Howard D. White

The prepower stroke conformation of myosin V

eW have used electron microscopy and single-particle image processing to study head conformation in myosin V molecules. We find that in the presence of ATP, many heads have a sharply angled conformation that is rare in its absence. The sharply angled conformation is similar to a myosin II atomic structure proposed to mimic the prepower stroke state. The leading head in molecules attached to actin by both heads has a similar conformation, but is also sharply angled in a second plane by tethering through the trail head. The lead head lever joins the motor domain ∼5 nm axially from where it joins the trail motor. These positions locate the converter subdomain and show the lead motor is in the prepower stroke conformation. Tethering by the trail head places the lead head motor domain at the correct axial position along the actin for binding, but at the wrong orientation. Attachment is achieved either by bending the lead head lever throughout its length or at the pliant point. The microscopy shows that most of the walking stride is produced by changes in lever angle brought about by converter movement, but is augmented by distortion produced by thermal energy.

Combining bibliometrics, information retrieval, and relevance theory, Part 1: First examples of a synthesis

In Sperber and Wilsons relevance theory (RT), the ratio Cognitive Effects/Processing Effort defines the relevance of a communication. The tf*idf formula from information retrieval is used to operationalize this ratio for any item co‐occurring with a user‐supplied seed term in bibliometric distributions. The tf weight of the item predicts its effect on the user in the context of the seed term, and its idf weight predicts the users processing effort in relating the item to the seed term. The idf measure, also known as statistical specificity, is shown to have unsuspected applications in quantifying interrelated concepts such as topical and nontopical relevance, levels of user expertise, and levels of authority. A new kind of visualization, the pennant diagram, illustrates these claims. The bibliometric distributions visualized are the works cocited with a seed work (Moby Dick), the authors cocited with a seed author (White HD, for maximum interpretability), and the books and articles cocited with a seed article (S.A. Harters “Psychological Relevance and Information Science,” which introduced RT to information scientists in 1992). Pennant diagrams use bibliometric data and information retrieval techniques on the system side to mimic a relevance‐theoretic model of cognition on the user side. Relevance theory may thus influence the design of new visual information retrieval interfaces. Generally, when information retrieval and bibliometrics are interpreted in light of RT, the implications are rich: A single sociocognitive theory may serve to integrate research on literature‐based systems with research on their users, areas now largely separate.

Combining Bibliometrics, Information Retrieval, and Relevance Theory, Part 2: Some Implications for Information Science

When bibliometric data are converted to term frequency (tf) and inverse document frequency (idf) values, plotted as pennant diagrams, and interpreted according to Sperber and Wilson’s relevance theory (RT), the results evoke major variables of information science (IS). These include topicality, in the sense of intercohesion and intercoherence among texts; cognitive effects of texts in response to people’s questions; people’s levels of expertise as a precondition for cognitive effects; processing effort as textual or other messages are received; specificity of terms as it affects processing effort; relevance, defined in RT as the effects/effort ratio; and authority of texts and their authors. While such concerns figure automatically in dialogues between people, they become problematic when people create or use or judge literature-based information systems. The difficulty of achieving worthwhile cognitive effects and acceptable processing effort in human-system dialogues explains why relevance is the central concern of IS. Moreover, since relevant communication with both systems and unfamiliar people is uncertain, speakers tend to seek cognitive effects that cost them the least effort. Yet hearers need greater effort, often greater specificity, from speakers if their responses are to be highly relevant in their turn. This theme of mismatch manifests itself in vague reference questions, underdeveloped online searches, uncreative judging in retrieval evaluation trials, and perfunctory indexing. Another effect of least effort is a bias toward topical relevance over other kinds. RT can explain these outcomes as well as more adaptive ones. Pennant diagrams, applied here to a literature search and a Bradford-style journal analysis, can model them. Given RT and the right context, bibliometrics may predict psychometrics.

Author-centered bibliometrics through CAMEOs: Characterizations automatically made and edited online

This article describes ways of automatically generating 15 kinds of personal profiles of authors from bibliographic data on their publications in databases. Nicknamed CAMEOs, the profiles can be used for retrieval of documents by human searchers or computerized agents. They can also be used for mapping an authors subject matter (in terms of descriptors, identifiers, and natural language) and studying his or her publishing career. Finally, they can be used to map the intellectual and social networks evident in citations to and from authors and in co-authorships.

Term Co-occurrence Analysis as an Interface for Digital Libraries

We examine the relationship between term co-occurrence analysis and a user interface for digital libraries. We describe a current working implementation of a dynamic visual information retrieval system based on co-cited author maps that assists in browsing and retrieving records from a large-scale database, ten years of the Arts & Humanities Citation Index, in real time. Any figure in the arts or humanities, including scholars and critics, can be mapped, and the maps are live interfaces for retrieving co-citing documents.

Mechanism of regulation of phosphate dissociation from actomyosin-ADP-Pi by thin filament proteins

Regulation by calcium and myosin-S1 of the acceleration of the rate of phosphate release from myosin-ADP-inorganic phosphate (M-ADP-Pi) by the thin filament actin-tropomyosin (Tm)-troponin (Tn), was measured directly by using double mixing stopped-flow experiments with fluorescent phosphate binding protein. At low calcium and without rigor myosin-S1, saturating concentrations of thin filaments accelerate the rate of phosphate dissociation from M-ADP-Pi 8-fold, from 0.08 to 0.64 s−1. If either myosin-S1 or calcium is bound to the thin filaments, phosphate release is a biphasic process in which the fast phase is the dissociation of Pi from actoTmTnM-ADP-Pi and the slow phase is limited by the hydrolysis of actoTmTnM-ATP to actoTmTnM-ADP-Pi. The maximum accelerations of the fast components by saturating thin filaments (relative to M-ADP-Pi alone) are: ≈200-fold, 16 s−1 (calcium only); ≈400-fold, 30 s−1 (EGTA and rigor S1); and ≈1,000-fold, 75 s−1 (calcium and rigor S1). The maximum rate of phosphate dissociation attained with S1 and calcium bound to the thin filament is the same as for unregulated actin. Regulation of the rate of phosphate dissociation by calcium and myosin-S1 is partially explained by the model of Geeves [McKillop, D. F. and Geeves, M. A. (1993) Biophys. J. 65, 693–701], in which calcium and rigor S1 perturb the equilibria among three states of the thin filament (blocked, closed, and open). However, a quantitative description of the regulatory mechanism requires acceleration by calcium of an additional step of the mechanism, either phosphate dissociation or a preceding conformational change.

A cocitation map of the social indicators movement

Author cocitations form the base of a general technique of bibliogrpahic retrieval and of mapping the strucutre of literatures. The technique was used here in a largescale retrieval of the Social Indicators (SI) literature and a computerized mapping, through multidimensional scaling and clustering, of key SI contributors as perceived by citers during 1972-1980. Clusters of points on the map are interpreted as authors similar in perceived subject matter and style of work; other interpretable features also eemerge. The map conforms well with independent reviews of the SI literature, actually illustrating some of the judgments they contain. It is suggested that such mappings may become a stimulus and complement to literature reviews in the future.

Maximal Activation of Skeletal Muscle Thin Filaments Requires Both Rigor Myosin S1 and Calcium

The regulation by calcium and rigor-bound myosin-S1 of the rate of acceleration of 2′-deoxy-3′-O-(N-methylanthraniloyl)ADP (mdADP) release from myosin-mdADP-Pi by skeletal muscle thin filaments (reconstituted from actin-tropomyosin-troponin) was measured using double mixing stopped-flow fluorescence with the nucleotide substrate 2′-deoxy-3′-O-(N-methylanthraniloyl). The predominant mechanism of regulation is the acceleration of product dissociation by a factor of ∼200 by thin filaments in the fully activated conformation (bound calcium and rigor S1) relative to the inhibited conformation (no bound calcium or rigor S1). In contrast, only 2–3-fold regulation is due to a change in actin affinity such as would be expected by “steric blocking” of the myosin binding site of the thin filament by tropomyosin. The binding of one ligand (either calcium or rigor-S1) produces partial activation of the rate of product dissociation, but the binding of both is required to maximally accelerate product dissociation to a rate similar to that obtained with F-actin in the absence of regulatory proteins. The data support an allosteric regulation model in which the binding of either calcium or rigor S1 alone to the thin filament shifts the equilibrium in favor of the active conformation, but full activation requires binding of both ligands.

Quality of indexing in online data bases

Abstract We describe practical tests by which the quality of subject indexing in online bibliographic data bases can be compared and judged. The tests are illustrated with 18 clusters of documents from the medical behavioral science literature and with terms drawn from MEDLINE, PsycINFO, BIOSIS, and Excerpta Medica. Each test involves obtaining a cluster of about five documents known on some grounds to be related in subject matter, and retrieving their descriptors from at least two data bases. We then tabulate the average number of descriptors applied to the documents, the number of descriptors applied to all and to a majority of the documents in the cluster, and the relative rarity of the applied descriptors. Comparable statistics emerge on how each data base links related documents and discriminates broadly and finely among documents. We also gain qualitative insights into the expressiveness and pertinence of the available indexing terms.

Comparing retrieval performance in online data bases

Abstract This study systematically compares retrievals on 11 topics across five well-known data bases, with MEDLINEs subject indexing as a focus. Each topic was posed by a researcher in the medical behavioral sciences. Each was searched in MEDLINE, EXCERPTA MEDICA, and PSYCINFO, which permit descriptor searches, and in SCISEARCH and SOCIAL SCISEARCH, which express topics through cited references. Searches on each topic were made with (1) descriptors, (2) cited references, and (3) natural language (a capability common to all five data bases). The researchers who posed the topics judged the results. In every case, the set of records judged relevant was used to calculate recall, precision, and novelty ratios. Overall, MEDLINE had the highest recall percentage (37%), followed by SSCI (31%). All searches resulted in high precision ratios; novelty ratios of data bases and searches varied widely. Differences in record format among data bases affected the success of the natural language retrievals. Some 445 documents judged relevant were not retrieved from MEDLINE using its descriptors; they were found in MEDLINE through natural language or in an alternative data base. An analysis was performed to examine possible faults in MEDLINE subject indexing as the reason for their nonretrieval. However, no patterns of indexing failure could be seen in those documents subsequently found in MEDLINE through known-item searches. Documents not found in MEDLINE primarily represent failures of coverage—articles were from nonindexed or selectively indexed journals. Recommendations to MEDLINE managers include expansion of record format and modification of journal and article selection policies.