Finding overlapping communities in networks by label propagation

We propose an algorithm for finding overlapping community structure in very large networks. The algorithm is based on the label propagation technique of Raghavan, Albert, and Kumara, but is able to detect communities that overlap. Like the original algorithm, vertices have labels that propagate between neighbouring vertices so that members of a community reach a consensus on their community membership. Our main contribution is to extend the label and propagation step to include information about more than one community: each vertex can now belong to up to v communities, where v is the parameter of the algorithm. Our algorithm can also handle weighted and bipartite networks. Tests on an independently designed set of benchmarks, and on real networks, show the algorithm to be highly effective in recovering overlapping communities. It is also very fast and can process very large and dense networks in a short time

Non-invasive MRI quantification of cerebrospinal fluid dynamics in amyotrophic lateral sclerosis patients.

BACKGROUND: Developing novel therapeutic agents to treat amyotrophic lateral sclerosis (ALS) has been difficult due to multifactorial pathophysiologic processes at work. Intrathecal drug administration shows promise due to close proximity of cerebrospinal fluid (CSF) to affected tissues. Development of effective intrathecal pharmaceuticals will rely on accurate models of how drugs are dispersed in the CSF. Therefore, a method to quantify these dynamics and a characterization of differences across disease states is needed. METHODS: Complete intrathecal 3D CSF geometry and CSF flow velocities at six axial locations in the spinal canal were collected by T2-weighted and phase-contrast MRI, respectively. Scans were completed for eight people with ALS and ten healthy controls. Manual segmentation of the spinal subarachnoid space was performed and coupled with an interpolated model of CSF flow within the spinal canal. Geometric and hydrodynamic parameters were then generated at 1 mm slice intervals along the entire spine. Temporal analysis of the waveform spectral content and feature points was also completed. RESULTS: Comparison of ALS and control groups revealed a reduction in CSF flow magnitude and increased flow propagation velocities in the ALS cohort. Other differences in spectral harmonic content and geometric comparisons may support an overall decrease in intrathecal compliance in the ALS group. Notably, there was a high degree of variability between cases, with one ALS patient displaying nearly zero CSF flow along the entire spinal canal. CONCLUSION: While our sample size limits statistical confidence about the differences observed in this study, it was possible to measure and quantify inter-individual and cohort variability in a non-invasive manner. Our study also shows the potential for MRI based measurements of CSF geometry and flow to provide information about the hydrodynamic environment of the spinal subarachnoid space. These dynamics may be studied further to understand the behavior of CSF solute transport in healthy and diseased states

Multi-species population indices for sets of species including rare, disappearing or newly occurring species

NI is funded by Natural Environment Research Council award NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.Multi-species indices (MSI) are widely used as ecological indicators and as instruments to inform environmental policies. Many of these indices combine species-specific estimates of relative population sizes using the geometric mean. Because the geometric mean is not defined when values of zero occur, usually only commoner species are included in MSIs and zero values are replaced by a small non-zero value. The latter can exhibit an arbitrary influence on the geometric mean MSI. Here, we show how the compound Poisson and the negative binomial model can be used in such cases to obtain an MSI that has similar features to the geometric mean, including weighting halving and doubling of a species’ population equally. In contrast to the geometric mean, these two statistical models can handle zero values in population sizes and thus accommodate newly occurring and temporarily or permanently disappearing species in the MSI. We compare the MSIs obtained by the two statistical models with the geometric mean MSI and measure sensitivity to changes in evenness and to population trends in rare and abundant species. Additionally, we outline sources of uncertainty and discuss how to measure them. We found that, in contrast to the geometric mean and the negative binomial MSI, the compound Poisson MSI is less sensitive to changes in evenness when total abundance is constant. Further, we found that the compound Poisson model can be influenced more than the other two methods by trends of species showing a low interannual variance. The negative binomial MSI is less sensitive to trends in rare species compared with the other two methods, and similarly sensitive to trends in abundant species as the geometric mean. While the two new MSIs have the advantage that they are not arbitrarily influenced by rare, newly appearing and disappearing species, both do not weight all species equally. We recommend replacing the geometric mean MSI with either compound Poisson or negative binomial when there are species with a population size of zero in some years having a strong influence on the geometric mean MSI. Further, we recommend providing additional information alongside the MSIs. For example, it is particularly important to give an evenness index in addition to the compound Poisson MSI and to indicate the number of disappearing and newly occurring species alongside the negative binomial MSI.Publisher PDFPeer reviewe

Potato Breeding and Variety Development for Improved Quality and Pest Resistance in the Eastern United States

The eastern U.S. potato industry needs new potato varieties to overcome pest problems while reducing agricultural chemical use and to enhance marketing opportunities. This project will conduct potato breeding, germplasm enhancement, and selection studies to improve potato productivity and quality for important eastern U.S. markets. Novel and highly improved potato germplasm and varieties will be developed to reduce the impact of economically important potato pests, such as golden nematode, late blight, pink rot, and scab

Outcomes in hepatitis C virus–infected recipients of living donor vs. deceased donor liver transplantation

In this retrospective study of hepatitis C virus (HCV)–infected transplant recipients in the 9-center Adult to Adult Living Donor Liver Transplantation Cohort Study, graft and patient survival and the development of advanced fibrosis were compared among 181 living donor liver transplant (LDLT) recipients and 94 deceased donor liver transplant (DDLT) recipients. Overall 3-year graft and patient survival were 68% and 74% in LDLT, and 80% and 82% in DDLT, respectively. Graft survival, but not patient survival, was significantly lower for LDLT compared to DDLT ( P = 0.04 and P = 0.20, respectively). Further analyses demonstrated lower graft and patient survival among the first 20 LDLT cases at each center (LDLT 20; P = 0.002 and P = 0.002, respectively) and DDLT recipients ( P 20 and DDLT were not significantly different ( P = 0.66 and P = 0.74, respectively). Overall, 3-year graft survival for DDLT, LDLT >20, and LDLT 20 were not significantly different. Important predictors of graft loss in HCV-infected patients were limited LDLT experience, pretransplant HCC, and higher MELD at transplantation. Liver Transpl 13:122–129, 2007. © 2006 AASLD.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55915/1/20995_ftp.pd

The Moral of the Tale: Stories, Trust, and Public Engagement with Clinical Ethics via Radio and Theatre.

Trust is frequently discussed with reference to the professional-patient relationship. However, trust is less explored in relation to the ways in which understanding of, and responses to, questions of ethics are discussed by both the "public" and "experts." Public engagement activity in healthcare ethics may invoke "trust" in analysing a moral question or problem but less frequently conceives of trust as integral to "public engagement" itself. This paper explores the relationship between trust and the ways in which questions of healthcare ethics are identified and negotiated by both "experts" and the public. Drawing on two examples from the author's "public engagement" work-a radio programme for the British Broadcasting Corporation and work with a playwright and theatre-the paper interrogates the ways in which "public engagement" is often characterized. The author argues that the common approach to public engagement in questions of ethics is unhelpfully constrained by a systemic disposition which continues to privilege the professional or expert voice at the expense of meaningful exchange and dialogue. By creating space for novel interactions between the "expert" and the "public," authentic engagement is achieved that enables not only the participants to flourish but also contributes to trust itself

Developing a placebo-controlled trial in surgery:issues of design, acceptability and feasibility

BACKGROUND: Surgical placebos are controversial. This in-depth study explored the design, acceptability, and feasibility issues relevant to designing a surgical placebo-controlled trial for the evaluation of the clinical and cost effectiveness of arthroscopic lavage for the management of people with osteoarthritis of the knee in the UK. METHODS: Two surgeon focus groups at a UK national meeting for orthopaedic surgeons and one regional surgeon focus group (41 surgeons); plenary discussion at a UK national meeting for orthopaedic anaesthetists (130 anaesthetists); three focus groups with anaesthetists (one national, two regional; 58 anaesthetists); two focus groups with members of the patient organisation Arthritis Care (7 participants); telephone interviews with people on consultant waiting lists from two UK regional centres (15 participants); interviews with Chairs of UK ethics committees (6 individuals); postal surveys of members of the British Association of Surgeons of the Knee (382 surgeons) and members of the British Society of Orthopaedic Anaesthetists (398 anaesthetists); two centre pilot (49 patients assessed). RESULTS: There was widespread acceptance that evaluation of arthroscopic lavage had to be conducted with a placebo control if scientific rigour was not to be compromised. The choice of placebo surgical procedure (three small incisions) proved easier than the method of anaesthesia (general anaesthesia). General anaesthesia, while an excellent mimic, was more intrusive and raised concerns among some stakeholders and caused extensive discussion with local decision-makers when seeking formal approval for the pilot.Patients were willing to participate in a pilot with a placebo arm; although some patients when allocated to surgery became apprehensive about the possibility of receiving placebo, and withdrew. Placebo surgery was undertaken successfully. CONCLUSIONS: Our study illustrated the opposing and often strongly held opinions about surgical placebos, the ethical issues underpinning this controversy, and the challenges that exist even when ethics committee approval has been granted. It showed that a placebo-controlled trial could be conducted in principle, albeit with difficulty. It also highlighted that not only does a placebo-controlled trial in surgery have to be ethically and scientifically acceptable but that it also must be a feasible course of action. The place of placebo-controlled surgical trials more generally is likely to be limited and require specific circumstances to be met. Suggested criteria are presented. TRIAL REGISTRATION NUMBER: The trial was assigned ISRCTN02328576 through http://controlled-trials.com/ in June 2006. The first patient was randomised to the pilot in July 2007