Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference

<p>Abstract</p> <p>Background</p> <p>With the rapid development of high-throughput genotyping technologies, efficient methods for identifying linked regions using high-density SNP genotype data have become more and more important. Recently, a deterministic method that works very well on SNP genotyping data has been developed (Lin et al. Bioinformatics 2008, 24(1): 86–93). However, that program can only work on a limited number of family structures. In particular, the results (if any) will be poor when the genotype data for the whole chromosome of one of the parents in a nuclear family is missing.</p> <p>Results</p> <p>We have developed a software package (LIden) for identifying linked regions using high-density SNP genotype data. We focus on handling the case where the genotype data for the whole chromosome of one of the parents in a nuclear family is missing. We use the minimum recombinant model for haplotype inference in pedigrees. Several local optimization algorithms are used to infer the haplotype of each individual and determine the linked regions based on the inferred haplotype data. We have developed a more flexible method to combine nuclear families to further refine (reduce the length of) the linked regions.</p> <p>Conclusion</p> <p>Our new package (LIden) is efficient software for linked region detection using high-density SNP genotype data. LIden can handle some important cases where the existing programs do not work well. In particular, the new package can handle many cases where the genotype data of one of the two parents is missing for the entire chromosome. The running time of the program is <it>O</it>(<it>mn</it>), where <it>m </it>is the number of members in the family and <it>n </it>is the number of SNP sites in the chromosome. LIden is specifically suitable for handling big sized families. This research also demonstrates another practical use of the minimum recombinant model for haplotype inference in pedigrees.</p> <p>The software package can be downloaded at <url>http://www.cs.cityu.edu.hk/~lwang/software/Link</url>.</p

Cationic chitosan derivatives as potential antifungals: A review of structural optimization and applications

The increasing resistance of pathogen fungi poses a global public concern. There are several limitations in current antifungals, including few available fungicides, severe toxicity of some fungicides, and drug resistance. Therefore, there is an urgent need to develop new antifungals with novel targets. Chitosan has been recognized as a potential antifungal substance due to its good biocompatibility, biodegradability, non-toxicity, and availability in abundance, but its applications are hampered by the low charge density results in low solubility at physiological pH. It is believed that enhancing the positive charge density of chitosan may be the most effective approach to improve both its solubility and antifungal activity. Hence, this review mainly focuses on the structural optimization strategy of cationic chitosan and the potential antifungal applications. This review also assesses and comments on the challenges, shortcomings, and prospect of cationic chitosan derivatives as antifungal therapy

NO除去光触媒性能を向上させるためのカーボンナイトライドベース光触媒修飾

Tohoku University殷澍課

Adult type granulosa cell tumor in adult testis: report of a case and review of the literature

Granulosa cell tumors can be classified into juvenile and adult types and more commonly occur in ovaries. Adult testicular granulosa cell tumors are extremely rare and only 29 cases of adult type have previously been reported. We report here a 28-year old Caucasian man with a left testicular adult type granulosa cell tumor. The tumor measured 2.6×2.6×2.5 cm and was mitotically active (10/10 HPF). Immunohistochemical stains showed the tumor diffusely positive for inhibin and vimentin, and negative for epithelial membrane antigen, cytokeratins, synaptophysin, HMB-45, OCT-4, placental-like alkaline phosphatase and lymphoid markers. The reported granulosa cell tumors in adult testis were briefly reviewed

Laboratory evaluation of Rediset modified bitumen based on rheology and adhesion properties

Warm mix asphalt (WMA) could significantly reduce the production temperature of asphalt mixtures. Lower production temperature meaning reduced fossil fuel consumption and greenhouse gas emission which in turn avoid environmental pollution in the road construction process. This study aims to characterise the properties of bitumen with the addition of a type of WMA additive – Rediset. The influence of Rediset on bitumen surface energy was evaluated by using the Dynamic Contact Angle (DCA) test. Complex modulus and phase angle of bitumen were evaluated through frequency sweep test using Dynamic Shear Rheometer (DSR). The high-temperature viscosity of bitumen was measured using a corn and plate system which installed in the DSR equipment. Finally, the Pneumatic Adhesion Tensile Testing Instrument (PATTI) test was performed to measure the tensile strength and moisture susceptibility of aggregate-bitumen combinations. The results show that the Rediset reduces the surface energy of bitumen. Moreover, as seen in the DSR test, the complex modulus increased while the phase angle decreased at the low frequency range due to the addition of Rediset. The decreased bitumen viscosity because of the addition of Rediset demonstrating reduced mixing and compaction temperature of asphalt mixture. In addition, the addition of Rediset could improve the bonding strength of aggregate-bitumen combinations at medium and high service temperatures but has no influence at low temperature. Furthermore, the Rediset is able to increase the retained tensile strength which in turn reduces the moisture susceptibility of asphalt mixture

Synthetic Collateral Debt Obligation Pricing

Portfolio credit products, such as CDO and Single Tranche CDO (STCDO) have gained their popularity in financial industry. The key problem facing by the financial engineers is how to price these portfolio credit derivatives, especially how to model the dependent default structure. Copula model proposed by Li (2000) is widely used in practice. Comparing with simulation, factor copula model and conditional independent framework provide good balance between accuracy and computational efficiency, but it is hard to achieve good performance if sticking to normal distribution. There are a few ways to improve it: introducing Levy distributions, using generic copula functions, and the semi parametric estimation. In this paper the Levy distribution and conditional independent factor copula model are examined. The flexibility and accuracy improvement comes from calibrating the skewness and heavy tail of Levy distribution for the underlying marginal distributions. The simulation result and short period prediction result are discussed too. One of the other benefits of this model is that once calibrating to the standard market tranches spreads, the model can handle the customized CDO, e.g. Single Tranche CDO. Key words: factor copula model, portfolio credit derivatives, Levy proces

RISE: Robust Wireless Sensing Using Probabilistic and Statistical Assessments

Peer reviewe