Population Size Influences Amphibian Detection Probability: Implications for Biodiversity Monitoring Programs

Monitoring is an integral part of species conservation. Monitoring programs must take imperfect detection of species into account in order to be reliable. Theory suggests that detection probability may be determined by population size but this relationship has not yet been assessed empirically. Population size is particularly important because it may induce heterogeneity in detection probability and thereby cause bias in estimates of biodiversity. We used a site occupancy model to analyse data from a volunteer-based amphibian monitoring program to assess how well different variables explain variation in detection probability. An index to population size best explained detection probabilities for four out of six species (to avoid circular reasoning, we used the count of individuals at a previous site visit as an index to current population size). The relationship between the population index and detection probability was positive. Commonly used weather variables best explained detection probabilities for two out of six species. Estimates of site occupancy probabilities differed depending on whether the population index was or was not used to model detection probability. The relationship between the population index and detectability has implications for the design of monitoring and species conservation. Most importantly, because many small populations are likely to be overlooked, monitoring programs should be designed in such a way that small populations are not overlooked. The results also imply that methods cannot be standardized in such a way that detection probabilities are constant. As we have shown here, one can easily account for variation in population size in the analysis of data from long-term monitoring programs by using counts of individuals from surveys at the same site in previous years. Accounting for variation in population size is important because it can affect the results of long-term monitoring programs and ultimately the conservation of imperiled species

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Impact of Chronic Neonicotinoid Exposure on Honeybee Colony Performance and Queen Supersedure

Background Honeybees provide economically and ecologically vital pollination services to crops and wild plants. During the last decade elevated colony losses have been documented in Europe and North America. Despite growing consensus on the involvement of multiple causal factors, the underlying interactions impacting on honeybee health and colony failure are not fully resolved. Parasites and pathogens are among the main candidates, but sublethal exposure to widespread agricultural pesticides may also affect bees. Methodology/Principal Findings To investigate effects of sublethal dietary neonicotinoid exposure on honeybee colony performance, a fully crossed experimental design was implemented using 24 colonies, including sister-queens from two different strains, and experimental in-hive pollen feeding with or without environmentally relevant concentrations of thiamethoxam and clothianidin. Honeybee colonies chronically exposed to both neonicotinoids over two brood cycles exhibited decreased performance in the short-term resulting in declining numbers of adult bees (−28%) and brood (−13%), as well as a reduction in honey production (−29%) and pollen collections (−19%), but colonies recovered in the medium-term and overwintered successfully. However, significantly decelerated growth of neonicotinoid-exposed colonies during the following spring was associated with queen failure, revealing previously undocumented long-term impacts of neonicotinoids: queen supersedure was observed for 60% of the neonicotinoid-exposed colonies within a one year period, but not for control colonies. Linked to this, neonicotinoid exposure was significantly associated with a reduced propensity to swarm during the next spring. Both short-term and long-term effects of neonicotinoids on colony performance were significantly influenced by the honeybees’ genetic background. Conclusions/Significance Sublethal neonicotinoid exposure did not provoke increased winter losses. Yet, significant detrimental short and long-term impacts on colony performance and queen fate suggest that neonicotinoids may contribute to colony weakening in a complex manner. Further, we highlight the importance of the genetic basis of neonicotinoid susceptibility in honeybees which can vary substantially

Unbiased Recursive Partitioning Enables Robust and Reliable Outcome Prediction in Acute Spinal Cord Injury

Neurological disorders usually present very heterogeneous recovery patterns. Nonetheless, accurate prediction of future clinical end-points and robust definition of homogeneous cohorts are necessary for scientific investigation and targeted care. For this, unbiased recursive partitioning with conditional inference trees (URP-CTREE) have received increasing attention in medical research, especially, but not limited to traumatic spinal cord injuries (SCIs). URP-CTREE was introduced to SCI as a clinical guidance tool to explore and define homogeneous outcome groups by clinical means, while providing high accuracy in predicting future clinical outcomes. The validity and predictive value of URP-CTREE to provide improvements compared with other more common approaches applied by clinicians has recently come under critical scrutiny. Therefore, a comprehensive simulation study based on traumatic, cervical complete spinal cord injuries provides a framework to investigate and quantify the issues raised. First, we assessed the replicability and robustness of URP-CTREE to identify homogeneous subgroups. Second, we implemented a prediction performance comparison of URP-CTREE with traditional statistical techniques, such as linear or logistic regression, and a novel machine learning method. URP-CTREE's ability to identify homogeneous subgroups proved to be replicable and robust. In terms of prediction, URP-CTREE yielded a high prognostic performance comparable to a machine learning algorithm. The simulation study provides strong evidence for the robustness of URP-CTREE, which is achieved without compromising prediction accuracy. The slightly lower prediction performance is offset by URP-CTREE's straightforward interpretation and application in clinical settings based on simple, data-driven decision rules

Autoregressive transitional ordinal model to test for treatment effect in neurological trials with complex endpoints

Background: A number of potential therapeutic approaches for neurological disorders have failed to provide convincing evidence of efficacy, prompting pharmaceutical and health companies to discontinue their involvement in drug development. Limitations in the statistical analysis of complex endpoints have very likely had a negative impact on the translational process. Methods: We propose a transitional ordinal model with an autoregressive component to overcome previous limitations in the analysis of Upper Extremity Motor Scores, a relevant endpoint in the field of Spinal Cord Injury. Statistical power and clinical interpretation of estimated treatment effects of the proposed model were compared to routinely employed approaches in a large simulation study of two-arm randomized clinical trials. A revisitation of a key historical trial provides further comparison between the different analysis approaches. Results: The proposed model outperformed all other approaches in virtually all simulation settings, achieving on average 14 % higher statistical power than the respective second-best performing approach (range: -1 %, +34 %). Only the transitional model allows treatment effect estimates to be interpreted as conditional odds ratios, providing clear interpretation and visualization. Conclusion: The proposed model takes into account the complex ordinal nature of the endpoint under investigation and explicitly accounts for relevant prognostic factors such as lesion level and baseline information. Superior statistical power, combined with clear clinical interpretation of estimated treatment effects and widespread availability in commercial software, are strong arguments for clinicians and trial scientists to adopt, and further extend, the proposed approach.Other UBCNon UBCReviewedFacult

Pollen collections.

<p>Mean (±SD) fresh weights of pollen collections for control (black) and neonicotinoid-exposed (white) colonies over the course of the treatment period (pollen-trap contents were weighed in 2-2–3 days intervals throughout the study).</p

Dynamics of honeybee colony performance.

<p>Data of all three endpoints number of adult bees (A), eggs and larvae (B) and pupae (C) for the different pollen feeding treatments (black  =  control; red  =  neonicotinoids) and honeybee strains (circles  =  strain A; crosses  =  strain B). The data were obtained at four successive colony assessment dates (X-axis subpanels within figures) performed before (Spring 2011) and directly after the 1.5 months of experimental pollen feeding (Summer 2011), 3.5 months after the treatment (Autumn 2011) and one year later (Spring 2012). Estimated numbers on the Y-axes are truncated for adult bees and pupae for better overview.</p

Model-based estimates of contrasts and corresponding significance levels of the treatment effect (neonicotinoid <i>versus</i> control) and honeybee genetics (strain A <i>vs.</i> strain B).

<p>Results are shown in the transformed scale for the three response variables adult bees, eggs and larvae and pupae assessed directly after the 1.5 months of treatment (Summer 2011), 3.5 months later (Autumn 2011) and 1 year later (Spring 2012). For adult bees and eggs and larvae (the models that included a significant threefold interaction between treatment, honeybee strain and assessment date) contrasts for treatment effects were also computed within individual honeybee strains at each assessment date. <i>P</i> values are adjusted for multiple testing. ***<i>P</i><0.001; **<i>P</i><0.01; *<i>P</i><0.05; <b>·</b> 0.05<<i>P</i><0.1.</p

Identifying homogeneous subgroups in neurological disorders: unbiased recursive partitioning in cervical complete spinal cord injury

BACKGROUND: The reliable stratification of homogeneous subgroups and the prediction of future clinical outcomes within heterogeneous neurological disorders is a particularly challenging task. Nonetheless, it is essential for the implementation of targeted care and effective therapeutic interventions. OBJECTIVE: This study was designed to assess the value of a recently developed regression tool from the family of unbiased recursive partitioning methods in comparison to established statistical approaches (eg, linear and logistic regression) for predicting clinical endpoints and for prospective patients' stratification for clinical trials. METHODS: A retrospective, longitudinal analysis of prospectively collected neurological data from the European Multicenter study about Spinal Cord Injury (EMSCI) network was undertaken on C4-C6 cervical sensorimotor complete subjects. Predictors were based on a broad set of early (<2 weeks) clinical assessments. Endpoints were based on later clinical examinations of upper extremity motor scores and recovery of motor levels, at 6 and 12 months, respectively. Prediction accuracy for each statistical analysis was quantified by resampling techniques. RESULTS: For all settings, overlapping confidence intervals indicated similar prediction accuracy of unbiased recursive partitioning to established statistical approaches. In addition, unbiased recursive partitioning provided a direct way of identification of more homogeneous subgroups. The partitioning is carried out in a data-driven manner, independently from a priori decisions or predefined thresholds. CONCLUSION: Unbiased recursive partitioning techniques may improve prediction of future clinical endpoints and the planning of future SCI clinical trials by providing easily implementable, data-driven rationales for early patient stratification based on simple decision rules and clinical read-outs