IL-10 is necessary and sufficient for autoimmune diabetes in conjunction with NOD MHC homozygosity.

Contrary to expectations based on in vitro experiments, we previously found that pancreatic IL-10 did not inhibit autoimmune diabetes but accelerated it in an MHC-dependent manner. Therefore, the ability of IL-10 to overcome the absence of all non-MHC diabetes susceptibility (Idd) alleles was studied in transgenic mice expressing pancreatic IL-10 backcrossed to B10.H2g7 congenic mice, which have no Idd alleles other than NOD MHC (H2g7). IL-10 transgenic backcross 1 (BC1) mice with H2g7/g7 haplotype developed clear-cut insulitis and diabetes, but neither transgenic mice with the H2g/b haplotype nor nontransgenic BC1 mice did so. Further implicating IL-10 in autoimmune diabetes, anti-IL-10 antibody treatment inhibited the development of insulitis in NOD mice. These results suggest that IL-10 may be necessary and sufficient for producing autoimmune diabetes in conjunction with NOD MHC homozygosity and that some Idd genes may be related to the regulation of IL-10

In Vitro Validation of Finite-Element Model of AAA Hemodynamics Incorporating Realistic Outlet Boundary Conditions

The purpose of this study is to validate numerical simulations of flow and pressure in an abdominal aortic aneurysm (AAA) using phase-contrast magnetic resonance imaging (PCMRI) and an in vitro phantom under physiological flow and pressure conditions. We constructed a two-outlet physical flow phantom based on patient imaging data of an AAA and developed a physical Windkessel model to use as outlet boundary conditions. We then acquired PCMRI data in the phantom while it operated under conditions mimicking a resting and a light exercise physiological state. Next, we performed in silico numerical simulations and compared experimentally measured velocities, flows, and pressures in the in vitro phantom to those computed in the in silico simulations. There was a high degree of agreement in all of the pressure and flow waveform shapes and magnitudes between the experimental measurements and simulated results. The average pressures and flow split difference between experiment and simulation were all within 2%. Velocity patterns showed good agreement between experimental measurements and simulated results, especially in the case of whole-cycle averaged comparisons. We demonstrated methods to perform in vitro phantom experiments with physiological flows and pressures, showing good agreement between numerically simulated and experimentally measured velocity fields and pressure waveforms in a complex patient-specific AAA geometry

Stochastic search and joint fine-mapping increases accuracy and identifies previously unreported associations in immune-mediated diseases

Abstract: Thousands of genetic variants are associated with human disease risk, but linkage disequilibrium (LD) hinders fine-mapping the causal variants. Both lack of power, and joint tagging of two or more distinct causal variants by a single non-causal SNP, lead to inaccuracies in fine-mapping, with stochastic search more robust than stepwise. We develop a computationally efficient multinomial fine-mapping (MFM) approach that borrows information between diseases in a Bayesian framework. We show that MFM has greater accuracy than single disease analysis when shared causal variants exist, and negligible loss of precision otherwise. MFM analysis of six immune-mediated diseases reveals causal variants undetected in individual disease analysis, including in IL2RA where we confirm functional effects of multiple causal variants using allele-specific expression in sorted CD4+ T cells from genotype-selected individuals. MFM has the potential to increase fine-mapping resolution in related diseases enabling the identification of associated cellular and molecular phenotypes

Electrical Switching Dynamics in Circular and Rectangular Ge2Sb2Te5 Nanopillar Phase Change Memory Devices

We have measured the critical phase change conditions induced by electrical pulses in Ge2Sb2Te5 nanopillar phase change memory devices by constructing a comprehensive resistance map as a function of pulse parameters (width, amplitude and trailing edge). Our measurements reveal that the heating scheme and the details of the contact geometry play the dominant role in determining the final phase composition of the device such that a non-uniform heating scheme promotes partial amorphization/crystallization for a wide range of pulse parameters enabling multiple resistance levels for data storage applications. Furthermore we find that fluctuations in the snap-back voltage and set/reset resistances in repeated switching experiments are related to the details of the current distribution such that a uniform current injection geometry (i.e. circular contact) favors more reproducible switching parameters. This shows that possible geometrical defects in nanoscale phase change memory devices may play an essential role in the performance of the smallest possible devices through modification of the exact current distribution in the active chalcogenide layer. We present a three-dimensional finite element model of the electro-thermal physics to provide insights into the underlying physical mechanisms of the switching dynamics as well as to quantitatively account for the scaling behaviour of the switching currents in both circular and rectangular contact geometries. The calculated temporal evolution of the heat distribution within the pulse duration shows distinct features in rectangular contacts providing evidence for locally hot spots at the sharp corners of the current injection site due to current crowding effects leading to the observed behaviour

Sequencing of BAC pools by different next generation sequencing platforms and strategies

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable.</p> <p>Results</p> <p>Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library.</p> <p>Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%.</p> <p>Conclusion</p> <p>Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.</p

Idd9.2 and Idd9.3 Protective Alleles Function in CD4+ T-Cells and Nonlymphoid Cells to Prevent Expansion of Pathogenic Islet-Specific CD8+ T-Cells

OBJECTIVE - Multiple type 1 diabetes susceptibility genes have now been identified in both humans and mice, yet mechanistic understanding of how they impact disease pathogenesis is still minimal. We have sought to dissect the cellular basis for how the highly protective mouse Idd9 region limits the expansion of autoreactive CD8 T-cells, a key cell type in destruction of the islets. RESEARCH DESIGN AND METHODS - We assess the endogenous CD8 T-cell repertoire for reactivity to the islet antigen glucose-6-phosphatase-related protein (IGRP). Through the use of adoptively transferred T-cells, bone marrow chimeras, and reconstituted severe combined immunodeficient mice, we identify the protective cell types involved. RESULTS - IGRP-specific CD8 T-cells are present at low frequency in the insulitic lesions of Idd9 mice and could not be recalled in the periphery by viral expansion. We show that Idd9 genes act extrinsically to the CD8 T-cell to prevent the massive expansion of pathogenic effectors near the time of disease onset that occurs in NOD mice. The subregions Idd9.2 and Idd9.3 mediated this effect. Interestingly, the Idd9.1 region, which provides significant protection from disease, did not prevent the expansion of autoreactive CD8 T-cells. Expression of Idd9 genes was required by both CD4 T-cells and a nonlymphoid cell to induce optimal tolerance. CONCLUSIONS - Idd9 protective alleles are associated with reduced expansion of IGRP-specific CD8 T-cells. Intrinsic expression of protective Idd9 alleles in CD4 T-cells and nonlymphoid cells is required to achieve an optimal level of tolerance. Protective alleles in the Idd9.2 congenic subregion are required for the maximal reduction of islet-specific CD8 T-cells

\u3ci\u3eIn Vitro\u3c/i\u3e Validation of Finite Element Analysis of Blood Flow in Deformable Models

The purpose of this article is to validate numerical simulations of flow and pressure incorporating deformable walls using in vitro flow phantoms under physiological flow and pressure conditions. We constructed two deformable flow phantoms mimicking a normal and a restricted thoracic aorta, and used a Windkessel model at the outlet boundary. We acquired flow and pressure data in the phantom while it operated under physiological conditions. Next, in silico numerical simulations were performed, and velocities, flows, and pressures in the in silico simulations were compared to those measured in the in vitro phantoms. The experimental measurements and simulated results of pressure and flow waveform shapes and magnitudes compared favorably at all of the different measurement locations in the two deformable phantoms. The average difference between measured and simulated flow and pressure was approximately 3.5 cc/s (13% of mean) and 1.5 mmHg (1.8% of mean), respectively. Velocity patterns also showed good qualitative agreement between experiment and simulation especially in regions with less complex flow patterns. We demonstrated the capabilities of numerical simulations incorporating deformable walls to capture both the vessel wall motion and wave propagation by accurately predicting the changes in the flow and pressure waveforms at various locations down the length of the deformable flow phantoms

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

<p>Abstract</p> <p>Background</p> <p>We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using <it>in silico </it>simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence.</p> <p>Results</p> <p>The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on <it>Arabidopsis</it>. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most.</p> <p>Conclusions</p> <p>BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.</p