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Cognition, Vol. 109, No. 1. (October 2008), pp. 89-104.We investigated how human adults orient in enclosed virtual environments, when discrete landmark information is not available and participants have to rely on geometric and featural information on the environmental surfaces. In contrast to earlier studies, where, for women, the featural information from discrete landmarks overshadowed the encoding of the geometric information, Experiment 1 showed that when featural information is conjoined with the environmental surfaces, men and women encoded both types of information. Experiment 2 showed that, although both types of information are encoded, performance in locating a goal position is better if it is close to a geometrically or featurally distinct location. Furthermore, although features are relied upon more strongly than geometry, initial experience with an environment influences the relative weighting of featural and geometric cues. Taken together, these results show that human adults use a flexible strategy for encoding spatial information.D Kelly, W Bischof, citeulike.org

Nucl. Acids Res., Vol. 31, No. 9. (1 May 2003), pp. 2443-2450.Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques and quasi-bipartites) of complicated protein-protein interaction networks. Our analyses suggest that these hidden topological structures consist of biologically relevant functional groups. This result motivates a new method to predict the function of uncharacterized proteins based on the classification of known proteins within topological structures. Using this spectral analysis method, 48 quasi-cliques and six quasi-bipartites were isolated from a network involving 11 855 interactions among 2617 proteins in budding yeast, and 76 uncharacterized proteins were assigned functions. 10.1093/nar/gkg340Dongbo Bu, Yi Zhao, Lun Cai, Hong Xue, Xiaopeng Zhu, Hongchao Lu, Jingfen Zhang, Shiwei Sun, Lunjiang Ling, Nan Zhang, Guojie Li, Runsheng Chen, citeulike.org

Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2283-2290.MOTIVATION: Identification of functional modules in protein interaction networks is a first step in understanding the organization and dynamics of cell functions. To ensure that the identified modules are biologically meaningful, network-partitioning algorithms should take into account not only topological features but also functional relationships, and identified modules should be rigorously validated. RESULTS: In this study we first integrate proteomics and microarray datasets and represent the yeast protein-protein interaction network as a weighted graph. We then extend a betweenness-based partition algorithm, and use it to identify 266 functional modules in the yeast proteome network. For validation we show that the functional modules are indeed densely connected subgraphs. In addition, genes in the same functional module confer a similar phenotype. Furthermore, known protein complexes are largely contained in the functional modules in their entirety. We also analyze an example of a functional module and show that functional modules can be useful for gene annotation. CONTACT: yuan.33@osu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.Chen Jingchun, Yuan Bo, citeulike.org

Am. J. Roentgenol., Vol. 188, No. 6. (1 June 2007), pp. 1622-1635.OBJECTIVE. In this article, we present the basic principles of diffusion-weighted imaging (DWI) that can aid radiologists in the qualitative and quantitative interpretation of DW images. However, a detailed discussion of the physics of DWI is beyond the scope of this article. A short discussion ensues on the technical aspects of performing DWI in the body. The emerging applications of DWI for tumor detection, tumor characterization, distinguishing tumor tissue from nontumor tissue, and monitoring and predicting treatment response are highlighted. The challenges to widespread adoption of the technique for cancer imaging in the body are discussed. CONCLUSION. DWI derives its image contrast from differences in the motion of water molecules between tissues. Such imaging can be performed quickly without the need for the administration of exogenous contrast medium. The technique yields qualitative and quantitative information that reflects changes at a cellular level and provides unique insights about tumor cellularity and the integrity of cell membranes. Recent advances enable the technique to be widely applied for tumor evaluation in the abdomen and pelvis and have led to the development of whole-body DWI. 10.2214/AJR.06.1403Dow-Mu Koh, David Collins, citeulike.org

Am. J. Roentgenol., Vol. 188, No. 1. (1 January 2007), pp. 91-98.OBJECTIVE. The objective of our study was to establish the sensitivity and specificity for prostate cancer detection using a combined 1H MR spectroscopy and diffusion-weighted MRI approach. SUBJECTS AND METHODS. Forty-two men (mean age +/- SD, 69.3 +/- 4.7 years) with prostate cancer were studied using endorectal T2-weighted imaging, 2D chemical shift imaging (CSI), and isotropic apparent diffusion coefficient (ADC) maps. Regions of interest (ROIs) were drawn around the entire gland, central gland, and peripheral zone tumor, diagnostically defined as low signal intensity on T2-weighted images within a sextant that was biopsy-positive for tumor. Lack of susceptibility artifact on a gradient-echo B0 map through the slice selected for CSI and no high signal intensity on external array T1-weighted images confirmed the absence of significant hemorrhage after biopsy. CSI voxels were classified as nonmalignant or as tumor (ROI included 30% or 3 70% tumor). Choline-citrate (Cho/Cit) ratios and average ADCs were calculated for every voxel. A plot of Cho/Cit ratios versus ADCs yielded a line of best separation of tumor voxels from nonmalignant voxels. Receiver operating characteristic (ROC) curves were plotted for Cho/Cit ratios alone, ADCs alone, and a combination of the two. RESULTS. The Cho/Cit ratios were significantly higher (p < 0.001) and the ADCs were significantly lower (p < 0.006) in tumor-containing voxels than in non-tumor-containing voxels. When voxels containing 30% or more tumor were considered positive, the area under the ROC curves using combined MR spectroscopy and ADC (0.81) was similar to that of Cho/Cit alone (0.79) and better than ADC alone (0.66). When voxels containing 70% or more tumor were considered positive and cutoffs to achieve a 90%-or-greater sensitivity chosen, a combination of Cho/Cit and ADC achieved a significant improvement in specificity compared with Cho/Cit alone (p < 0.0001) or ADC alone (p < 0.0001). CONCLUSION. When voxels containing 70% tumor are considered positive, the combined use of MR spectroscopy and diffusion-weighted MRI increases the specificity for prostate cancer detection while retaining the sensitivity compared with MR spectroscopy alone or diffusion-weighted MRI alone. 10.2214/AJR.05.2198Stefan Reinsberg, Geoffrey Payne, Sophie Riches, Sue Ashley, Jonathan Brewster, Veronica Morgan, Nandita Desouza, citeulike.org

Physica A: Statistical Mechanics and its Applications, Vol. 350, No. 2-4. (15 May 2005), pp. 643-656.In order to take the weight of connection into consideration and to find a natural measurement of weight, we have collected papers in Econophysics and constructed a network of scientific communication to integrate idea transportation among econophysicists by collaboration, citation and personal discussion. Some basic statistics such as weight per degree are discussed in Fan et al. J. Mod. Phys. B (17-19) (2004) 2505. In this paper, by including the papers published recently, further statistical results for the network are reported. Clustering coefficient of weighted networks is introduced and empirically studied in this network. We also compare the typical statistics on this network under different weight assignments, including random and inverse weight. The conclusion from weight-redistributed network is helpful to the investigation of the topological role of weight.Menghui Li, Ying Fan, Jiawei Chen, Liang Gao, Zengru Di, Jinshan Wu, citeulike.org

New J. Phys., Vol. 9, No. 6. (June 2007), 180.Illés Farkas, Dániel Ábel, Gergely Palla, Tamás Vicsek, citeulike.org

Am. J. Roentgenol., Vol. 189, No. 2. (1 August 2007), pp. 323-328.OBJECTIVE. The objective of our study was to compare T2-weighted MRI alone and T2 combined with diffusion-weighted imaging (DWI) for the localization of prostate cancer. SUBJECTS AND METHODS. T2-weighted imaging and DWI (b value = 600 s/mm2) were performed in 49 patients before radical prostatectomy using an endorectal coil at 1.5 T in this prospective trial. The peripheral zone of the prostate was divided into sextants and the transition zone into left and right halves. T2 images alone and then T2 images combined with apparent diffusion coefficient (ADC) maps (T2 + DWI) were scored for the likelihood of tumor and were compared with whole-mount histology results. Fixed window and level settings were used to display the ADC maps. Only tumors with an area of more than 0.13 cm2 (> 4 mm diameter) and a Gleason score of 6 were considered significant. The area under the receiver operating characteristic curve (Az) was used to assess accuracy. RESULTS. In the peripheral zone, the Az value was significantly higher (p = 0.004) for T2 plus DWI (Az = 0.89) than for T2 imaging alone (Az = 0.81). Performance was poorer in the transition zone for both T2 plus DWI (Az = 0.78) and T2 (Az = 0.79). For the whole prostate, sensitivity was significantly higher (p < 0.001) with T2 plus DWI (81% ) than with T2 imaging alone (54% ), with T2 plus DWI showing only a slight loss in specificity compared with T2 imaging alone (84% vs 91% , respectively). CONCLUSION. Combined T2 and DWI MRI is better than T2 imaging alone in the detection of significant cancer (Gleason score 6 and diameter > 4 mm) within the peripheral zone of the prostate. 10.2214/AJR.07.2211Masoom Haider, Theodorus van der Kwast, Jeff Tanguay, Andrew Evans, Ali-Tahir Hashmi, Gina Lockwood, John Trachtenberg, citeulike.org

Comput Biol Chem, Vol. 30, No. 1. (February 2006), pp. 72-76.On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structures by searching the stem structure with maximum weight summation step-by-step. This algorithm not only avoids the complicated free energy calculation, but also it could attain higher prediction accuracy. Moreover, our algorithm can predict most types of potential pseudoknots in the RNA structure.H Liu, D Xu, J Shao, Y Wang, citeulike.org

J. Autom. Lang. Comb., Vol. 9, No. 2-3. (2004), pp. 257-267.Simulation of nondeterministic automata is often required in algorithms for string matching and image compression. We give three algorithms for NWFA simulation and compare them with known methods. When we consider the problem of computing the acceptance weight of all words of a given finite length, we find that the best of the three algorithms is comparable with a recursive version of a known sparse matrix based algorithm with respect to time, but offers an implementation with simpler data structures.Mark Eramian, citeulike.org