FooPar: A Functional Object Oriented Parallel Framework in Scala

We present FooPar, an extension for highly efficient Parallel Computing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates functional programming features. Our framework FooPar combines these features with parallel computing techniques. FooPar is designed modular and supports easy access to different communication backends for distributed memory architectures as well as high performance math libraries. In this article we use it to parallelize matrix matrix multiplication and show its scalability by a isoefficiency analysis. In addition, results based on a empirical analysis on two supercomputers are given. We achieve close-to-optimal performance wrt. theoretical peak performance. Based on this result we conclude that FooPar allows to fully access Scala's design features without suffering from performance drops when compared to implementations purely based on C and MPI

Retinal phenotyping of variants of Alzheimer's disease using ultra-widefield retinal images

Background: Posterior cortical atrophy (PCA) is the most common atypical variant of Alzheimer's disease (AD). Changes associated with PCA in the brain affect the visual cortex, but little is known about retinal changes in PCA. In this study, we explored retinal phenotypic variations in typical AD (tAD) and PCA. Methods: Retinal phenotyping was carried out on ultra-widefield (UWF) images of 69 control, 24 tAD, and 25 PCA participants. Results: Individuals with tAD (odds ratio [OR] = 2.76 [confidence interval (CI):1.24 to 6.10], P = .012) and PCA (OR = 3.40 [CI:1.25 to 9.22], P = .016) were more likely phenotyped as hard drusen. tAD (OR = 0.34 [CI:0.12 to 0.92], P = .035) were less likely to have soft drusen compared to control. Almost 3-fold increase in reticular pseudodrusen formation in tAD (OR = 2.93 [CI:1.10 to 7.76], P = .030) compared to control was estimated. Discussion: Studying the peripheral retina may contribute to a better understanding of differences in retinal phenotypes of different AD variants

Predictors of mortality for delirium in palliative care

© Mary Ann Liebert, Inc. 2016. Introduction: Delirium has a high mortality rate. Understanding predictors of prognosis in patients with delirium will aid treatment decisions and communication. This study aimed to explore variables associated with death during an established episode of delirium in palliative care when haloperidol treatment had been commenced. Methods: A consecutive cohort of palliative care patients, from 14 centers across four countries, is reported. The outcome of interest was death within 14 days from commencement of haloperidol treatment for delirium. Clinicodemographic variables explored were delirium severity, age, gender, primary life limiting illness, body mass index (BMI), total daily haloperidol dose at baseline (mg), functional status, and comorbidities. Results: One hundred and sixteen palliative care patients where vital status was known were included in the analysis; 45% (n = 52) died within 10 days, and 56% (n = 65) died within 14 days. In multivariate analyses no clinical or demographic variables predicted death, apart from lower BMI in noncancer patients. Conclusion: This study has shown a very high mortality rate within two weeks of commencing haloperidol for delirium in palliative care, with no clear clinical predictors for those with a higher chance of dying. Having a higher BMI offered some benefit in survival, but only in noncancer patients. When delirium occurs in advanced illness, discussion should be initiated about the gravity of the clinical situation

Pharmacovigilance in hospice/palliative care: Net effect of haloperidol for delirium

Introduction: Prescribing practice in hospice/palliative care is largely extrapolated from other areas of clinical practice, with few studies of net medication effects (benefits and harms) in hospice/palliative care to guide prescribing decisions. Hospice/palliative care patients differ in multiple ways from better studied participant groups, hence the applicability of studies in other participant groups is uncertain. Haloperidol, a butyrophenone derivative and dopamine antagonist, is commonly prescribed for nausea, vomiting, and delirium in hospice/palliative care. Its frequent use in delirium occurs despite little evidence of the effect of antipsychotics on the untreated course of delirium. The aim of this study was to examine the immediate and short-term clinical benefits and harms of haloperidol for delirium in hospice/palliative care patients. Method: A consecutive cohort of participants from 14 centers across four countries who had haloperidol commenced for delirium were recruited. Data were collected at three time points: baseline, 48 hours (clinical benefits), and day 10 (clinical harms). Investigators were also able to report clinical harms at any time up to 14 days after it was commenced. Results: Of the 119 participants included, the average dose was 2.1 mg per 24 hours; 42 of 106 (35.2%) reported benefit at 48 hours. Harm was reported in 14 of 119 (12%) at 10 days, the most frequent being somnolence (n=11) and urinary retention (n=6). Seven participants had their medication ceased due to harms (2 for somnolence and 2 for rigidity). Approximately half (55/119) were still being treated with haloperidol after 10 days. Conclusion: Overall, 1 in 3 participants gained net clinical benefit at 10 days. © Copyright 2013, Mary Ann Liebert, Inc. 2013

How will transitioning from cytology to HPV testing change the balance between the benefits and harms of cervical cancer screening? Estimates of the impact on cervical cancer, treatment rates and adverse obstetric outcomes in Australia, a high vaccination coverage country

Primary HPV screening enables earlier diagnosis of cervical lesions compared to cytology, however, its effect on the risk of treatment and adverse obstetric outcomes has not been extensively investigated. We estimated the cumulative lifetime risk (CLR) of cervical cancer and excisional treatment, and change in adverse obstetric outcomes in HPV unvaccinated women and cohorts offered vaccination (>70% coverage in 12-13 years) for the Australian cervical screening program. Two-yearly cytology screening (ages 18-69 years) was compared to 5-yearly primary HPV screening with partial genotyping for HPV16/18 (ages 25-74 years). A dynamic model of HPV transmission, vaccination, cervical screening and treatment for precancerous lesions was coupled with an individual-based simulation of obstetric complications. For cytology screening, the CLR of cervical cancer diagnosis, death and treatment was estimated to be 0.649%, 0.198% and 13.4% without vaccination and 0.182%, 0.056% and 6.8%, in vaccinated women, respectively. For HPV screening, relative reductions of 33% and 22% in cancer risk for unvaccinated and vaccinated women are predicted, respectively, compared to cytology. Without the implementation of vaccination, a 4% increase in treatment risk for HPV versus cytology screening would have been expected, implying a possible increase in pre-term delivery (PTD) and low birth weight (LBW) events of 19 to 35 and 14 to 37, respectively, per 100,000 unvaccinated women. However, in vaccinated women, treatment risk will decrease by 13%, potentially leading to 4 to 41 fewer PTD events and from 2 more to 52 fewer LBW events per 100,000 vaccinated women. In unvaccinated women in cohorts offered vaccination as 12-13 year olds, no change to lifetime treatment risk is expected with HPV screening. In unvaccinated women in cohorts offered vaccination as 12-13 year olds, no change to lifetime treatment risk is expected with HPV screening. HPV screening starting at age 25 in populations with high vaccination coverage, is therefore expected to both improve the benefits (further decrease risk of cervical cancer) and reduce the harms (reduce treatments and possible obstetric complications) associated with cervical cancer screening

Pharmacovigilance in hospice/palliative care: Net effect of gabapentin for neuropathic pain

Objective Hospice/palliative care patients may differ from better studied populations, and data from other populations cannot necessarily be extrapolated into hospice/palliative care clinical practice. Pharmacovigilance studies provide opportunities to understand the harms and benefits of medications in routine practice. Gabapentin, a γ-amino butyric acid analogue antiepileptic drug, is commonly prescribed for neuropathic pain in hospice/palliative care. Most of the evidence however relates to nonmalignant, chronic pain syndromes (diabetic neuropathy, postherpetic neuralgia, central pain syndromes, fibromyalgia). The aim of this study was to quantify the immediate and short-term clinical benefits and harms of gabapentin in routine hospice/palliative care practice. Design Multisite, prospective, consecutive cohort. Population 127 patients, 114 of whom had cancer, who started gabapentin for neuropathic pain as part of routine clinical care. Settings 42 centres from seven countries. Data were collected at three time points-at baseline, at day 7 (and at any time; immediate and shortterm harms) and at day 21 (clinical benefits). Results At day 21, the average dose of gabapentin for those still using it (n=68) was 653mg/24h (range 0-1800mg) and 54 (42%) reported benefits, of whom 7 (6%) experienced complete pain resolution. Harms were reported in 39/127 (30%) patients at day 7, the most frequent of which were cognitive disturbance, somnolence, nausea and dizziness. Ten patients had their medication ceased due to harms. The presence of significant comorbidities, higher dose and increasing age increased the likelihood of harm. Conclusions Overall, 42% of people experienced benefit at a level that resulted in continued use at 21 days

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study the following model for population abundances in $n$ patches: the conditional law of $X_{t+dt}$ given $X_t=x$ is such that when $dt$ is small the conditional mean of $X_{t+dt}^i-X_t^i$ is approximately $[x^i\mu_i+\sum_j(x^j D_{ji}-x^i D_{ij})]dt$, where $X_t^i$ and $\mu_i$ are the abundance and per capita growth rate in the $i$-th patch respectivly, and $D_{ij}$ is the dispersal rate from the $i$-th to the $j$-th patch, and the conditional covariance of $X_{t+dt}^i-X_t^i$ and $X_{t+dt}^j-X_t^j$ is approximately $x^i x^j \sigma_{ij}dt$. We show for such a spatially extended population that if $S_t=(X_t^1+...+X_t^n)$ is the total population abundance, then $Y_t=X_t/S_t$, the vector of patch proportions, converges in law to a random vector $Y_\infty$ as $t\to\infty$, and the stochastic growth rate $\lim_{t\to\infty}t^{-1}\log S_t$ equals the space-time average per-capita growth rate \sum_i\mu_i\E[Y_\infty^i] experienced by the population minus half of the space-time average temporal variation \E[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j] experienced by the population. We derive analytic results for the law of $Y_\infty$, find which choice of the dispersal mechanism $D$ produces an optimal stochastic growth rate for a freely dispersing population, and investigate the effect on the stochastic growth rate of constraints on dispersal rates. Our results provide fundamental insights into "ideal free" movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology.Comment: 47 pages, 4 figure

Better off dead: assessment of aquatic disinfectants and thermal shock treatments to prevent the spread of invasive freshwater bivalves

Biosecurity protocols designed to prevent further spread of invasive alien species have become a key component of invader management strategies. Yet, the species-specific efficacy of many biosecurity treatments are frequently unclear or unknown. Invasive quagga, Dreissena bugensis, and zebra mussels, D. polymorpha, are a serious threat to freshwater ecosystems worldwide. Here, we examine the effectiveness of immersion (≤ 90 min) within 2% or 4% solutions for two commonly used disinfectants (Virasure® Aquatic and Virkon® Aquatic) to cause mortality of adult Dreissena bivalves. Further, we assessed the effectiveness of thermal treatments: steam spray (≥ 100 °C; ≤ 120 s); hot air (− 500 °C; ≤ 60 s); and dry ice exposure (− 78 °C; ≤ 300 g; 15 min). Complete mortality of D. polymorpha was observed following exposure to both disinfectants for 90 min, at both concentrations. However, high but incomplete mortality (40–90%) was recorded for D. bugensis across disinfectant treatments. For both species, complete mortality was achieved following 30 s of steam. In addition, 10 s of hot air and 15 min exposure to 300 g of dry ice can both completely killed groups of D. polymorpha. Overall, although the disinfectants did not cause complete mortality, it appears that relatively brief exposure to thermal treatments could be used to curtail the further spread of Dreissena species

The effectiveness of hot water pressurized spray in field conditions to slow the spread of invasive alien species

An array of vectors have been identified that pose a risk of spreading invasive alien species (IAS), from personal protective equipment to large equipment such as vehicles and boats. Biosecurity practices that remove and/or kill IAS reduce the risk of accidental spread. The effectiveness of biosecurity protocols suitable for large equipment is little tested and requires development. One widely-used biosecurity method for large equipment is high-pressure hot water spray machines. This study tests the effectiveness of high-pressure hot water spray to induce mortality in two invasive aquatic plants: floating pennywort (Hydrocotyle ranunculoides) and Australian swamp-stonecrop (Crassula helmsii); and two invasive invertebrates: killer shrimp (Dikerogammarus villosus) and zebra mussel (Dreissena polymorpha) in field conditions. IAS were exposed to hot water spray for a range of durations (5–15 seconds) and from a range of distances (10–30 cm). Further treatments of up to 90 seconds were applied to C. helmsii. Complete survival of D. polymorpha, D. villosus and C. helmsii was seen in all control treatments following exposure to cold water spray. Hot water spray caused complete mortality of D. polymorpha and D. villosus at 10 cm for 15 seconds, demonstrating the effectiveness of the hot water treatment in inducing mortality. However, treatments were less effective when applied at longer distances and shorter durations. In contrast, hot water spray was ineffective in causing mortality in C. helmsii, even at 90 seconds of exposure. Fragmentation and complete mortality was seen in H. ranunculoides following exposure to hot and cold water spray, therefore the pressure of the spray was associated with H. ranunculoides mortality. The use of hot water spray is effective against the aquatic invasive animals tested here, however to ensure complete mortality, the importance of both duration and distance of hot water spray application is highlighted. Hot water spray did cause complete mortality in H. ranunculoides but not in C. helmsii, therefore the need for treatment water containment and safe disposal is paramount to prevent spread of potentially viable propagules