Durga: An R package for effect size estimation and visualisation.

Statistical analysis and data visualisation are integral parts of science communication. One of the major issues in current data analysis practice is an over-dependency on - and misuse of - p-values. Researchers have been advocating for the estimation and reporting of effect sizes for quantitative research to enhance the clarity and effectiveness of data analysis. Reporting effect sizes in scientific publications has until now been mainly limited to numeric tables, even though effect size plotting is a more effective means of communicating results. We have developed the Durga R package for estimating and plotting effect sizes for paired and unpaired group comparisons. Durga allows users to estimate unstandardised and standardised effect sizes and bootstrapped confidence intervals of the effect sizes. The central functionality of Durga is to combine effect size visualisations with traditional plotting methods. Durga is a powerful statistical and data visualisation package that is easy to use, providing the flexibility to estimate effect sizes of paired and unpaired data using different statistical methods. Durga provides a plethora of options for plotting effect size, which allows users to plot data in the most informative and aesthetic way. Here, we introduce the package and its various functions. We further describe a workflow for estimating and plotting effect sizes using example data sets.

Nest excavators' learning walks in the Australian desert ant Melophorus bagoti.

The Australian red honey ant, Melophorus bagoti, stands out as the most thermophilic ant in Australia, engaging in all outdoor activities during the hottest periods of the day during summer months. This species of desert ants often navigates by means of path integration and learning landmark cues around the nest. In our study, we observed the outdoor activities of M. bagoti workers engaged in nest excavation, the maintenance of the nest structure, primarily by taking excess sand out of the nest. Before undertaking nest excavation, the ants conducted a single exploratory walk. Following their initial learning expedition, these ants then engaged in nest excavation activities. Consistent with previous findings on pre-foraging learning walks, after just one learning walk, the desert ants in our study demonstrated the ability to return home from locations 2 m away from the nest, although not from locations 4 m away. These findings indicate that even for activities like dumping excavated sand within a range of 5-10 cm outside the nest, these ants learn and utilize the visual landmark panorama around the nest.

Estimation of maternal and foetal risk of radiation-induced cancer from a survey of computed tomography pulmonary angiography and ventilation/perfusion lung scanning for diagnosing pulmonary embolism during pregnancy.

INTRODUCTION: While there are many papers on maternal and foetal radiation doses from computed tomography pulmonary angiography (CTPA) and ventilation/perfusion (V/Q) lung scanning examinations for diagnosing pulmonary embolism in pregnant patients, few have used clinical data to examine the patient lifetime attributable risk (LAR) of different cancer types. This paper aims to estimate the cancer risk from maternal radiation doses from CTPA and V/Q examinations and associated foetal doses. METHODS: Dosimetric data were determined for 267 pregnant patients who received CTPA and/or V/Q examinations over 8 years. Organ and foetal doses were determined using software allowing patient size variations for CTPA and using two different activity-to-organ dose conversion methods for V/Q scans. The LAR of cancer incidence was estimated using International Commission on Radiological Protection (ICRP) modelling including estimates of detriment. RESULTS: Estimated total cancer incidence was 23 and 22 cases per 100,000 for CTPA and V/Q examinations, respectively, with detriment estimates of 18 and 20 cases. Cancer incidence was evenly divided between lung and breast cancer for CTPA with lung cancer being 80% of all cancer for V/Q. The median foetal doses were 0.03 mSv for CTPA and 0.29 mSv for V/Q. Significant differences in estimated foetal dose for V/Q scans were obtained by the two different methods used. The differences in dose between the modes of CTPA scan acquisition highlight the importance of optimisation. CONCLUSION: Maternal cancer incidence and detriment were remarkably similar for each examination. Optimisation of examinations is critical for low-dose outcomes, particularly for CTPA examination.

Morphological ant mimics: constrained to imperfection?

Adaptive evolution relies on both heritable variation and selection. Variation is the raw material upon which selection acts, so any mechanism that limits or prevents the generation of heritable variation reduces the power of selection to lead to adaptation. Such limitations are termed evolutionary constraints. While it is widely accepted that constraints play an important role in shaping evolutionary outcomes, their relative importance, as opposed to adaptation, in determining evolutionary outcomes remains a subject of debate. Evolutionary constraints are often evoked as the reason behind the persistence of inaccurate mimicry. Here, we compared the variation and accuracy of body-shape mimicry in ant-mimicking spiders with that of ant-mimicking insects, predicting greater constraints, and hence inaccuracy, in spiders mimicking ants, due to their evolutionary distance from the ant model. We found high inter-species variation in mimetic accuracy, but dorsally, no overall difference in mimetic accuracy between spider and insect mimics, which is inconsistent with a constraint causing inaccurate mimicry. Our study provides empirical evidence suggesting that imperfect mimicry in spiders and insects is predominantly shaped by adaptive processes rather than constraints or chance. Our findings contribute to our understanding of the mechanisms underlying evolutionary diversity and the processes that shape phenotypic outcomes.

Intraspecific body size variation and allometry of genitalia in the orb-web spider-Argiope lobata.

The current consensus is that sexual selection is responsible for the rapid and diverse evolution of genitalia, with several mutually exclusive mechanisms under debate, including non-antagonistic, antagonistic and stabilizing mechanisms. We used the orb-web spider, Argiope lobata (Araneidae), as a study model to quantify the allometric relationship between body size and genitalia, and to test for any impact of genital structures on male mating success or outcome in terms of copulation duration, leg loss or cannibalism. Our data do not support the 'one-size-fits-all' hypothesis that predicts a negative allometric slope between genitalia and body size. Importantly, we measured both male and female genitalia, and there was no sex specific pattern in allometric slopes. Unexpectedly, we found no predictor for reproductive success as indicated by copulation duration, cannibalism, and leg loss.

Fast acrobatic maneuvers enable arboreal spiders to hunt dangerous prey.

Spiders, the most specious taxon of predators, have evolved an astounding range of predatory strategies, including group hunting, specialized silk traps, pheromone-loaded bolas, and aggressive mimicry. Spiders that hunt prey defended with behavioral, mechanical, or chemical means are under additional selection pressure to avoid injury and death. Ants are considered dangerous because they can harm or kill their predators, but some groups of spiders, such as the Theridiidae, have a very high diversification of ant-hunting species and strategies [J. Liu et al., Mol. Phylogenet. Evol. 94, 658-675 (2016)]. Here, we provide detailed behavioral analyses of the highly acrobatic Australian ant-slayer spider, Euryopis umbilicata (Theridiidae), that captures much larger and defended Camponotus ants on vertical tree trunks. The hunting sequence consists of ritualized steps performed within split seconds, resulting in an exceptionally high prey capture success rate.

AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size.

Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.

Novel decorating behaviour of silk retreats in a challenging habitat.

Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat.

Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?

Many animals mimic dangerous or undesirable prey as a defence from predators. We would expect predators to reliably avoid animals that closely resemble dangerous prey, yet imperfect mimics are common across a wide taxonomic range. There have been many hypotheses suggested to explain imperfect mimicry, but comparative tests across multiple mimicry systems are needed to determine which are applicable, and which-if any-represent general principles governing imperfect mimicry. We tested four hypotheses on Australian ant mimics and found support for only one of them: the information limitation hypothesis. A predator with incomplete information will be unable to discriminate some poor mimics from their models. We further present a simple model to show that predators are likely to operate with incomplete information because they forage and make decisions while they are learning, so might never learn to properly discriminate poor mimics from their models. We found no evidence that one accurate mimetic trait can compensate for, or constrain, another, or that rapid movement reduces selection pressure for good mimicry. We argue that information limitation may be a general principle behind imperfect mimicry of complex traits, while interactions between components of mimicry are unlikely to provide a general explanation for imperfect mimicry.

Analysis of patient breast dose from a mammographic biopsy unit.

Further assessment of suspicious lesions found during asymptomatic breast cancer screening is critical and involves mammographic follow up with biopsy. The X-ray procedure is complex and variable in nature and until now there is little information on the radiation dose to the breast or associated risks. A survey of radiation doses from a Siemens MammoTest prone biopsy with the support of a Sectra L30 AIR mammographic unit for workup and post clip images has been completed. Procedure details and outcomes, including radiographic and patient related variables have been collected and analysed using standard dosimetric formulation. The partial irradiation of the breast in biopsy and magnification views was considered. The average mean glandular breast dose was 5.13 mGy, comprising of 3.52 mGy from the biopsy procedure and 1.61 mGy from the workup and post clip images, with an average of 8.4 biopsy images and 5.8 workup and post clip images. The risk from these dose levels are dependent on the age of the woman, however are not considered high for a symptomatic X-ray procedure.

Dosimetric impact of breast density in breast tomosynthesis: A comparative study.

A radiation dose survey has been undertaken involving 256 patients to investigate the dosimetric impact of breast tomosynthesis screening by employing different breast densities estimated by the Dance model, 50-50 breast model, and patient-specific density software: Volpara. Mean glandular dose (MGD) based on the Dance model provided the most realistic dose estimate with an average difference of -3.3 ± 4.8% from the patient-specific estimation. Average differences of -8.2 ± 6.5% and -7.3 ± 4.7% were observed for the 50-50 breast model and console MGD, respectively. We conclude that the Dance model should be used for dose calculations in radiation dose surveys and establishing diagnostic reference levels (DRL).

Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests.

Clearwing moths are known for their physical resemblance to hymenopterans, but the extent of their behavioural mimicry is unknown. We describe zigzag flights of sesiid bee mimics that are nearly indistinguishable from those of sympatric bees, whereas sesiid wasp mimics display faster, straighter flights more akin to those of wasps. In particular, the flight of the sesiids Heterosphecia pahangensis, Aschistophleps argentifasciata and Pyrophleps cruentata resembles both Tetragonilla collina and T. atripes stingless bees and, to a lesser extent, dwarf honeybees Apis andreniformis, whereas the sesiid Pyrophleps sp. resembles Tachysphex sp. wasps. These findings represent the first experimental evidence for behavioural mimicry in clearwing moths.

The impact of patient table on size-specific dose estimate (SSDE).

The use of parameters water equivalent diameter (D W ) and size-specific dose estimate (SSDE) are becoming increasingly established as a recognised method to relate patient dose from a CT examination to the dose indicator volume CT dose index (CTDIVOL). However, the role of the attenuation due to the patient table in these estimations requires careful consideration and is the subject of this study. The aim of this study is to investigate the impact of a minimal part of the patient table when calculating the D W and SSDE. We investigated 164 patients who had undergone CT examinations for the pelvis, abdomen, thorax and head. We subsequently calculated D W and SSDE using two methods: one using a small circular region of interest (ROI) including a minimal part of the patient table and the other using a ROI fitted to the patient border alone. The results showed that the water equivalent diameter calculated with the table included in the ROI (D W,t ) is greater, compared to that without the consideration of the patient table (D W,nt ), by 1.5-6.2% depending on the anatomy being imaged. On the other hand, the SSDE calculated with inclusion of the patient table (SSDEt) is smaller than otherwise (SSDEnt) by 1.0-5.5% again depending on the anatomy being imaged. The effect of the patient table on D W and SSDE in the thorax CT examination was statistically significant, but its effect on D W and SSDE in the other examinations of head, pelvis and abdomen was relatively small and not statistically significant.

Liver retraction system by C3-muco-adhesive polymer films for laparoscopic surgery.

BACKGROUND: Conventional laparoscopic instruments used for retraction may cause trauma at the retraction site. Alternative retraction/lifting especially of heavy solid organs such as the liver may be obtained by other means. The present study was designed to explore the use of C3-muco-adhesive polymers (C3-MAPs), which exhibit strong binding to the liver shortly after application to the organ and which retain strong adhesion for sufficient time, to enable sustained retraction during laparoscopic operations. METHODS AND MATERIALS: C3-muco-adhesive polymers were produced specifically for the study. In an ex vivo experimental set-up, discs of C3-MAPs were placed on the surface of porcine livers for adhesion and retraction studies involving objective measurements by tensiometry. RESULTS: Experiments were carried out on 14 porcine livers. The force required to detach the C3-MAPs from the liver exceeded 2.0 N 30 s after application. The adhesion force by C3-MAPs files was sufficient to enable sustained retraction force necessary for exposure of the gall bladder, which was achieved by a mean retraction force of 4.85 N (SD = 0.63). This was sustained for a mean of 130 min (range 17.0-240.0). In the adhesion studies, the forces at 30 s required to detach the polymer discs from the liver exceeded 20 N (upper limit of the load cells of the Instron). The duration of the adhesion enabled sustained optimal gall bladder exposure for periods ranging from 17 to 240 min, with a mean of 130 ± 91 min. CONCLUSIONS: The results of the present study demonstrate that the adhesion and retraction properties of the engineered C3-MAP films are sufficient to enable complete exposure of the gall bladder for a period exceeding 1 h, confirming their potential for atraumatic retraction in laparoscopic and other minimal-access surgical approaches.

Investigation of the clinical performance of a novel solid-state diagnostic dosimeter.

This study investigated the clinical performance of a novel solid-state diagnostic dosimeter, the RaySafe Xi transparent detector, by comparing its performance to a reference-class ionization chamber. Firstly a comparison of dosimeter response "free-in-air" with standard beam qualities was made, followed by an investigation into its relative transparency in an X-ray field and angular sensitivity dependence. The second part of the study looked at the overall performance of the transparent detector under scatter conditions with a number of beam qualities, including standard beam and those hardened by copper (Cu) filtration of thickness up to 0.9 mm, as would be encountered in the equipment testing of fluoroscopy systems. Overall, the transparent detector has demonstrated equivalent measurement properties to the ionization chamber under standard conditions and provided similar X-ray attenuation as reflected by the nearly identical radiographic parameters selected for both dosimeters by the automatic dose rate control (ADRC) system. Yet, it also possessed an asymmetric angular response which respectively under- and overestimated the dose contribution from the rear and lateral directions by the same amount of 50%. The transparent detector provided comparable dose reading of ± 3% to the ionization chamber with standard beam qualities and backscatter radiation present. These results were in good agreement with those of free-in-air measurement, indicating that the angular under- and overresponse might potentially compensate one another for accurate measurement. However, for identical Cu filtered beam qualities and setups, the transparent detector on average overresponded by 5.4% across the useful tube voltage range. In conclusion, the transparent detector, with its novel design, is essentially equivalent, within a 5% tolerance, to an ionization chamber, except in situations where beams hardened with Cu filtration are used with backscatter radiation present requiring larger uncertainty error estimations.

Measurement of radiotherapy CBCT dose in a phantom using different methods.

Cone beam computed tomography (CBCT) is used widely for the precise and accurate patient set up needed during radiation therapy, notably for hypo fractionated treatments, such as intensity modulated radiation therapy and stereotactic radiation therapy. Reported doses associated with CBCT indicate the potential to approach radiation tolerance levels for some critical organs. However while some manufacturers state the CBCT dose for each standard protocol, currently there are no standard or recognised protocols for CBCT dosimetry. This study has applied wide beam computed tomography dosimetry approaches as reported by the International Atomic Energy Agency and the American Association of Physicists in Medicine to investigate dosimetry for the Varian Trilogy linear accelerator with on-board imager v1.5. Three detection methods were used including (i) the use of both 100 mm and 300 mm pencil ionisation chambers, (ii) a 0.6 cm(3) ionisation chamber and (iii) gafchromic film. Measurements were performed using custom built 45 cm long PMMA phantoms as well as standard 15 cm long phantoms for both head and body simulation. The results showed good agreement between each other detector system (within 3 %). The measured CBCT dose for the above methods showed a large difference to the dose stated by Varian, with the measured dose being 40 % over the stated dose for the standard head protocol. This shows the importance of independently verifying the stated dose given by the vendor for standard procedures.

Benefits of dual-axis rotational coronary angiography in routine clinical practice.

Dual-axis rotational coronary angiography (DARCA) is a new imaging technique involving three-dimensional rotation of the gantry around the patient with simultaneous left to right and craniocaudal movements. This allows complete imaging of the left or right coronary tree with a single acquisition run. Previous small studies have indicated that DARCA is associated with reduced radiation dose and contrast use in comparison with standard coronary angiography (SCA). We conducted a registry of unselected patients undergoing DARCA or SCA. DARCA was used in 107 patients and SCA in 105 patients. Mean number of acquisition runs was 2.6 for DARCA and 6.9 for SCA (P < 0.0001). Mean radiation dose (dose-area product, DAP) was 30.4 Gy cm(2) for SCA and 15.9 Gy cm(2) for DARCA (P < 0.0001). Mean contrast volume was 41.7 ml for SCA and 25.7 ml for DARCA (P < 0.0001). Case time for DARCA in the first half of the study was 20.8 ± 1.4 min compared with 15.2 ± 2.0 min in the second half of the study (P = 0.0015), suggesting a learning curve. In the DARCA group, 64 % of patients required only two acquisition runs for complete and satisfactory imaging. There were no adverse effects resulting from DARCA. Two cases are presented to illustrate the diagnostic ability of DARCA. DARCA was associated with a 48 % reduction in radiation dose and 36 % reduction in contrast volume in comparison with SCA, with comparable diagnostic ability.

Mucoadhesive polymer films for tissue retraction in laparoscopic surgery: Ex-vivo study on their mechanical properties.

Safe and effective manipulation of soft tissue during laparoscopic procedures can be achieved by the use of mucoadhesive polymer films. A series of novel adhesive polymer films were formulated in house based on either Carbopol or Chitosan modified systems. The mechanical properties of the polymers and their adherence to bowel were evaluated using ex-vivo pig bowel immersed in 37°C water bath and connected to an Instron tensiometer. Young's modulus was 300 kPa for the Carbopol-polymer and 5 kPa for the Chitosan-polymer. The Chitosan-polymer exhibited much larger shear adhesion than its tensile adhesion: 3.4 N vs. 1.2. Both tensile and shear adhesions contributed to the large retraction force (2.6 N) obtained during l polymer-bowel retraction testing. Work of adhesion at the polymer/serosa interface, defined as the area under the force curve, was 64 mJ, which is appreciably larger than that reported with existing polymers. In conclusion, adhesive polymers can stick to the serosal side of the bowel with an adhesive force, which is sufficient to lift the bowel, providing a lower retraction stress than that caused by laparoscopic grasping which induces high localized pressures on the tissue.