Search results for " Methods"
showing 10 items of 4102 documents
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
2015
Abstract Motivation: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. Results: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are inc…
Structure Learning in Nested Effects Models
2007
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell. In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we…
Infant mortality across species. A global probe of congenital abnormalities
2019
Infant mortality, by which we understand the postnatal stage during which mortality is declining, is a manifestation and embodiment of congenital abnormalities. Severe defects will translate into death occurring shortly after birth whereas slighter anomalies may contribute to death much later, possibly only in adult age. While for many species birth defects would be nearly impossible to identify, infant mortality provides a convenient global assessment. In the present paper we examine a broad range of species from mammals to fish to gastropods to insects. One of the objectives of our comparative analysis is to test a conjecture suggested by reliability engineering according to which the fre…
Contributed discussion on article by Pratola
2016
The author should be commended for his outstanding contribution to the literature on Bayesian regression tree models. The author introduces three innovative sampling approaches which allow for efficient traversal of the model space. In this response, we add a fourth alternative.
Systematic handling of missing data in complex study designs : experiences from the Health 2000 and 2011 Surveys
2016
We present a systematic approach to the practical and comprehensive handling of missing data motivated by our experiences of analyzing longitudinal survey data. We consider the Health 2000 and 2011 Surveys (BRIF8901) where increased non-response and non-participation from 2000 to 2011 was a major issue. The model assumptions involved in the complex sampling design, repeated measurements design, non-participation mechanisms and associations are presented graphically using methodology previously defined as a causal model with design, i.e. a functional causal model extended with the study design. This tool forces the statistician to make the study design and the missing-data mechanism explicit…
Synthesis and Structural Characterization of Substituted 2-Phenacylbenzoxazoles
2013
1 H and 13C NMR spectra of eleven 2-phenacylbenzoxazoles (ketimine form) show that their CDCl3-solutions contains also (Z)-2-(benzo[d]oxazol-2-yl)-1-phenylethenols (enolimine form). Intramolecular hydrogen bonding in the latter tautomer was found to be significantly weaker than that one in respective (Z)-2-(2-hydroxy-2-phenylvinyl)pyridines. Integrals of the 1 H NMR signals were used to evaluate the molar ratio of the tautomers. Strong electron-donating substituents were found to stabilize the ketimine tautomer. pKT (negative logarithm of the equilibrium constant, KT = [ketimine]/[enolimine]) was found to be linearly dependent on the Hammett substituent constant σ. The results of the MP2 ab…
A Hydrogen-Bonded Supramolecular meso-Helix
2003
[EN] A new one-dimensional hydrogen-bonded polymer with a unique meso-helical structure has been prepared from the spontaneous self-assembly in the solid-state of meta-substituted phenylene dioxamic acid diethyl ester monomers. The helical nature of this molecule and its self-complementary character, through intermolecular hydrogen bonding between oxamic acid ester functions, are the two main factors responsible for the crystalline aggregation process, as confirmed by both experimental X-ray crystallographic data and theoretical ab initio calculations.
Rotational Isomerism in Acetic Acid: The First Experimental Observation of the High-Energy Conformer
2003
The high-energy conformer of acetic acid (cis-AA) is produced in an Ar matrix by vibrational excitation of the OH stretching overtone of the ground conformational state (trans-AA). IR-absorption spectroscopy provides a clear identification of the reaction product. cis-AA converts back to trans-AA in a time scale of minutes at 8 K by tunneling. http://dx.doi.org/10.1021/ja038341a
A Density Functional Study of Open-Shell Cyclopentadienyl−Molybdenum(II) Complexes. A Comparison of Stabilizing Factors: Spin-Pairing, Mo−X π Bonding…
2000
International audience; The dissociation of PH3 from the 18-electron system CpMoX(PH3)3 to afford the corresponding 16-electron CpMoX(PH3)2 fragment has been investigated theoretically by density functional theory for X = H, CH3, F, Cl, Br, I, OH, and PH2. The product is found to prefer a triplet spin state for all X ligands except PH2, the singlet−triplet gap varying between 1.7 kcal/mol for OH to 8.7 kcal/mol for F. The Mo−PH3 bond dissociation energy to the 16-electron ground state varies dramatically across the series, from 4.5 kcal/mol for OH to 23.5 kcal/mol for H, and correlates with experimental observations on trisubstituted phosphine derivatives. Geometry-optimized spin doublet Cp…
An ab initio study of the enolboration of 3-pentanone mediated by boron monochlorides L2BCl
2001
Abstract Using ab initio methods at the HF/6-31G∗∗ level, we have studied the mechanism of the enolboration of 3-pentanone mediated by boron monochlorides L2BCl (L=H, methyl and isopropyl) and trimethyl amine. The size of the L group has been found to have a decisive influence on the configuration (E or Z) of the formed boron enolate. Thus, whereas our calculations predict that dimethylboron chloride yields the Z enolate with high stereoselectivity, diisopropylboron chloride is found to yield predominantly the E enolate. The difference in behavior is due mainly to steric features related to the conformational bias of the respective ketone–boron chloride complexes formed reversibly in the fi…