Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

Raman And Infrared Spectroscopy Of Sr2b′uo6 (b′ = Ni; Co) Double Perovskites

Temperature dependent normal modes and lattice thermal expansion of Sr 2B′UO6 (B′ = Ni, Co) double perovskites were investigated by Raman/infrared spectroscopies and synchrotron X-ray diffraction, respectively. Monoclinic crystal structures with space group P21/n were confirmed for both compounds, with no clear structural phase transition between 10 and 400 K. As predicted for this structure, the first-order Raman and infrared spectra show a plethora of active modes. In addition, the Raman spectra reveal an enhancement of the integrated area of an oxygen stretching mode, which is also observed in higher-order Raman modes, and an anomalous softening of ∼1 cm-1 upon cooling below T* ∼ 300 K. In contrast, the infrared spectra show conventional temperature dependence. The band profile phonon anomalies are possibly related to an unspecified electronic property of Sr2B′UO6 (B′ = Ni, Co). © 2010 Elsevier B.V. All rights reserved.542142147Serrate, D., Serrate, D., De Teresa, J.M., Ibarra, M.R., (2007) J. Phys.: Condens. Matter, 19, p. 023201Kobayashi, K.-I., Kimura, T., Sawada, H., Terakura, K., Tokura, Y., (1998) Nature (London), 395, p. 677Kobayashi, K.I., Kimura, T., Tomioka, Y., Sawada, H., Terakura, K., (1999) Phys. Rev. B, 59, p. 11159Prellier, W., Smolyaninova, V., Biswas, A., Galley, C., Greene, R.L., Ramesha, K., Gopalakrishnan, J., (2000) J. Phys. C, 12, p. 965Gopalakrishnan, J., Chattopadhyay, A., Ogale, S.B., Venkatesan, T., Greene, R.L., Millis, A.J., Ramesha, K., Marest, G., (2000) Phys. Rev. B, 62, p. 9538Maignan, A., Raveau, B., Martin, C., Hervieu, M., (1999) J. Solid State Chem., 144, p. 224Dai, J.M., Song, W.H., Wang, S.G., Ye, S.L., Wang, K.Y., Du, J.J., Sun, Y.P., Gao, B.J., (2001) Mat. Sci. Eng. B, 83, p. 217Granado, E., Hung, Q., Lynn, J.W., Gopalakrishnan, J., Greene, R.L., Ramesha, K., (2002) Phys. Rev. B, 66, p. 064409Azimonte, C., Cezar, J.C., Granado, E., Huang, Q., Lynn, J.W., Campoy, J.C.P., Gopalakrishnan, J., Ramesha, K., (2007) Phys. Rev. Lett., 98, p. 017204Azimonte, C., Granado, E., Cezar, J.C., Gopalakrishnan, J., Ramesha, K., (2007) J. Appl. Phys., 101, pp. 09H115Serrate, D., De Teresa, J.M., Algarabel, P.A., Galibert, J., Ritter, C., Blasco, J., Ibarra, M.R., (2007) Phys. Rev. B, 75, p. 165109Sikora, M., Mathon, O., Van Der Linden, P., Michalik, J.M., De Teresa, J.M., Kapusta, C., Pascarelli, S., (2009) Phys. Rev. B, 79, p. 220402Pinacca, R.M., Viola, M.C., Pedregosa, J.C., Muñoz, A., Alonso, J.A., Martínez-Lope, M.J., Carbonio, R.E., (2005) Dalton Trans., p. 447Pinacca, R.M., Viola, M.C., Pedregosa, J.C., Martínez-Lope, M.J., Carbonio, R.E., Alonso, J.A., (2007) J. Solid State Chem., 180, p. 1582Ferreira, F.F., Granado, E., Carvalho Jr., W., Kycia, S.W., Bruno, D., Droppa Jr., R., (2006) J. Synchrotron Rad., 13, p. 46Larson, A.C., Von Dreele, R.B., (2000) Los Alamos National Laboratory Report LAUR 86-748Toby, B.H., (2001) J. Appl. Cryst., 34, pp. 210-213Prosandeev, S.A., Waghmare, U., Levin, I., Maslar, J., (2005) Phys. Rev. B, 71, p. 214307Iliev, M.N., Abrashev, M.V., Litvinchuk, A.P., Hadjiev, V.G., Guo, H., Gupta, A., (2007) Phys. Rev. B, 75, p. 104118Balkanski, M., Wallis, R.F., Haro, E., (1983) Phys. Rev. B, 28, p. 1928Andreasson, J., Holmlund, J., Knee, C.S., Käll, M., Börjesson, L., Naler, S., Bäckström, J., Eriksson, S.-G., (2007) Phys. Rev. B, 75, p. 104302Fujioka, Y., Frantti, J., Kakihana, M., (2004) J. Phys. Chem. B, 108, p. 17012Fujioka, Y., Frantti, J., Kakihana, M., (2006) J. Phys. Chem. B, 110, p. 777Kurosawa, T., (1961) J. Phys. Soc. Jpn., 16, p. 1208Siny, I.G., Katiyar, R.S., Bhalla, A.S., (2000) Ferroelectr. Rev., 2, p. 51Granado, E., García, A., Sanjurjo, J.A., Rettori, C., Torriani, I., Prado, F., Sánchez, R.D., Oseroff, S.B., (1999) Phys. Rev. B, 60, p. 11879Iliev, M.N., Guo, H., Gupta, A., (2007) Appl. Phys. Lett., 90, p. 15191

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background: Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods: The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results: A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion: Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)