A simulation model of the Devils Hole pupfish population using monthly length-frequency distributions

The Devils Hole pupfish, Cyprinodon diabolis, is a federally-endangered fish that is endemic to Devils Hole, a discontiguous part of Death Valley National Park in Nye County, Nevada. Due to its status, Devils Hole pupfish monitoring must be non-obtrusive and thereby exclude techniques that require handling fish. Due to a recent decline in pupfish abundance, Devils Hole pupfish managers have expressed a need for a model that describes population dynamics. This population model would be used to identify vulnerable life history stage(s) and inform management actions. We constructed a set of individualbased simulation models designed to explore effects of population processes and evaluate assumptions. We developed a baseline model, whose output best resembled both observed length-frequency data and predicted intraannual abundance patterns. We then ran simulations with 5 % increases in egg-larval, juvenile, and adult survival rates to better understand Devils Hole pupfish life history, thereby helping identify vulnerable life history stages that should become the target of management actions. Simulation models with temporally constant adult, juvenile, and egg-larval survival rates were able to reproduce observed length-frequency distributions and predicted intra-annual population patterns. In particular, models with monthly adult and juvenile survival rates of 80 % and an egg-larval survival rate of 4.7 % replicated patterns in observed data. Population growth was most affected by 5 % increases in egg-larval survival, whereas adult and juvenile survival rates had similar but lesser effects on population growth. Outputs from the model were used to assess factors suspected of influencing Devils Hole pupfish population decline

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

<p>Abstract</p> <p>Background</p> <p>Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets.</p> <p>Results</p> <p>The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of <it>translators</it> required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data.</p> <p>Conclusions</p> <p>Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: <url>http://pypi.python.org/pypi/rpy2-bioconductor-extensions/</url></p

The influence of fine-scale topography on the impacts of Holocene fire in a Tasmanian montane landscape

Copyright © 2019 John Wiley & Sons, Ltd. Tasmania's montane temperate rainforests contain some of Australia's most ancient and endemic flora. Recent landscape-scale fires have impacted a significant portion of these rainforest ecosystems. The complex and rugged topography of Tasmania results in a highly variable influence of fire across the landscape, rendering predictions of ecosystem response to fire difficult. We assess the role of topographic variation in buffering the influence of fire in these endemic rainforest communities. We developed a new 14000-year (14-ka) palaeoecological dataset from Lake Perry, southern Tasmania, and compared it to neighbouring Lake Osborne

Inhibition of cell proliferation does not slow down echinoderm neural regeneration

BACKGROUND: Regeneration of the damaged central nervous system is one of the most interesting post-embryonic developmental phenomena. Two distinct cellular events have been implicated in supplying regenerative neurogenesis with cellular material – generation of new cells through cell proliferation and recruitment of already existing cells through cell migration. The relative contribution and importance of these two mechanisms is often unknown. METHODS: Here, we use the regenerating radial nerve cord (RNC) of the echinoderm Holothuria glaberrima as a model of extensive post-traumatic neurogenesis in the deuterostome central nervous system. To uncouple the effects of cell proliferation from those of cell migration, we treated regenerating animals with aphidicolin, a specific inhibitor of S-phase DNA replication. To monitor the effect of aphidicolin on DNA synthesis, we used BrdU immunocytochemistry. The specific radial glial marker ERG1 was used to label the regenerating RNC. Cell migration was tracked with vital staining with the lipophilic dye DiI. RESULTS: Aphidicolin treatment resulted in a significant 2.1-fold decrease in cell proliferation. In spite of this, the regenerating RNC in the treated animals did not differ in histological architecture, size and cell number from its counterpart in the control vehicle-treated animals. DiI labeling showed extensive cell migration in the RNC. Some cells migrated from as far as 2 mm away from the injury plane to contribute to the neural outgrowth. CONCLUSIONS: We suggest that inhibition of cell division in the regenerating RNC of H. glaberrima is compensated for by recruitment of cells, which migrate into the RNC outgrowth from deeper regions of the neuroepithelium. Neural regeneration in echinoderms is thus a highly regulative developmental phenomenon, in which the size of the cell pool can be controlled either by cell proliferation or cell migration, and the latter can neutralize perturbations in the former. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12983-017-0196-y) contains supplementary material, which is available to authorized users

CEO Compensation

This paper surveys the recent literature on CEO compensation. The rapid rise in CEO pay over the past 30 years has sparked an intense debate about the nature of the pay-setting process. Many view the high level of CEO compensation as the result of powerful managers setting their own pay. Others interpret high pay as the result of optimal contracting in a competitive market for managerial talent. We describe and discuss the empirical evidence on the evolution of CEO pay and on the relationship between pay and firm performance since the 1930s. Our review suggests that both managerial power and competitive market forces are important determinants of CEO pay, but that neither approach is fully consistent with the available evidence. We briefly discuss promising directions for future research

Game fence presence and permeability influences the local movement and distribution of South African mammals

Fences are utilized throughout the world to restrict the movements of wildlife, protecting them from threats and reducing human-wildlife conflict. In South Africa the number of privately-owned fenced game reserves has greatly increased in recent years, but little is known about how fencing affects the distribution and movements of target and non-target mammals. We surveyed 2m either side of the complete fence line of a recently established commercial game reserve in South Africa, identifying signs of animal presence (spoor, scat, foraging or other field signs) while also recording damage (holes) to the fence. Every 250m we carried out 100m perpendicular transects either side of the fence, recording vegetation cover and height at 10m intervals along the transect. We found that livestock (largely cattle) were excluded from the reserve. However, 12% of records of large animal species were recorded outside of the fence line. These species had been introduced to the reserve, strongly suggesting that they had crossed the boundary into the surrounding farmland. Sixteen naturally present wild species were found on both sides of the fence, but we found more evidence of their presence inside the reserve. Observational evidence suggests that they were regularly crossing the boundary, particularly where the fence was damaged, with hole size affecting species recorded. We also found evidence that the construction of the fence had led to a difference in vegetation structure with plant diversity and percentage of non-woody plant cover significantly higher inside the fence. While fencing was highly effective at preventing movement of livestock, introduced and wild animals were able to cross the boundary, via holes in the fence. This work shows that the efficacy of the most common approach to preventing animal movement around protected areas depends on the species being considered and fence condition

Variation of health-related quality of life assessed by caregivers and patients affected by severe childhood infections.

BACKGROUND: The agreement between self-reported and proxy measures of health status in ill children is not well established. This study aimed to quantify the variation in health-related quality of life (HRQOL) derived from young patients and their carers using different instruments. METHODS: A hospital-based cross-sectional survey was conducted between August 2010 and March 2011. Children with meningitis, bacteremia, pneumonia, acute otitis media, hearing loss, chronic lung disease, epilepsy, mild mental retardation, severe mental retardation, and mental retardation combined with epilepsy, aged between five to 14 years in seven tertiary hospitals were selected for participation in this study. The Health Utilities Index Mark 2 (HUI2), and Mark 3 (HUI3), and the EuroQoL Descriptive System (EQ-5D) and Visual Analogue Scale (EQ-VAS) were applied to both paediatric patients (self-assessment) and caregivers (proxy-assessment). RESULTS: The EQ-5D scores were lowest for acute conditions such as meningitis, bacteremia, and pneumonia, whereas the HUI3 scores were lowest for most chronic conditions such as hearing loss and severe mental retardation. Comparing patient and proxy scores (n = 74), the EQ-5D exhibited high correlation (r = 0.77) while in the HUI2 and HUI3 patient and caregiver scores were moderately correlated (r = 0.58 and 0.67 respectively). The mean difference between self and proxy-assessment using the HUI2, HUI3, EQ-5D and EQ-VAS scores were 0.03, 0.05, -0.03 and -0.02, respectively. In hearing-impaired and chronic lung patients the self-rated HRQOL differed significantly from their caregivers. CONCLUSIONS: The use of caregivers as proxies for measuring HRQOL in young patients affected by pneumococcal infection and its sequelae should be employed with caution. Given the high correlation between instruments, each of the HRQOL instruments appears acceptable apart from the EQ-VAS which exhibited low correlation with the others

Community health workers improve contact tracing among immigrants with tuberculosis in Barcelona

Background: The important increase in immigration during recent years has changed the epidemiology and control strategies for tuberculosis (TB) in many places. This study evaluates the effectiveness of intervention with community health workers (CHW) to improve contact tracing among immigrants. Methods: The study included all TB cases detected by the Barcelona TB Program from 2000 to 2005 and compared a period without CHW intervention (2000-2002) to a period with CHW intervention (2003-2005). The influence on contact tracing of sex, age, hospital of diagnosis, district of residence, birthplace, HIV, homeless and CHW intervention was analysed by logistic regression. Odds ratio (OR) and 95 % confidence intervals (CI) were calculated. Results: 960 foreign born TB cases were detected, 388 in the intervention period. Contact tracing was performed on 65,7 % of 201 smear-positive cases during the pre-intervention period compared to 81.6 % of 152 smear-positive TB cases during the intervention period (p &lt; 0.001). Risk factors associated with incomplete contact tracing of smear-positive index cases included being diagnosed in two hospitals without contact tracing TB unit (OR = 3.5; CI:1.4-8.9) and (OR = 4.6; CI:1.6-13.5) respectively, birth place in India-Pakistan (OR = 4.4; CI:1.9-10.3) or North Africa (OR = 4.3; CI:1.8-10.5), having an unknown residence (OR = 5.4; CI:1.6-18.0), being HIV-infected (OR = 6.1; CI:2.5-14.8