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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Least-Squares Analysis

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Disease relevance of Least-Squares Analysis

  • The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution [1].
  • The crystal structure of the apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined by the method of isomorphous replacement and refined at 2.4 A resolution using a restrained least-squares method [2].
  • Comparisons of last 14-day, least-squares means among groups did not reveal differences in data treated by lean body weight [3MH/(kg LBW X d)] or by urinary creatinine excretion [3MH/(kg UCE X d)], but 3MH/(kg LBW X d) excretions were higher for exercise than no-exercise subjects [3].
  • Using broken-line least-squares analysis, weight gain reached a plateau (6.8 g/d) at a thiamin concentration of 0.55 +/- 0.07 mg/kg [4].
  • Adopting this general approach, we fitted human pulmonary O2 toxicity data to the hyperbolic equation % delta VC = Bs.(PO2 - B1).(time)B3 using a nonlinear least squares analysis [5].

Psychiatry related information on Least-Squares Analysis


High impact information on Least-Squares Analysis

  • A restrained least squares refinement of the solution structure of the double-stranded DNA undecamer 5'd(AAGTGT-GACAT).5'd(ATGTCACACTT) comprising a portion of the specific target site of the cAMP receptor protein in the gal operon is presented [9].
  • Selected backbone segments of the model representing regions of prominent sequence similarity between antibodies and TCRs were least-squares superimposed onto the corresponding segments of the crystallographically resolved 4-4-20 antibody complexed with its antigen, fluorescein [10].
  • Use of the van't Hoff equation plus least-squares fitting to determine a more probable baseline gives delta H = 1.3 kcal/mol per residue [11].
  • The structure of human recombinant interleukin 1 beta (IL-1 beta) has been refined by a restrained least-squares method to a crystallographic R factor of 17.2% to 2.0 A resolution [12].
  • The crystal structure of Lys-7-(dinitrophenylene)-Lys-41-cross-linked ribonuclease A has been determined by molecular replacement and refined by restrained least-squares methods to an R factor of 0.18 at 2.0-A resolution [13].

Chemical compound and disease context of Least-Squares Analysis


Biological context of Least-Squares Analysis

  • Absolute metabolic fluxes in isolated perfused hearts have been determined by a nonlinear least squares analysis of glutamate labeling kinetics from [1-13C]glucose, [4-13C]beta-hydroxybutyrate, or [2-13C]acetate using 13C NMR spectroscopy [17].
  • Partial least squares (PLS) has proven to be a important multivariate analytic tool for positron emission tomographic and, more recently, event-related potential (ERP) data [18].
  • The models were refined to R-factors of 0.19 (maleate complex) and 0.18 (2-methylaspartate complex) by molecular dynamics and restrained least squares methods [19].
  • Isotope excretion ratios of urinary folates were used as criteria of bioavailability (pooled SE = 0.10): PteGlu (1.53, least squares mean), 10-formyl-H4folate (1.02), 5-methyl-H4folate (0.99), 5-formyl-H4folate (0.1.13), and H4folate (0.71) [20].
  • RESULTS: Vildagliptin significantly increased the insulin secretory rate at 7 mmol/liter glucose (secretory tone), calculated from the dose response; the difference in least squares mean (deltaLSM) was 101 +/- 51 pmol.min(-1).m(-2) (P = 0.002) [21].

Anatomical context of Least-Squares Analysis

  • Computer simulation studies showed that RLS analysis yielded k(3) with almost the same accuracy as the standard nonlinear least squares (NLS) analysis in brain regions with low (such as neocortex and hippocampus) and moderately high (thalamus) k(3) values [22].
  • Enhanced synchronous spectrofluorometric determination of tetracycline in blood serum by chemometric analysis. Comparison of partial least-squares and hybrid linear analysis calibrations [23].
  • The algorithms presented here are used to perform nonlinear least-squares analyses of ST-EPR spectra of the anion exchange protein of the human erythrocyte membrane, band 3, which has been affinity spin-labeled with a recently developed dihydrostilbene disulfonate derivative, [15N,2H13]-SL-H2DADS-MAL [24].
  • The pharmacology of the receptors was studied using computerized, non-linear least-squares regression analysis of [3H]flunitrazepam displacement by flunitrazepam, CL218,872 and ethyl beta-carboline-3-carboxylate binding to membranes [25].
  • The accumulation of choline into PC12 cells proceeded through two uptake systems with high (Km = 3.20 microM) and low (Km = 65.2 muM) affinities as revealed by least-squares iterative fitting of a substrate-velocity curve to the data [26].

Associations of Least-Squares Analysis with chemical compounds

  • The slope of the regression line obtained by a least squares method was steepest for all the treatment groups, followed by the heat plus 5 g/kg glucose and heat plus 3 g/kg glucose groups [27].
  • Urinary 15N-nitrogen excretion as ammonia and urea was measured during the 210-min infusion period, and urea synthesis and ammonia conversion to amino acids were analyzed with a three-compartment model using the nonlinear least-squares method [28].
  • At a late stage of the refinement, atomic parameters for only the Fe4S4 cluster plus the 4 associated cystein S-gamma atoms were adjusted by least squares methods and kept fixed during the rest of the refinement [29].
  • The structure of cytoplasmic malate dehydrogenase has been partially refined by crystallographic least squares methods [30].
  • Nonlinear least squares fitting of these data to the model gave nonrandomly distributed residuals for the 13C fractional enrichments of glutamate C-4, suggesting an incomplete model, but a well determined cycle flux of 11.9 mumol/g dry weight X min for an oxygen uptake of 35 mumol/g dry weight X min [31].

Gene context of Least-Squares Analysis

  • Dissociation constants determined by least-squares non-linear regression indicated that the affinity of UCP2 for these fluorescently tagged nucleotides was 3-5 microM or perhaps an order of magnitude stronger, depending on the model used [32].
  • Metabolic profiles from (1)H nuclear magnetic resonance spectroscopy have been used to describe both one and two protein systems in four mouse models related to Duchenne muscular dystrophy using the pattern recognition technique partial least squares [33].
  • The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method [34].
  • The structure of a Y35G mutant of bovine pancreatic trypsin inhibitor (BPTI) was solved by molecular replacement and was refined by both simulated annealing and restrained least-squares at 1.8 A resolution [35].
  • The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108 [36].

Analytical, diagnostic and therapeutic context of Least-Squares Analysis


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  2. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. Goldberg, J.D., Yoshida, T., Brick, P. J. Mol. Biol. (1994) [Pubmed]
  3. Exercise and protein intake effects on urinary 3-methylhistidine excretion. Hickson, J.F., Hinkelmann, K. Am. J. Clin. Nutr. (1985) [Pubmed]
  4. Minimum thiamin requirement of weanling Sprague-Dawley outbred rats. Rains, T.M., Emmert, J.L., Baker, D.H., Shay, N.F. J. Nutr. (1997) [Pubmed]
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  6. Ziprasidone and haloperidol in the treatment of acute exacerbation of schizophrenia and schizoaffective disorder: comparison of intramuscular and oral formulations in a 6-week, randomized, blinded-assessment study. Brook, S., Walden, J., Benattia, I., Siu, C.O., Romano, S.J. Psychopharmacology (Berl.) (2005) [Pubmed]
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  9. The solution structure of a B-DNA undecamer comprising a portion of the specific target site for the cAMP receptor protein in the gal operon. Refinement on the basis of interproton distance data. Clore, G.M., Gronenborn, A.M. EMBO J. (1985) [Pubmed]
  10. Similarity between fluorescein-specific T-cell receptor and antibody in chemical details of antigen recognition. Ganju, R.K., Smiley, S.T., Bajorath, J., Novotny, J., Reinherz, E.L. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  11. Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Scholtz, J.M., Marqusee, S., Baldwin, R.L., York, E.J., Stewart, J.M., Santoro, M., Bolen, D.W. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  12. Crystallographic refinement of interleukin 1 beta at 2.0 A resolution. Priestle, J.P., Schär, H.P., Grütter, M.G. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  13. The 2-A resolution structure of a thermostable ribonuclease A chemically cross-linked between lysine residues 7 and 41. Weber, P.C., Sheriff, S., Ohlendorf, D.H., Finzel, B.C., Salemme, F.R. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  14. The use of FT-IR for quantitative studies of the apparent pKa of lipid carboxyl groups and the dehydration degree of the phosphate group of phospholipids. Gómez-Fernández, J.C., Villalaín, J. Chem. Phys. Lipids (1998) [Pubmed]
  15. Periparturient endocrine changes of conceptus and maternal units in Holstein heifers bearing genetically different conceptuses. Guilbault, L.A., Thatcher, W.W., Collier, R.J., Wilcox, C.J. J. Anim. Sci. (1985) [Pubmed]
  16. Serial epidemiological surveys in an urban Indian population demonstrate increasing coronary risk factors among the lower socioeconomic strata. Gupta, R., Gupta, V.P., Sarna, M., Prakash, H., Rastogi, S., Gupta, K.D. The Journal of the Association of Physicians of India. (2003) [Pubmed]
  17. Calculation of absolute metabolic flux and the elucidation of the pathways of glutamate labeling in perfused rat heart by 13C NMR spectroscopy and nonlinear least squares analysis. Chatham, J.C., Forder, J.R., Glickson, J.D., Chance, E.M. J. Biol. Chem. (1995) [Pubmed]
  18. Spatiotemporal analysis of event-related fMRI data using partial least squares. McIntosh, A.R., Chau, W.K., Protzner, A.B. Neuroimage (2004) [Pubmed]
  19. Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms. Jäger, J., Moser, M., Sauder, U., Jansonius, J.N. J. Mol. Biol. (1994) [Pubmed]
  20. Relative bioavailability of deuterium-labeled monoglutamyl tetrahydrofolates and folic acid in human subjects. Gregory, J.F., Bhandari, S.D., Bailey, L.B., Toth, J.P., Baumgartner, T.G., Cerda, J.J. Am. J. Clin. Nutr. (1992) [Pubmed]
  21. Vildagliptin, a dipeptidyl peptidase-IV inhibitor, improves model-assessed beta-cell function in patients with type 2 diabetes. Mari, A., Sallas, W.M., He, Y.L., Watson, C., Ligueros-Saylan, M., Dunning, B.E., Deacon, C.F., Holst, J.J., Foley, J.E. J. Clin. Endocrinol. Metab. (2005) [Pubmed]
  22. Kinetic analysis of [(11)C]MP4A using a high-radioactivity brain region that represents an integrated input function for measurement of cerebral acetylcholinesterase activity without arterial blood sampling. Nagatsuka Si, S., Fukushi, K., Shinotoh, H., Namba, H., Iyo, M., Tanaka, N., Aotsuka, A., Ota, T., Tanada, S., Irie, T. J. Cereb. Blood Flow Metab. (2001) [Pubmed]
  23. Enhanced synchronous spectrofluorometric determination of tetracycline in blood serum by chemometric analysis. Comparison of partial least-squares and hybrid linear analysis calibrations. Goicoechea, H.C., Olivieri, A.C. Anal. Chem. (1999) [Pubmed]
  24. Analysis of saturation transfer electron paramagnetic resonance spectra of a spin-labeled integral membrane protein, band 3, in terms of the uniaxial rotational diffusion model. Hustedt, E.J., Beth, A.H. Biophys. J. (1995) [Pubmed]
  25. Multiple benzodiazepine receptors in the human basal ganglia: a detailed pharmacological and anatomical study. Faull, R.L., Villiger, J.W. Neuroscience (1988) [Pubmed]
  26. Cholinergic differentiation of clonal rat pheochromocytoma cells (PC12) induced by factors contained in glioma-conditioned medium: enhancement of high-affinity choline uptake system and reduction of norepinephrine uptake system. Matsuoka, I., Satake, R., Kurihara, K. Brain Res. (1986) [Pubmed]
  27. Comparison between tumor pH and cell sensitivity to heat in RIF-1 tumors. Hiraoka, M., Hahn, G.M. Cancer Res. (1989) [Pubmed]
  28. Metabolism of 15N-ammonia in patients with cirrhosis: a three-compartmental analysis. Fujii, T., Kohno, M., Hirayama, C. Hepatology (1992) [Pubmed]
  29. Crystallographic structure refinement of Chromatium high potential iron protein at two Angstroms resolution. Freer, S.T., Alden, R.A., Carter, C.W., Kraut, J. J. Biol. Chem. (1975) [Pubmed]
  30. The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase. Birktoft, J.J., Banaszak, L.J. J. Biol. Chem. (1983) [Pubmed]
  31. Mathematical analysis of isotope labeling in the citric acid cycle with applications to 13C NMR studies in perfused rat hearts. Chance, E.M., Seeholzer, S.H., Kobayashi, K., Williamson, J.R. J. Biol. Chem. (1983) [Pubmed]
  32. Nucleotide binding to human uncoupling protein-2 refolded from bacterial inclusion bodies. Jekabsons, M.B., Echtay, K.S., Brand, M.D. Biochem. J. (2002) [Pubmed]
  33. Metabolic profiles of dystrophin and utrophin expression in mouse models of Duchenne muscular dystrophy. Griffin, J.L., Sang, E., Evens, T., Davies, K., Clarke, K. FEBS Lett. (2002) [Pubmed]
  34. Refined structure of glutathione reductase at 1.54 A resolution. Karplus, P.A., Schulz, G.E. J. Mol. Biol. (1987) [Pubmed]
  35. Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor. Housset, D., Kim, K.S., Fuchs, J., Woodward, C., Wlodawer, A. J. Mol. Biol. (1991) [Pubmed]
  36. Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+. Ahmed, F.R., Przybylska, M., Rose, D.R., Birnbaum, G.I., Pippy, M.E., MacManus, J.P. J. Mol. Biol. (1990) [Pubmed]
  37. Imaging of collagen and proteoglycan in cartilage sections using Fourier transform infrared spectral imaging. Potter, K., Kidder, L.H., Levin, I.W., Lewis, E.N., Spencer, R.G. Arthritis Rheum. (2001) [Pubmed]
  38. Detection of phospholipid phase separation. A multifrequency phase fluorimetry study of 1,6-diphenyl-1,3,5-hexatriene fluorescence. Parasassi, T., Conti, F., Glaser, M., Gratton, E. J. Biol. Chem. (1984) [Pubmed]
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