional manner. We previously reported a formal approach to verifying function blocks (FBs) using tabular expressions and the PVS proof assistant. By applying our approach to the IEC 61131-3 standard of Programmable Logic Controllers (PLCs), we constructed a repository of precise specification and reusable (proven) theorems of feasibility and correctness for FBs. However, we previously did not apply our approach to verify FBs against timing requirements, since IEC 61131-3 does not define composite FBs built from timers. In this paper, based on our experience in the nuclear domain, we conduct two realistic case studies, consisting of the software requirements and the proposed FB implementations for two subsystems of an industrial control system. The implementations are built from IEC 61131-3 FBs, including the on-delay timer. We find issues during the verification process and suggest solutions.Comment: In Proceedings ESSS 2015, arXiv:1506.0325

Band gap bowing in NixMg1-xO.

Epitaxial transparent oxide NixMg1-xO (0 ≤ x ≤ 1) thin films were grown on MgO(100) substrates by pulsed laser deposition. High-resolution synchrotron X-ray diffraction and high-resolution transmission electron microscopy analysis indicate that the thin films are compositionally and structurally homogeneous, forming a completely miscible solid solution. Nevertheless, the composition dependence of the NixMg1-xO optical band gap shows a strong non-parabolic bowing with a discontinuity at dilute NiO concentrations of x  0.074 and account for the anomalously large band gap narrowing in the NixMg1-xO solid solution system

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS

The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates

Studies on the relationships between oligonucleotide probe properties and hybridization signal intensities

Microarray technology is a commonly used tool in biomedical research for assessing global gene expression, surveying DNA sequence variations, and studying alternative gene splicing. Given the wide range of applications of this technology, comprehensive understanding of its underlying mechanisms is of importance. The focus of this work is on contributions from microarray probe properties (probe secondary structure: ?Gss, probe-target binding energy: ?G, probe-target mismatch) to the signal intensity. The benefits of incorporating or ignoring these properties to the process of microarray probe design and selection, as well as to microarray data preprocessing and analysis, are reported. Four related studies are described in this thesis. In the first, probe secondary structure was found to account for up to 3% of all variation on Affymetrix microarrays. In the second, a dinucleotide affinity model was developed and found to enhance the detection of differentially expressed genes when implemented as a background correction procedure in GeneChip preprocessing algorithms. This model is consistent with physical models of binding affinity of the probe target pair, which depends on the nearest-neighbor stacking interactions in addition to base-pairing. In the remaining studies, the importance of incorporating biophysical factors in both the design and the analysis of microarrays ‘percent bound’, predicted by equilibrium models of hybridization, is a useful factor in predicting and assessing the behavior of long oligonucleotide probes. However, a universal probe-property-independent three-parameter Langmuir model has also been tested, and this simple model has been shown to be as, or more, effective as complex, computationally expensive models developed for microarray target concentration estimation. The simple, platform-independent model can equal or even outperform models that explicitly incorporate probe properties, such as the model incorporating probe percent bound developed in Chapter Three. This suggests that with a “spiked-in” concentration series targeting as few as 5-10 genes, reliable estimation of target concentration can be achieved for the entire microarray

Design fabrication and characterization of high performance in GaAs/InP focal plane array in the 1-2.6 µm wavelength region

This research thesis describes a new InxGa1-xAs/InAysP1-y/InP technology for long wavelength photodetectors and photodetector arrays. A unique and novel detector structure was designed and fabricated using Hydride Vapor Phase Epitaxy, for low leakage current photodetector arrays in the 1-2.6 µm wavelength region. Potential applications of InGaAs focal plane arrays include near-infrared spectroscopy, fluorescence, remote sensing, environmental sensing, space and astronomical applications. The unique design concepts included the step grading of InAsP layers, lower lattice mismatch between the two InAsP graded layers, lattice matched InAsP cap layer and InGaAs absorption layer, sulphur doping of InGaAs absorption layer and InAsP layers. Improved device fabrication techniques including rapid thermal annealing and precisely controlled diffusion were implemented during the processing of 1024 element linear photodetector arrays to reduce the dislocation density. An analysis of dark current, which is the critical parameter was required and is described in detail. The dark current analysis and the experimental results showed that the dark current is bulk dominated and is due to the crystal defects and dislocation density. Each element of the focal plane array consisted of a 13 X 500 µm2 active area with an element to element spacing (pitch) of 25 µm The focal plane architecture designed had two 512 element (left and right) multiplexers and a 1024 element detector array and was integrated in a 24 pin dual-in-line package. A unique and novel Si read-out multiplexer was designed and fabricated using radiation hardened N-well CMOS process. Each multiplexer unit cell consisted of a capacitive transimpedance amplifier, correlated double sampling circuit, threshold non uniformity correction circuit and an output buffer stage. Integration and testing of InGaAs focal plane arrays with cut-off wavelengths of 1.7 µm, 2.2 µm and 2.6 µm are described. The performance of the focal plane arrays was analyzed in detail and the results showed that the 10 fA dark current levels could be achievable with 1024 element InGaAs/InP focal plane arrays in the 1-2.6 urn wavelength region. The dark current achieved from the test focal plane arrays was \u3c I fA for 1.7 µm \u3c 20 fA for 2.2 µm and \u3c 50 fA for 2.6 µm cutoff wavelength. Radiation testing using proton, gamma and electron particle radiation on InGaAs photodetectors and photodetector arrays showed that InGaAs/InP focal plane arrays can with stand upto 15 Krad (Si) particle radiation. Comparison of the results achieved with published results of other technology (HgCdTe) operating at the same temperature shows that InGaAs/InP Focal Plane Arrays have lower dark current by a factor of 10-100

Modulation of the DNA-binding activity of Saccharomyces cerevisiae MSH2–MSH6 complex by the high-mobility group protein NHP6A, in vitro

DNA mismatch repair corrects mispaired bases and small insertions/deletions in DNA. In eukaryotes, the mismatch repair complex MSH2–MSH6 binds to mispairs with only slightly higher affinity than to fully paired DNA in vitro. Recently, the high-mobility group box1 protein, (HMGB1), has been shown to stimulate the mismatch repair reaction in vitro. In yeast, the closest homologs of HMGB1 are NHP6A and NHP6B. These proteins have been shown to be required for genome stability maintenance and mutagenesis control. In this work, we show that MSH2–MSH6 and NHP6A modulate their binding to DNA in vitro. Binding of the yeast MSH2–MSH6 to homoduplex regions of DNA significantly stimulates the loading of NHP6A. Upon binding of NHP6A to DNA, MSH2–MSH6 is excluded from binding unless a mismatch is present. A DNA binding-impaired MSH2–MSH6F337A significantly reduced the loading of NHP6A to DNA, suggesting that MSH2–MSH6 binding is a requisite for NHP6A loading. MSH2–MSH6 and NHP6A form a stable complex, which is responsive to ATP on mismatched substrates. These results suggest that MSH2–MSH6 binding to homoduplex regions of DNA recruits NHP6A, which then prevents further binding of MSH2–MSH6 to these sites unless a mismatch is present