Zigzag persistence for coral reef resilience using a stochastic spatial model.

A complex interplay between species governs the evolution of spatial patterns in ecology. An open problem in the biological sciences is characterizing spatio-temporal data and understanding how changes at the local scale affect global dynamics/behaviour. Here, we extend a well-studied temporal mathematical model of coral reef dynamics to include stochastic and spatial interactions and generate data to study different ecological scenarios. We present descriptors to characterize patterns in heterogeneous spatio-temporal data surpassing spatially averaged measures. We apply these descriptors to simulated coral data and demonstrate the utility of two topological data analysis techniques-persistent homology and zigzag persistence-for characterizing mechanisms of reef resilience. We show that the introduction of local competition between species leads to the appearance of coral clusters in the reef. We use our analyses to distinguish temporal dynamics stemming from different initial configurations of coral, showing that the neighbourhood composition of coral sites determines their long-term survival. Using zigzag persistence, we determine which spatial configurations protect coral from extinction in different environments. Finally, we apply this toolkit of multi-scale methods to empirical coral reef data, which distinguish spatio-temporal reef dynamics in different locations, and demonstrate the applicability to a range of datasets.

How well do farmers know their badgers? Relating farmer knowledge to ecological survey data.

Knowledge of badger distribution is important for the management of bovine tuberculosis. At the farm level, typically the only information on badger activity available is from the farmers themselves. This study compares how well farmer perceptions of badger activity match data obtained from ecological surveys. Farmer estimates of numbers of badger setts (burrows) surrounding their farms were generally correlated with field survey results, but tended to be underestimates. Farmers correctly recorded 50 per cent of setts recorded in surveys, with larger setts and active setts more likely to be correctly recorded. Badger visits to farm buildings and yards were also monitored using surveillance cameras. The majority of farmers were aware of badger visits to their farm buildings, but in 22 per cent of cases farmers were not aware of badger visits. At the farm level, knowledge of badger activity will be useful in informing vets and animal health professionals of the potential risks of disease transmission, and hence directing management interventions. However, the tendency to underestimate activity, combined with a lack of detailed knowledge of sett locations, means that farmer estimates of badger activity should be interpreted with caution and in isolation may not be sufficient to inform management interventions.

lncRNA/MicroRNA interactions in the vasculature.

MicroRNA (miRNA) have gained widespread attention for their role in diverse vascular processes including angiogenesis, apoptosis, proliferation, and migration. Despite great understanding of miRNA expression and function, knowledge of long noncoding RNA (lncRNA) molecular mechanisms still remains limited. The influence of miRNA on lncRNA function, and the converse, is now beginning to emerge. lncRNA may regulate miRNA function by acting as endogenous sponges to regulate gene expression and miRNA have been shown to bind and regulate lncRNA stability. A detailed understanding of the molecular and cellular effects of lncRNA-miRNA-mediated interactions in vascular pathophysiology could pave the way for new diagnostic markers and therapeutic approaches, but first there is a requirement for a more detailed understanding of the impact of such regulatory networks.

Widespread exposure to lead affects the body condition of free-living whooper swans Cygnus cygnus wintering in Britain.

Lead poisoning, through the ingestion of spent lead gunshot, is an established cause of morbidity and mortality in waterbirds globally, but the thresholds at which blood levels begin to affect the physiology of birds in the wild are less well known. Here we determine the prevalence of lead exposure in whooper swans and, for the first time, identify the level of blood lead associated with initial reductions in body condition. Blood lead elevated above background levels (i.e. >20 µg dL(-1)) was found in 41.7% (125/300) of swans tested. Blood lead was significantly negatively associated with winter body condition when levels were ≥44 µg dL(-1) (27/260 = 10%). Our findings indicating that sub-lethal impacts of lead on body condition occur at the lower end of previously established clinical thresholds and that a relatively high proportion of individuals in this population may be affected, reaffirm the importance of reducing contamination of the environment with lead shot.

An invasive non-native mammal population conserves genetic diversity lost from its native range.

Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species' native range in Great Britain, we reveal the opposite effect. We demonstrate that the New Zealand stoat population contains four mitochondrial haplotypes that have not been found in the native range. Stoats in Britain rely heavily on introduced rabbits Oryctolagus cuniculus as their primary prey and were introduced to New Zealand in a misguided attempt at biological control of rabbits, which had also been introduced there. While invasive stoats have since decimated the New Zealand avifauna, native stoat populations were themselves decimated by the introduction to Britain of Myxoma virus as a control measure for rabbits. We highlight the irony that while introduced species (rabbits) and subsequent biocontrol (myxomatosis) have caused population crashes of native stoats, invasive stoats in New Zealand, which were also introduced for biological control, now contain more genetic haplotypes than their most likely native source.

Sex-related heterogeneity in the life-history correlates of Mycobacterium bovis infection in European badgers (Meles meles).

Heterogeneity in the progression of disease amongst individual wild animals may impact on both pathogen and host dynamics at the population level, through differential effects on transmission, mortality and reproductive output. The role of the European badger (Meles meles) as a reservoir host for Mycobacterium bovis infection in the UK and Ireland has been the focus of intense research for many years. Here, we investigate life-history correlates of infection in a high-density undisturbed badger population naturally infected with M. bovis. We found no evidence of a significant impact of M. bovis infection on female reproductive activity or success, with evidence of reproduction continuing successfully for several years in the face of M. bovis excretion. We also found evidence to support the hypothesis that female badgers are more resilient to established M. bovis infection than male badgers, with longer survival times following the detection of bacterial excretion. We discuss the importance of infectious breeding females in the persistence of M. bovis in badger populations, and how our findings in male badgers are consistent with testosterone-induced immunosuppression. In addition, we found significant weight loss in badgers with evidence of disseminated infection, based on the culture of M. bovis from body systems other than the respiratory tract. For females, there was a gradual loss of weight as infection progressed, whereas males only experienced substantial weight loss when infection had progressed to the point of dissemination. We discuss how these differences may be explained in terms of resource allocation and physiological trade-offs.

Heterogeneity in the risk of Mycobacterium bovis infection in European badger (Meles meles) cubs.

The behaviour of certain infected individuals within socially structured populations can have a disproportionately large effect on the spatio-temporal distribution of infection. Endemic infection with Mycobacterium bovis in European badgers (Meles meles) in Great Britain and Ireland is an important source of bovine tuberculosis in cattle. Here we quantify the risk of infection in badger cubs in a high-density wild badger population, in relation to the infection status of resident adults. Over a 24-year period, we observed variation in the risk of cub infection, with those born into groups with resident infectious breeding females being over four times as likely to be detected excreting M. bovis than cubs from groups where there was no evidence of infection in adults. We discuss how our findings relate to the persistence of infection at both social group and population level, and the potential implications for disease control strategies.

Patterns of direct and indirect contact between cattle and badgers naturally infected with tuberculosis.

Tuberculosis (TB) due to infection with Mycobacterium bovis is transmitted between cattle and badgers (Meles meles) in the UK and Ireland but it is unclear where or when transmission occurs. We investigated direct and indirect interactions between badgers and cattle using automated proximity loggers on animals and at badger latrines located on pasture, in an area of south-west England with a high-density badger population. Direct contacts (interactions within 1.4 m) between badgers and cattle at pasture were very rare (four out of >500000 recorded animal-to-animal contacts) despite ample opportunity for interactions to occur. Indirect interactions (visits to badger latrines by badgers and cattle) were two orders of magnitude more frequent than direct contacts: 400 visits by badgers and 1700 visits by cattle were recorded. This suggests that indirect contacts might be more important than direct contacts in terms of disease transmission at pasture. The TB infection status of individual badgers (ascribed with 93% accuracy using three diagnostic tests) did not affect the frequency or duration of their visits to latrines located on pasture grazed by cattle. Nevertheless, there was wide variation in contact behaviour between individuals, which highlights the importance of understanding heterogeneity in contact patterns when developing strategies to control disease spread in wildlife and livestock.

Multi-state modelling reveals sex-dependent transmission, progression and severity of tuberculosis in wild badgers.

Statistical models of epidemiology in wildlife populations usually consider diseased individuals as a single class, despite knowledge that infections progress through states of severity. Bovine tuberculosis (bTB) is a serious zoonotic disease threatening the UK livestock industry, but we have limited understanding of key epidemiological processes in its wildlife reservoirs. We estimated differential survival, force of infection and progression in disease states in a population of Eurasian badgers (Meles meles), naturally infected with bTB. Our state-dependent models overturn prevailing categorizations of badger disease states, and find novel evidence for early onset of disease-induced mortality in male but not female badgers. Males also have higher risk of infection and more rapid disease progression which, coupled with state-dependent increases in mortality, could promote sex biases in the risk of transmission to cattle. Our results reveal hidden complexities in wildlife disease epidemiology, with implications for the management of TB and other zoonotic diseases.

Farm-scale risk factors for bovine tuberculosis incidence in cattle herds during the Randomized Badger Culling Trial.

We analysed the incidence of cattle herd breakdowns due to bovine tuberculosis (Mycobacterium bovis) in relation to experimental badger culling, badger populations and farm characteristics during the Randomized Badger Culling Trial (RBCT). Mixed modelling and event history analysis were used to examine the individual risk factors. The interdependencies of covariates were examined using structural equation modelling. There were consistent findings among the different analyses demonstrating that during a badger culling programme farms experiencing: reactive culling, larger herd sizes, larger holdings and holdings with multiple parcels of land were all at greater risk of a herd breakdown. Proactive culling reduced risks within the culling area, but we did not assess any potential effects in the periphery of the treatment area. Badger-related variables measured prior to the start of culling (number of social groups and length of badger territorial boundaries) did not consistently point to an increase in risk, when set against a background of ongoing badger culling. This could be because (1) the collected variables were not important to risk in cattle, or (2) there were insufficient data to demonstrate their importance. Our findings highlight the difficulty in identifying simple predictors of spatial variation in transmission risks from badger populations and the consequent challenge of tailoring management actions to any such field data.

Does small mammal prey guild affect the exposure of predators to anticoagulant rodenticides?

Ireland has a restricted small mammal prey guild but still includes species most likely to consume anticoagulant rodenticide (AR) baits. This may enhance secondary exposure of predators to ARs. We compared liver AR residues in foxes (Vulpes vulpes) in Northern Ireland (NI) with those in foxes from Great Britain which has a more diverse prey guild but similar agricultural use of ARs. Liver ARs were detected in 84% of NI foxes, more than in a comparable sample of foxes from Scotland and similar to that of suspected AR poisoned animals from England and Wales. High exposure in NI foxes is probably due to greater predation of commensal rodents and non-target species most likely to take AR baits, and may also partly reflect greater exposure to highly persistent brodifacoum and flocoumafen. High exposure is likely to enhance risk and Ireland may be a sentinel for potential effects on predator populations.

KDIGO clinical practice guideline for the care of kidney transplant recipients: a summary

The 2009 Kidney Disease: Improving Global Outcomes (KDIGO) clinical practice guideline on the monitoring, management, and treatment of kidney transplant recipients is intended to assist the practitioner caring for adults and children after kidney transplantation. The guideline development process followed an evidence-based approach, and management recommendations are based on systematic reviews of relevant treatment trials. Critical appraisal of the quality of the evidence and the strength of recommendations followed the Grades of Recommendation Assessment, Development, and Evaluation (GRADE) approach. The guideline makes recommendations for immunosuppression and graft monitoring, as well as prevention and treatment of infection, cardiovascular disease, malignancy, and other complications that are common in kidney transplant recipients, including hematological and bone disorders. Limitations of the evidence, especially the lack of definitive clinical outcome trials, are discussed and suggestions are provided for future research. This summary includes a brief description of methodology and the complete guideline recommendations but does not include the rationale and references for each recommendation, which are published elsewhere.

Point transect sampling along linear features.

Distance sampling is a widely used methodology for assessing animal abundance. A key requirement of distance sampling is that samplers (lines or points) are placed according to a randomized design, which ensures that samplers are positioned independently of animals. Often samplers are placed along linear features such as roads, so that bias is expected if animals are not uniformly distributed with respect to distance from the linear feature. We present an approach for analyzing distance data from a survey when the samplers are points placed along a linear feature. Based on results from a simulation study and from a survey of Irish hares in Northern Ireland conducted from roads, we conclude that large bias may result if the position of samplers is not randomized, and analysis methods fail to account for nonuniformity.

Element patterns in albatrosses and petrels: influence of trophic position, foraging range, and prey type.

We investigated the concentrations of 22 essential and non-essential elements among a community of Procellariiformes (and their prey) to identify the extent to which trophic position and foraging range governed element accumulation. Stable isotope analysis (SIA) was used to characterise trophic (delta(15)N) and spatial patterns (delta(13)C) among species. Few consistent patterns were observed in element distributions among species and diet appeared to be highly influential in some instances. Arsenic levels in seabird red blood cells correlated with delta(15)N and delta(13)C, demonstrating the importance of trophic position and foraging range for arsenic distribution. Arsenic concentrations in prey varied significantly across taxa, and in the strength of association with delta(15)N values (trophic level). In most instances, element patterns in Procellariiformes showed the clearest separation among species, indicating that a combination of prey selection and other complex species-specific characteristics (e.g. moult patterns) were generally more important determining factors than trophic level per se.

The relationship of donor source and age on short- and long-term allograft survival in pediatric renal transplantation.

Limited pediatric data on allograft survival from advanced aged kidney donors exist. To determine the influence of donor source and age on allograft survival in pediatric renal transplant recipients, we analyzed the OPTN database. Allograft survival for 7291 pediatric renal transplants was evaluated. Up to five yr post-transplantation, graft survival was higher for LD vs. DD recipients. At seven yr, allograft survival was 71% in 18-54 yr-old LD recipients, 59.1% in >or=55 yr-old LD, and 45.1% in >or=50 yr-old DD recipients. An approximate 35% improvement in allograft survival in 18-54 yr-old LD recipients was observed. Multivariate results showed that recipients of LD 35-49 (aRR 0.66, 95% CI 0.55-0.80) and LD 50-54 (aRR 0.65, 95% CI 0.45-0.94) have a graft survival advantage over the ideal DD. In LD >or=55 yr, no improvement in graft survival was observed when compared with the 18-34 yr-old DD. In summary, we observed in a pediatric population, <55 yr-old LD kidneys afford improved long-term allograft survival when compared with DD kidney recipients. Increasing awareness of the long-term graft survival advantage for children receiving an LD kidney, even from older donors, should be a priority.

Should pediatric patients wait for HLA-DR-matched renal transplants?

Graft survival rates from deceased donors aged 35 years or less among all primary pediatric kidney transplant recipients in the United States between 1996 and 2004 were retrospectively examined to determine the effect of HLA-DR mismatches on graft survival. Zero HLA-DR-mismatched kidneys had statistically comparable 5-year graft survival (71%), to 1-DR-mismatched kidneys (69%) and 2-DR-mismatched kidneys (71%). When compared to donors less than 35 years of age, the relative rate of allograft failure was 1.32 (p = 0.0326) for donor age greater than or equal to age 35. There was no statistical increase in the odds of developing a panel-reactive antibody (PRA) greater than 30% at the time of second waitlisting, based upon the degree of HLA-A, -B or -DR mismatch of the first transplant, nor was there a 'dose effect' when more HLA antigens were mismatched between the donor and recipient. Therefore, pediatric transplant programs should utilize the recently implemented Organ Procurement and Transplantation Network's (OPTN)allocation policy, which prioritizes pediatric recipients to receive kidneys from deceased donors less than 35 years of age, and should not turn down such kidney offers to wait for a better HLA-DR-matched kidney.

Survival advantage of pediatric recipients of a first kidney transplant among children awaiting kidney transplantation.

The mortality rate in children with ESRD is substantially lower than the rate experienced by adults. However, the risk of death while awaiting kidney transplantation and the impact of transplantation on long-term survival has not been well characterized in the pediatric population. We performed a longitudinal study of 5961 patients under age 19 who were placed on the kidney transplant waiting list in the United States. Of these, 5270 received their first kidney transplant between 1990 and 2003. Survival was assessed via a time-varying nonproportional hazards model adjusted for potential confounders. Transplanted children had a lower mortality rate (13.1 deaths/1000 patient-years) compared to patients on the waiting list (17.6 deaths/1000 patient-years). Within the first 6 months of transplant, there was no significant excess in mortality compared to patients remaining on the waiting list (adjusted Relative Risk (aRR) = 1.01; p = 0.93). After 6 months, the risk of death was significantly lower: at 6-12 months (aRR = 0.37; p < 0.001) and at 30 months (aRR 0.26; p < 0.001). Compared to children who remain on the kidney transplant waiting list, those who receive a transplant have a long-term survival advantage. With the potential for unmeasured bias in this observational data, the results of the analysis should be interpreted conservatively.

Incidence of PTLD in pediatric renal transplant recipients receiving basiliximab, calcineurin inhibitor, sirolimus and steroids.

Pediatric renal transplant recipients were enrolled in a multicenter, randomized, double-blind trial of steroid withdrawal. Subjects received basiliximab, calcineurin inhibitor, sirolimus and steroids. Of 274 subjects enrolled, 19 (6.9%) subjects developed posttransplant lymphoproliferative disorder (PTLD). The relative hazard (RH) for PTLD was 5.3-fold higher in children aged < or =5 versus those >12 years (p = 0.0017). EBV seronegative subjects had a 4.7-fold higher RH compared to EBV positive subjects (p = 0.02). Among EBV donor+/recipient- (D+/R-) subjects, the RH increased by 6.1-fold (p = 0.0001). In a multivariate model, risk factors included recipient age < or =5 years (RH 3.2, 95% CI: 1.1-9.6, p = 0.034) and EBV D+/R- status (RH 7.7, 95% CI: 1.6-35.9, p = 0.010). Of 19 patients with PTLD, 17 are alive with functioning grafts and 2 lost their grafts, 1 of whom subsequently died of recurrent PTLD. This 'robust' immunosuppression protocol was associated with low rejection rates but an unacceptably high incidence of PTLD. The combination of basiliximab, calcineurin inhibitor, sirolimus and steroids resulted in over-immunosuppression in a high-risk pediatric population and we do not recommend its use. Future studies must include routine viral monitoring to permit early identification of viral activity and a protocol driven reduction of immunosuppression aimed at avoiding complications.

Decreased risk of renal allograft thrombosis associated with interleukin-2 receptor antagonists: a report of the NAPRTCS.

Graft thrombosis is the most common cause of first year graft failure in pediatric renal transplantation. The North American Pediatric Renal Transplant Cooperative Study (NAPRTCS) database was analyzed for cases of graft failure due to thrombosis among patients transplanted from 1998 to 2004. The impact of interleukin-2 (IL-2) receptor antagonists as induction therapy was determined. There were a total of 51 graft failures due to thrombosis among the 2750 reported renal transplants (1.85%) (95% CI (1.39%, 2.41%)). This represents the most common cause of graft loss during the first year post-transplant accounting for 35% of first year losses and 18% of all graft losses. The incidence of thrombosis among patients who received IL-2 receptor antibodies was 1.07% (12/1126) compared to 2.40% (39/1624) among patients who did not (OR 0.44, 95% CI 0.23, 0.84, p = 0.014). Use of IL-2 receptor blockade was the only significant prognostic factor in a multivariate model with previously identified risk factors. Analysis of NAPRTCS data found that the use of IL-2 receptor antibodies as induction therapy is associated with a significantly decreased risk of graft failure due to thrombosis. This provocative finding requires further investigation to determine whether thrombotic failure can be decreased by this therapeutic strategy.

Relationship between V3 genotype, biologic phenotype, tropism, and coreceptor use for primary isolates of human immunodeficiency virus type 1.

OBJECTIVES: The predictive value of positively charged amino acids at positions 11 and 25 within the V3 loop region of the human immunodeficiency virus type 1 (HIV-1) envelope gene for the syncytium-inducing (SI) phenotype was assessed. STUDY DESIGN/METHODS: Sequencing was performed on DNA extracted from primary peripheral blood mononuclear cells (PBMCs) and complementary DNA (cDNA) prepared from serial viral isolates from 10 HIV-1-seropositive subjects. Proviral DNA sequencing was also performed on biologic clones from most of these subjects. RESULTS: Positive charge at position 11 and/or 25 in 257 isolate cDNA, PBMC DNA, and biologic clone PBMC DNA sequences was compared with 69 phenotypic determinations, of which 62.3% were SI. V3 genotype was 51.2% sensitive and 85.8% specific for the SI phenotype, with positive and negative predictive values of 62.8% and 79.0%, respectively. Cellular tropism failed to correlate with V3 genotype, coreceptor use, or biologic phenotype. Exclusive use of CCR5 was associated with the nonsyncytium-inducing (NSI) phenotype. Overall, V3 loop charge was higher in SI than in NSI isolates (5.01 and 3.78, respectively; p = 0.0211). CONCLUSIONS: The predictive power of SI phenotype from V3 genotype is relatively weak, especially in a low SI prevalence population. The direct measurement of viral phenotype, cellular tropism, and coreceptor use in HIV-1 isolates is essential for accurate biologic characterization.