The Small Subunit rRNA Modification Database

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods

Semantic memory redux: an experimental test of hierarchical category representation

Four experiments investigated the classic issue in semantic memory of whether people organize categorical information in hierarchies and use inference to retrieve information from them, as proposed by Collins & Quillian (1969). Past evidence has focused on RT to confirm sentences such as “All birds are animals” or “Canaries breathe.” However, confounding variables such as familiarity and associations between the terms have led to contradictory results. Our experiments avoided such problems by teaching subjects novel materials. Experiment 1 tested an implicit hierarchical structure in the features of a set of studied objects (e.g., all brown objects were large). Experiment 2 taught subjects nested categories of artificial bugs. In Experiment 3, subjects learned a tree structure of novel category hierarchies. In all three, the results differed from the predictions of the hierarchical inference model. In Experiment 4, subjects learned a hierarchy by means of paired associates of novel category names. Here we finally found the RT signature of hierarchical inference. We conclude that it is possible to store information in a hierarchy and retrieve it via inference, but it is difficult and avoided whenever possible. The results are more consistent with feature comparison models than hierarchical models of semantic memory

Degradation of electroless Ni(P) under-bump metallization in Sn3.5Ag and Sn37Pb solders during high-temperature storage

The interfacial reaction between electroless Ni(P) under-bump metallization (UBM) and solders is studied. A P-rich layer forms in the UBM along the solder side after reflow and thermal aging. Crack formation inside the P-rich layer can sometimes penetrate throughout the entire UBM layer structure. The Ni(P) UBM degradation occurs earlier in the Sn3.5Ag solder than in Sn37Pb because of its higher reflow temperature. Despite the formation of a P-rich layer and cracks inside the UBM, it still keeps its original function within the high-temperature storage period in this study. Explanations for the formation of the P-rich layer and cracks in the UBM are outlined along with explanations for the Ni(P) UBM degradation process

A probabilistic threshold model: Analyzing semantic categorization data with the Rasch model

According to the Threshold Theory (Hampton, 1995, 2007) semantic categorization decisions come about through the placement of a threshold criterion along a dimension that represents items' similarity to the category representation. The adequacy of this theory is assessed by applying a formalization of the theory, known as the Rasch model (Rasch, 1960; Thissen & Steinberg, 1986), to categorization data for eight natural language categories and subjecting it to a formal test. In validating the model special care is given to its ability to account for inter- and intra-individual differences in categorization and their relationship with item typicality. Extensions of the Rasch model that can be used to uncover the nature of category representations and the sources of categorization differences are discussed

Effects of classification context on categorization in natural categories

The patterns of classification of borderline instances of eight common taxonomic categories were examined under three different instructional conditions to test two predictions: first, that lack of a specified context contributes to vagueness in categorization, and second, that altering the purpose of classification can lead to greater or lesser dependence on similarity in classification. The instructional conditions contrasted purely pragmatic with more technical/quasi-legal contexts as purposes for classification, and these were compared with a no-context control. The measures of category vagueness were between-subjects disagreement and within-subjects consistency, and the measures of similarity based categorization were category breadth and the correlation of instance categorization probability with mean rated typicality, independently measured in a neutral context. Contrary to predictions, none of the measures of vagueness, reliability, category breadth, or correlation with typicality were generally affected by the instructional setting as a function of pragmatic versus technical purposes. Only one subcondition, in which a situational context was implied in addition to a purposive context, produced a significant change in categorization. Further experiments demonstrated that the effect of context was not increased when participants talked their way through the task, and that a technical context did not elicit more all-or-none categorization than did a pragmatic context. These findings place an important boundary condition on the effects of instructional context on conceptual categorization

Community structure of Pleistocene coral reefs of Curaçao, Netherlands Antilles

The Quaternary fossil record of living coral reefs is fundamental for understanding modern ecological patterns. Living reefs generally accumulate in place, so fossil reefs record a history of their former biological inhabitants and physical environments. Reef corals record their ecological history especially well because they form large, resistant skeletons, which can be identified to species. Thus, presence-absence and relative abundance data can be obtained with a high degree of confidence. Moreover, potential effects of humans on reef ecology were absent or insignificant on most reefs until the last few hundred years, so that it is possible to analyze "natural" distribution patterns before intense human disturbance began. We characterized Pleistocene reef coral assemblages from Curacao, Netherlands Antilles, Caribbean Sea, focusing on predictability in species abundance patterns from different reef environments over broad spatial scales. Our data set is composed of >2 km of surveyed Quaternary reef. Taxonomic composition showed consistent differences between environments and along secondary environmental gradients within environments. Within environments, taxonomic composition of communities was markedly similar indicating nonrandom species associations and communities composed of species occurring in characteristic abundances. This community similarity was maintained with little change over a 40-km distance. The nonrandom patterns in species abundances were similar to those found in the Caribbean before the effects of extensive anthropogenic degradation of reefs in the late 1970s and early 1980s. The high degree of order observed in species abundance patterns of fossil reef coral communities on a scale of tens of kilometers contrasts markedly with patterns observed in previous small-scale studies of modern reefs. Dominance of Acropora palmata in the reef crest zone and patterns of overlap and nonoverlap of species in the Montastraea ''annularis'' sibling species complex highlight the tendency for distribution and abundance patterns of Pleistocene corals to reflect environmental preferences at multiple spatial scales. Wave energy is probably the most important physical environmental variable structuring these coral communities. The strong similarity between ancient and pre-1980s Caribbean reefs and the nonrandom distribution of coral species in space and time indicate that recent variability noted at much smaller time scales may be due to either unprecedented anthropogenic influences on reefs or fundamentally different patterns at varying spatio-temporal scales

Feature integration in natural language concepts

Two experiments measured the joint influence of three key sets of semantic features on the frequency with which artifacts (Experiment 1) or plants and creatures (Experiment 2) were categorized in familiar categories. For artifacts, current function outweighed both originally intended function and current appearance. For biological kinds, appearance and behavior, an inner biological function, and appearance and behavior of offspring all had similarly strong effects on categorization. The data were analyzed to determine whether an independent cue model or an interactive model best accounted for how the effects of the three feature sets combined. Feature integration was found to be additive for artifacts but interactive for biological kinds. In keeping with this, membership in contrasting artifact categories tended to be superadditive, indicating overlapping categories, whereas for biological kinds, it was subadditive, indicating conceptual gaps between categories. It is argued that the results underline a key domain difference between artifact and biological concepts

A holistic and comprensive data approach validates the distribution of the critically endangered flapper skate (Dipturus intermedius)

Morphological similarities between skates of the genus Dipturus in the north-eastern Atlantic and mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as ‘D. batis’). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the ‘common skate’, with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.acceptedVersio

Feminist Economics, Setting out the Parameters

___Introduction___ Feminist economics has developed its position over the past decade, towards a firmer embeddedness in economic science and a source of inspiration for activists, policy makers, and social science researchers in a wide variety of fields of research. This development has come about in a relatively short period of time, as is reflected, for example, in the follow-up book of the feminist economic primer Beyond Economic Man (Ferber/Nelson 1993), published ten years later: Feminist Economics Today (Ferber/Nelson, 2003) The strengthened position of feminist economics also shows in the 10-year anniversary of the prize-winning journal Feminist Economics, the flourishing of the International Association for Feminist Economics (IAFFE), as well as the more regular demand for feminist economic policy advise by institutions like the UN, OECD and governments in developed and developing countries, and in well-established training courses in feminist economics, such as at the Institute of Social Studies and University of Utah . It is impossible to give a fair overview of the state of the art of feminist economics in the number of pages available, even when limited to issues pertaining to development and macroeconomics . As a consequence, this is a very sketchy and subjective overview of what I perceive to be recent developments in feminist economics that have relevance for feminist development analysis and policy. The next section recognizes three trends in feminist economics, in particular the engagement of feminist economists with heterodox schools of economics. The following sections will briefly review developments in methodology and methods in feminist economics. These will be followed by three sections on topics that have recently become key themes or areas of research in feminist economics, in particular in the area of development economics: unpaid labour and the care economy; the two-way relationship between gender and trade; and gender, efficiency and growth. Each of these topics will be introduced, with references to the main literature, and some links to policy recommendations. The paper will end with a conclusion