On the Estimation of the Population Mean with Known Coefficient of Variation

For the estimation of population mean a class of estimators has been proposed when the coefficient of variation is known and its efficiency is compared with the usual unbiased estimator and the estimators suggested by various researchers. The properties of the proposed class of estimators have been also discussed in the case of normal population.     

Field test of an automated radio‐telemetry system: tracking local space use of aerial insectivores

Documenting local space use of birds that move rapidly, but are too small to carry GPS tags, such as swallows and swifts, can be challenging. For these species, tracking methods such as manual radio‐telemetry and visual observation are either inadequate or labor‐ and time‐intensive. Another option is use of an automated telemetry system, but equipment for such systems can be costly when many receivers are used. Our objective, therefore, was to determine if an automated radio‐telemetry system, consisting of just two receivers, could provide an alternative to manual tracking for gathering data on local space use of six individuals of three species of aerial insectivores, including one Cliff Swallow (Petrochelidon pyrrhonota), one Eastern Phoebe (Sayornis phoebe), and four Barn Swallows (Hirundo rustica). We established automated radio‐telemetry systems at three sites near the city of Peterborough in eastern Ontario, Canada, from May to August 2015. We evaluated the location error of our two‐receiver system using data from moving and stationary test transmitters at known locations, and used telemetry data from the aerial insectivores as a test of the system's ability to track rapidly moving birds under field conditions. Median location error was ~250 m for automated telemetry test locations after filtering. More than 90% of estimated locations had large location errors and were removed from analysis, including all locations > 1 km from receiver stations. Our automated telemetry receivers recorded 17,634 detections of the six radio‐tagged birds. However, filtering removed an average of 89% of bird location estimates, leaving only the Cliff Swallow with enough locations for analysis of space use. Our results demonstrate that a minimal automated radio‐telemetry system can be used to assess local space use by small, highly mobile birds, but the resolution of the data collected using only two receiver stations was coarse and had a limited range. To improve both location accuracy and increase the percentage of usable location estimates collected, we suggest that, in future studies, investigators use receivers that simultaneously record signals detected by all antennas, and use of a minimum of three receiver stations with more antennas at each station.     

Scale‐dependent biases in species counts in a grassland

Abstract. Numbers of plant species were recorded in species‐rich meadows in the Bílé Karpaty Mts., SE Czech Republic, with the aim to evaluate the sampling error made by well‐trained observers. Five observers recorded vascular plants in seven plots ranging from 9.8 cm² to 4 m² independently and were not time‐limited. In larger plots a discrepancy of 10–20% was found between individual estimates, in smaller plots discrepancy increased to 33%, on average. The gain in observed species richness by combining records of individual observers (in comparison with the mean numbers estimated by single observers) decreased from the smallest plot (27–82% for two to five observers) to the largest one (13–25%). However, after misidentified and suspicious records were eliminated, the gain was much lower and became scale‐independent; two observers added 12% species, on average, and the increase by combining species lists made by three or more observers was negligible (3% more on average). It is concluded that most discrepancies between individual observers were caused by misidentification of rare seedlings and young plants. We suggest that in species‐rich meadows plants should be recorded by at least three observers together and that they should consult all problematic plant specimens together in the field, to minimize errors.     

Higher patient doses through X-ray imaging procedures

Medical imaging using X-rays has been one of the most popular imaging modalities ever since the discovery of X-rays 125 years ago. With unquestionable benefits, concerns about radiation risks have frequently been raised. Computed tomography (CT) and fluoroscopic guided interventional procedures have the potential to impart higher radiation exposure to patients than radiographic examinations. Despite technological advances, there have been instances of increased doses per procedure mainly because of better diagnostic information in images. However, cumulative dose from multiple procedures is creating new concerns as effective doses >100 mSv are not uncommon. There is a need for action at all levels. Manufacturers must produce equipment that can provide a quality diagnostic image at substantially lesser dose and better implementation of optimization strategies by users. There is an urgent need for the industry to develop CT scanners with sub-mSv radiation dose, a goal that has been lingering. It appears that a new monochromatic X-ray source will lead to replacement of X-ray tubes all over the world in coming years and will lead to a drastic reduction in radiation doses. This innovation will impact all X-ray imaging and will help dose reduction. For interventional procedures, the likely employment of robotic systems in practice may drastically reduce radiation exposures to operators- but patient exposure will still remain an issue. Training needs always need to be emphasized and practiced.     

EMG gait data from indwelling electrodes is attenuated over time and changes independent of any experimental effect

The effect of time on the validity of electromyography (EMG) signals from indwelling fine-wire electrodes has not been explored. This is important because experiments using intramuscular electrodes are often long and biochemical and mechanical factors, may impair measurement accuracy over time. Measures over extended periods might therefore be erroneous. Twelve healthy participants (age = 33 ± 8 years) walked for 50 min at a controlled speed. Fine-wire electrodes were inserted into tibialis anterior and a surface EMG sensor attached near the fine-wire insertion site. EMG signals progressively and significantly decreased with time with the fine-wire electrode, but not the surface electrode. For the fine-wire electrode, after 25 min mean amplitude had reduced by 11% (p < 0.001) and after 50 min by 16% (p < 0.001), and peak amplitude reduced 22% at 20 min (p = 0.006) and 37% at 50 min (p < 0.001). Reduced amplitude with indwelling EMG without concurrent changes in surface EMG signal suggests an important inconsistency in data from fine-wire EMG electrodes. Changes in EMG signal will occur over time independent of the experimental condition and this questions their use in experiments of more than 30 min. These results should impact on experimental study design. They also invite reinterpretation of prior literature and sensor innovation to improve measurement performance.     

Can we manage fisheries with the inherent uncertainty from eDNA?

Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.     

Observations on the Staining of Corynebacterium Diphtheriae

Albert's method, of staining diphtheria cultures consists of staining a fixed smear for one minute (some laboratories stain for five minutes) with a solution containing toluidine blue and malachite (or methyl) green, washing with water, and applying Albert's iodine for one minute. This procedure is discussed and criticized, and in addition the mechanism of the stain is elucidated. Also, the procedure which involves staining a fixed smear for one minute with Loeffler's alkaline methylene blue solution is discussed and criticized.

To overcome the objections to the above staining methods, a different method is proposed. This consists of staining a fixed smear with an acid solution of toluidine blue, washing with water, applying Albert's iodine for one minute, washing with water, and finally applying a safranin solution for 15-20 seconds. The theoretical basis for this method is presented.     

Colon tumour secretopeptidome: Insights into endogenous proteolytic cleavage events in the colon tumour microenvironment

The secretopeptidome comprises endogenous peptides derived from proteins secreted into the tumour microenvironment through classical and non-classical secretion. This study characterised the low-M_r (< 3 kDa) component of the human colon tumour (LIM1215, LIM1863) secretopeptidome, as a first step towards gaining insights into extracellular proteolytic cleavage events in the tumour microenvironment. Based on two biological replicates, this secretopeptidome isolation strategy utilised differential centrifugal ultrafiltration in combination with analytical RP-HPLC and nanoLC-MS/MS. Secreted peptides were identified using a combination of Mascot and post-processing analyses including MSPro re-scoring, extended feature sets and Percolator, resulting in 474 protein identifications from 1228 peptides (≤ 1% q-value, ≤ 5% PEP) — a 36% increase in peptide identifications when compared with conventional Mascot (homology ionscore thresholding). In both colon tumour models, 122 identified peptides were derived from 41 cell surface protein ectodomains, 23 peptides (12 proteins) from regulated intramembrane proteolysis (RIP), and 12 peptides (9 proteins) generated from intracellular domain proteolysis. Further analyses using the protease/substrate database MEROPS, (http://merops.sanger.ac.uk/), revealed 335 (71%) proteins classified as originating from classical/non-classical secretion, or the cell membrane. Of these, peptides were identified from 42 substrates in MEROPS with defined protease cleavage sites, while peptides generated from a further 205 substrates were fragmented by hitherto unknown proteases. A salient finding was the identification of peptides from 88 classical/non-classical secreted substrates in MEROPS, implicated in tumour progression and angiogenesis (FGFBP1, PLXDC2), cell–cell recognition and signalling (DDR1, GPA33), and tumour invasiveness and metastasis (MACC1, SMAGP); the nature of the proteases responsible for these proteolytic events is unknown. To confirm reproducibility of peptide fragment abundance in this study, we report the identification of a specific cleaved peptide fragment in the secretopeptidome from the colon-specific GPA33 antigen in 4/14 human CRC models. This improved secretopeptidome isolation and characterisation strategy has extended our understanding of endogenous peptides generated through proteolysis of classical/non-classical secreted proteins, extracellular proteolytic processing of cell surface membrane proteins, and peptides generated through RIP. The novel peptide cleavage site information in this study provides a useful first step in detailing proteolytic cleavage associated with tumourigenesis and the extracellular environment. This article is part of a Special Issue entitled: An Updated Secretome.     

Validation of discrete time-to-event prediction models in the presence of competing risks

Clinical prediction models play a key role in risk stratification, therapy assignment and many other fields of medical decision making. Before they can enter clinical practice, their usefulness has to be demonstrated using systematic validation. Methods to assess their predictive performance have been proposed for continuous, binary, and time-to-event outcomes, but the literature on validation methods for discrete time-to-event models with competing risks is sparse. The present paper tries to fill this gap and proposes new methodology to quantify discrimination, calibration, and prediction error (PE) for discrete time-to-event outcomes in the presence of competing risks. In our case study, the goal was to predict the risk of ventilator-associated pneumonia (VAP) attributed to Pseudomonas aeruginosa in intensive care units (ICUs). Competing events are extubation, death, and VAP due to other bacteria. The aim of this application is to validate complex prediction models developed in previous work on more recently available validation data.     

Outlier detection methods are still effective even using virtual species created with the probabilistic approach

Liu et al. (Journal of Biogeography, 2018, 45 :164–176) presented an approach to detect outliers in species distribution data by developing virtual species created using the threshold approach. Meynard et al. (Journal of biogeography, 2019, 46 :2141–2144) raised concerns about this approach stating that ‘using a probabilistic approach … may significantly change results’. Here we provide a new series of simulations using the two approaches and demonstrate that the outlier detection approach based on pseudo species distribution models was still effective when using the probabilistic approach, although the detection rate was lower than when using the threshold approach.