A unified statistical framework for sequence comparison and structure comparison

We present an approach for assessing the significance of sequence and structure comparisons by using nearly identical statistical formalisms for both sequence and structure. Doing so involves an all-vs.-all comparison of protein domains [taken here from the Structural Classification of Proteins (scop) database] and then fitting a simple distribution function to the observed scores. By using this distribution, we can attach a statistical significance to each comparison score in the form of a P value, the probability that a better score would occur by chance. As expected, we find that the scores for sequence matching follow an extreme-value distribution. The agreement, moreover, between the P values that we derive from this distribution and those reported by standard programs (e.g., blast and fasta validates our approach. Structure comparison scores also follow an extreme-value distribution when the statistics are expressed in terms of a structural alignment score (essentially the sum of reciprocated distances between aligned atoms minus gap penalties). We find that the traditional metric of structural similarity, the rms deviation in atom positions after fitting aligned atoms, follows a different distribution of scores and does not perform as well as the structural alignment score. Comparison of the sequence and structure statistics for pairs of proteins known to be related distantly shows that structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. The comparison also indicates that there are very few pairs with significant similarity in terms of sequence but not structure whereas many pairs have significant similarity in terms of structure but not sequence.

Altered surfactant function and structure in SP-A gene targeted mice.

The surfactant protein A (SP-A) gene was disrupted by homologous recombination in embryonic stem cells that were used to generate homozygous SP-A-deficient mice. SP-A mRNA and protein were not detectable in the lungs of SP-A(-/-) mice, and perinatal survival of SP-A(-/-) mice was not altered compared with wild-type mice. Lung morphology, surfactant proteins B-D, lung tissue, alveolar phospholipid pool sizes and composition, and lung compliance in SP-A(-/-) mice were unaltered. At the highest concentration tested, surfactant from SP-A(-/-) mice produced the same surface tension as (+/+) mice. At lower concentrations, minimum surface tensions were higher for SP-A(-/-) mice. At the ultrastructural level, type II cell morphology was the same in SP-A(+/+) and (-/-) mice. While alveolar phospholipid pool sizes were unperturbed, tubular myelin figures were decreased in the lungs of SP-A(-/-) mice. A null mutation of the murine SP-A gene interferes with the formation of tubular myelin without detectably altering postnatal survival or pulmonary function.

The problems of the origin and structure of chondrules in stony meteorites / Sharat Kumar Roy --

v.10:no.31(1957)

Mean grain size and structure of ODP Hole 140-504B samples

Microstructural investigations of ocean crust samples provide a complementary approach to both marine surveys and laboratory experiments. The recovery of relatively undeformed diabases from Deep Sea Drilling Project (DSDP)/Ocean Drilling Program (ODP) Hole 504B provides a first opportunity to examine a reference section of microstructural features that influence strain localization at depths of 2 km in the ocean crust. Syn- and post-crystallization features in plagioclase and augite crystals have been examined by optical microscopy and secondary and backscattered electron imaging. These features show a strong influence of modal composition and primary textures on early sites of strain localization. Thermal cracking and subsequent alteration intensities and distribution are strongly phase dependent. A consistently higher intragranular fracture density is observed in augite crystals relative to plagioclase. The impact of alteration on the mechanical response of diabases is likely to depend on the primary textural characteristics. Even where extensive augite alteration occurs, the rock remains supported by a framework of weakly altered plagioclase crystals. The Hole 504B diabases from Leg 140 provide a valuable comparison for future studies of more deformed sections likely to be encountered at depth. Advances in constraining the detailed rheology of the ocean crust at spreading centers would benefit from experimental deformation of texturally diverse diabase and gabbro samples.

The development and structure of the U.S. electric lamp industry : staff report of the Federal Trade Commission /

Cover title: Staff report on the development and structure of the U.S. electric lamp industry.

Williamsburg: a Jewish community in transition; a study of the factors and patterns of change in the organization and structure of a community in transition.

The author's thesis, first issued on microfilm in 1954, now brought up to date.

Timber: growth and structure : felling, converting and buying; measuring; seasoning; properties and defects; preservation; varieties.

"A comprehensive digest of the knowledge of timber scattered over seventeen volumes of Building World".

The vitreous body, its origin, development, and structure as observed in the eye of the pig,

"Contribution from the Biological Laboratory of the Catholic University of America, no. 4."

The apostolical authority of the Epistle to the Hebrews: an inquiry, in which the received title of the Greek epistle is vindicated, against the cavils of objectors, ancient and modern, from Origen to Sir J. D. Michaëlis, chiefly upon grounds of internal evidence hitherto unnoticed: comprising a comparative analysis of the style and structure of this epistle, and of the undisputed epistles of St. Paul, tending to throw light upon their interpretation.

Mode of access: Internet.

Sacred literature; comprising a review of the principles of composition laid down by the late Robert Lowth ... in his Praelections, and Isaiah: and an application of the principles so reviewed, to the illustration of the New Testament; in a series of critical observations on the style and structure of that sacred volume. By the Rev. John Jebb.

Mode of access: Internet.

Personality: a biosocial approach to origins and structure.

Bibliography: p. [945]-968.