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"Stanley, David"
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A research agenda for transport policy
Everyone has an opinion on transport: it significantly affects daily lives. This book highlights key transport opportunities and challenges, and identifies research requirements to inform policy discussion and support better societal outcomes. It does this by scanning across modes, continents, technologies and socio-economic settings, looking for common threads, points of difference and opportunities to make a difference. The book should appeal to prospective post-graduate students, professionals in transport and related fields, and those interested in better places and good discussions.
Book
Eicosanoid Signaling in Insect Immunology: New Genes and Unresolved Issues
This paper is focused on eicosanoid signaling in insect immunology. We begin with eicosanoid biosynthesis through the actions of phospholipase A2, responsible for hydrolyzing the C18 polyunsaturated fatty acid, linoleic acid (18:2n-6), from cellular phospholipids, which is subsequently converted into arachidonic acid (AA; 20:4n-6) via elongases and desaturases. The synthesized AA is then oxygenated into one of three groups of eicosanoids, prostaglandins (PGs), epoxyeicosatrienoic acids (EETs) and lipoxygenase products. We mark the distinction between mammalian cyclooxygenases and insect peroxynectins, both of which convert AA into PGs. One PG, PGI2 (also called prostacyclin), is newly discovered in insects, as a negative regulator of immune reactions and a positive signal in juvenile development. Two new elements of insect PG biology are a PG dehydrogenase and a PG reductase, both of which enact necessary PG catabolism. EETs, which are produced from AA via cytochrome P450s, also act in immune signaling, acting as pro-inflammatory signals. Eicosanoids signal a wide range of cellular immune reactions to infections, invasions and wounding, including nodulation, cell spreading, hemocyte migration and releasing prophenoloxidase from oenocytoids, a class of lepidopteran hemocytes. We briefly review the relatively scant knowledge on insect PG receptors and note PGs also act in gut immunity and in humoral immunity. Detailed new information on PG actions in mosquito immunity against the malarial agent, Plasmodium berghei, has recently emerged and we treat this exciting new work. The new findings on eicosanoid actions in insect immunity have emerged from a very broad range of research at the genetic, cellular and organismal levels, all taking place at the international level.
Journal Article
Prediction Interval: What to Expect When You’re Expecting … A Replication
A challenge when interpreting replications is determining whether the results of a replication \"successfully\" replicate the original study. Looking for consistency between two studies is challenging because individual studies are susceptible to many sources of error that can cause study results to deviate from each other and the population effect in unpredictable directions and magnitudes. In the current paper, we derive methods to compute a prediction interval, a range of results that can be expected in a replication due to chance (i.e., sampling error), for means and commonly used indexes of effect size: correlations and d-values. The prediction interval is calculable based on objective study characteristics (i.e., effect size of the original study and sample sizes of the original study and planned replication) even when sample sizes across studies are unequal. The prediction interval provides an a priori method for assessing if the difference between an original and replication result is consistent with what can be expected due to sample error alone. We provide open-source software tools that allow researchers, reviewers, replicators, and editors to easily calculate prediction intervals.
Journal Article
Team of teams : new rules of engagement for a complex world
As commander of Joint Special Operations Command (JSOC), General Stanley McChrystal played a crucial role in the War on Terror. But when he took the helm in 2004, America was losing that war badly: despite vastly inferior resources and technology, Al Qaeda was outmaneuvering America's most elite warriors. McChrystal came to realize that today's faster, more interdependent world had overwhelmed the conventional, top-down hierarchy of the U.S. military. Al Qaeda had seen the future: a decentralized network that could move quickly and strike ruthlessly. To defeat such an enemy, JSOC would have to discard a century of management wisdom, and pivot from a pursuit of mechanical efficiency to organic adaptability. Under McChrystal's leadership, JSOC remade itself, in the midst of a grueling war, into something entirely new: a network that combined robust centralized communication with decentralized managerial authority. As a result, they beat back Al Qaeda. In this book, McChrystal shows not only how the military made that transition, but also how similar shifts are possible in all organizations, from large companies to startups to charities to governments. In a turbulent world, the best organizations think and act like a team of teams, embracing small groups that combine the freedom to experiment with a relentless drive to share what they've learned. Drawing on a wealth of evidence from his military career, the private sector, and sources as diverse as hospital emergency rooms and NASA's space program, McChrystal frames the existential challenge facing today's organizations, and proposes a compelling, effective solution.
Book
High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
Rapid advancements in long-read sequencing technologies have transformed read lengths from bps to Mbps, which has enabled chromosome-scale genome assemblies. However, read lengths are now becoming limited by the extraction of pure high-molecular weight DNA suitable for long-read sequencing, which is particularly challenging in plants and fungi. To overcome this, we present a protocol collection; high-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. We optimised a gentle magnetic bead based high-molecular weight DNA extraction, which is presented here in detail. The protocol circumvents spin columns and high-centrifugation, to limit DNA fragmentation. The protocol is scalable based on tissue input, which can be used on many species of plants, fungi, reptiles and bacteria. It is also cost effective compared to kit-based protocols and hence applicable at scale in low resource settings. An optional sorbitol wash is listed and is highly recommended for plant and fungal tissues. To further remove any remaining contaminants such as phenols and polysaccharides, optional DNA clean-up and size selection strategies are given. This protocol collection is suitable for all common long-read sequencing platforms, such as technologies offered by PacBio and Oxford Nanopore. Using these protocols, sequencing on the Oxford Nanopore MinION can achieve read length N50 values of 30–50 kb, with reads exceeding 200 kb and outputs ranging from 15–30 Gbp. This has been routinely achieved with various plant, fungi, animal and bacteria samples.
Journal Article
Democracy in a hotter time : climate change and democratic transformation
\"A stellar roster of essayists share their reimagings of the institutions of democracy and governance necessary to resolve the climate crisis, and call on the reader to do so as well\"-- Provided by publisher.
Book
A PLA2 deletion mutant using CRISPR/Cas9 coupled to RNASeq reveals insect immune genes associated with eicosanoid signaling
Eicosanoids mediate insect immune responses and synthesized by the catalytic activity of phospholipase A 2 (PLA 2 ). A uniquely encoded secretory PLA 2 (sPLA 2 ) is associated with immune responses of a lepidopteran insect, Spodoptera exigua . Its deletion mutant was generated using a CRISPR/Cas9 genome editing technology. Both wild and mutant lines were then immune-challenged, and the resulting transcripts were compared with their naïve transcripts by RNASeq using the Illumina-HiSeq platform. In total, 12,878 unigenes were further analyzed by differentially expressed gene tools. Over 69% of the expressed genes in S . exigua larvae are modulated in their expression levels by eicosanoids, recorded from CRISPR/Cas9 mutagenesis against an eicosanoid-synthetic gene, Se-sPLA 2 . Further, about 36% of the immune-associated genes are controlled by the eicosanoids in S . exigua . Indeed, the deletion mutant suffered significant immunosuppression in both cellular and humoral responses in response to bacterial challenge as well as severely reduced developmental and reproductive potentials.
Journal Article
Expectations for Replications: Are Yours Realistic?
Failures to replicate published psychological research findings have contributed to a \"crisis of confidence.\" Several reasons for these failures have been proposed, the most notable being questionable research practices and data fraud. We examine replication from a different perspective and illustrate that current intuitive expectations for replication are unreasonable. We used computer simulations to create thousands of ideal replications, with the same participants, wherein the only difference across replications was random measurement error. In the first set of simulations, study results differed substantially across replications as a result of measurement error alone. This raises questions about how researchers should interpret failed replication attempts, given the large impact that even modest amounts of measurement error can have on observed associations. In the second set of simulations, we illustrated the difficulties that researchers face when trying to interpret and replicate a published finding. We also assessed the relative importance of both sampling error and measurement error in producing variability in replications. Conventionally, replication attempts are viewed through the lens of verifying or falsifying published findings. We suggest that this is a flawed perspective and that researchers should adjust their expectations concerning replications and shift to a meta-analytic mind-set.
Journal Article