Strong “bottom‐up” influences on small mammal populations: State‐space model analyses from long‐term studies

“Bottom‐up” influences, that is, masting, plus population density and climate, commonly influence woodland rodent demography. However, “top‐down” influences (predation) also intervene. Here, we assess the impacts of masting, climate, and density on rodent populations placed in the context of what is known about “top‐down” influences. To explain between‐year variations in bank vole Myodes glareolus and wood mouse Apodemus sylvaticus population demography, we applied a state‐space model to 33 years of catch‐mark‐release live‐trapping, winter temperature, and precise mast‐collection data. Experimental mast additions aided interpretation. Rodent numbers in European ash Fraxinus excelsior woodland were estimated (May/June, November/December). December–March mean minimum daily temperature represented winter severity. Total marked adult mice/voles (and juveniles in May/June) provided density indices validated against a model‐generated population estimate; this allowed estimation of the structure of a time‐series model and the demographic impacts of the climatic/biological variables. During two winters of insignificant fruit‐fall, 6.79 g/m² sterilized ash seed (as fruit) was distributed over an equivalent woodland similarly live‐trapped. September–March fruit‐fall strongly increased bank vole spring reproductive rate and winter and summer population growth rates; colder winters weakly reduced winter population growth. September–March fruit‐fall and warmer winters marginally increased wood mouse spring reproductive rate and September–December fruit‐fall weakly elevated summer population growth. Density dependence significantly reduced both species' population growth. Fruit‐fall impacts on demography still appeared after a year. Experimental ash fruit addition confirmed its positive influence on bank vole winter population growth with probable moderation by colder temperatures. The models show the strong impact of masting as a “bottom‐up” influence on rodent demography, emphasizing independent masting and weather influences; delayed effects of masting; and the importance of density dependence and its interaction with masting. We conclude that these rodents show strong “bottom‐up” and density‐dependent influences on demography moderated by winter temperature. “Top‐down” influences appear weak and need further investigation.     

The short‐ and long‐term fitness consequences of natal dispersal in a wild bird population

Dispersal is a key process in population and evolutionary ecology. Individual decisions are affected by fitness consequences of dispersal, but these are difficult to measure in wild populations. A long‐term dataset on a geographically closed bird population, the Mauritius kestrel, offers a rare opportunity to explore fitness consequences. Females dispersed further when the availability of local breeding sites was limited, whereas male dispersal correlated with phenotypic traits. Female but not male fitness was lower when they dispersed longer distances compared to settling close to home. These results suggest a cost of dispersal in females. We found evidence of both short‐ and long‐term fitness consequences of natal dispersal in females, including reduced fecundity in early life and more rapid aging in later life. Taken together, our results indicate that dispersal in early life might shape life history strategies in wild populations.     

Long‐term cytological and histological outcomes in women managed with loop excision treatment under local anaesthetic for high‐grade cervical intraepithelial neoplasia

Y. L. Woo, C. Badley, E. Jackson and R. Crawford Long‐term cytological and histological outcomes in women managed with loop excision treatment under local anaesthetic for high‐grade cervical intraepithelial neoplasia Objective: This study examines the impact of excision margin status after large loop excision of the transformation zone (LLETZ) under local anaesthetic for high‐grade cervical intraepithelial neoplasia (HG‐CIN) on the cytological and histological outcomes up to 5 years after treatment. Methods: Prospective cytological and histological data were obtained by examination of the colposcopy database at Addenbrooke’s Hospital, Cambridge, UK. All women aged between 19 and 50 years who underwent treatment for HG‐CIN by LLETZ under local anaesthetic were included in the study. Patients without follow‐up data were excluded from the study. The excision margin status was correlated with the subsequent cytological and histological outcomes. Results: A series of 967 women with CIN2 and CIN3 underwent LLETZ excision under local anaesthetic. Overall, 42% of women had disease present at the excision margin following LLETZ. Women with CIN3 were more likely than those with CIN2 to have an involved excision margin (P < 0.0001). Cytological recurrence was highest at 12 months (16%) and did not correlate with the CIN grade or excision margin status. Histological recurrence/persistence was also highest at 12 months follow‐up (15%) and this correlated with grade of CIN and margin status (P < 0.0001). Conclusions: Histological recurrence/persistence correlates with grade of CIN and excision margin status. Management of HG‐CIN in an outpatient setting under local anaesthetic is safe, cost effective and yields a favourable long‐term outcome.     

Risk‐adjusted monitoring of time to event in the presence of long‐term survivors

The use of control charts for monitoring schemes in medical context should consider adjustments to incorporate the specific risk for each individual. Some authors propose the use of a risk‐adjusted survival time cumulative sum (RAST CUSUM) control chart to monitor a time‐to‐event outcome, possibly right censored, using conventional survival models, which do not contemplate the possibility of cure of a patient. We propose to extend this approach considering a risk‐adjusted CUSUM chart, based on a cure rate model. We consider a regression model in which the covariates affect the cure fraction. The CUSUM scores are obtained for Weibull and log‐logistic promotion time model to monitor a scale parameter for nonimmune individuals. A simulation study was conducted to evaluate and compare the performance of the proposed chart (RACUF CUSUM) with RAST CUSUM, based on optimal control limits and average run length in different situations. As a result, we note that the RAST CUSUM chart is inappropriate when applied to data with a cure rate, while the proposed RACUF CUSUM chart seems to have similar performance if applied to data without a cure rate. The proposed chart is illustrated with simulated data and with a real data set of patients with heart failure treated at the Heart Institute (InCor), at the University of São Paulo, Brazil.     

Estimation in the progressive illness‐death model: A nonexhaustive review

Multistate models can be successfully used for describing complex event history data, for example, describing stages in the disease progression of a patient. The so‐called “illness‐death” model plays a central role in the theory and practice of these models. Many time‐to‐event datasets from medical studies with multiple end points can be reduced to this generic structure. In these models one important goal is the modeling of transition rates but biomedical researchers are also interested in reporting interpretable results in a simple and summarized manner. These include estimates of predictive probabilities, such as the transition probabilities, occupation probabilities, cumulative incidence functions, and the sojourn time distributions. We will give a review of some of the available methods for estimating such quantities in the progressive illness‐death model conditionally (or not) on covariate measures. For some of these quantities estimators based on subsampling are employed. Subsampling, also referred to as landmarking, leads to small sample sizes and usually to heavily censored data leading to estimators with higher variability. To overcome this issue estimators based on a preliminary estimation (presmoothing) of the probability of censoring may be used. Among these, the presmoothed estimators for the cumulative incidences are new. We also introduce feasible estimation methods for the cumulative incidence function conditionally on covariate measures. The proposed methods are illustrated using real data. A comparative simulation study of several estimation approaches is performed and existing software in the form of R packages is discussed.     

A Bayesian Long‐term Survival Model Parametrized in the Cured Fraction

The main goal of this paper is to investigate a cure rate model that comprehends some well‐known proposals found in the literature. In our work the number of competing causes of the event of interest follows the negative binomial distribution. The model is conveniently reparametrized through the cured fraction, which is then linked to covariates by means of the logistic link. We explore the use of Markov chain Monte Carlo methods to develop a Bayesian analysis in the proposed model. The procedure is illustrated with a numerical example.     

Mesophyll CO2 conductance and leakiness are not responsive to short‐ and long‐term soil water limitations in the C4 plant Sorghum bicolor

Breeding economically important C₄ crops for enhanced whole‐plant water‐use efficiency (WUE_plant) is needed for sustainable agriculture. WUE_plant is a complex trait and an efficient phenotyping method that reports on components of WUE_plant, such as intrinsic water‐use efficiency (WUE_i, the rate of leaf CO₂ assimilation relative to water loss via stomatal conductance), is needed. In C₄ plants, theoretical models suggest that leaf carbon isotope composition (δ¹³C), when the efficiency of the CO₂‐concentrating mechanism (leakiness, ?) remains constant, can be used to screen for WUE_i. The limited information about how ? responds to water limitations confines the application of δ¹³C for WUE_i screening of C₄ crops. The current research aimed to test the response of ? to short‐ or long‐term moderate water limitations, and the relationship of δ¹³C with WUE_i and WUE_plant, by addressing potential mesophyll CO₂ conductance (g_m) and biochemical limitations in the C₄ plant Sorghum bicolor. We demonstrate that g_m and ? are not responsive to short‐ or long‐term water limitations. Additionally, δ¹³C was not correlated with gas‐exchange estimates of WUE_i under short‐ and long‐term water limitations, but showed a significant negative relationship with WUE_plant. The observed association between the δ¹³C and WUE_plant suggests an intrinsic link of δ¹³C with WUE_i in this C₄ plant, and can potentially be used as a screening tool for WUE_plant in sorghum.     

The contrasting effects of short‐ and long‐term habitat drainage on the population dynamics of freshwater turtles in a human‐dominated landscape

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Effects of long‐term straw return on soil organic carbon storage and sequestration rate in North China upland crops: A meta‐analysis

Soil organic carbon (SOC) is essential for soil fertility and climate change mitigation, and carbon can be sequestered in soil through proper soil management, including straw return. However, results of studies of long‐term straw return on SOC are contradictory and increasing SOC stocks in upland soils is challenging. This study of North China upland agricultural fields quantified the effects of several fertilizer and straw return treatments on SOC storage changes and crop yields, considering different cropping duration periods, soil types, and cropping systems to establish the relationships of SOC sequestration rates with initial SOC stocks and annual straw C inputs. Our meta‐analysis using long‐term field experiments showed that SOC stock responses to straw return were greater than that of mineral fertilizers alone. Black soils with higher initial SOC stocks also had lower SOC stock increases than did soils with lower initial SOC stocks (fluvo‐aquic and loessial soils) following applications of nitrogen‐phosphorous‐potassium (NPK) fertilizer and NPK+S (straw). Soil C stocks under the NPK and NPK+S treatments increased in the more‐than‐20‐year duration period, while significant SOC stock increases in the NP and NP+S treatment groups were limited to the 11‐ to 20‐year period. Annual crop productivity was higher in double‐cropped wheat and maize under all fertilization treatments, including control (no fertilization), than in the single‐crop systems (wheat or maize). Also, the annual soil sequestration rates and annual straw C inputs of the treatments with straw return (NP+S and NPK+S) were significantly positively related. Moreover, initial SOC stocks and SOC sequestration rates of those treatments were highly negatively correlated. Thus, long‐term straw return integrated with mineral fertilization in upland wheat and maize croplands leads to increased crop yields and SOC stocks. However, those effects of straw return are highly dependent on fertilizer management, cropping system, soil type, duration period, and the initial SOC content.     

Revegetation,restoration and reptiles in rural landscapes: Insights from long‐term monitoring programmes in the temperate eucalypt woodlands of south‐eastern Australia

Over the past decade, there has been a concerted effort to better understand the distribution and abundance of reptiles in agricultural landscapes and to specifically evaluate their response to revegetation (tree and shrub plantings) and habitat restoration in the wheat‐sheep belt of south‐eastern Australia. This article reviews the response of reptiles to revegetation and woodland management and provides ten insights and lessons that can be applied to help improve reptile conservation in temperate eucalypt woodlands and fragmented agricultural landscapes in Australia. The review focuses primarily on revegetation programmes conducted by Landcare and Greening Australia, and management interventions funded by Local Land Services in NSW and Catchment Management Authorities in Victoria.     

Effects of changes in the driving forces on water quality and plankton dynamics in three Swiss lakes – long‐term simulations with BELAMO

1. With a modified version of the lake model BELAMO, we were able to describe the essential features of the dynamics of nutrients, dissolved oxygen, phyto‐ and zooplankton in three lakes of different trophic status over periods of 19–30 years, with essentially the same model parameters for all three lakes. This is remarkable, as the measured nutrient inputs decreased considerably during the simulated time period. 2. Despite having done this before for a period of 4 years with an earlier version of the model, a considerable effort was required that led to a series of model modifications without which the data could not be matched. This demonstrates that long‐term calibration of a model that combines processes in the water column with mineralisation in the sediment can be difficult. 3. Due to the necessarily simplified processes within the model, there is a bias in its output. We applied a recently developed technique for model calibration and uncertainty analysis to address bias and multiple calibration criteria. To account for the demanding long‐term simulations, a simplified numerical implementation of this technique was used. 4. Our results demonstrate good understanding of the chemical state of the lake during the calibration period but less of the biological variables. The credibility intervals used to visualise this knowledge widen substantially during the prediction period (consisting of the last 10 years of the simulation). 5. The joint calibration of the model with long‐term data from lakes of different trophic status is possible but only with considerable prediction uncertainty. Due to the explicit consideration of bias in our calibration technique, we are able to estimate quantitatively the uncertainty of our knowledge about chemical and biological variables in the lake.