On a two-truths phenomenon in spectral graph clustering.

Clustering is concerned with coherently grouping observations without any explicit concept of true groupings. Spectral graph clustering-clustering the vertices of a graph based on their spectral embedding-is commonly approached via K-means (or, more generally, Gaussian mixture model) clustering composed with either Laplacian spectral embedding (LSE) or adjacency spectral embedding (ASE). Recent theoretical results provide deeper understanding of the problem and solutions and lead us to a "two-truths" LSE vs. ASE spectral graph clustering phenomenon convincingly illustrated here via a diffusion MRI connectome dataset: The different embedding methods yield different clustering results, with LSE capturing left hemisphere/right hemisphere affinity structure and ASE capturing gray matter/white matter core-periphery structure.

Linking Antarctic krill larval supply and recruitment along the Antarctic Peninsula.

Antarctic krill (Euphausia superba) larval production and overwinter survival drive recruitment variability, which in turn determines abundance trends. The Antarctic Peninsula has been described as a recruitment hot spot and as a potentially important source region for larval and juvenile krill dispersal. However, there has been no analysis to spatially resolve regional-scale krill population dynamics across life stages. We assessed spatiotemporal patterns in krill demography using two decades of austral summer data collected along the North and West Antarctic Peninsula since 1993. We identified persistent spatial segregation in the summer distribution of euphausiid larvae (E. superba plus other species), which were concentrated in oceanic waters along the continental slope, and E. superba recruits, which were concentrated in shelf and coastal waters. Mature females of E. superba were more abundant over the continental shelf than the slope or coast. Euphausiid larval abundance was relatively localized and weakly correlated between the North and West Antarctic Peninsula, while E. superba recruitment was generally synchronized throughout the entire region. Euphausiid larval abundance along the West Antarctic Peninsula slope explained E. superba recruitment in shelf and coastal waters the next year. Given the localized nature of krill productivity, it is critical to evaluate the connectivity between upstream and downstream areas of the Antarctic Peninsula and beyond. Krill fishery catch distributions and population projections in the context of a changing climate should account for ontogenetic habitat partitioning, regional population connectivity, and highly variable recruitment.

Lesion Size Index in Maximum Voltage-Guided Cavotricuspid Ablation for Atrial Flutter.

The application of optimum contact force (CF) can be used to improve ablation procedure success and safety. The lesion size index (LSI) is a novel dimensionless contact force parameter that allows for an accurate estimation of lesion volume in real time by integrating contact force (grams), duration (seconds) and power (watts). The aim was to correlate LSI values with current contact force parameters to achieve successful and safe bidirectional block of the cavotricuspid isthmus (CTI) using a maximum voltage-guided (MVG) ablation strategy. Fifteen consecutive patients (age 69 ± 7.9 years, nine males) with symptomatic atrial flutter (AFL) were evaluated and compared with 23 control (age 66.3 ± 10.4 years, 16 males) non-contact force-guided ablation cases. Irrigated-tip force-sensing ablation catheters (TactiCath Quartz™, St. Jude Medical, St. Paul, MN, USA) were used in the CF group to achieve the primary endpoint of complete bidirectional block of the isthmus. In the CF group, a total of 233 radiofrequency (RF) applications were examined. A mean LSI of 6.4 ±1.0 correlated with a force-time integral (FTI) of 581.2 ±230.9 g/s and an average CF of 13.9 ±4.9 g concurrently. Intraprocedural, fluoroscopy time and RF time demonstrated lower trends in the CF group, but no significance with respect to these trends was observed. The secondary endpoint of no reconnection within 20 min after the procedure was equally attained in both groups, and, likewise, the level of safety was comparable. An LSI value of >5 represents a new effective parameter in MVG ablation for the cavotricuspid region that demonstrates a safe profile. Guidance of CTI ablation using LSI and other contact force parameters of CF 13.9 ±4.9 g and FTI 581.2 ±230.9 g/s demonstrated highly effective and safe outcomes.

Fast approximate quadratic programming for graph matching.

Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance.

A resource to acquire and summarize pharmacogenetics knowledge in the literature.

To determine how genetic variations contribute the variations in drug response, we need to know the genes that are related to drugs of interest. But there are no publicly available data-bases of known gene-drug relationships, and it is time-consuming to search the literature for this information. We have developed a resource to support the storage, summarization, and dissemination of key gene-drug interactions of relevance to pharmacogenetics. Extracting all gene-drug relationships from the literature is a daunting task, so we distributed a tool to acquire this knowledge from the scientific community. We also developed a categorization scheme to classify gene-drug relationships according to the type of pharmacogenetic evidence that supports them. Our resource (http://www.pharmgkb.org/home/project-community.jsp) can be queried by gene or drug, and it summarizes gene-drug relationships, categories of evidence, and supporting literature. This resource is growing, containing entries for 138 genes and 215 drugs of pharmacogenetics significance, and is a core component of PharmGKB, a pharmacogenetics knowledge base (http://www.pharmgkb.org).

Beyond captions: linking figures with abstract sentences in biomedical articles.

Although figures in scientific articles have high information content and concisely communicate many key research findings, they are currently under utilized by literature search and retrieval systems. Many systems ignore figures, and those that do not typically only consider caption text. This study describes and evaluates a fully automated approach for associating figures in the body of a biomedical article with sentences in its abstract. We use supervised methods to learn probabilistic language models, hidden Markov models, and conditional random fields for predicting associations between abstract sentences and figures. Three kinds of evidence are used: text in abstract sentences and figures, relative positions of sentences and figures, and the patterns of sentence/figure associations across an article. Each information source is shown to have predictive value, and models that use all kinds of evidence are more accurate than models that do not. Our most accurate method has an F1-score of 69% on a cross-validation experiment, is competitive with the accuracy of human experts, has significantly better predictive accuracy than state-of-the-art methods and enables users to access figures associated with an abstract sentence with an average of 1.82 fewer mouse clicks. A user evaluation shows that human users find our system beneficial. The system is available at http://FigureItOut.askHERMES.org.

Toward a microchip-based solid-phase extraction method for isolation of nucleic acids.

A silica-based solid-phase extraction system suitable for incorporation into a microchip platform (nu-total analytical system; nu-TAS) would find utility in a variety of genetic analysis protocols, including DNA sequencing. The extraction procedure utilized is based on adsorption of the DNA onto bare silica. The procedure involves three steps: (i) DNA adsorption in the presence of a chaotropic salt, (ii) removal of contaminants with an alcohol/water solution, and (iii) elution of the adsorbed DNA in a small volume of buffer suitable for polymerase chain reaction (PCR) amplification. Multiple approaches for incorporation of this protocol into a microchip were examined with regard to extraction efficiency, reproducibility, stability, and the potential to provide PCR-amplifiable DNA. These included packing microchannels with silica beads only, generating a continuous silica network via sol-gel chemistry, and combinations of these. The optimal approach was found to involve immobilizing silica beads packed into the channel using a sol-gel network. This method allowed for successful extraction and elution of nanogram quantities of DNA in less than 25 min, with the DNA obtained in the elution buffer fraction. Evaluation of the eluted DNA indicated that it was of suitable quality for subsequent amplification by PCR.