Prospective reporting of statistical analysis plans for randomised controlled trials

In 2017, JAMA published a statistical analysis plan (SAP) guidance document for randomised clinical trials (RCTs). This guidance is part of the EQUATOR Network of reporting resources and includes a checklist of minimum items for reporting details of statistical analysis of RCTs [1]. While the clinical trial protocol should describe the principal features of the statistical analysis, a separate detailed SAP containing sufficient information to support replication by an independent statistician may be needed [2,3,4]

Combining Phylogeography with Distribution Modeling: Multiple Pleistocene Range Expansions in a Parthenogenetic Gecko from the Australian Arid Zone

Phylogenetic and geographic evidence suggest that many parthenogenetic organisms have evolved recently and have spread rapidly. These patterns play a critical role in our understanding of the relative merits of sexual versus asexual reproductive modes, yet their interpretation is often hampered by a lack of detail. Here we present a detailed phylogeographic study of a vertebrate parthenogen, the Australian gecko Heteronotia binoei, in combination with statistical and biophysical modeling of its distribution during the last glacial maximum. Parthenogenetic H. binoei occur in the Australian arid zone and have the widest range of any known vertebrate parthenogen. They are broadly sympatric with their sexual counterparts, from which they arose via hybridization. We have applied nested clade phylogeographic, effective migration, and mismatch distribution analyses to mitochondrial DNA (mtDNA) sequences obtained for 319 individuals sampled throughout the known geographic ranges of two parthenogenetic mitochondrial lineages. These analyses provide strong evidence for past range expansion events from west to east across the arid zone, and for continuing eastward range expansion. Parthenogen formation and range expansion events date to the late Pleistocene, with one lineage expanding from the northwest of its present range around 240,000 years ago and the second lineage expanding from the far west around 70,000 years ago. Statistical and biophysical distribution models support these inferences of recent range expansion, with suitable climatic conditions during the last glacial maximum most likely limited to parts of the arid zone north and west of much of the current ranges of these lineages. Combination of phylogeographic analyses and distribution modeling allowed considerably stronger inferences of the history of this complex than either would in isolation, illustrating the power of combining complementary analytical approaches

Interplay between Fermi gamma-ray lines and collider searches

We explore the interplay between lines in the gamma-ray spectrum and LHC searches involving missing energy and photons. As an example, we consider a singlet Dirac fermion dark matter with the mediator for Fermi gamma-ray line at 130 GeV. A new chiral or local U(1) symmetry makes weak-scale dark matter natural and provides the axion or Z 0 gauge boson as the mediator connecting between dark matter and electroweak gauge bosons. In these models, the mediator particle can be produced in association with a monophoton at colliders and it produces large missing energy through the decays into a DM pair or ZZ; Z with at least one Z decaying into a neutrino pair. We adopt the monophoton searches with large missing energy at the LHC and impose the bounds on the coupling and mass of the mediator field in the models. We show that the parameter space of the Z 0 mediation model is already strongly constrained by the LHC 8TeV data, whereas a certain region of the parameter space away from the resonance in axion-like mediator models are bounded. We foresee the monophoton bounds on the Z 0 and axion mediation models at the LHC 14 TeV

Predicting the Impact of Climate Change on Threatened Species in UK Waters

Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis) and angelshark (Squatina squatina)

Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10-30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements of mussel tissue temperature indicated errors of similar to 2.0-2.5 degrees C, during daily fluctuations that often exceeded 15 degrees-20 degrees C. Geographic patterns in thermal stress based on biomimetic logger measurements were generally far more complex than anticipated based only on 'habitat-level' measurements of air or sea surface temperature. This unique data set provides an opportunity to link physiological measurements with spatially-and temporally-explicit field observations of body temperature

Using quantitative breath sound measurements to predict lung function following resection

<p>Abstract</p> <p>Background</p> <p>Predicting postoperative lung function is important for estimating the risk of complications and long-term disability after pulmonary resection. We investigated the capability of vibration response imaging (VRI) as an alternative to lung scintigraphy for prediction of postoperative lung function in patients with intrathoracic malignancies.</p> <p>Methods</p> <p>Eighty-five patients with intrathoracic malignancies, considered candidates for lung resection, were prospectively studied. The projected postoperative (ppo) lung function was calculated using: perfusion scintigraphy, ventilation scintigraphy, and VRI. Two sets of assessments made: one for lobectomy and one for pneumonectomy. Clinical concordance was defined as both methods agreeing that either a patient was or was not a surgical candidate based on a ppoFEV₁% and ppoDLCO% > 40%.</p> <p>Results</p> <p>Limits of agreement between scintigraphy and VRI for ppo following lobectomy were -16.47% to 15.08% (mean difference = -0.70%;95%CI = -2.51% to 1.12%) and for pneumonectomy were -23.79% to 19.04% (mean difference = -2.38%;95%CI = -4.69% to -0.07%). Clinical concordance between VRI and scintigraphy was 73% for pneumonectomy and 98% for lobectomy. For patients who had surgery and postoperative lung function testing (<it>n </it>= 31), ppoFEV₁% using scintigraphic methods correlated with measured postoperative values better than projections using VRI, (adjusted R²= 0.32 scintigraphy; 0.20 VRI), however the difference between methods failed to reach statistical significance. Limits of agreement between measured FEV₁% postoperatively and ppoFEV₁% based on perfusion scintigraphy were -16.86% to 23.73% (mean difference = 3.44%;95%CI = -0.29% to 7.16%); based on VRI were -19.56% to 28.99% (mean difference = 4.72%;95%CI = 0.27% to 9.17%).</p> <p>Conclusions</p> <p>Further investigation of VRI as an alternative to lung scintigraphy for prediction of postoperative lung function is warranted.</p

A Novel Method to Adjust Efficacy Estimates for Uptake of Other Active Treatments in Long-Term Clinical Trials

BACKGROUND: When rates of uptake of other drugs differ between treatment arms in long-term trials, the true benefit or harm of the treatment may be underestimated. Methods to allow for such contamination have often been limited by failing to preserve the randomization comparisons. In the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) study, patients were randomized to fenofibrate or placebo, but during the trial many started additional drugs, particularly statins, more so in the placebo group. The effects of fenofibrate estimated by intention-to-treat were likely to have been attenuated. We aimed to quantify this effect and to develop a method for use in other long-term trials. METHODOLOGY/PRINCIPAL FINDINGS: We applied efficacies of statins and other cardiovascular drugs from meta-analyses of randomized trials to adjust the effect of fenofibrate in a penalized Cox model. We assumed that future cardiovascular disease events were reduced by an average of 24% by statins, and 20% by a first other major cardiovascular drug. We applied these estimates to each patient who took these drugs for the period they were on them. We also adjusted the analysis by the rate of discontinuing fenofibrate. Among 4,900 placebo patients, average statin use was 16% over five years. Among 4,895 assigned fenofibrate, statin use was 8% and nonuse of fenofibrate was 10%. In placebo patients, use of cardiovascular drugs was 1% to 3% higher. Before adjustment, fenofibrate was associated with an 11% reduction in coronary events (coronary heart disease death or myocardial infarction) (P = 0.16) and an 11% reduction in cardiovascular disease events (P = 0.04). After adjustment, the effects of fenofibrate on coronary events and cardiovascular disease events were 16% (P = 0.06) and 15% (P = 0.008), respectively. CONCLUSIONS/SIGNIFICANCE: This novel application of a penalized Cox model for adjustment of a trial estimate of treatment efficacy incorporates evidence-based estimates for other therapies, preserves comparisons between the randomized groups, and is applicable to other long-term trials. In the FIELD study example, the effects of fenofibrate on the risks of coronary heart disease and cardiovascular disease events were underestimated by up to one-third in the original analysis. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN64783481

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Evolutionary Origin and Phylogeography of the Diploid Obligate Parthenogen Artemia parthenogenetica (Branchiopoda: Anostraca)

Background: Understanding the evolutionary origin and the phylogeographic patterns of asexual taxa can shed light on the origin and maintenance of sexual reproduction. We assessed the geographic origin, genetic diversity, and phylogeographic history of obligate parthenogen diploid Artemia parthenogenetica populations, a widespread halophilic crustaceanPeer reviewe