One Hub-One Process: A Tool Based View on Regulatory Network Topology

The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We find that the topology of the regulatory network show weak remnants of its history of network reorganizations, but strong features of co-regulated proteins associated to similar tasks. This suggests that local topological features of regulatory networks, including broad degree distributions, emerge as an implicit result of matching a number of needed processes to a finite toolbox of proteins.Comment: 18 pages, 3 figures, 5 supplementary figure

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Conditions for Interference Versus Facilitation During Sequential Sensorimotor Adaptation

We investigated how sensorimotor adaptation acquired during one experimental session influenced the adaptation in a subsequent session. The subjects' task was to track a visual target using a joystick-controlled cursor, while the relationship between joystick and cursor position was manipulated to introduce a sensorimotor discordance. Each subject participated in two sessions, separated by a pause of 2 min to 1 month duration. We found that adaptation was achieved within minutes, and persisted in the memory for at least a month, with only a small decay (experiment A). When the discordances administered in the two sessions were in mutual conflict, we found evidence for task interference (experiment B). However, when the discordances were independent, we found facilitation rather than interference (experiment C); the latter finding could not be explained by the use of an "easier" discordance in the second session (experiment D). We conclude that interference is due to an incompatibility between task requirements, and not to a competition of tasks for short-term memory. We further conclude that the ability to adapt to a sensorimotor discordance

Degree Landscapes in Scale-Free Networks

We generalize the degree-organizational view of real-world networks with broad degree-distributions in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). For example, correlated degrees between adjacent nodes corresponds to smooth landscapes (social networks), hierarchical networks to one-mountain landscapes (the Internet), and degree-disassortative networks without hierarchical features to rough landscapes with several mountains. We also generate ridge landscapes to model networks organized under constraints imposed by the space the networks are embedded in, associated to spatial or, in molecular networks, to functional localization. To quantify the topology, we here measure the widths of the mountains and the separation between different mountains.Comment: 4 pages, 5 figure

Laparoscopic lavage is superior to colon resection for perforated purulent diverticulitis:a meta-analysis

PURPOSE: Perforated diverticulitis often requires surgery with a colon resection such as Hartmann’s procedure, with inherent morbidity. Recent studies suggest that laparoscopic lavage may be an alternative surgical treatment. The aim of this study was to compare re-operations, morbidity, and mortality as well as health economic outcomes between laparoscopic lavage and colon resection for perforated purulent diverticulitis. METHODS: PubMed, Cochrane, Centre for Reviews and Dissemination, and Embase were searched. Published randomized controlled trials and prospective and retrospective cohorts with laparoscopic lavage and colon resection as interventions were identified. Trial limitations were assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology. Re-operations, complications at 90 days classified according to Clavien-Dindo and mortality were extracted. RESULTS: Three randomized trials published between 2005 and 2015 were included in the analysis. The studies included a total of 358 patients with 185 patients undergoing laparoscopic lavage. At 12 months, the relative risk of having a re-operation was lower for laparoscopic lavage compared to colon resection in the two trials that had a 12 month follow-up. We found no significant differences in Clavien-Dindo complications classified more than level IIIB or mortality at 90 days. CONCLUSIONS: The risk for re-operations within the first 12 months after index surgery was lower for laparoscopic lavage compared to colon resection, with overall comparable morbidity and mortality. Furthermore, Hartmann’s resection was more costly than laparoscopic lavage. We therefore consider laparoscopic lavage a valid alternative to surgery with resection for perforated purulent diverticulitis

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Background: The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results: We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster, and H. sapiens. It was found that the histogram of sequence identities p generated by an all-to-all alignment of all protein sequences encoded in a genome is well fitted with a power-law form ∼ p−γ with the value of the exponent γ around 4 for the majority of organisms used in this study. This implies that the intra-protein variability of substitution rates is best described by the Gamma-distribution with the exponent α ≈ 0.33. Different features of the shape of such histograms allow us to quantify the ratio between the genome-wide average deletion/duplication rates and the amino-acid substitution rate. 1 Conclusions: We separately measure the short-term (“raw”) duplication and deletion rates r ∗ dup, r ∗ del whic

Species–area relationships always overestimate extinction rates from habitat loss : comment

Author Posting. © Ecological Society of America, 2013. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecology 94 (2013): 761–763, doi:10.1890/12-0047.1.The species–area relationship summarizes the relationship between the average number of species in a region and its area. This relationship provides a basis for predicting the loss of species associated with loss of habitat (e.g., Pimm and Raven 2000). The approach involves two steps. First, as discussed in more detail below, the species–area relationship is used to predict the number of species that are endemic to the habitat at risk based on its area. Second, these endemic species are assumed to become extinct should this habitat be lost. In a controversial paper, He and Hubbell (2011) argued that the way in which the species–area relationship is used to predict the number of endemic species is incorrect when individual organisms are aggregated in space and argued that this explains a discrepancy between predicted and observed extinction rates associated with habitat loss. The controversy surrounding the paper focused primarily on the second part of their argument (Brooks 2011, Evans et al. 2011, He and Hubbell 2012, Pereira et al. 2012, Thomas and Williamson 2012). Here, we focus on the details underlying the first part.U. Roll is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities. L. Stone is supported by the Israeli Science Foundation

Mid-infrared Variability from the Spitzer Deep Wide-field Survey

We use the multi-epoch, mid-infrared Spitzer Deep Wide-Field Survey to investigate the variability of objects in 8.1 deg^2 of the NOAO Deep Wide Field Survey Boötes field. We perform a Difference Image Analysis of the four available epochs between 2004 and 2008, focusing on the deeper 3.6 and 4.5 μm bands. Out of 474, 179 analyzed sources, 1.1% meet our standard variability selection criteria that the two light curves are strongly correlated (r > 0.8) and that their joint variance (σ_(12)) exceeds that for all sources with the same magnitude by 2σ. We then examine the mid-IR colors of the variable sources and match them with X-ray sources from the XBoötes survey, radio catalogs, 24 μm selected active galactic nucleus (AGN) candidates, and spectroscopically identified AGNs from the AGN and Galaxy Evolution Survey (AGES). Based on their mid-IR colors, most of the variable sources are AGNs (76%), with smaller contributions from stars (11%), galaxies (6%), and unclassified objects, although most of the stellar, galaxy, and unclassified sources are false positives. For our standard selection criteria, 11%-12% of the mid-IR counterparts to X-ray sources, 24 μm AGN candidates, and spectroscopically identified AGNs show variability. The exact fractions depend on both the search depth and the selection criteria. For example, 12% of the 1131 known z>1 AGNs in the field and 14%-17% of the known AGNs with well-measured fluxes in all four Infrared Array Camera bands meet our standard selection criteria. The mid-IR AGN variability can be well described by a single power-law structure function with an index of γ ≈ 0.5 at both 3.6 and 4.5 μm, and an amplitude of S _0 ≃ 0.1 mag on rest-frame timescales of 2 yr. The variability amplitude is higher for shorter rest-frame wavelengths and lower luminosities

Social Media Use and Prevention of HIV and Other Sexually Transmitted Infections among At-Risk College Students in the United States

The purpose of this study was to evaluate college students\u27 self-perceptions of HIV/STI risk, potential barriers to HIV/STI testing, use of social media, and technology-based HIV/STI health interventions. Surveys were administered to 97 US college students. Participants were categorized into three groups based on sexual behaviors: (1) men who have sex with men (MSM), (2) men who have sex with women (MSW), and (3) women who have sex with men (WSM). MSM (n=24) were significantly more likely MSW/WSM (n=72) to report being tested in the past year for HIV (p\u3c.01) and other STIs (p\u3c.01). Only 35% reported HIV testing and 24% reported STI testing in the past year. MSM were more likely than MSW to report having met a sexual partner through social media (p\u3c.01), while no WSM reported doing so. The average number of partners met online in the past year was 7.8 (range=1-20). Those who had met a partner online were more willing to receive e-mail or text message HIV/STI testing reminders (p\u3c.05)

Retrospective Surveillance for Intussusception in Children Aged Less than Five Years in a South Indian Tertiary-care Hospital

To facilitate the assessment of the safety profile of rotavirus vaccines effectively, baseline data on intussusception are important for comparison with intussusception rates following the introduction of vaccine. The aim of the study was to describe epidemiological and clinical features of intussusception in children aged less than five years in an Indian medical facility. Hospital data on intussusception for children discharged during 1 January 2001–30 June 2004 from the Christian Medical College Hospital, Vellore, India, were reviewed. Relevant information was extracted from medical records to classify cases according to the criteria of the Brighton Collaboration Intussusception Working Group. Complete review of medical records for clinical and demographic information was only performed for those cases fulfilling level 1 diagnostic certainty (definite intussusception) (Study ID 101245). During the surveillance period, 31 infants and children with definite intussusception were identified. The majority (61.2%) of the cases occurred in the first year of life. The male : female ratio was 3.4 : 1. Intussusception cases occurred round the year with no distinct seasonality. No intussusception-associated death was recorded. This study provides baseline data on intussusception in South India. Cases identified in the study were similar in presentation and demographics as those observed in other Asian settings. Prospective surveillance systems, using standardized case definitions will further increase the understanding of the aetiology and epidemiology of intussusception, especially as new rotavirus vaccines are made available