Goertler instability on an airfoil

An effective computational scheme was developed to study the growth/damping of Goertler vortices along walls of variable curvature. Computational experiments indicate that when the amplification rates for the u-, v-, and w-perturbations are the same, the finite difference approach to solve the initial value problem and the normal mode approach give identical results for the Blasius boundary layer on constant curvature concave walls. The growth of Goertler vortices was rapid in the concave regions and was followed by sharp damping in the convex region. However, multiple sets of counter-rotating vortices were formed and remained far downstream in the convex region. The current computational scheme can be easily extended to more realistic problems including variable pressure gradients and suction effects

Frequency dependent core shifts and parameter estimation for the blazar 3C 454.3

We study the core shift effect in the parsec scale jet of the blazar 3C 454.3 using the 4.8 GHz - 36.8 GHz radio light curves obtained from three decades of continuous monitoring. From a piecewise Gaussian fit to each flare, time lags $\Delta t$ between the observation frequencies $\nu$ and spectral indices $\alpha$ based on peak amplitudes $A$ are determined. From the fit $\Delta t \propto \nu^{1/k_r}$, $k_r = 1.10 \pm 0.18$ indicating equipartition between the magnetic field energy density and the particle energy density. From the fit $A \propto \nu^\alpha$, $\alpha$ is in the range $-0.24$ to $1.52$. A mean magnetic field strength at 1 pc, $B_1 = 0.5 \pm 0.2$ G, and at the core, $B_{\rm core} = 46 \pm 16$ mG, are inferred, consistent with previous estimates. The measure of core position offset is $\Omega_{r\nu} = 6.4 \pm 2.8$ pc GHz$^{1/k_r}$ when averaged over all frequency pairs. Based on the statistical trend shown by the measured core radius $r_{\rm core}$ as a function of $\nu$, we infer that the synchrotron opacity model may not be valid for all cases. A Fourier periodogram analysis yields power law slopes in the range $-1.6$ to $-3.5$ describing the power spectral density shape and gives bend timescales in the range $0.52 - 0.66~$yr. This result, and both positive and negative $\alpha$, indicate that the flares originate from multiple shocks in a small region. Important objectives met in our study include: the demonstration of the computational efficiency and statistical basis of the piecewise Gaussian fit; consistency with previously reported results; evidence for the core shift dependence on observation frequency and its utility in jet diagnostics in the region close to the resolving limit of very long baseline interferometry observations.Comment: 12 pages, 11 figures (23 sub-figures), 5 tables. Accepted for publication in MNRA

A peculiar multi-wavelength flare in the Blazar 3C 454.3

The blazar 3C454.3 exhibited a strong flare seen in gamma-rays, X-rays, and optical/NIR bands during 3--12 December 2009. Emission in the V and J bands rose more gradually than did the gamma-rays and soft X-rays, though all peaked at nearly the same time. Optical polarization measurements showed dramatic changes during the flare, with a strong anti-correlation between optical flux and degree of polarization (which rose from ~ 3% to ~ 20%) during the declining phase of the flare. The flare was accompanied by large rapid swings in polarization angle of ~ 170 degree. This combination of behaviors appear to be unique. We have cm-band radio data during the same period but they show no correlation with variations at higher frequencies. Such peculiar behavior may be explained using jet models incorporating fully relativistic effects with a dominant source region moving along a helical path or by a shock-in-jet model incorporating three-dimensional radiation transfer if there is a dominant helical magnetic field. We find that spectral energy distributions at different times during the flare can be fit using modified one-zone models where only the magnetic field strength and particle break frequencies and normalizations need change. An optical spectrum taken at nearly the same time provides an estimate for the central black hole mass of ~ 2.3 * 10^9 M_sun. We also consider two weaker flares seen during the $\sim 200$ d span over which multi-band data are available. In one of them, the V and J bands appear to lead the $\gamma$-ray and X-ray bands by a few days; in the other, all variations are simultaneous.Comment: 11 pages, 4 figures, 2 tables; MNRAS in pres

Multiwavelength Intraday Variability of the BL Lac S5 0716+714

We report results from a 1 week multi-wavelength campaign to monitor the BL Lac object S5 0716+714 (on December 9-16, 2009). In the radio bands the source shows rapid (~ (0.5-1.5) day) intra-day variability with peak amplitudes of up to ~ 10 %. The variability at 2.8 cm leads by about 1 day the variability at 6 cm and 11 cm. This time lag and more rapid variations suggests an intrinsic contribution to the source's intraday variability at 2.8 cm, while at 6 cm and 11 cm interstellar scintillation (ISS) seems to predominate. Large and quasi-sinusoidal variations of ~ 0.8 mag were detected in the V, R and I-bands. The X-ray data (0.2-10 keV) do not reveal significant variability on a 4 day time scale, favoring reprocessed inverse-Compton over synchrotron radiation in this band. The characteristic variability time scales in radio and optical bands are similar. A quasi-periodic variation (QPO) of 0.9 - 1.1 days in the optical data may be present, but if so it is marginal and limited to 2.2 cycles. Cross-correlations between radio and optical are discussed. The lack of a strong radio-optical correlation indicates different physical causes of variability (ISS at long radio wavelengths, source intrinsic origin in the optical), and is consistent with a high jet opacity and a compact synchrotron component peaking at ~= 100 GHz in an ongoing very prominent flux density outburst. For the campaign period, we construct a quasi-simultaneous spectral energy distribution (SED), including gamma-ray data from the FERMI satellite. We obtain lower limits for the relativistic Doppler-boosting of delta >= 12-26, which for a BL\,Lac type object, is remarkably high.Comment: 16 pages, 15 figures, table 2; Accepted for Publication in MNRA

A comparison of common programming languages used in bioinformatics

<p>Abstract</p> <p>Background</p> <p>The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.</p> <p>Results</p> <p>Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found.</p> <p>Source code and additional information are available from <url>http://www.bioinformatics.org/benchmark/</url></p> <p>Conclusion</p> <p>This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.</p

DQB1*0602 rather than DRB1*1501 confers susceptibility to multiple sclerosis-like disease induced by proteolipid protein (PLP)

<p>Abstract</p> <p>Background</p> <p>Multiple sclerosis (MS) is associated with pathogenic autoimmunity primarily focused on major CNS-myelin target antigens including myelin basic protein (MBP), proteolipidprotein (PLP), myelin oligodendrocyte protein (MOG). MS is a complex trait whereby the HLA genes, particularly class-II genes of HLA-DR15 haplotype, dominate the genetic contribution to disease-risk. Due to strong linkage disequilibrium in HLA-II region, it has been hard to establish precisely whether the functionally relevant effect derives from the DRB1*1501, DQA1*0102-DQB1*0602, or DRB5*0101 loci of HLA-DR15 haplotype, their combinations, or their epistatic interactions. Nevertheless, most genetic studies have indicated DRB1*1501 as a primary risk factor in MS. Here, we used 'HLA-humanized' mice to discern the potential relative contribution of DRB1*1501 and DQB1*0602 alleles to susceptibility to "humanized" MS-like disease induced by PLP, one of the most prominent and encephalitogenic target-antigens implicated in human MS.</p> <p>Methods</p> <p>The HLA-DRB1*1501- and HLA-DQB1*0602-Tg mice (MHC-II^-/-), and control non-HLA-DR15-relevant-Tg mice were immunized with a set of overlapping PLP peptides or with recombinant soluble PLP for induction of "humanized" MS-like disease, as well as for ex-vivo analysis of immunogenic/immunodominant HLA-restricted T-cell epitopes and associated cytokine secretion profile.</p> <p>Results</p> <p>PLP autoimmunity in both HLA-DR15-Tg mice was focused on 139-151 and 175-194 epitopes. Strikingly, however, the HLA-DRB1*1501-transgenics were refractory to disease induction by any of the overlapping PLP peptides, while HLA-DQB1*0602 transgenics were susceptible to disease induction by PLP139-151 and PLP175-194 peptides. Although both transgenics responded to both peptides, the PLP139-151- and PLP175-194-reactive T-cells were directed to Th1/Th17 phenotype in DQB1*0602-Tg mice and towards Th2 in DRB1*1501-Tg mice.</p> <p>Conclusions</p> <p>While genome studies map a strong MS susceptibility effect to the region of DRB1*1501, our findings offer a rationale for potential involvement of pathogenic DQ6-associated autoimmunity in MS. Moreover, that DQB1*0602, but not DRB1*1501, determines disease-susceptibility to PLP in HLA-transgenics, suggests a potential differential, functional role for DQB1*0602 as a predisposing allele in MS. This, together with previously demonstrated disease-susceptibility to MBP and MOG in DRB1*1501-transgenics, also suggests a differential role for DRB1*1501 and DQB1*0602 depending on target antigen and imply a potential complex 'genotype/target antigen/phenotype' relationship in MS heterogeneity.</p

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons

BACKGROUND: Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines. RESULTS: InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein – protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports. CONCLUSION: As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements

Optical variability of PKS 0736+017

We present BVR photometric observations of the blazar PKS 0736+017. These observations were carried out with three telescopes in Mexico and two in Spain between December 1998 and April 2003. PKS 0736+017 shows remarkable variation at different timescales and amplitudes. Maximum brightness was detected on December 19, 2001 (B=14.90+/-0.01, V=14.34+/-0.01, and R=13.79+/-0.01). A peculiar tendency to redden with increased brightness was detected throughout our observations. Moreover, in one season a good correlation between flux level and spectral slope is shown. This "anomalous" behaviour cannot be described by common flare models of blazars. The flux vs. spectral slope correlation observed in this and other blazars is worth further study.Comment: 8 pages, 6 figures, accepted for publication in Astronomy & Astrophysic

Reconstitution of huPBL-NSG Mice with Donor-Matched Dendritic Cells Enables Antigen-Specific T-cell Activation

Humanized mouse models provide a unique opportunity to study human immune cells in vivo, but traditional models have been limited to the evaluation of non-specific T-cell interactions due to the absence of antigen-presenting cells. In this study, immunodeficient NOD/SCID/IL2r-γnull (NSG) mice were engrafted with human peripheral blood lymphocytes alone or in combination with donor-matched monocyte-derived dendritic cells (DC) to determine whether antigen-specific T-cell activation could be reconstituted. Over a period of 3 weeks, transferred peripheral blood lymphocytes reconstituted the spleen and peripheral blood of recipient mice with predominantly human CD45-positive lymphocytes. Animals exhibited a relatively normal CD4/CD8 ratio (average 1.63:1) as well as reconstitution of CD3/CD56 (averaging 17.8%) and CD20 subsets (averaging 4.0%). Animals reconstituted with donor-matched CD11c+ DC also demonstrated a CD11c+ population within their spleen, representing 0.27% to 0.43% of the recovered human cells with concurrent expression of HLA-DR, CD40, and CD86. When immunized with adenovirus, either as free replication-incompetent vector (AdV) or as vector-transduced DC (DC/AdV), there was activation and expansion of AdV-specific T-cells, an increase in Th1 cytokines in serum, and skewing of T-cells toward an effector/memory phenotype. T-cells recovered from animals challenged with AdV in vivo proliferated and secreted a Th1-profile of cytokines in response to DC/AdV challenge in vitro. Our results suggest that engrafting NSG mice with a combination of lymphocytes and donor-matched DC can reconstitute antigen responsiveness and allow the in vivo assessment of human immune response to viruses, vaccines, and other immune challenges

Mouse Transgenesis Identifies Conserved Functional Enhancers and cis-Regulatory Motif in the Vertebrate LIM Homeobox Gene Lhx2 Locus

The vertebrate Lhx2 is a member of the LIM homeobox family of transcription factors. It is essential for the normal development of the forebrain, eye, olfactory system and liver as well for the differentiation of lymphoid cells. However, despite the highly restricted spatio-temporal expression pattern of Lhx2, nothing is known about its transcriptional regulation. In mammals and chicken, Crb2, Dennd1a and Lhx2 constitute a conserved linkage block, while the intervening Dennd1a is lost in the fugu Lhx2 locus. To identify functional enhancers of Lhx2, we predicted conserved noncoding elements (CNEs) in the human, mouse and fugu Crb2-Lhx2 loci and assayed their function in transgenic mouse at E11.5. Four of the eight CNE constructs tested functioned as tissue-specific enhancers in specific regions of the central nervous system and the dorsal root ganglia (DRG), recapitulating partial and overlapping expression patterns of Lhx2 and Crb2 genes. There was considerable overlap in the expression domains of the CNEs, which suggests that the CNEs are either redundant enhancers or regulating different genes in the locus. Using a large set of CNEs (810 CNEs) associated with transcription factor-encoding genes that express predominantly in the central nervous system, we predicted four over-represented 8-mer motifs that are likely to be associated with expression in the central nervous system. Mutation of one of them in a CNE that drove reporter expression in the neural tube and DRG abolished expression in both domains indicating that this motif is essential for expression in these domains. The failure of the four functional enhancers to recapitulate the complete expression pattern of Lhx2 at E11.5 indicates that there must be other Lhx2 enhancers that are either located outside the region investigated or divergent in mammals and fishes. Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers