Spectral partitioning with multiple eigenvectors

AbstractThe graph partitioning problem is to divide the vertices of a graph into disjoint clusters to minimize the total cost of the edges cut by the clusters. A spectral partitioning heuristic uses the graph's eigenvectors to construct a geometric representation of the graph (e.g., linear orderings) which are subsequently partitioned. Our main result shows that when all the eigenvectors are used, graph partitioning reduces to a new vector partitioning problem. This result implies that as many eigenvectors as are practically possible should be used to construct a solution. This philosophy is in contrast to that of the widely used spectral bipartitioning (SB) heuristic (which uses only a single eigenvector) and several previous multi-way partitioning heuristics [8, 11, 17, 27, 38] (which use k eigenvectors to construct k-way partitionings). Our result motivates a simple ordering heuristic that is a multiple-eigenvector extension of SB. This heuristic not only significantly outperforms recursive SB, but can also yield excellent multi-way VLSI circuit partitionings as compared to [1, 11]. Our experiments suggest that the vector partitioning perspective opens the door to new and effective partitioning heuristics. The present paper updates and improves a preliminary version of this work [5]

Hydrophobic interaction chromatography for bottom-up proteomics analysis of single proteins and protein complexes

Hydrophobic interaction chromatography (HIC) is a robust standard analytical method to purify proteins while preserving their biological activity. It is widely used to study post-translational modifications of proteins and drug–protein interactions. In the current manuscript we employed HIC to separate proteins, followed by bottom-up LC–MS/MS experiments. We used this approach to fractionate antibody species followed by comprehensive peptide mapping as well as to study protein complexes in human cells. HIC–reversed-phase chromatography (RPC)–mass spectrometry (MS) is a powerful alternative to fractionate proteins for bottom-up proteomics experiments making use of their distinct hydrophobic properties

Perceptions of Criminal and Gang Involvement Among College Student-Athletes

The involvement of youth and young adults in gangs and other criminal activities continues to be a serious threat and grounds for concern among a variety of stakeholders on college campuses and beyond. The extant literature examining the criminality of intercollegiate student-athletes is limited to media accounts or research focused on few types of offenses or athletics programs. The presence and impact of gangs in institutions such as secondary education and the military has been documented, but the expansion of gangs to college athletics has not been empirically verified despite media portrayals. The current study addresses these gaps in knowledge of criminally and gang-involved college student-athletes with information provided by athletics directors and campus police chiefs. Findings from both groups of key informants show that individuals involved with gangs and other criminal offenses participate in college athletics. However, few athletics directors and campus police chiefs reported the presence of gang-involved athletes on their own campuses

Peptide Orientation Affects Selectivity in Ion-Exchange Chromatography

Here we demonstrate that separation of proteolytic peptides, having the same net charge and one basic residue, is affected by their specific orientation toward the stationary phase in ion-exchange chromatography. In electrostatic repulsion−hydrophilic interaction chromatography (ERLIC) with an anion-exchange material, the C-terminus of the peptides is, on average, oriented toward the stationary phase. In cation exchange, the average peptide orientation is the opposite. Data with synthetic peptides, serving as orientation probes, indicate that in tryptic/Lys-C peptides the C-terminal carboxyl group appears to be in a zwitterionic bond with the side chain of the C-terminal Lys/Arg residue. In effect, the side chain is then less basic than the N-terminus, accounting for the specific orientation of tryptic and Lys-C peptides. Analyses of larger sets of peptides, generated from lysates by either Lys-N, Lys-C, or trypsin, reveal that specific peptide orientation affects the ability of charged side chains, such as phosphate residues, to influence retention. Phosphorylated residues that are remote in the sequence from the binding site affect retention less than those that are closer. When a peptide contains multiple charged sites, then orientation is observed to be less rigid and retention tends to be governed by the peptide’s net charge rather than its sequence. These general observations could be of value in confirming a peptide’s identification and, in particular, phosphosite assignments in proteomics analyses. More generally, orientation accounts for the ability of chromatography to separate peptides of the same composition but different sequence

Genome Resources for Climate‐Resilient Cowpea, an Essential Crop for Food Security

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited‐input small‐holder farming and climate stress

Effectiveness of an Ultrasound Training Module for Internal Medicine Residents

<p>Abstract</p> <p>Background</p> <p>Few internal medicine residency programs provide formal ultrasound training. This study sought to assess the feasibility of simulation based ultrasound training among first year internal medicine residents and measure their comfort at effectively using ultrasound to perform invasive procedures before and after this innovative model of ultrasound training.</p> <p>Methods</p> <p>A simulation based ultrasound training module was implemented during intern orientation that incorporated didactic and practical experiences in a simulation and cadaver laboratory. Participants completed anonymous pre and post surveys in which they reported their level of confidence in the use of ultrasound technology and their comfort in identifying anatomic structures including: lung, pleural effusion, bowel, peritoneal cavity, ascites, thyroid, and internal jugular vein. Survey items were structured on a 5-point Likert scales (1 = extremely unconfident, 5 = extremely confident).</p> <p>Results</p> <p>Seventy-five out of seventy-six interns completed the pre-intervention survey and 55 completed the post-survey. The mean confidence score (SD) increased to 4.00 (0.47) (p < 0.0001). The mean (SD) comfort ranged from 3.61 (0.84) for peritoneal cavity to 4.48 (0.62) for internal jugular vein. Confidence in identifying all anatomic structures showed an increase over the pre-intervention means (p < 0.002).</p> <p>Conclusion</p> <p>A simulation based ultrasound learning module can improve the self-reported confidence with which residents identify structures important in performing invasive ultrasound guided procedures. Incorporating an ultrasound module into residents' education may address perceived need for ultrasound training, improve procedural skills, and enhance patient safety.</p

Reply to: New Meta- and Mega-analyses of Magnetic Resonance Imaging Findings in Schizophrenia: Do They Really Increase Our Knowledge About the Nature of the Disease Process?

This work was supported by National Institute of Biomedical Imaging and Bioengineering Grant No. U54EB020403 (to the ENIGMA consortium)