Why plant diversity and distribution matter

This article is the Editorial for the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora

Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

Ten golden rules for reforestation to optimize carbon sequestration, biodiversity recovery and livelihood benefits

Urgent solutions to global climate change are needed. Ambitious tree-planting initiatives, many already underway, aim to sequester enormous quantities of carbon to partly compensate for anthropogenic CO₂ emissions, which are a major cause of rising global temperatures. However, tree planting that is poorly planned and executed could actually increase CO₂ emissions and have long-term, deleterious impacts on biodiversity, landscapes and livelihoods. Here, we highlight the main environmental risks of large-scale tree planting and propose 10 golden rules, based on some of the most recent ecological research, to implement forest ecosystem restoration that maximizes rates of both carbon sequestration and biodiversity recovery while improving livelihoods. These are as follows: (1) Protect existing forest first; (2) Work together (involving all stakeholders); (3) Aim to maximize biodiversity recovery to meet multiple goals; (4) Select appropriate areas for restoration; (5) Use natural regeneration wherever possible; (6) Select species to maximize biodiversity; (7) Use resilient plant material (with appropriate genetic variability and provenance); (8) Plan ahead for infrastructure, capacity and seed supply; (9) Learn by doing (using an adaptive management approach); and (10) Make it pay (ensuring the economic sustainability of the project). We focus on the design of long-term strategies to tackle the climate and biodiversity crises and support livelihood needs. We emphasize the role of local communities as sources of indigenous knowledge, and the benefits they could derive from successful reforestation that restores ecosystem functioning and delivers a diverse range of forest products and services. While there is no simple and universal recipe for forest restoration, it is crucial to build upon the currently growing public and private interest in this topic, to ensure interventions provide effective, long-term carbon sinks and maximize benefits for biodiversity and people.

Evaluating very high energy electron RBE from nanodosimetric pBR322 plasmid DNA damage

This paper presents the first plasmid DNA irradiations carried out with Very High Energy Electrons (VHEE) over 100-200 MeV at the CLEAR user facility at CERN to determine the Relative Biological Effectiveness (RBE) of VHEE. DNA damage yields were measured in dry and aqueous environments to determine that ~ 99% of total DNA breaks were caused by indirect effects, consistent with other published measurements for protons and photons. Double-Strand Break (DSB) yield was used as the biological endpoint for RBE calculation, with values found to be consistent with established radiotherapy modalities. Similarities in physical damage between VHEE and conventional modalities gives confidence that biological effects of VHEE will also be similar-key for clinical implementation. Damage yields were used as a baseline for track structure simulations of VHEE plasmid irradiation using GEANT4-DNA. Current models for DSB yield have shown reasonable agreement with experimental values. The growing interest in FLASH radiotherapy motivated a study into DSB yield variation with dose rate following VHEE irradiation. No significant variations were observed between conventional and FLASH dose rate irradiations, indicating that no FLASH effect is seen under these conditions.

Revisiting the taxonomy of the Neotropical Haemodoraceae (Commelinales)

Based on extensive herbarium, field, botanical illustration, and molecular phylogenetic research, five genera and eight species are recognised for the Neotropical Haemodoraceae. New taxa include Cubanicula Hopper et al., Xiphidium pontederiiflorum M.Pell. et al. and Schiekia timida M.Pell. et al. Two new combinations are made, Cubanicula xanthorrhizos (C.Wright ex Griseb.) Hopper et al. and Schiekia silvestris (Maas & Stoel) Hopper et al. We also correct the author citation for Xiphidium, provide the necessary typifications for several names and present an updated identification key, comments, and photo plates for all species. Finally, we provide high-quality illustrations for most of the recognised species and their diagnostic characters.

Ultra-high-bandwidth polarization interferometry and optimal quadratic phase detection

A novel homodyne interferometer and analysis method are described which use orthogonal polarization components to measure large rapid changes in interferometric phase, in quadrature, in the presence of strong time-dependent attenuation of the scene beam. This approach overcomes the major sources of error associated with homodyne interferometry (sensitivity nulls, ambiguity in the direction of phase change when passing through a sensitivity null, and intolerance to beam power variations) while maintaining its intrinsic simplicity and speed, enabling extremely high-bandwidth, high-dynamic range measurements limited only by available detector technology. Using this technique, electron density in a magnetized plasma shock was measured with unprecedented bandwidth and resolution, revealing short-timescale features not previously observed.

A combined millimeter wave and CO2 interferometer on the C-2W Jet plasma

A two wavelength tangentially viewing multi-chord interferometer has been built for the Jet plasma of the C-2W experiment at TAE Technologies. A novel 1 mm wavelength interferometer has been developed to be used simultaneously with a CO₂ laser interferometer to provide full coverage of the Jet plasma and the translating field-reversed configuration (FRC) plasma before merging. With CO₂ and millimeter wave sources, the interferometer proposes to cover a combined dynamic range of line integrated density of more than 1000 although the CO₂ interferometer sub-system is not yet operational. Sited at the axial location of the mirror field of C-2W, the interferometer will play a pivotal role in assessing the FRC before merging and the operation of the inner and outer divertors and particle outflow. The performance of the millimeter wave interferometer and recent measurements is discussed.

Practical Appraisal of a New Rating Scale (MRSS) for Rehabilitation

Rating scales are available to assess patients undergoing rehabilitation for chronic psychiatric disorders. Few are universally acceptable because of pitfalls in their structure or administration. This study examines the recently printed Morningside Rehabilitation Status Scale in one rehabilitation network. The MRSS was found to be suitable in discriminating between severely and moderately disabled groups but not between mildly and moderately disabled groups.

A streak camera based fiber optic pulsed polarimetry technique for magnetic sensing to sub-mm resolution

The technique of fiber optic pulsed polarimetry, which provides a distributed (local) measurement of the magnetic field along an optical fiber, has been improved to the point where, for the first time, photocathode based optical detection of backscatter is possible with sub-mm spatial resolutions. This has been realized through the writing of an array of deterministic fiber Bragg gratings along the fiber, a so-called backscatter-tailored optical fiber, producing a 34 000-fold increase in backscatter levels over Rayleigh. With such high backscatter levels, high repetition rate lasers are now sufficiently bright to allow near continuous field sensing in both space and time with field resolutions as low as 0.005 T and as high as 170 T over a ∼mm interval given available fiber materials.

Atlanto-Axial Infection after Acupuncture

A 67-year-old man presented with neck cellulitis following acupuncture for cervical spondylosis. Blood cultures were positive for methicillin-sensitive Staphylococcus aureus. Increased neck pain and bacteraemia prompted MRI, which showed atlanto-axial septic arthritis without signs of infection of the tissues between the superficial cellulitic area and the atlanto-axial joint, thus making direct extension of infection unlikely. It is more likely that haematogenous spread of infection resulted in seeding in the atlanto-axial joint, with the proximity of the arthritis and acupuncture site being coincidental. Acupuncture is a treatment option for some indolent pain conditions. As such, acupuncture services are likely to be more frequently utilised. A history of acupuncture is rarely requested by the admitting doctor and seldom offered voluntarily by the patient, especially where the site of infection due to haematogenous spread is distant from the needling location. Awareness of infectious complications following acupuncture can reduce morbidity through early intervention.

Applications of mathematical modeling in managing the spread of chronic wasting disease (CWD) in wild deer under alternative harvesting scenarios

The application of a recently developed mathematical model for predicting the spread of chronic wasting disease (CWD) in wild deer was assessed under different scenarios where harvesting is employed in disease management. A process-based mathematical model for CWD transmission in wild deer populations was recently developed and parameterized by Al-arydah et al. (2011) to provide a scientific basis for understanding the factors that affect spread of CWD and evaluate concomitant disease-control strategies. The impact of gender on CWD transmission was shown to have a significant influence on the spread of the disease in the wild. Our model demonstrates a range of harvesting rates in which CWD is controlled and deer populations survive. However, if harvesting rates are too low, the disease remains endemic for decades. Conversely, the Canadian deer population is eradicated if harvesting rates are excessive. Future investigation includes building the model to assess the spread of CWD under different disease-management scenarios.

Atlanto-axial infection after acupuncture

A 67-year-old man presented with neck cellulitis following acupuncture for cervical spondylosis. Blood cultures were positive for methicillin-sensitive Staphylococcus aureus. Increased neck pain and bacteraemia prompted MRI, which showed atlanto-axial septic arthritis without signs of infection of the tissues between the superficial cellulitic area and the atlanto-axial joint, thus making direct extension of infection unlikely. It is more likely that haematogenous spread of infection resulted in seeding in the atlanto-axial joint, with the proximity of the arthritis and acupuncture site being coincidental. Acupuncture is a treatment option for some indolent pain conditions. As such, acupuncture services are likely to be more frequently utilised. A history of acupuncture is rarely requested by the admitting doctor and seldom offered voluntarily by the patient, especially where the site of infection due to haematogenous spread is distant from the needling location. Awareness of infectious complications following acupuncture can reduce morbidity through early intervention.

Precise measurement of the neutrino mixing parameter θ23 from muon neutrino disappearance in an off-axis beam

New data from the T2K neutrino oscillation experiment produce the most precise measurement of the neutrino mixing parameter θ23. Using an off-axis neutrino beam with a peak energy of 0.6 GeV and a data set corresponding to 6.57×10(20) protons on target, T2K has fit the energy-dependent νμ oscillation probability to determine oscillation parameters. The 68% confidence limit on sin(2)(θ23) is 0.514(-0.056)(+0.055) (0.511±0.055), assuming normal (inverted) mass hierarchy. The best-fit mass-squared splitting for normal hierarchy is Δm32(2)=(2.51±0.10)×10(-3)  eV(2)/c(4) (inverted hierarchy: Δm13(2)=(2.48±0.10)×10(-3)  eV(2)/c(4)). Adding a model of multinucleon interactions that affect neutrino energy reconstruction is found to produce only small biases in neutrino oscillation parameter extraction at current levels of statistical uncertainty.

Observation of electron neutrino appearance in a muon neutrino beam

The T2K experiment has observed electron neutrino appearance in a muon neutrino beam produced 295 km from the Super-Kamiokande detector with a peak energy of 0.6 GeV. A total of 28 electron neutrino events were detected with an energy distribution consistent with an appearance signal, corresponding to a significance of 7.3σ when compared to 4.92±0.55 expected background events. In the Pontecorvo-Maki-Nakagawa-Sakata mixing model, the electron neutrino appearance signal depends on several parameters including three mixing angles θ12, θ23, θ13, a mass difference Δm(32)(2) and a CP violating phase δ(CP). In this neutrino oscillation scenario, assuming |Δm(32)(2)|=2.4×10(-3)  eV(2), sin(2)θ(23)=0.5, and Δm322>0 (Δm(32)(2)<0), a best-fit value of sin(2)2θ(13)=0.140(-0.032)(+0.038) (0.170(-0.037)(+0.045)) is obtained at δ(CP)=0. When combining the result with the current best knowledge of oscillation parameters including the world average value of θ(13) from reactor experiments, some values of δ(CP) are disfavored at the 90% C.L.

Phomopsis Dieback: A Grapevine Trunk Disease Caused by Phomopsis viticola in California

Field surveys recently conducted in California and in other grape-growing regions in the United States showed Phomopsis viticola to be one of the most prevalent fungi isolated from grapevine perennial cankers in declining vines. The current study has not only confirmed the presence of P. viticola from grapevine cankers in California but also has for the first time revealed the occurrence of Diaporthe ambigua, D. eres, and D. neotheicola in symptomatic grapevine wood in California by means of morphological studies and multi-gene sequence analysis. Pathogenicity trials conducted on mature cordons of Vitis vinifera 'Syrah' and 'Red Globe', as well as on lignified Syrah dormant canes, showed P. viticola isolates from California to be capable of causing perennial cankers. Lengths of vascular discoloration caused by P. viticola were similar to those caused by Eutypa lata and several Botryosphaeriaceae spp., which are well-known grapevine trunk disease pathogens. Additionally, a lack of spring growth was commonly observed in dormant canes inoculated with P. viticola spore suspensions in two pathogenicity trials. As part of this study, V. vinifera 'Cabernet Sauvignon' and 'Zinfandel' wood was shown to be more susceptible to infection by P. viticola than 'Barbera', 'Chardonnay', 'Merlot', and 'Thompson Seedless' wood. After more than 40 years overlooking P. viticola as a grapevine wood pathogen, this study provides strong evidence of the role of P. viticola as a canker-causing organism, and suggests its addition to the fungi involved in the grapevine trunk disease complex. Results from this study suggest D. ambigua and D. neotheicola to be saprophytes or weak pathogens on grapevine wood.

Measurement of neutrino oscillation parameters from muon neutrino disappearance with an off-axis beam

The T2K Collaboration reports a precision measurement of muon neutrino disappearance with an off-axis neutrino beam with a peak energy of 0.6 GeV. Near detector measurements are used to constrain the neutrino flux and cross section parameters. The Super-Kamiokande far detector, which is 295 km downstream of the neutrino production target, collected data corresponding to 3.01×10(20) protons on target. In the absence of neutrino oscillations, 205±17 (syst) events are expected to be detected while only 58 muon neutrino event candidates are observed. A fit to the neutrino rate and energy spectrum, assuming three neutrino flavors and normal mass hierarchy yields a best-fit mixing angle sin2(θ23)=0.514±0.082 and mass splitting |Δm(32)(2)|=2.44(-0.15)(+0.17)×10(-3) eV2/c4. Our result corresponds to the maximal oscillation disappearance probability.

Chemical labeling of northern pike (Esox lucius) by the alarm pheromone of fathead minnows (Pimephales promelas)

In previous experiments, chemical stimuli from northern pike (Esox lucius) elicited fright responses from pike-naive fathead minnows (Pimephales promelas) only if the pike had recently eaten conspecific minnows. We used a behavioral assay to determine if the fright response is the result of the incorporation of the minnow alarm pheromone into the chemical signature of the pike. Because the alarm substance cells (epidermal club cells) of fathead minnows are seasonally lost by males, we used chemical stimuli from pike that had eaten breeding male minnows as a control stimulus. In independent laboratory and field experiments, pike-naive minnows exhibited fright reactions (e.g., increased shelter use, avoidance) when exposed to water from tanks containing pike that had eaten nonbreeding fatheads (with alarm substance cells), but not to water from tanks containing pike that had eaten breeding male fatheads (without alarm substance cells). These data indicate that the fathead minnow alarm pheromone chemically labels northern pike as dangerous to pike-naive receivers.

Early warning in the predation sequence: A disturbance pheromone in Iowa darters (Etheostoma exile)

The probability of prey avoiding a predator's attack should increase if the predator's presence is detected at an early stage in the predation sequence. In this study, we tested whether threatened Iowa darters (Etheostoma exile) release disturbance pheromones that warn conspecifics of the presence of predation threat. Pairs of aquaria were visually isolated from one another, but connected chemically by water circulating between them. Darters in one aquarium were observed before and after darters in the other aquarium were chased with a model predator. In control tests, the model was moved in the same manner but there were no darters in the upstream tank. Darters receiving water from threatened fish increased vigilance behavior and decreased movement. Vigilant fish raised their head above the substratum, propping themselves up on their pectoral fins and/or arching their neck dorsally, pointing the snout upward. Exposure to water from disturbed darters suppressed exploratory behavior and resulted in movement by short rapid hops that ended abruptly in a rigid, alert posture. This study suggests that Iowa darters release a disturbance pheromone that can provide conspecifics with an early warning of predation risk.

Tailored eculizumab therapy in the management of complement factor H-mediated atypical hemolytic uremic syndrome in an adult kidney transplant recipient: a case report

Atypical hemolytic uremic syndrome (aHUS) is characterized by thrombocytopenia, microangiopathic hemolytic anemia, and acute kidney injury (AKI) which frequently progresses to end-stage renal disease (ESRD). In 50% of affected patients, mutations in complement regulatory proteins cause inappropriate complement activation with endothelial injury. Complement factor H (CFH) mutations cause 25% of aHUS cases; these patients have an 80% recurrence risk after kidney transplantation. Eculizumab, an anti-C5 antibody, is effective in limiting hemolysis episodes in patients with aHUS, but less is known about preventing recurrence after kidney transplantation. Herein we report the use of prophylactic eculizumab in an adult with aHUS who underwent kidney transplantation. A 31-year-old female presented with aHUS and progressive AKI associated with low complement 3 level leading to ESRD despite plasmapheresis and corticosteroids. She had a heterozygous nonsense mutation in CFH and reduced plasma CFH levels. She was given preoperative plasmapheresis and eculizumab and underwent living unrelated renal transplantation. Postoperatively, eculizumab was dosed to achieve low functional complement 5 levels and low soluble membrane attack complex levels and she has maintained excellent graft function without aHUS recurrence. We propose that eculizumab with titrated dosing should be used in CFH-mediated aHUS patients who are at a high risk of recurrence.

Medical emergencies in the imaging department of a university hospital: event and imaging characteristics

We aimed to describe the characteristics of medical emergencies that occurred in the medical imaging department (MID) of a university hospital in Melbourne, Australia. A database of 'Respond Medical Emergency Team (MET)' and 'Respond Blue' calls was retrospectively examined for the period June 2003 to November 2010 in relation to events that occurred in the MID. The hospital medical imaging database was also examined in relation to these events and, where necessary, patients' notes were reviewed. Ethics approval was granted by the hospital ethics review board. There were 124 medical emergency calls in the MID during the study period, 28% Respond Blue and 72% Respond MET. Of these 124 calls, 26% occurred outside of usual work hours and 12% involved cardiac arrest. The most common reasons for the emergency calls were seizures (14%) and altered conscious state (13%). Contrast anaphylaxis precipitated the emergency in 4% of cases. In 83% of cases the emergency calls were for patients attending the MID for diagnostic imaging, the remainder being for a procedure. Of the scheduled imaging techniques, 45% were for computed tomography. The scheduled imaging was abandoned due to the emergency in 12% of cases. When performed, imaging informed patient management in 34% of cases in diagnostic imaging and in all cases in the context of image-guided procedures. Medical emergency calls in the MID often occurred outside usual work hours and were attributed to a range of medical problems. The emergencies occurred in relation to all imaging techniques and imaging informed patient management in many cases.

Association between red blood cell distribution width and macrovascular and microvascular complications in diabetes

AIMS/HYPOTHESIS

Red blood cell distribution width (RDW) has been reported to be a risk marker of morbidity and mortality for cardiovascular disease in various study populations. However, no studies have investigated the relationship between RDW and diabetes complications. We therefore evaluated RDW as a marker of macrovascular and microvascular complications in a nationally representative sample of the adult diabetes population in the USA.

METHODS

A cross-sectional study was performed using the nationwide 1988 to 1994 data set from the Third National Health and Nutrition Examination Survey. The association between RDW quartiles and macrovascular and microvascular complications was evaluated in 2,497 non-pregnant adults aged 20 years and older and affected by diabetes. Logistic regression modelling was used to adjust for potential confounding.

RESULTS

Compared with the lowest RDW quartile, higher RDW values (3rd and 4th quartiles) were associated with increased adjusted odds of any vascular complication (OR 4th quartile 2.06 [95% CI 1.11, 3.83]), myocardial infarction (OR 4th quartile 2.45 [95% CI 1.13, 5.28]), heart failure (OR 4th quartile 4.40 [95% CI 1.99, 9.72]), stroke (OR 4th quartile 2.56 [95% CI 1.21, 5.42]) and nephropathy (OR 4th quartile 2.33 [95% CI 1.42, 3.82]). The odds of developing diabetic retinopathy were not significantly increased across RDW quartiles.

CONCLUSIONS/INTERPRETATION

Higher RDW values are associated with increased odds of developing cardiovascular disease and nephropathy in a nationally representative sample of USA adults with diabetes. RDW may be an important clinical marker of vascular complications in diabetes and one that is independent of traditional risk factors and disease duration.

Evidence for separatrix formation and sustainment with steady inductive helicity injection

The first sustainment of toroidal plasma current of 50 kA at up to 3 times the injected currents, added in quadrature, using steady inductive helicity injection is described. Separatrix currents-currents not linking the helicity injectors-are sustained up to 40 kA. Decreases in the n=1 toroidal mode of the poloidal magnetic field at higher current amplifications indicate more quiescent, direct toroidal current drive. Results are achieved in HIT-SI (with a spheromak of major radius 0.3 m) during deuterium operations immediately after helium operation. These results represent a breakthrough in the development of this new current drive method for magnetic confinement fusion.

Indication of electron neutrino appearance from an accelerator-produced off-axis muon neutrino beam

The T2K experiment observes indications of ν(μ) → ν(e) appearance in data accumulated with 1.43×10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Δm(23)(2)| = 2.4×10(-3)  eV(2), sin(2)2θ(23) = 1 and sin(2)2θ(13) = 0, the expected number of such events is 1.5±0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7×10(-3), equivalent to 2.5σ significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2θ(13) < 0.28(0.34) for δ(CP) = 0 and a normal (inverted) hierarchy.

Production of high titre disabled infectious single cycle (DISC) HSV from a microcarrier culture

Disabled Infectious Single Cycle (DISC) HSV-2 has been cultured in the complimentary cell line CR2 to provide high titre bulk material suitable for the purification of the virus as a live viral vaccine. CR2 cells are cultured on the microcarrier Cytodex-1 at 5 g l-1 in small scale (1 l) and larger scale (15 l) reactors. The cells are infected at an MOI of 0.01 pfu cell-1 and the culture harvested 60–72 h later. The infected cells are removed from the microcarriers by the addition of a hypotonic saline and the virus released by low-pressure disruption techniques. Virus titres achieved are compared to the standard roller bottle process. The resulting material is the starting point for the purification of the DISC-HSV virus.

Imaging of the magnetic field structure in megagauss plasmas by combining pulsed polarimetry with an optical Kerr effect shutter technique

Pulsed polarimetry in combination with a high speed photographic technique based on the optical Kerr effect is described. The backscatter in a pulsed polarimeter is directed through a scattering cell and photographed using an ∼1 ps shutter, essentially freezing the intensity pattern. The image provides both the local electron density and magnetic field distributions along and transverse to the laser sightline. Submillimeter spatial resolution is possible for probing wavelengths in the visible due to the high densities and strong optical activity. Pulsed polarimetry is thereby extended to centimeter-sized plasmas with n(e)>10(19)-10(20) cm(-3) and B>20-100 T (MG) produced by multiterawatt, multimega-ampere electrical drivers, wire Z pinches, and liner imploded magnetized plasmas.

Air force takes aim at a big bird

Early this year, the U.S. land-based force of nuclear missiles became vulnerable to destruction in a preemptive attack by the Soviet Union. The Air Force has worried about this situation for a long time, searching high and low for a better place to put both the existing silo-based missiles and a new missile, the MX. The first article in this series examined the reasons that U.S. officials became alarmed about missile vulberability, and the second examined the short-term plan to put missiles into silos. This article explores the Ait Force's least favourite long-term basing mode. Subsequent articles will explore the alternatives.

Botryosphaeriaceae Species Spore-Trapping Studies in California Vineyards

The seasonal abundance of Botryosphaeriaceae spp. spores was studied in California vineyards by using glass microscope slides covered with petroleum jelly placed on grapevine cordons and Burkard volumetric spore traps at seven and two different locations, respectively. Correlation analysis was used to determine which meteorological variables (precipitation, relative humidity, temperature, and wind speed) influenced Botryosphaeriaceae spp. spore release. Among all variables, regression analysis resulted in a strong relationship between spore release and precipitation. Additionally, a positive relationship between irrigation and spore release was also observed in the Riverside County vineyard. During the study period, spore discharge of Botryosphaeriaceae spp. occurred from the first fall rain through the last spring rains, coinciding with September to April. However, based on the results obtained from the spore traps, most spores (over 60%) were trapped following rain events during the winter months of December, January, and February, which coincides with the grapevine pruning season. Botryosphaeriaceae spp. spore release was much lower in fall and early spring (22%) and very few or no spores were trapped in late spring and summer (3%). This work suggests that a delay of pruning time in California may be warranted to reduce grapevine infection because the current timing coincides with the greatest period of spore discharge.

Identification of imprinted loci by methylation: use of methylation-sensitive representational difference analysis (Me-RDA)

The technique of representational difference analysis (RDA) was originally described by Lisitsyn et al. (1993) as a means of identifying differences between complex genomes by the use of subtractive hybridisation (1). This protocol for methylation-sensitive RDA (Me-RDA) describes adaptations to the original technique that, by the use of oligonucleotides for HpaII or Hin6I sites, allow the identification of sequences whose methylation differs between two sources of DNA. Differences in the methylation of the maternal and paternal alleles of imprinted genes have been described for most imprinted genes studied to date (2). The importance of methylation in the control of imprinted gene expression has been clearly demonstrated by the perturbation of allelic expression in mice deficient in Dnmt1, the major mammalian DNA methyltransferase (3), and methylation has been suggested to fulfill the necessary requirements of an "imprint" (4).

Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range

BACKGROUND AND AIMS

Species may occur over a wide geographical range within which populations can display large variation in reproductive success and genetic diversity. Neotinea maculata is a rare orchid of conservation concern at the edge of its range in Ireland, where it occurs in small populations. However, it is relatively common throughout the Mediterranean region. Here, factors that affect rarity of N. maculata in Ireland are investigated by comparing Irish populations with those found in Italy, where it is more common.

METHODS

Vegetation communities, breeding system and genetic diversity were compared using three amplified fragment length polymorphism (AFLP) primer pairs in populations in Ireland and Italy. Vegetation was quantified using quadrats taken along transects in study populations, and hand pollination experiments were performed to assess reliance of N. maculata on pollinators in both Irish and Italian populations.

KEY RESULTS

Neotinea maculata occupies different vegetation communities in Italian and Irish populations. Breeding system experiments show that N. maculata is 100 % autogamous, and there are no differences in fruit and seed production in selfed, outcrossed and unmanipulated plants. AFLP markers revealed that Irish and Italian populations have similar genetic diversity and are distinct from each other.

CONCLUSIONS

Neotinea maculata does not suffer any negative effects of autogamous reproduction; it self-pollinates and sets seed readily in the absence of pollinators. It occupies a variety of habitats in both Ireland and Italy; however, Irish populations are small and rare and should be conserved. This could be due to climatic factors and the absence of suitable soil mycorrhizas to allow recruitment from seed.

Sexual intercourse involving giant sperm in Cretaceous ostracode

Reproduction with giant sperm occurs in distinct groups scattered over the animal kingdom. Although experiments in Drosophila assessed the influence of different selection pressures on this character, no information was available on its long-term stability. Sub-micrometer-resolution synchrotron quantitative phase tomography (holotomography) of exceptionally well-preserved three-dimensional Cretaceous ostracode fossils from the Brazilian Santana Formation indicates that ostracode reproduction with giant sperm persisted for at least over the past 100 million years. Remnants of the male sperm pumps as well as giant, inflated female sperm receptacles evidence that, despite high costs, reproduction with giant sperm can be an evolutionary successful strategy.

Development of a fibre size-specific job-exposure matrix for airborne asbestos fibres

OBJECTIVE

To develop a method for estimating fibre size-specific exposures to airborne asbestos dust for use in epidemiological investigations of exposure-response relations.

METHODS

Archived membrane filter samples collected at a Charleston, South Carolina asbestos textile plant during 1964-8 were analysed by transmission electron microscopy (TEM) to determine the bivariate diameter/length distribution of airborne fibres by plant operation. The protocol used for these analyses was based on the direct transfer method published by the International Standards Organization (ISO), modified to enhance fibre size determinations, especially for long fibres. Procedures to adjust standard phase contrast microscopy (PCM) fibre concentration measures using the TEM data in a job-exposure matrix (JEM) were developed in order to estimate fibre size-specific exposures.

RESULTS

A total of 84 airborne dust samples were used to measure diameter and length for over 18,000 fibres or fibre bundles. Consistent with previous studies, a small proportion of airborne fibres were longer than >5 microm in length, but the proportion varied considerably by plant operation (range 6.9% to 20.8%). The bivariate diameter/length distribution of airborne fibres was expressed as the proportion of fibres in 20 size-specific cells and this distribution demonstrated a relatively high degree of variability by plant operation. PCM adjustment factors also varied substantially across plant operations.

CONCLUSIONS

These data provide new information concerning the airborne fibre characteristics for a previously studied textile facility. The TEM data demonstrate that the vast majority of airborne fibres inhaled by the workers were shorter than 5 mum in length, and thus not included in the PCM-based fibre counts. The TEM data were used to develop a new fibre size-specific JEM for use in an updated cohort mortality study to investigate the role of fibre dimension in the development of asbestos-related lung diseases.

The size of scalable brain components in the human evolutionary lineage: with a comment on the paradox of Homo floresiensis

The discovery of a diminutive, small-brained hominin skeleton (LB1) from the Pleistocene of Flores, Indonesia, seems to present a paradox concerning the interpretation of overall brain size in an evolutionary context. This specimen forms the holotype of a purportedly new hominin species, Homo floresiensis. As inferred from the archaeological record, it has been suggested that this species of Homo, existing as recently as 12,000 years ago, engaged in sophisticated cultural behaviors with an adult brain size equivalent to that seen in modern chimpanzees and one that in modern humans would be defined as "high degree microcephaly" and "always associated with idiocy". The alternative explanation for these behaviors at the observed brain size would require that H. floresiensis deviate from existing patterns of primate brain scaling at either a macroscopic or microscopic level. Here we develop predictive equations and confidence intervals for estimating the size of various brain components in the human evolutionary lineage by calculating scaling relationships among overall brain size and 11 components of the primate brain using phylogenetically independent contrasts (PIC) methods. Using these equations, paleoanthropologists can: (a) estimate brain component size (and confidence intervals) for any primate in the fossil record if overall brain size is known; and (b) calculate some reasonable outside limits as to how far species-specific departures from allometric constraints (i.e., brain "reorganization") can be taken in assessing human brain evolution. We conclude that if the original assessment of LB1 is correct, i.e., that it samples a population from a new species of Homo, H. floresiensis, that was capable of Homo sapiens-like cultural attributes (fire, blade manufacturing, etc.), while having a chimpanzee-sized brain, then we are faced with the paradox that 1 cm(3) of H. floresiensis brain could not be functionally equivalent to 1cm(3) of a modern human or modern chimpanzee brain.

Spheromak formation by steady inductive helicity injection

A spheromak is formed for the first time using a new steady state inductive helicity injection method. Using two inductive injectors with odd symmetry and oscillating at 5.8 kHz, a steady state spheromak with even symmetry is formed and sustained through nonlinear relaxation. A spheromak with about 13 kA of toroidal current is formed and sustained using about 3 MW of power. This is a much lower power threshold for spheromak production than required for electrode-based helicity injection. Internal magnetic probe data, including oscillations driven by the injectors, agree with the plasma being in the Taylor state. The agreement is remarkable considering the only fitting parameter is the amplitude of the spheromak component of the state.

Adherence to antiretroviral HIV drugs: how many doses can you miss before resistance emerges?

The question of determining how many doses may be skipped before HIV treatment response is adversely affected by the emergence of drug-resistance is addressed. Impulsive differential equations are used to develop a prescription to minimize the emergence of drug-resistance for protease-sparing regimens. A threshold for the maximal number of missable doses is determined. If the number of missed doses is below this threshold, then resistance levels are negligible and dissipate quickly, assuming perfect adherence subsequently. If the number of missed doses exceeds this threshold, even for 24h, resistance levels are extremely high and will not dissipate for weeks, even assuming perfect adherence subsequently. After this interruption, the minimum number of successive doses that should be taken is determined. Estimates are provided for all protease-sparing drugs approved by the US Food and Drug Administration. Estimates for the basic reproductive ratios for the wild-type and mutant strains of the virus are also calculated, for a long-term average fractional degree of adherence. There are regions within this fraction of adherence where the outcome is not predictable and may depend on a patient's entire history of drug-taking.

Drug resistance in an immunological model of HIV-1 infection with impulsive drug effects

We consider an SIR-type model of immunological behaviour for HIV dynamics, including the effects of reverse transcriptase inhibitors and other drugs which prevent cellular infection. We use impulsive differential equations to model drug behaviour. We classify different regimes according to whether the drug efficacy is negligible, intermediate or high. We consider two strains of the virus: a wild-type strain that can be controlled by both intermediate and high drug concentrations, and a mutant strain that can only be controlled by high drug concentrations. Drug regimes may take trajectories through one, two or all three regimes, depending on the dosage and the dosing schedule. We demonstrate that drug resistance arises at both intermediate and high drug levels. At low drug levels resistance does not emerge, but the total T cell count is proven to be significantly lower than in the disease-free state. At intermediate drug levels, drug resistance is guaranteed to emerge. At high drug levels, either the drug-resistant strain will dominate or, in the absence of longer-lived reservoirs of infected cells, both viral sub-populations will be cleared. In the latter case the immune system is maintained by a population of T cells which have absorbed sufficient quantities of the drug to prevent infection by even the drug-resistant strain. We provide estimates of a range of dosages and dosing schedules which would, if physiologically tolerable, theoretically eliminate free virus in this system. Our results predict that to control viral load, decreasing the interval between doses is more effective than increasing the dose.

Datura contamination of hay as the suspected cause of an extensive outbreak of impaction colic in horses : clinical communication

atura poisoning of horses is extensively reviewed. An outbreak of intractable impaction colic affecting 18 of 83 horses was stopped by withdrawing dried tef hay contaminated with young Datura plants. The dried, botanically identified Datura stramonium and D. ferox contained respectively 0.15 % mass/mass (m/m) hyoscyamine as well as 0.16 % m/m hyoscine (scopolamine) and only hyoscine at a concentration of 0.11 % m/m. Immature, unidentifiable plants resembling D. stramonium, contained 0.14 % m/m and 0.12 % m/m of the 2 respective tropane alkaloids. The outbreak was characterised by protracted and repeated colic attacks due to impaction of the large colon and/or caecum without any other anti-muscarinic signs. Comparative analyses of single specimens of dried seed of the 2 species collected from both fertilised and waste areas revealed that young South African Datura spp. had levels of tropane alkaloids comparable to those in the well-known toxic seed and were, consequently, equally toxic. The inherent danger of tef hay being contaminated with Datura is emphasised. To our knowledge this is the 1st field case of poisoning in horses ascribed to the vegetative parts of Datura spp.

Design and acceptability of patient-oriented computerized diabetes care reminders for use at the point of care

Despite the widespread availability of guidelines for caring for patients with diabetes and decades of research on computerized reminder systems, large gaps in quality remain in diabetes care remain and computerized reminder systems are rarely used for patients with diabetes. We set out to develop and test the feasibility of a system that would overcome many of the barriers preventing the widespread use of point-of-care computerized reminders to improve diabetes care. Five primary care physicians and 32 patients with type 2 diabetes pilot tested the system. We set out to design and measure the preliminary acceptability of patient-oriented point of care computerized diabetes care reminders. The main findings of our study were that (1) the reports were well accepted by both patients and providers and (2) survey and audiotape data suggest that they may be helpful at improving the quality of outpatient care for patients with diabetes.

Distinct effects of protease and reverse transcriptase inhibition in an immunological model of HIV-1 infection with impulsive drug effects

We present an immunological model that considers the dynamics of CD4+ T cells interacting with free virions, reverse transcriptase inhibiting drugs and protease inhibiting drugs. We divide the T cells into multiple classes and use impulsive differential equations to describe the drug activity. As expected, we find that insufficient dosing of either drug corresponds to high viral load and a large population of infectious T cells. The model further predicts that, in the absence of physiological limits on tolerable drug concentrations, sufficiently frequent dosing with the reverse transcriptase inhibitor alone could theoretically maintain the CD4+ T cell count arbitrarily close to the T cell count in the uninfected immune system. However, for frequent dosing of the protease inhibitor alone, the limiting T cell populations may not be enough to maintain the immune system. Furthermore, frequent dosing of both drugs has the same net effect on the T cell population as frequent dosing of the reverse transcriptase inhibitor only. Thus, the two drug classes can have fundamentally different effects on the long-term dynamics and the reverse transcriptase inhibitor, in particular, plays a crucial role in maintaining the immune system. We also provide estimates for the dosing intervals of each drug that could theoretically sustain the T cell population at a desired level.