New resampling method for evaluating stability of clusters

<p>Abstract</p> <p>Background</p> <p>Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are required to distinguish between real and random clusters. Several methods for assessing cluster stability have been published, including resampling methods such as the bootstrap.</p> <p>We propose a new resampling method based on continuous weights to assess the stability of clusters in hierarchical clustering. While in bootstrapping approximately one third of the original items is lost, continuous weights avoid zero elements and instead allow non integer diagonal elements, which leads to retention of the full dimensionality of space, i.e. each variable of the original data set is represented in the resampling sample.</p> <p>Results</p> <p>Comparison of continuous weights and bootstrapping using real datasets and simulation studies reveals the advantage of continuous weights especially when the dataset has only few observations, few differentially expressed genes and the fold change of differentially expressed genes is low.</p> <p>Conclusion</p> <p>We recommend the use of continuous weights in small as well as in large datasets, because according to our results they produce at least the same results as conventional bootstrapping and in some cases they surpass it.</p

A Naturally Occurring Plant Cysteine Protease Possesses Remarkable Toxicity against Insect Pests and Synergizes Bacillus thuringiensis Toxin

When caterpillars feed on maize (Zea maize L.) lines with native resistance to several Lepidopteran pests, a defensive cysteine protease, Mir1-CP, rapidly accumulates at the wound site. Mir1-CP has been shown to inhibit caterpillar growth in vivo by attacking and permeabilizing the insect's peritrophic matrix (PM), a structure that surrounds the food bolus, assists in digestion and protects the midgut from microbes and toxins. PM permeabilization weakens the caterpillar defenses by facilitating the movement of other insecticidal proteins in the diet to the midgut microvilli and thereby enhancing their toxicity. To directly determine the toxicity of Mir1-CP, the purified recombinant enzyme was directly tested against four economically significant Lepidopteran pests in bioassays. Mir1-CP LC50 values were 1.8, 3.6, 0.6, and 8.0 ppm for corn earworm, tobacco budworm, fall armyworm and southwestern corn borer, respectively. These values were the same order of magnitude as those determined for the Bacillus thuringiensis toxin Bt-CryIIA. In addition to being directly toxic to the larvae, 60 ppb Mir1-CP synergized sublethal concentrations of Bt-CryIIA in all four species. Permeabilization of the PM by Mir1-CP probably provides ready access to Bt-binding sites on the midgut microvilli and increases its activity. Consequently, Mir1-CP could be used for controlling caterpillar pests in maize using non-transgenic approaches and potentially could be used in other crops either singly or in combination with Bt-toxins

Perspectives on global leadership and the Covid-19 crisis

As the world struggled to come to grips with the Covid-19 pandemic, over twenty scholars, practitioners, and global leaders wrote brief essays for this curated chapter on the role of global leadership in this extreme example of a global crisis. Their thoughts span helpful theoretical breakthroughs to essential, pragmatic adaptations by companies

Efficacy of a cry1Ab Gene for Control of Maruca vitrata (Lepidoptera: Crambidae) in Cowpea (Fabales: Fabaceae)

Cowpea [Vigna unguiculata (L) Walp.] is an important staple legume in the diet of many households in sub-Saharan Africa. Its production, however, is negatively impacted by many insect pests including bean pod borer, Maruca vitrata F., which can cause 20–80% yield loss. Several genetically engineered cowpea events that contain a cry1Ab gene from Bacillus thuringiensis (Bt) for resistance against M. vitrata were evaluated in Nigeria, Burkina Faso, and Ghana (West Africa), where cowpea is commonly grown. As part of the regulatory safety package, these efficacy data were developed and evaluated by in-country scientists. The Bt-cowpea lines were planted in confined field trials under Insect-proof netting and artificially infested with up to 500 M. vitrata larvae per plant during bud formation and flowering periods. Bt-cowpea lines provided nearly complete pod and seed protection and in most cases resulted in significantly increased seed yield over non-Bt control lines. An integrated pest management strategy that includes use of Bt-cowpea augmented with minimal insecticide treatment for protection against other insects is recommended to control pod borer to enhance cowpea production. The insect resistance management plan is based on the high-dose refuge strategy where non-Btcowpea and natural refuges are expected to provide M. vitrata susceptible to Cry1Ab protein. In addition, there will be a limited release of this product until a two-toxin cowpea pyramid is released. Other than South African genetically engineered crops, Bt-cowpea is the first genetically engineered food crop developed by the public sector and approved for release in sub-Saharan Africa

Annual cycle of the legume pod borer Maruca vitrata Fabricius (Lepidoptera: Crambidae) in southwestern Burkina Faso

Maruca vitrata is an economically significant insect pest of cowpea in sub-Saharan Africa. Understanding the seasonal population patterns of M. vitrata is essential for the establishment of effective pest management strategies. M. vitrata larval populations on cultivated cowpea and adult flying activities were monitored in addition to scouting for host plants and parasitoids during 2 consecutive years in 2010 and 2011 in southwestern Burkina Faso. Our data suggest that M. vitrata populations overlapped on cultivated cowpea and alternate host plants during the rainy season. During the cowpea off-season, M. vitrata maintained a permanent population on the wild host plants Mucuna poggei and Daniella oliveri. The parasitoid fauna include three species, Phanerotoma leucobasis Kri., Braunsia kriegeri End. and Bracon sp. Implications of these finding for pest management strategies are discussed

Measurement of the tt̄W and tt̄Z production cross sections in pp collisions at √s = 8 TeV with the ATLAS detector

The production cross sections of top-quark pairs in association with massive vector bosons have been measured using data from pp collisions at s√ = 8 TeV. The dataset corresponds to an integrated luminosity of 20.3 fb−¹ collected by the ATLAS detector in 2012 at the LHC. Final states with two, three or four leptons are considered. A fit to the data considering the tt̄W and tt̄Z processes simultaneously yields a significance of 5.0σ (4.2σ) over the background-only hypothesis for tt¯Wtt¯W (tt̄Z) production. The measured cross sections are σtt̄W = 369 + 100−91 fb and σtt̄Z = 176 + 58−52 fb. The background-only hypothesis with neither tt̄W nor tt̄Z production is excluded at 7.1σ. All measurements are consistent with next-to-leading-order calculations for the tt̄W and tt̄Z processes

An assessment of the risk of Bt-cowpea to non-target organisms in West Africa

Cowpea (Vigna unguiculata Walp.) is the most economically important legume crop in arid regions of sub-Saharan Africa. Cowpea is grown primarily by subsistence farmers who consume the leaves, pods and grain on farm or sell grain in local markets. Processed cowpea foods such as akara (a deep-fat fried fritter) are popular in the rapidly expanding urban areas. Demand far exceeds production due, in part, to a variety of insect pests including, in particular, the lepidopteran legume pod borer (LPB) Maruca vitrata. Genetically engineered Bt-cowpea, based on cry1Ab (Event 709) and cry2Ab transgenes, is being developed for use in sub-Saharan Africa to address losses from the LBP. Before environmental release of transgenic cowpeas, the Bt Cry proteins they express need to be assessed for potential effects on non-target organisms, particularly arthropods. Presented here is an assessment of the potential effects of those Cry proteins expressed in cowpea for control of LPB. Based on the history of safe use of Bt proteins, as well as the fauna associated with cultivated and wild cowpea in sub-Saharan Africa results indicate negligible effects on non-target organisms

Observation of Long-Range Elliptic Azimuthal Anisotropies in root s=13 and 2.76 TeV pp Collisions with the ATLAS Detector

ATLAS has measured two-particle correlations as a function of the relative azimuthal angle, Δϕ, and pseudorapidity, Δη, in sqrt[s]=13 and 2.76 TeV pp collisions at the LHC using charged particles measured in the pseudorapidity interval |η|<2.5. The correlation functions evaluated in different intervals of measured charged-particle multiplicity show a multiplicity-dependent enhancement at Δϕ∼0 that extends over a wide range of Δη, which has been referred to as the "ridge." Per-trigger-particle yields, Y(Δϕ), are measured over 2<|Δη|<5. For both collision energies, the Y(Δϕ) distribution in all multiplicity intervals is found to be consistent with a linear combination of the per-trigger-particle yields measured in collisions with less than 20 reconstructed tracks, and a constant combinatoric contribution modulated by cos(2Δϕ). The fitted Fourier coefficient, v_{2,2}, exhibits factorization, suggesting that the ridge results from per-event cos(2ϕ) modulation of the single-particle distribution with Fourier coefficients v_{2}. The v_{2} values are presented as a function of multiplicity and transverse momentum. They are found to be approximately constant as a function of multiplicity and to have a p_{T} dependence similar to that measured in p+Pb and Pb+Pb collisions. The v_{2} values in the 13 and 2.76 TeV data are consistent within uncertainties. These results suggest that the ridge in pp collisions arises from the same or similar underlying physics as observed in p+Pb collisions, and that the dynamics responsible for the ridge has no strong sqrt[s] dependence

Thoracic Endovascular Aortic Repair of Aortic Arch Pathologies with the Conformable Thoracic Aortic Graft: Early and 2 year Results from a European Multicentre Registry

Objective: To assess safety, effectiveness and clinical outcome of the conformable thoracic aortic endograft (CTAG) in the treatment of aortic arch pathologies. Methods: Between October 2009 and December 2010, 100 consecutive patients (65 men; mean age 65 years) with aortic arch pathologies were treated with the CTAG device in five European centres. Indications were thoracic aortic aneurysm (n = 57), Type B dissection (n = 24), intramural haematoma (n = 4), penetrating aortic ulcer (n = 9), and traumatic transection (n = 6). Emergency procedures were performed in 33%.The proximal landing zone (LZ) was LZ 0 in 7%, LZ 1 in14%, LZ 2 in 43%, and LZ 3 in 36%. Data were collected prospectively and analysed for technical and clinical success. Conformability and deployment accuracy were analysed on intra-operative angiography and postoperative computed tomography. Mean follow up was 24 +/- 19 months (range, 0.3-36 months). Results: The 30 day, 1 and 2 year survival rates were 90%, 81%, and 74% respectively. The 2 year survival was 80% in the elective and 62% in the emergency groups (p = .20). The major 30 day complication rate was 34%: primary Type la endoleak affected 1%, retrograde dissection in 1%, and the paraplegia and stroke rates at 30 days were 4% and 11%. Age > 70 years was an independent predictor for mortality and complications. The primary technical success rate was 92%; device deployment was successful in 100% and accurate in 99%. Conformability to the aortic arch was achieved in 95%. Conclusion: The CTAG stent graft shows high deployment accuracy, good conformability, and clinical effectiveness in the treatment of aortic arch pathologies. However, thoracic endovascular aortic repair in the arch is associated with a relatively high stroke rate. Further studies with more patients and longer follow up are needed to evaluate the long-term results. (C) 2016 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved