Accurate and Fast Retrieval for Complex Non-metric Data via Neighborhood Graphs

We demonstrate that a graph-based search algorithm-relying on the construction of an approximate neighborhood graph-can directly work with challenging non-metric and/or non-symmetric distances without resorting to metric-space mapping and/or distance symmetrization, which, in turn, lead to substantial performance degradation. Although the straightforward metrization and symmetrization is usually ineffective, we find that constructing an index using a modified, e.g., symmetrized, distance can improve performance. This observation paves a way to a new line of research of designing index-specific graph-construction distance functions

Cue Integration in Categorical Tasks: Insights from Audio-Visual Speech Perception

Previous cue integration studies have examined continuous perceptual dimensions (e.g., size) and have shown that human cue integration is well described by a normative model in which cues are weighted in proportion to their sensory reliability, as estimated from single-cue performance. However, this normative model may not be applicable to categorical perceptual dimensions (e.g., phonemes). In tasks defined over categorical perceptual dimensions, optimal cue weights should depend not only on the sensory variance affecting the perception of each cue but also on the environmental variance inherent in each task-relevant category. Here, we present a computational and experimental investigation of cue integration in a categorical audio-visual (articulatory) speech perception task. Our results show that human performance during audio-visual phonemic labeling is qualitatively consistent with the behavior of a Bayes-optimal observer. Specifically, we show that the participants in our task are sensitive, on a trial-by-trial basis, to the sensory uncertainty associated with the auditory and visual cues, during phonemic categorization. In addition, we show that while sensory uncertainty is a significant factor in determining cue weights, it is not the only one and participants' performance is consistent with an optimal model in which environmental, within category variability also plays a role in determining cue weights. Furthermore, we show that in our task, the sensory variability affecting the visual modality during cue-combination is not well estimated from single-cue performance, but can be estimated from multi-cue performance. The findings and computational principles described here represent a principled first step towards characterizing the mechanisms underlying human cue integration in categorical tasks

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG) that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars) that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability

Engaging Undergraduates in Science Research: Not Just About Faculty Willingness.

Despite the many benefits of involving undergraduates in research and the growing number of undergraduate research programs, few scholars have investigated the factors that affect faculty members' decisions to involve undergraduates in their research projects. We investigated the individual factors and institutional contexts that predict faculty members' likelihood of engaging undergraduates in their research project(s). Using data from the Higher Education Research Institute's 2007-2008 Faculty Survey, we employ hierarchical generalized linear modeling to analyze data from 4,832 science, technology, engineering, and mathematics (STEM) faculty across 194 institutions to examine how organizational citizenship behavior theory and social exchange theory relate to mentoring students in research. Key findings show that faculty who work in the life sciences and those who receive government funding for their research are more likely to involve undergraduates in their research project(s). In addition, faculty at liberal arts or historically Black colleges are significantly more likely to involve undergraduate students in research. Implications for advancing undergraduate research opportunities are discussed

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks premorphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll’s ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths

Calibration of GENEActiv accelerometer wrist cut-points for the assessment of physical activity intensity of pre-school aged children

This study sought to validate cut-points for use of wrist worn GENEActiv accelerometer data, to analyse preschool children’s (4 to 5 year olds) physical activity (PA) levels via calibration with oxygen consumption values (VO2). This was a laboratory based calibration study. Twenty-one preschool children, aged 4.7 ± 0.5 years old, completed six activities (ranging from lying supine to running) whilst wearing the GENEActiv accelerometers at two locations (left and right wrist), these being the participants’ non-dominant and dominant wrist, and a Cortex face mask for gas analysis. VO2 data was used for the assessment of criterion validity. Location specific activity intensity cut points were established via Receiver Operator Characteristic curve (ROC) analysis. The GENEActiv accelerometers, irrespective of their location, accurately discriminated between all PA intensities (sedentary, light, and moderate and above), with the dominant wrist monitor providing a slightly more precise discrimination at light PA and the non-dominant at the sedentary behaviour and moderate and above intensity levels (Area Under the Curve (AUC) for non-dominant = 0.749-0.993, compared to AUC dominant = 0.760-0.988). Conclusion: This study establishes wrist-worn physical activity cut points for the GENEActiv accelerometer in pre-schoolers.N/

Recent ASA presidents and ‘top’ journals: observed publication patterns, alleged cartels and varying careers

It has been common for studies presented as about American sociology as a whole to rely on data compiled from leading journals (American Sociological Review [ASR] and American Journal of Sociology [AJS]), or about presidents of the American Sociological Association [ASA], to represent it. Clearly those are important, but neither can be regarded as providing a representative sample of American sociology. Recently, Stephen Turner has suggested that dominance in the ASA rests with a ‘cartel’ initially formed in graduate school, and that it favors work in a style associated with the leading journals. The adequacy of these ideas is examined in the light of available data on the last 20 years, which show that very few of the presidents were in the same graduate schools at the same time. All presidents have had distinguished academic records, but it is shown that their publication strategies have varied considerably. Some have had no ASR publications except their presidential addresses, while books and large numbers of other journals not normally mentioned in this context have figured in their contributions, as well as being more prominent in citations. It seems clear that articles in the leading journals have not been as closely tied to prestigious careers as has sometimes been suggested, and that if there is a cartel it has not included all the presidents

An integrated MR/PET system: prospective applications

Radiology is strongly depending on medical imaging technology and consequently directing technological progress. A novel technology can only be established, however, if improved diagnostic accuracy influence on therapeutic management and/or overall reduced cost can be evidenced. It has been demonstrated recently that Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) can technologically be integrated into one single hybrid system. Some scientific arguments on the benefits are obvious, e.g., that simultaneous imaging of morphological and functional information will improve tissue characterization. However, crossfire of questions still remains: What unmet radiological needs are addressed by the novel system? What level of hardware integration is reasonable, or would software-based image co-registration be sufficient? Will MR/PET achieve higher diagnostic accuracy compared to separate imaging? What is the added value compared to other hybrid imaging modalities like PET/CT? And finally, is the system economically reasonable and has the potential to reduce overall costs for therapy planning and monitoring? This article tries to highlight some perspectives of applying an integrated MR/PET system for simultaneous morphologic and functional imaging