Performance comparison of ASN.1 encoder/decoders using FTAM

Abstract Syntax Notation-One (ASN.1) is a standard external data representation language used to define messages of application layer protocols. Its encoding rules, the Basic Encoding Rules (BER), are also international standards that define the encoding/decoding of data values into/from a transfer syntax. Various approaches to automating BER encoding/decoding are examined; in particular, two widely used software packages (ISODE and CASN 1) are studied. A hardware BER encoder/decoder called VASN 1 is presented. Performance of software and hardware approaches are evaluated on real instances of file transfer using a standard FTAM protocol. Benchmarks obtained from running CASN 1 on one of the fastest workstations and from running VHDL simulations of VASN 1 indicate the superiority of the hardware approach. © 1993

Estimation of nasal cavity and conchae volumes by stereological method

Background: Studies evaluating the mean volumes of nasal cavity and concha are very rare. Since there is little date on the mentioned topic, we aimed to carry out the presented study to obtain a volumetric index showing the relation between the nasal cavity and concha. Material and methods: The volumes of the nasal cavity and concha were measured in 30 males and 30 females (18&#8211;40 years old) on computed tomography images using stereological methods. Results: The mean volumes of nasal cavity, concha nasalis media, and concha nasalis inferior were 5.95 &#177; 0.10 cm3, 0.56 &#177; 0.22 cm3, and 1.45 &#177; 0.68 cm3; 7.01 &#177; 0.18 cm3, 0.67 &#177; 0.31 cm3 and 1.59 &#177; 0.98 cm3 in females and males, respectively. There were statistically significant differences in the volume of the nasal cavity and concha nasalis media (p < 0.05) between males and females, except for concha nasalis inferior (p > 0.05). Conclusions: Our results could provide volumetric indexes for the nasal cavity and concha, which could help the physician to manage surgical procedures related to the nasal cavity and concha

Estimation of Fiber Orientations Using Neighborhood Information

Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted l1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.Comment: Journal paper accepted in Medical Image Analysis. 35 pages and 16 figure

Effective and Efficient Similarity Index for Link Prediction of Complex Networks

Predictions of missing links of incomplete networks like protein-protein interaction networks or very likely but not yet existent links in evolutionary networks like friendship networks in web society can be considered as a guideline for further experiments or valuable information for web users. In this paper, we introduce a local path index to estimate the likelihood of the existence of a link between two nodes. We propose a network model with controllable density and noise strength in generating links, as well as collect data of six real networks. Extensive numerical simulations on both modeled networks and real networks demonstrated the high effectiveness and efficiency of the local path index compared with two well-known and widely used indices, the common neighbors and the Katz index. Indeed, the local path index provides competitively accurate predictions as the Katz index while requires much less CPU time and memory space, which is therefore a strong candidate for potential practical applications in data mining of huge-size networks.Comment: 8 pages, 5 figures, 3 table

Development of a multiplex PCR assay for simultaneous detection of Theileria annulata, Babesia bovis and Anaplasma marginale in cattle

Tropical theileriosis, bovine babesiosis and anaplasmosis are tick-borne protozoan diseases that impose serious constraints on the health and productivity of domestic cattle in tropical and sub-tropical regions of the world. A common feature of these diseases is that, following recovery from primary infection, animals become persistent carriers of the pathogen and continue to play a critical role in disease epidemiology, acting as reservoirs of infection. This study describes development and evaluation of multiplex and single PCR assays for simultaneous detection of Theileria annulata, Babesia bovis and Anaplasma marginale in cattle. Following in silico screening for candidate target genes representing each of the pathogens, an optimised multiplex PCR assay was established using three primer sets, cytob1, MAR1bB2 and bovar2A, for amplification of genomic DNA of T. annulata, A. marginale and B. bovis respectively. The designed primer sets were found to be species-specific, generating amplicons of 312, 265 and 166 base pairs, respectively and were deemed suitable for the development of a multiplex assay. The sensitivity of each primer pair was evaluated using serial dilutions of parasite DNA, while specificity was confirmed by testing for amplification from DNA of different stocks of each pathogen and other Theileria, Babesia and Anaplasma species. Additionally, DNA preparations derived from field samples were used to evaluate the utility of the single and multiplex PCRs for determination of infection status. The multiplex PCR was found to detect each pathogen species with the same level of sensitivity, irrespective of whether its DNA was amplified in isolation or together with DNA representing the other pathogens. Moreover, single and multiplex PCRs were able to detect each species with equal sensitivity in serially diluted DNA representing mixtures of T. annulata, B. bovis and A. marginale, and no evidence of non-specific amplification from non-target species was observed. Validation that the multiplex PCR efficiently detects single and mixed infections from field samples was demonstrated. The developed assay represents a simple and efficient diagnostic for co-detection of tropical theileriosis, bovine babesiosis and anaplasmosis, and may be a valuable tool for epidemiological studies aimed at assessing the burden of multiple infection with tick-borne pathogens and improving control of the associated diseases in endemic regions

Cultures of conflict:Protests, violent repression, and community values

What are the cultural origins of societal conflicts that revolve around democratization, women’s rights, and modern libertarian values? We propose that deep-seated differences in community-based collective values (at the micro-level) may be related to why people support anti-government protest and why they support repression of such protests (at the macro-level). The hypothesis was examined among residents of Turkey (N = 500). Cultural values, measured at the individual level and community level with the community collectivism scale, correlated with political orientation and emotions, as well as with subsequent support for anti-governmental protest or its repression. The main conclusions are that both support for protest and support for repression are related to the cultural values people hold and their subsequent political orientations and emotions. Micro-level cultural values in local communities may thus play a role in explaining macro-level socio-political divides

Mutation Frequency of the Major Frontotemporal Dementia Genes, MAPT, GRN and C9ORF72 in a Turkish Cohort of Dementia Patients

‘Microtubule-associated protein tau’ (MAPT), ‘granulin’ (GRN) and ‘chromosome 9 open reading frame72’ (C9ORF72) gene mutations are the major known genetic causes of frontotemporal dementia (FTD). Recent studies suggest that mutations in these genes may also be associated with other forms of dementia. Therefore we investigated whether MAPT, GRN and C9ORF72 gene mutations are major contributors to dementia in a random, unselected Turkish cohort of dementia patients. A combination of whole-exome sequencing, Sanger sequencing and fragment analysis/Southern blot was performed in order to identify pathogenic mutations and novel variants in these genes as well as other FTD-related genes such as the ‘charged multivesicular body protein 2B’ (CHMP2B), the ‘FUS RNA binding protein’ (FUS), the ‘TAR DNA binding protein’ (TARDBP), the ‘sequestosome1’ (SQSTM1), and the ‘valosin containing protein’ (VCP). We determined one pathogenic MAPT mutation (c.1906C>T, p.P636L) and one novel missense variant (c.38A>G, p.D13G). In GRN we identified a probably pathogenic TGAG deletion in the splice donor site of exon 6. Three patients were found to carry the GGGGCC expansions in the non-coding region of the C9ORF72 gene. In summary, a complete screening for mutations in MAPT, GRN and C9ORF72 genes revealed a frequency of 5.4% of pathogenic mutations in a random cohort of 93 Turkish index patients with dementia

A novel compound heterozygous mutation in TREM2 found in a Turkish frontotemporal dementia-like family

Triggering receptor expressed on myeloid cells 2 (TREM2) homozygous mutations cause Nasu-Hakola disease, an early-onset recessive form of dementia preceded by bone cysts and fractures. The same type of mutations has recently been shown to cause frontotemporal dementia (FTD) without the presence of any bone phenotype. Here, we further confirm the association of TREM2 mutations with FTD-like phenotypes by reporting the first compound heterozygous mutation in a Turkish family

Fast Multi-contrast MRI Reconstruction

Abstract. This paper proposes an efficient algorithm to simultaneously reconstruct multiple T1/T2-weighted images of the same anatomical cross section from partially sampled k-space data. The simultaneous re-construction problem is formulated as minimizing a linear combination of three terms corresponding to a least square data fitting, joint total-variation (TV) and group wavelet-sparsity regularization. It is rooted in two observations: 1) the variance of image gradients should be similar for the same spatial position across multiple contrasts; 2) the wavelet coeffi-cients of all images from the same anatomical cross section should have similar sparse modes. To efficiently solve this formulation, we decompose it into group sparsity and joint TV regularization subproblems, respec-tively. Finally, the reconstructed image is obtained from the weighted average of solutions from two subproblems in an iterative framework. We compare the proposed algorithm with previous methods on SRT24 multi-channel Brain Atlas Data. Experiments demonstrate its superior performance for multi-contrast MR image reconstruction.