Population viability analysis of endangered plant species : an evaluation of stochastic methods and an application to a rare prairie plant

Transition matrix models are one of the most widely used tools for assessing population viability. The technique allows inclusion of environmental variability, thereby permitting estimation of probabilistic events, such as extinction. However, few studies use the technique to compare the effects of management treatments on population viability, and fewer still have evaluated the implications of using different model assumptions. In this dissertation, I provide an example of the use of stochastic matrix models to assess the effects of prescribed fire on Lomatium bradshawii (Apiaceae), an endangered prairie plant. Using empirically derived data from 27 populations of five perennial plant species collected over a span of five to ten years, I compare the effects of using different statistical distributions to model stochasticity, and different methods of constraining stage-specific survival to [less than or equal to] 100% on population viability estimates. Finally, the importance of correlation among transition elements is tested, along with interactions between stochastic distributions and study species, on population viability estimates. Fire significantly increased population viability of L. bradshawii, regardless of stochastic method (matrix selection or element selection). Different processes of incorporating stochasticity (i.e., matrix selection vs. these statistical distributions for element selection: beta, truncated normal, truncated gamma, triangular, uniform, and bootstrap) and constraining survival (resampling vs. rescaling procedures) yielded divergent estimates of stochastic growth rate, and there was a significant interaction between these methods. These effects were largely explained by the degree of bias the different methods caused in transition elements. Incorporating correlation among elements caused a significant, but small, reduction in estimated stochastic growth rate in two of five species examined, yet there was no interaction with stochastic method in this effect. Much of the variation in average response to correlation structure among species was due to the relative balance between positive and negative associations among the vital rates. Although alternative techniques may lead to very strong differences in estimates of population viability, conclusions about the relative ranking of populations or treatments are robust to differences in stochastic methods

Factors Influencing Germination of a Functionally Important Grassland Plant, Iris tenax

Grassland prairies of western Oregon and Washington are among the most endangered ecosystems in the United States. Active management and restoration are needed to promote biodiversity in the region. To support plant production for use in habitat restoration, we developed germination protocols for greenhouse propagation of Iris tenax (Oregon iris). Dormancy was most effectively overcome (63% germination) by four weeks of warm stratification at 20/30°C followed by 6–12 weeks of cold stratification at 5°C suggesting that I. tenax may have morphophysiological dormancy. This result was consistent across multiple source populations

Selective Serotonin Reuptake Inhibitors and Associated Bleeding Risks: A Narrative and Clinical Review.

Major Depressive Disorder (MDD) is a major cause of disability worldwide and is associated with serious lasting impairment. A leading hypothesis of the pathophysiology of MDD is the monoamine deficiency hypothesis which suggests that depression is caused by depletion of serotonin, norepinephrine, or dopamine in the central nervous system. Serotonin is the most widely studied neurotransmitter in the pathophysiology of depression, with studies showing that reduced central serotonin synthesis leads to depressive symptoms in individuals at risk for depression. Selective Serotonin Reuptake Inhibitors (SSRI) inhibit serotonin reuptake and subsequently increase the amount of serotonin available in synapses. Common side effects of SSRIs include increased suicidality of patients under the age of 25, sexual dysfunction, anxiety, dizziness, weight gain, gastrointestinal distress, and headache. Other side effects include prolonging the QT interval, coagulopathy, and the risk of serotonin syndrome, as well as SSRI discontinuation syndrome. Sites of increased bleeding related to SSRI use have been reported to occur in the upper gastrointestinal tract, as well as intracranially. Based on the current literature, three studies have found that SSRIs are not associated with increased bleeding and/or increased perioperative risk, while others have demonstrated that SSRIs are associated with an increased risk in perioperative use. The inhibition of serotonin reuptake can affect platelet aggregation since platelets also express the serotonin transporter. SSRIs can result in decreased storage of serotonin in platelet dense granules. Increased serotonin can also increase gastric acid secretion, which increases the risk for ulceration. SSRIs in combination with NSAIDs also show a significantly increased risk of upper GI bleeding. Some studies show an increased bleeding risk from 30% to 70% when taking a combination of vitamin K antagonists and SSRIs in hospitalized patients. Related to the high prevalence of conditions that are treated with SSRIs, the bleeding risk associated with this class of medication merits further study

Telemedicine During COVID-19 and Beyond: A Practical Guide and Best Practices Multidisciplinary Approach for the Orthopedic and Neurologic Pain Physical Examination.

BACKGROUND:The COVID pandemic has impacted almost every aspect of human interaction, causing global changes in financial, health care, and social environments for the foreseeable future. More than 1.3 million of the 4 million cases of COVID-19 confirmed globally as of May 2020 have been identified in the United States, testing the capacity and resilience of our hospitals and health care workers. The impacts of the ongoing pandemic, caused by a novel strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have far-reaching implications for the future of our health care system and how we deliver routine care to patients. The adoption of social distancing during this pandemic has demonstrated efficacy in controlling the spread of this virus and has been the only proven means of infection control thus far. Social distancing has prompted hospital closures and the reduction of all non-COVID clinical visits, causing widespread financial despair to many outpatient centers. However, the need to treat patients for non-COVID problems remains important despite this pandemic, as care must continue to be delivered to patients despite their ability or desire to report to outpatient centers for their general care. Our national health care system has realized this need and has incentivized providers to adopt distance-based care in the form of telemedicine and video medicine visits. Many institutions have since incorporated these into their practices without financial penalty because of Medicare\u27s 1135 waiver, which currently reimburses telemedicine at the same rate as evaluation and management codes (E/M Codes). Although the financial burden has been alleviated by this policy, the practitioner remains accountable for providing proper assessment with this new modality of health care delivery. This is a challenge for most physicians, so our team of national experts has created a reference guide for musculoskeletal and neurologic examination selection to retrofit into the telemedicine experience. OBJECTIVES:To describe and illustrate musculoskeletal and neurologic examination techniques that can be used effectively in telemedicine. STUDY DESIGN:Consensus-based multispecialty guidelines. SETTING:Tertiary care center. METHODS:Literature review of the neck, shoulder, elbow, wrist, hand, lumbar, hip, and knee physical examinations were performed. A multidisciplinary team comprised of physical medicine and rehabilitation, orthopedics, rheumatology, neurology, and anesthesia experts evaluated each examination and provided consensus opinion to select the examinations most appropriate for telemedicine evaluation. The team also provided consensus opinion on how to modify some examinations to incorporate into a nonhealth care office setting. RESULTS:Sixty-nine examinations were selected by the consensus team. Household objects were identified that modified standard and validated examinations, which could facilitate the examinations.The consensus review team did not believe that the modified tests altered the validity of the standardized tests. LIMITATIONS:Examinations selected are not validated for telemedicine. Qualitative and quantitative analyses were not performed. CONCLUSIONS:The physical examination is an essential component for sound clinical judgment and patient care planning. The physical examinations described in this manuscript provide a comprehensive framework for the musculoskeletal and neurologic examination, which has been vetted by a committee of national experts for incorporation into the telemedicine evaluation

Relation between falciparum malaria and bacteraemia in Kenyan children: a population-based, case-control study and a longitudinal study.

BACKGROUND: Many investigators have suggested that malaria infection predisposes individuals to bacteraemia. We tested this hypothesis with mendelian randomisation studies of children with the malaria-protective phenotype of sickle-cell trait (HbAS). METHODS: This study was done in a defined area around Kilifi District Hospital, Kilifi, Kenya. We did a matched case-control study to identify risk factors for invasive bacterial disease, in which cases were children aged 3 months to 13 years who were admitted to hospital with bacteraemia between Sept 16, 1999, and July 31, 2002. We aimed to match two controls, by age, sex, location, and time of recruitment, for every case. We then did a longitudinal case-control study to assess the relation between HbAS and invasive bacterial disease as malaria incidence decreased. Cases were children aged 0-13 years who were admitted to hospital with bacteraemia between Jan 1, 1999, and Dec 31, 2007. Controls were born in the study area between Jan 1, 2006, and June 23, 2009. Finally, we modelled the annual incidence of bacteraemia against the community prevalence of malaria during 9 years with Poisson regression. RESULTS: In the matched case-control study, we recruited 292 cases-we recruited two controls for 236, and one for the remaining 56. Sickle-cell disease, HIV, leucocyte haemozoin pigment, and undernutrition were positively associated with bacteraemia and HbAS was strongly negatively associated with bacteraemia (odds ratio 0·36; 95% CI 0·20-0·65). In the longitudinal case-control study, we assessed data from 1454 cases and 10,749 controls. During the study period, the incidence of admission to hospital with malaria per 1000 child-years decreased from 28·5 to 3·45, with a reduction in protection afforded by HbAS against bacteraemia occurring in parallel (p=0·0008). The incidence of hospital admissions for bacteraemia per 1000 child-years also decreased from 2·59 to 1·45. The bacteraemia incidence rate ratio associated with malaria parasitaemia was 6·69 (95% CI 1·31-34·3) and, at a community parasite prevalence of 29% in 1999, 62% (8·2-91) of bacteraemia cases were attributable to malaria. INTERPRETATION: Malaria infection strongly predisposes individuals to bacteraemia and can account for more than half of all cases of bacteraemia in malaria-endemic areas. Interventions to control malaria will have a major additional benefit by reducing the burden of invasive bacterial disease. FUNDING: Wellcome Trust

Plant traits – a tool for restoration?

Question: Most results of restoration efforts are species-specific and/or site-specific and therefore are not general enough to be easily applied to other species and other sites. Our research addresses the issue of species-specific results by investigating the feasibility of using plant traits instead of taxonomic species to characterize species responses to restoration treatments. Specifically, we test the explanatory power of plant traits, one necessary prerequisite for the development of predictive and general plant trait models. Location: Ten remnant bunchgrass prairie sites in the Pacific Northwest of North America (Oregon and Washington, USA; British Columbia, Canada). Methods: We developed two types of quantitative models for each of 10 prairie restoration sites: 1) plant trait models, which related plant traits to species field responses following restoration management treatments, and 2) species identity models, which related species taxonomic identity to species field responses following restoration management treatments. Species identity models determined the maximum amount of variability of field responses that can be explained by differences in individual species’ responses to management treatments. Plant trait models determined what proportion of this explanatory power can be attributed to plant traits. This approach contrasts with approaches often used in other plant trait studies that describe how traits vary with environmental conditions. Specifically, we used these two models to address the following questions: 1) How much of the variability in field responses of plants to restoration management treatments is explained by plant traits? 2) How well do plant traits explain the variability of field responses following restoration management treatments compared to models relating field responses to species identity? Our approach was to measure two aspects of explanatory power: R2 (variability explained) and AIC (a measure of model fit that accounts for parsimony, i.e., how well a model fits the data with relatively few explanatory variables). Results: 1) The plant trait models (relating plant traits with plant field responses) explained much of the variability within each of the ten restoration sites, with R2 values ranging between 31% and 69%. 2) The species identity models (relating species taxonomic identity with plant field responses) explained between 47% and 74% of variability in field performance (R2). Thus, the plant trait models explained nearly as much variability as the species identity models. In seven out of nine sites, the plant trait models were superior to the species identity models as measured by AIC; that is, the trait models did well at explaining variability with less model complexity (i.e., fewer explanatory variables). Conclusion: Development of general and predictive plant trait models is a multi-step process. Strong explanatory power by plant trait models, both on an absolute scale and as compared to species identity models, supports the feasibility of using plant traits instead of species taxonomic identity as a common language to characterize plant field responses to restoration treatments. Such high explanatory power is one necessary pre-requisite for the development of predictive and general plant trait models. Our results also indicate that the plant trait models are site-specific even though all sites were upland bunchgrass remnant prairies. We discuss the next steps in the development of more general and predictive models: incorporating environmental factors into the plant trait models to address the issue of site-specificity and testing the power of these models to predict vegetation responses.This is the post-print version of the article

On the heating mix of ITER (invited paper)

This paper considers the heating mix of ITER for the two main scenarios. Presently, 73MWof absorbed power are foreseen in the mix 20/33/20 for ECH, NBI and ICH. Given a sufficient edge stability, Q = 10 the goal of scenario 2 can be reached with 40MW power irrespective of the heating method but depends sensitively inter alia on the H-mode pedestal temperature, the density profile shape and on the characteristics of impurity transport. ICH preferentially heats the ions and would contribute specifically with Q 0.5, and strong off-axis current drive (CD). The findings presented here are based on revised CD efficiencies γ for ECCD and a detailed benchmark of several CD codes. With ECCD alone, the goals of scenario 4 can hardly be reached. Efficient off-axisCDis only possible with NBI.With beams, inductive discharges with fni > 0.8 can be maintained for 3000 s. The conclusion of this study is that the present heating mix of ITER is appropriate. It provides the necessary actuators to induce in a flexible way the best possible scenarios. The development risks of NBI at 1MeV can be reduced by operation at 0.85MeV

Ascospore discharge, germination and culture of fungal partners of tropical lichens, including the use of a novel culture technique

A total of 292 lichen samples, representing over 200 species and at least 65 genera and 26 families, were collected, mainly in Thailand; 170 of the specimens discharged ascospores in the laboratory. Generally, crustose lichens exhibited the highest discharge rates and percentage germination. In contrast, foliose lichen samples, although having a high discharge rate, had a lower percentage germination than crustose species tested. A correlation with season was indicated for a number of species. Continued development of germinated ascospores into recognizable colonies in pure culture was followed for a selection of species. The most successful medium tried was 2 % Malt-Yeast extract agar (MYA), and under static conditions using a liquid culture medium, a sponge proved to be the best of several physical carriers tested; this novel method has considerable potential for experimental work with lichen mycobionts

Early motion and directed exercise (EMADE) versus usual care post ankle fracture fixation: study protocol for a pragmatic randomised controlled trial

Background: Following surgical fixation of ankle fractures, the traditional management has included immobilisation for 6 weeks in a below-knee cast. However, this can lead to disuse atrophy of the affected leg and joint stiffness. While early rehabilitation from 2 weeks post surgery is viewed as safe, controversy remains regarding its benefits. We will compare the effectiveness of early motion and directed exercise (EMADE) ankle rehabilitation, against usual care, i.e. 6 weeks’ immobilisation in a below-knee cast. Method/design: We have designed a pragmatic randomised controlled trial (p-RCT) to compare the EMADE intervention against usual care. We will recruit 144 independently living adult participants, absent of tissue-healing comorbidities, who have undergone surgical stabilisation of isolated Weber B ankle fractures. The EMADE intervention consists of a non-weight-bearing progressive home exercise programme, complemented with manual therapy and education. Usual care consists of immobilisation in a non-weight-bearing below-knee cast. The intervention period is between week 2 and week 6 post surgery. The primary outcome is the Olerud and Molander Ankle Score (OMAS) patient-reported outcome measure (PROM) at 12 weeks post surgery. Secondary PROMs include the EQ-5D-5 L questionnaire, return to work and return to driving, with objective outcomes including ankle range of motion. Analysis will be on an intention-to-treat basis. An economic evaluation will be included. Discussion: The EMADE intervention is a package of care designed to address the detrimental effects of disuse atrophy and joint stiffness. An advantage of the OMAS is the potential of meta-analysis with other designs. Within the economic evaluation, the cost-utility analysis, may be used by commissioners, while the use of patient-relevant outcomes, such as return to work and driving, will ensure that the study remains pertinent to patients and their families. As it is being conducted in the clinical environment, this p-RCT has high external validity. Accordingly, if significant clinical benefits and cost-effectiveness are demonstrated, EMADE should become a worthwhile treatment option. A larger-scale, multicentre trial may be required to influence national guidelines. Trial registration: ISRCTN, ID: ISRCTN11212729. Registered retrospectively on 20 March 2017