Expression of stm4467-encoded arginine deiminase controlled by the stm4463 regulator contributes to salmonella enterica serovar typhimurium virulence

Arginine deiminase (ADI), carbamate kinase (CK), and ornithine transcarbamoylase (OTC) constitute the ADI system. In addition to metabolic functions, the ADI system has been implicated in the virulence of certain pathogens. The pathogenic intracellular bacterium Salmonella enterica serovar Typhimurium possesses the STM4467, STM4466, and STM4465 genes, which are predicted to encode ADI, CK, and OTC, respectively. Here we report that the STM4467 gene encodes an ADI and that ADI activity plays a role in the successful infection of a mammalian host by S. Typhimurium. An STM4467 deletion mutant was defective for replication inside murine macrophages and was attenuated for virulence in mice. We determined that a regulatory protein encoded by the STM4463 gene functions as an activator for STM4467 expression. The expression of the ADI pathway genes was enhanced inside macrophages in a process that required STM4463. Lack of STM4463 impaired the ability of S. Typhimurium to replicate within macrophages. A mutant defective in STM4467-encoded ADI displayed normal production of nitric oxide by macrophages

Wave equation calculation of most energetic traveltimes and amplitudes for Kirchhoff prestack migration

This work was conceived during a visit by Kurt Marfurt to Seoul National University, sponsored by the Korean Ministry of Science andTechnology.This work was financially supported by the Brain Korea 21 Project of the Ministry of Education of Korea and the National Research Laboratory project of the Ministry of Science and Technology. The authors acknowledge the support of the Korea Institute of Science and Technology Information (KISTI) under the Grand Challenge Support Program and the use of the Supercomputing Center

Identifying promoter features of co-regulated genes with similar network motifs

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2008, Philadelphia, PA, USA. 3–5 November 2008.Background: A large amount of computational and experimental work has been devoted to uncovering network motifs in gene regulatory networks. The leading hypothesis is that evolutionary processes independently selected recurrent architectural relationships among regulators and target genes (motifs) to produce characteristic expression patterns of its members. However, even with the same architecture, the genes may still be differentially expressed. Therefore, to define fully the expression of a group of genes, the strength of the connections in a network motif must be specified, and the cis-promoter features that participate in the regulation must be determined.Results: We have developed a model-based approach to analyze proteobacterial genomes for promoter features that is specifically designed to account for the variability in sequence, location and topology intrinsic to differential gene expression. We provide methods for annotating regulatory regions by detecting their subjacent cis-features. This includes identifying binding sites for a transcriptional regulator, distinguishing between activation and repression sites, direct and reverse orientation, and among sequences that weakly reflect a particular pattern; binding sites for the RNA polymerase, characterizing different classes, and locations relative to the transcription factor binding sites; the presence of riboswitches in the 5'UTR, and for other transcription factors. We applied our approach to characterize network motifs controlled by the PhoP/PhoQ regulatory system of Escherichia coli and Salmonella enterica serovar Typhimurium. We identified key features that enable the PhoP protein to control its target genes, and distinct features may produce different expression patterns even within the same network motif.Conclusion: Global transcriptional regulators control multiple promoters by a variety of network motifs. This is clearly the case for the regulatory protein PhoP. In this work, we studied this regulatory protein and demonstrated that understanding gene expression does not only require identifying a set of connexions or network motif, but also the cis-acting elements participating in each of these connexions.This research was supported in part by the Spanish Ministry of Science and Technology under project TIN2006-12879 and by Consejería de Innovacion, Investigación y Ciencia de la de la Junta de Andalucía under project TIC02788

Instant Privacy-Preserving Biometric Authentication for Hamming Distance

In recent years, there has been enormous research attention in privacy-preserving biometric authentication, which enables a user to verify him or herself to a server without disclosing raw biometric information. Since biometrics is irrevocable when exposed, it is very important to protect its privacy. In IEEE TIFS 2018, Zhou and Ren proposed a privacy-preserving user-centric biometric authentication scheme named PassBio, where the end-users encrypt their own templates, and the authentication server never sees the raw templates during the authentication phase. In their approach, it takes about 1 second to encrypt and compare 2000-bit templates based on Hamming distance on a laptop. However, this result is still far from practice because the size of templates used in commercialized products is much larger: according to NIST IREX IX report of 2018 which analyzed 46 iris recognition algorithms, size of their templates varies from 4,632-bit (579-byte) to 145,832-bit (18,229-byte). In this paper, we propose a new privacy-preserving user-centric biometric authentication (HDM-PPBA) based on Hamming distance, which shows a big improvement in efficiency to the previous works. It is based on our new single-key function-hiding inner product encryption, which encrypts and computes the Hamming distance of 145,832-bit binary in about 0.3 seconds on Intel Core i5 2.9GHz CPU. We show that it satisfies simulation-based security under the hardness assumption of Learning with Errors (LWE) problem. The storage requirements, bandwidth and time complexity of HDM-PPBA depend linearly on the bit-length of biometrics, and it is applicable to any large templates used in NIST IREX IX report with high efficiency

Efficient calculation of a partial-derivative wavefield using reciprocity for seismic imaging and inversion

Linearized inversion of surface seismic data for a model of the earths subsurface requires estimating the sensitivity of the seismic response to perturbations in the earths subsurface. This sensitivity, or Jacobian, matrix is usually quite expensive to estimate for all but the simplest model parameterizations.We exploit the numerical structure of the finite-element method, modern sparse matrix technology, and source–receiver reciprocity to develop an algorithm that explicitly calculates the Jacobian matrix at only the cost of a forward model solution. Furthermore, we show that we can achieve improved subsurface images using only one inversion iteration through proper scaling of the image by a diagonal approximation of the Hessian matrix, as predicted by the classical Gauss-Newton method. Our method is applicable to the full suite of wave scattering problems amenable to finiteelement forward modeling.We demonstrate our method through some simple 2-D synthetic examples

Prestack depth migration using straight ray technique(SRT)

Kirchhoff prestack depth migration requires an elaborate book-keeping effort and a massive IO process to construct Kirchhoff hyperbolas. In order to avoid the complexity of the programming code and the massive IO process, we propose a straight ray technique (SRT) for traveltimi calculations in Kirchhoff migration. Since all the rays are straight in. polar coordinates for the 2D velocity model,or in sphericalc oordinatesf or the 3D velocity model, traveltimesc an be simply computed along a straight ray for a given source-receiver configuration,without suffering from shadow zones and caustics, and used directly for building Kirchhoff hyperbolas. In this way, we clrcumvent the substantial IO process required for reading traveltimes on a disk and save computationals torage.N umerical examplesd emonstrateth at SRT computest raveltimesi ntermediate between first-arrival traveltimes and the most energetic arrival traveltimes, resulting in better images than the first arrival traveltimes for the 2D IFP Marmousi data. With the implementation of SRT for 2D Kirchhoff migration, we successfully extend our SRT to 3D Kirchhoff misration for the SECiEAGE salr dome data.This work was financially supported by the National Laboratory Project of the Ministry of Science and Technology, Brain Korea 21 Project of the Ministry of Education, grant No. R05-2000-00003 from the Basic Research Program of the Korea Science & Engineering Foundation, and grant No. PM10300 from the Korea Ocean Research & Development Institute

Traveltime calculations from frequency-domain downward-continuation algorithms

We present a new, fast 3D traveltime calculation algorithm that employs existing frequency-domain waveequation downward-continuation software. By modifying such software to solve for a few complex (rather than real) frequencies, we are able to calculate not only the first arrival and the approximately most energetic traveltimes at each depth point but also their corresponding amplitudes.We compute traveltimes by either taking the logarithm of displacements obtained by the oneway wave equation at a frequency or calculating derivatives of displacements numerically. Amplitudes are estimated from absolute value of the displacement at a frequency. By using the one-way downgoing wave equation, we also circumvent generating traveltimes corresponding to near-surface upcoming head waves not often needed in migration.We compare the traveltimes computed by our algorithm with those obtained by picking the most energetic arrivals from finite-difference solutions of the one-way wave equation, and show that our traveltime calculation method yields traveltimes comparable to solutions of the one-way wave equation. We illustrate the accuracy of our traveltime algorithm by migrating the 2D IFP Marmousi and the 3D SEG/EAGE salt models.This work was financially supported by National Laboratory Project of Ministry of Science and Technology, Brain Korea 21 project of theKorea Ministry of Education, and grant No. R03- 2000-000-00003-0 from the Basic Research Program of the Korea Science & Engineering Foundation