Virus-mediated transient expression techniques enable gene function studies in black-grass

Even though considerable progress has been made in weed ecology, weed molecular biology has been hindered by an inability to genetically manipulate weeds. Genetic manipulation is essential to demonstrate a causative relationship between genotype and phenotype. Herein we demonstrate that virus-mediated transient expression techniques developed for other monocots can be used in black-grass (Alopecurus myosuroides) for loss- and gain-of-function studies. We not only use virus induced gene silencing (VIGS) to create the black-grass exhibiting reduced PHYTOENE DESATURASE expression and virus-mediated overexpression (VOX) to drive GREEN FLUORESCENT PROTEIN, we demonstrate these techniques are applicable to testing hypotheses related to herbicide resistance in black-grass. We use VIGS to demonstrate that AmGSTF1 is necessary for the resistant biotype Peldon to survive fenoxaprop application and show the heterologous expression of the bialaphos resistance gene with VOX is sufficient to confer resistance to an otherwise lethal dose of glufosinate. Black-grass is the most problematic weed for winter-cereal farmers in the UK and Western Europe as it has rapidly evolved adaptions that allow it to effectively avoid current integrated weed management practices. Black-grass also reduces yields and therefore directly threatens food security and productivity. Novel disruptive technologies which mitigate resistance evolution and enable better control over this pernicious weed are therefore required. These virus-mediated protocols offer a step change in our ability to alter genes of interest under controlled laboratory conditions and therefore to gain a molecular-level understanding of how black-grass can survive in the agri-environment

Clustering and the hyperbolic geometry of complex networks

Clustering is a fundamental property of complex networks and it is the mathematical expression of a ubiquitous phenomenon that arises in various types of self-organized networks such as biological networks, computer networks or social networks. In this paper, we consider what is called the global clustering coefficient of random graphs on the hyperbolic plane. This model of random graphs was proposed recently by Krioukov et al. as a mathematical model of complex networks, under the fundamental assumption that hyperbolic geometry underlies the structure of these networks. We give a rigorous analysis of clustering and characterize the global clustering coefficient in terms of the parameters of the model. We show how the global clustering coefficient can be tuned by these parameters and we give an explicit formula for this function.Comment: 51 pages, 1 figur

A prospective randomized trial of tacrolimus and prednisone versus tacrolimus, prednisone and mycophenolate mofetil in primary adult liver transplantation: A single center report

Background. Tacrolimus (TAC) and mycophenolate mofetil (MMF) are currently approved immunosuppressants for prevention of rejection in liver transplantation (LTx). They have different modes of action and toxicity profiles, but the efficacy and safety of MMF in primary liver transplantation with TAC has not been determined. Methods. An Institutional Review Board-approved, open-label, single-center, prospective randomized trial was initiated to study the efficacy and toxicity of TAC and steroids (double-drug therapy (D)) versus TAC, steroids, and MMF (triple-drug therapy (T)) in primary adult LTx recipients. Both groups of patients were started on the same doses of TAC and steroids. Patients randomized to T also received 1 gm MMF twice a day. Results. Between August 1995 and May 1998, 350 patients were enrolled at a single center-175 in the D and 175 in the T groups. All patients were followed until May 1998, with a mean follow-up of 33.8±9.1 months. Using an intention-to-treat analysis, the 1-, 2-, 3-, and 4-year patient survival was 85.1%, 81.6%, 78.6%, and 75.8%, respectively, for D and 87.4%, 85.4%, 81.3%, and 79.9%, respectively, for T. The 4-year graft survival was 70% for D and 72.1% for T. Although the rate of acute rejection in the first 3 months was significantly lower for T than for D (28% for triple vs. 38.9% for double, P=0.03), the overall rate of rejection for T at the end of 1 year was not significantly lower than for the D (38.9% triple vs. 45.2% double). The median time to the first episode of rejection was 14 days for D versus 24 days for T (P=0.008). During the study period, 38 of 175 patients in D received MMF to control ongoing acute rejection, nephrotoxicity, and/or neurotoxicity. On the other hand, 103 patients in the T discontinued MMF for infection, myelosuppression, and/or gastrointestinal disturbances. The need for corticosteroids was less after 6 months for T and the perioperative need for dialysis was lower with use of MMF. Conclusion. This final report confirms similar patient survival and graft survival up to 4 years with a trend towards fewer episodes of rejection, lower need for steroids, and better perioperative renal function. However, the complex nature of LTx patients and their posttransplantation course prevents the routine application of MMF

Urban conservation : A framework for community involvement in Malaysia.

Whilst interest in conservation planning in Malaysia is growing, there is evidence that it contains several deficiencies, including the commitment and resources to support effective community involvement. This research investigates the underlying factors that contribute to these deficiencies in the system and aims to develop principles to be taken forward for application in a practice-oriented framework, drawn from a critical analysis of the relationships between best practice, as identified through the literature and contemporary practice in Malaysia, as identified through the empirical work.The research examines various examples of community involvement practice from selected developed countries, including the United Kingdom. This suggested a framework of community involvement best practice, which would achieve sustainable conservation results. The current community involvement approach practice in Malaysia (using the Case Study of Historical City of Malacca) was compared to this suggested framework. This comparison to best practice with Malaysia's present practice demonstrates, quite clearly, the vital need for an involvement framework in Malaysia to be improved to make the current practice and provisions more effective.The findings proved that the present process is inefficient. It lacks systematic techniques, adequate communication and awareness. Additionally, there is an imbalance of power and control which requires better coordination and collaboration between both stakeholder organisations (all levels of government, i.e. federal, state and local, as well as private and NGOs) and the communities. The summary of findings from both the authorities and communities was compared and arranged towards a concluding reconciliation of perspectives. This led to the proposed framework for community involvement based on the lessons of best practices explored for the improvement to the present conservation system.The recommended practice-oriented framework comprises of its key principles to guide the reform process and highlights on six main elements, i.e. the emphasis on community focus; policy and approach; involvement and consultation stages; process and procedures; consultation methods; and evaluation and monitoring. The implementation of the framework requires investment in terms of resources, as well as related education and awareness programmes to help secure its success

Online Convex Optimization Using Predictions

Making use of predictions is a crucial, but under-explored, area of online algorithms. This paper studies a class of online optimization problems where we have external noisy predictions available. We propose a stochastic prediction error model that generalizes prior models in the learning and stochastic control communities, incorporates correlation among prediction errors, and captures the fact that predictions improve as time passes. We prove that achieving sublinear regret and constant competitive ratio for online algorithms requires the use of an unbounded prediction window in adversarial settings, but that under more realistic stochastic prediction error models it is possible to use Averaging Fixed Horizon Control (AFHC) to simultaneously achieve sublinear regret and constant competitive ratio in expectation using only a constant-sized prediction window. Furthermore, we show that the performance of AFHC is tightly concentrated around its mean

Preconception Brief: Occupational/Environmental Exposures

In the last decade, more than half of U.S. children were born to working mothers and 65% of working men and women were of reproductive age. In 2004 more than 28 million women age 18–44 were employed full time. This implies the need for clinicians to possess an awareness about the impact of work on the health of their patients and their future offspring. Most chemicals in the workplace have not been evaluated for reproductive toxicity, and where exposure limits do exist, they were generally not designed to mitigate reproductive risk. Therefore, many toxicants with unambiguous reproductive and developmental effects are still in regular commercial or therapeutic use and thus present exposure potential to workers. Examples of these include heavy metals, (lead, cadmium), organic solvents (glycol ethers, percholoroethylene), pesticides and herbicides (ethylene dibromide) and sterilants, anesthetic gases and anti-cancer drugs used in healthcare. Surprisingly, many of these reproductive toxicants are well represented in traditional employment sectors of women, such as healthcare and cosmetology. Environmental exposures also figure prominently in evaluating a woman’s health risk and that to a pregnancy. Food and water quality and pesticide and solvent usage are increasingly topics raised by women and men contemplating pregnancy. The microenvironment of a woman, such as her choices of hobbies and leisure time activities also come into play. Caregivers must be aware of their patients’ potential environmental and workplace exposures and weigh any risk of exposure in the context of the time-dependent window of reproductive susceptibility. This will allow informed decision-making about the need for changes in behavior, diet, hobbies or the need for added protections on the job or alternative duty assignment. Examples of such environmental and occupational history elements will be presented together with counseling strategies for the clinician

Asymptotically optimal data analysis for rejecting local realism

Reliable experimental demonstrations of violations of local realism are highly desirable for fundamental tests of quantum mechanics. One can quantify the violation witnessed by an experiment in terms of a statistical p-value, which can be defined as the maximum probability according to local realism of a violation at least as high as that witnessed. Thus, high violation corresponds to small p-value. We propose a prediction-based-ratio (PBR) analysis protocol whose p-values are valid even if the prepared quantum state varies arbitrarily and local realistic models can depend on previous measurement settings and outcomes. It is therefore not subject to the memory loophole [J. Barrett et al., Phys. Rev. A 66, 042111 (2002)]. If the prepared state does not vary in time, the p-values are asymptotically optimal. For comparison, we consider protocols derived from the number of standard deviations of violation of a Bell inequality and from martingale theory [R. Gill, arXiv:quant-ph/0110137]. We find that the p-values of the former can be too small and are therefore not statistically valid, while those derived from the latter are sub-optimal. PBR p-values do not require a predetermined Bell inequality and can be used to compare results from different tests of local realism independent of experimental details.Comment: 11 pages, 4 figures; Software implementation of the PBR analysis protocol and its user guide attached as ancillary files; minor changes (add the software disclaimer, etc.

Recovery of mycorrhizal fungi from wild collected protocorms of Madagascan endemic orchidAerangis ellisii(BS Williams) Schltr. and their use in seed germination in vitro

Orchid mycorrhizal fungi (OMF) are critical for seed germination and maintaining natural populations of orchids, yet the degree of specificity of most orchids to their mycorrhizal associates remains unknown. Many orchids are at risk of extinction, whether generalists or specialists, but orchid species of narrow fungal specificity are arguably under increased threat due to their requirement for specific fungal symbionts. This study characterises the fungi associated with Aerangis ellisii, a lithophytic orchid from a site in the Central Highlands of Madagascar. Culturable OMF isolated from spontaneous protocorms of this species from the wild were used for seed germination. In vitro germination and seedling development of A. ellisii were achieved with fungi derived from A. ellisii and an isolate from a different Aerangis species 30 km away. The significance of these findings and their importance to conservation strategies for this species and other Aerangis spp. is discussed. These results have important implications for the conservation of A. ellisii populations in Madagascar

User-friendly tail bounds for sums of random matrices

This paper presents new probability inequalities for sums of independent, random, self-adjoint matrices. These results place simple and easily verifiable hypotheses on the summands, and they deliver strong conclusions about the large-deviation behavior of the maximum eigenvalue of the sum. Tail bounds for the norm of a sum of random rectangular matrices follow as an immediate corollary. The proof techniques also yield some information about matrix-valued martingales. In other words, this paper provides noncommutative generalizations of the classical bounds associated with the names Azuma, Bennett, Bernstein, Chernoff, Hoeffding, and McDiarmid. The matrix inequalities promise the same diversity of application, ease of use, and strength of conclusion that have made the scalar inequalities so valuable.Comment: Current paper is the version of record. The material on Freedman's inequality has been moved to a separate note; other martingale bounds are described in Caltech ACM Report 2011-0