Demography and Management of the Invasive Plant Species Hypericum perforatum. II. Construction and Use of an Individual-Based Model to Predict Population Dynamics and the Effects of Management Strategies

1. Hypericum perforatum , St John's wort, is an invasive weed of natural and agro-ecosystems in south-eastern Australia. In previous work we used a long-term data set to determine which plant traits and environmental factors influence population growth and persistence in this species. These results were then used to parameterize an individual-based model of the population dynamics of H. perforatum , and this model was used to make predictions about what control strategies will be most effective for populations in open and shaded sites. 2. The model was constructed using multi-level, mixed-effects statistical models of growth, survival, fecundity and damage, incorporating intrinsic plant variables, environmental variables, herbivory and spatial and temporal stochasticity. 3. We found that populations in shaded and open sites had different dynamics and responses to control strategies. Shaded populations took longer to reach infestation densities and were less affected by herbivory and reductions in survival than open populations. Open populations increased faster in response to increases in rainfall, but this was not so for shaded populations. 4. We used sensitivity testing and management simulations to predict that the most successful control strategies will involve a reduction in vegetative size in both open and shaded sites. Reductions in flowering stem size and survival in shaded and open sites, respectively, are predicted to be the next most successful strategies. Dry conditions in the austral autumn/winter adversely affect populations in both open and shaded sites. 5. Synthesis and applications . These models have enabled us to rank management strategies based on quantitative analysis of their potential effects on population size. This is an important tool not only for ecologists concerned with control of invasive species but for conservation biologists trying to understand the factors limiting a rare or endangered species

Demography and Management of the Invasive Plant Species Hypericum perforatum. I. Using Multi-Level Mixed-Effects Models For Characterizing Growth, Survival and Fecundity in a Long-Term Data Set

1. Hypericum perforatum , St John's wort, is an invasive perennial herb that is especially problematic on waste ground, roadsides, pastures and open woodland in south-eastern Australia. We use detailed data from a long-term observational study to develop quantitative models of the factors affecting growth, survival and fecundity of H. perforatum individuals. 2. Multi-level or hierarchical mixed-effects statistical models are used to analyse how environmental and intrinsic plant variables affect growth and reproduction within a complex nested spatial and temporal context. These techniques are relatively underused in ecology, despite the prevalence of multi-level and repeated-measures data generated from ecological studies. 3. We found that plant size (rosette or flowering stems) was strongly correlated with all life stages studied (growth, probability of flowering, asexual reproduction, survival and fruit production). Environmental variables such as herbivory, ground cover and rainfall had significant effects on several life stages. 4. Significant spatial variation at the quadrat level was found in the probability of flowering, flowering stem growth and fruit production models; variation at all other spatial levels in all models was non-significant. Yearly temporal variation was significant in all models where multi-year data were available. 5. Plants in shaded habitats were smaller but had higher survival probabilities than plants in open habitats. They are therefore likely to have slightly different population dynamics. 6. Synthesis and applications. Analysis of these models for H. perforatum has provided insights into which plant traits and environmental factors determine how populations increase and persist in exotic ecosystems, enabling population management strategies to be most effectively targeted. Spatially and temporally correlated data are often collected in long-term ecological studies and multi-level models are a way in which we can fully exploit the wealth of data available. Without these tools data are either underexploited or crucial assumptions of independence on which many statistics are based are contravene

Shearing Interferometer for Quantifying the Coherence of Hard X-Ray Beams

We report a quantitative measurement of the full transverse coherence function of the 14.4 keV x-ray radiation produced by an undulator at the Swiss Light Source. An x-ray grating interferometer consisting of a beam splitter phase grating and an analyzer amplitude grating has been used to measure the degree of coherence as a function of the beam separation out to 30 m. Importantly, the technique provides a model-free and spatially resolved measurement of the complex coherence function and is not restricted to high resolution detectors and small fields of view. The spatial characterization of the wave front has important applications in discovering localized defects in beam line optics

Longitudinal molecular microbial analysis of influenza-like illness in New York City, may 2009 through may 2010

<p>Abstract</p> <p>Background</p> <p>We performed a longitudinal study of viral etiology in samples collected in New York City during May 2009 to May 2010 from outpatients with fever or respiratory disease symptoms in the context of a pilot respiratory virus surveillance system.</p> <p>Methods</p> <p>Samples were assessed for the presence of 13 viruses, including influenza A virus, by MassTag PCR.</p> <p>Results</p> <p>At least one virus was detected in 52% of 940 samples analyzed, with 3% showing co-infections. The most frequently detected agents were rhinoviruses and influenza A, all representing the 2009 pandemic H1N1 strain. The incidence of influenza H1N1-positive samples was highest in late spring 2009, followed by a decline in summer and early fall, when rhinovirus infections became predominant before H1N1 reemerged in winter. Our study also identified a focal outbreak of enterovirus 68 in the early fall of 2009.</p> <p>Conclusion</p> <p>MassTag multiplex PCR affords opportunities to track the epidemiology of infectious diseases and may guide clinicians and public health practitioners in influenza-like illness and outbreak management. Nonetheless, a substantial proportion of influenza-like illness remains unexplained underscoring the need for additional platforms.</p

Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis.

Acute flaccid myelitis (AFM) has caused motor paralysis in &gt;560 children in the United States since 2014. The temporal association of enterovirus (EV) outbreaks with increases in AFM cases and reports of fever, respiratory, or gastrointestinal illness prior to AFM in &gt;90% of cases suggest a role for infectious agents. Cerebrospinal fluid (CSF) from 14 AFM and 5 non-AFM patients with central nervous system (CNS) diseases in 2018 were investigated by viral-capture high-throughput sequencing (VirCapSeq-VERT system). These CSF and serum samples, as well as multiple controls, were tested for antibodies to human EVs using peptide microarrays. EV RNA was confirmed in CSF from only 1 adult AFM case and 1 non-AFM case. In contrast, antibodies to EV peptides were present in CSF of 11 of 14 AFM patients (79%), significantly higher than controls, including non-AFM patients (1/5 [20%]), children with Kawasaki disease (0/10), and adults with non-AFM CNS diseases (2/11 [18%]) (P = 0.023, 0.0001, and 0.0028, respectively). Six of 14 CSF samples (43%) and 8 of 11 sera (73%) from AFM patients were immunoreactive to an EV-D68-specific peptide, whereas the three control groups were not immunoreactive in either CSF (0/5, 0/10, and 0/11; P = 0.008, 0.0003, and 0.035, respectively) or sera (0/2, 0/8, and 0/5; P = 0.139, 0.002, and 0.009, respectively).IMPORTANCE The presence in cerebrospinal fluid of antibodies to EV peptides at higher levels than non-AFM controls supports the plausibility of a link between EV infection and AFM that warrants further investigation and has the potential to lead to strategies for diagnosis and prevention of disease

Streptococcus pneumoniae Coinfection Is Correlated with the Severity of H1N1 Pandemic Influenza

Initial reports in May 2009 of the novel influenza strain H1N1pdm estimated a case fatality rate (CFR) of 0.6%, similar to that of seasonal influenza. In July 2009, however, Argentina reported 3056 cases with 137 deaths, representing a CFR of 4.5%. Potential explanations for increased CFR included virus reassortment or genetic drift, or infection of a more vulnerable population. Virus genomic sequencing of 26 Argentinian samples representing both severe and mild disease indicated no evidence of reassortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence. Furthermore, no evidence was found for increased frequency of risk factors for H1N1pdm disease.We examined nasopharyngeal swab samples (NPS) from 199 cases of H1N1pdm infection from Argentina with MassTag PCR, testing for 33 additional microbial agents. The study population consisted of 199 H1N1pdm-infected subjects sampled between 23 June and 4 July 2009. Thirty-nine had severe disease defined as death (n = 20) or hospitalization (n = 19); 160 had mild disease. At least one additional agent of potential pathogenic importance was identified in 152 samples (76%), including Streptococcus pneumoniae (n = 62); Haemophilus influenzae (n = 104); human respiratory syncytial virus A (n = 11) and B (n = 1); human rhinovirus A (n = 1) and B (n = 4); human coronaviruses 229E (n = 1) and OC43 (n = 2); Klebsiella pneumoniae (n = 2); Acinetobacter baumannii (n = 2); Serratia marcescens (n = 1); and Staphylococcus aureus (n = 35) and methicillin-resistant S. aureus (MRSA, n = 6). The presence of S. pneumoniae was strongly correlated with severe disease. S. pneumoniae was present in 56.4% of severe cases versus 25% of mild cases; more than one-third of H1N1pdm NPS with S. pneumoniae were from subjects with severe disease (22 of 62 S. pneumoniae-positive NPS, p = 0.0004). In subjects 6 to 55 years of age, the adjusted odds ratio (OR) of severe disease in the presence of S. pneumoniae was 125.5 (95% confidence interval [CI], 16.95, 928.72; p<0.0001).The association of S. pneumoniae with morbidity and mortality is established in the current and previous influenza pandemics. However, this study is the first to demonstrate the prognostic significance of non-invasive antemortem diagnosis of S. pneumoniae infection and may provide insights into clinical management

ICTV Virus Taxonomy Profile: Bornaviridae

Members of the family Bornaviridae produce enveloped virions containing a linear negative-sense non-segmented RNA genome of about 9 kb. Bornaviruses are found in mammals, birds, reptiles and fish. The most-studied viruses with public health and veterinary impact are Borna disease virus 1 and variegated squirrel bornavirus 1, both of which cause fatal encephalitis in humans. Several orthobornaviruses cause neurological and intestinal disorders in birds, mostly parrots. Endogenous bornavirus-like sequences occur in the genomes of various animals. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Bornaviridae, which is available at ictv.global/report/bornaviridae

Testing of cryogenic photomultiplier tubes for the MicroBooNE experiment

The MicroBooNE detector, to be located on axis in the Booster Neutrino Beamline (BNB) at the Fermi National Accelerator Laboratory (Fermilab), consists of two main components: a large liquid argon time projection chamber (LArTPC), and a light collection system. Thirty-two 8-inch diameter Hamamatsu R5912-02mod cryogenic photomultiplier tubes (PMTs) will detect the scintillation light generated in the liquid argon (LAr). This article first describes the MicroBooNE PMT performance test procedures, including how the light collection system functions in the detector, and the design of the PMT base. The design of the cryogenic test stand is then discussed, and finally the results of the cryogenic tests are reported