A Note on the Derivation of Epidemic Final Sizes

Final size relations are known for many epidemic models. The derivations are often tedious and difficult, involving indirect methods to solve a system of integro-differential equations. Often when the details of the disease or population change, the final size relation does not. An alternate approach to deriving final sizes has been suggested. This approach directly considers the underlying stochastic process of the epidemic rather than the approximating deterministic equations and gives insight into why the relations hold. It has not been widely used. We suspect that this is because it appears to be less rigorous. In this article, we investigate this approach more fully and show that under very weak assumptions (which are satisfied in all conditions we are aware of for which final size relations exist) it can be made rigorous. In particular, the assumptions must hold whenever integro-differential equations exist, but they may also hold in cases without such equations. Thus, the use of integro-differential equations to find a final size relation is unnecessary and a simpler, more general method can be applied.     

Recovery from Severe Mistletoe Infection After Heat- and Drought-Induced Mistletoe Death

Ecosystems - Mistletoes are emerging as important co-contributors to tree mortality across terrestrial ecosystems, particularly when infected trees are stressed by water limitations during drought....     

Ancestral Population Sizes and Species Divergence Times in the Primate Lineage on the Basis of Intron and BAC End Sequences

The effective sizes of ancestral populations and species divergence times of six primate species (humans, chimpanzees, gorillas, orangutans, and representatives of Old World monkeys and New World monkeys) are estimated by applying the two-species maximum likelihood (ML) method to intron sequences of 20 different loci. Examination of rate heterogeneity of nucleotide substitutions and intragenic recombination identifies five outrageous loci (ODC1, GHR, HBE, INS, and HBG). The estimated ancestral polymorphism ranges from 0.21 to 0.96% at major divergences in primate evolution. One exceptionally low polymorphism occurs when African and Asian apes diverged. However, taking into consideration the possible short generation times in primate ancestors, it is concluded that the ancestral population size in the primate lineage was no smaller than that of extant humans. Furthermore, under the assumption of 6 million years (myr) divergence between humans and chimpanzees, the divergence time of humans from gorillas, orangutans, Old World monkeys, and New World monkeys is estimated as 7.2, 18, 34, and 65 myr ago, respectively, which are generally older than traditional estimates. Beside the intron sequences, three other data sets of orthologous sequences are used between the human and the chimpanzee comparison. The ML application to these data sets including 58,156 random BAC end sequences (BES) shows that the nucleotide substitution rate is as low as 0.6–0.8 × 10^–9 per site per year and the extent of ancestral polymorphism is 0.33–0.51%. With such a low substitution rate and short generation time, the relatively high extent of polymorphism suggests a fairly large effective population size in the ancestral lineage common to humans and chimpanzees.[Reviewing Editor: Dr. Magnus Nordborg]     

Speculation on Pathogenesis in Death from Respiratory Syncytial Virus Infection

The lungs of three infants, two with bronchiolitis and one with pneumonia, were examined by fluorescent antibody techniques for the distribution of respiratory syncytial (R.S.) virus, and also for the presence of human globulin. In bronchiolitis the lungs contained little virus, whereas in pneumonia virus was abundant and widespread; and, paradoxically, while in bronchiolitis human globulin had the same scanty distribution as virus it was absent in pneumonia. It is suggested that the essential process in bronchiolitis is a widespread type 1 allergic reaction dependent on a second encounter with R.S. virus antigen, whereas in R.S. virus pneumonia the mucosal necrosis and alveolar and interstitial inflammation are the result of direct virus damage to the lungs. The alternative explanation put forward is that the process may be a type 3 allergic reaction.     

The Effects of Disease-Induced Juvenile Mortality on the Transient and Asymptotic Population Dynamics of Chinook Salmon (Oncorhynchus tshawytscha)

The effects of an increased disease mortality rate on the transient and asymptotic dynamics of Chinook salmon (Oncorhynchus tshawytscha) were investigated. Disease-induced mortality of juvenile salmon has become a serious concern in recent years. However, the overall effects of disease mortality on the asymptotic and transient dynamics of adult spawning abundance are still largely unknown. We explored various scenarios with regard to the density-dependent process, the distribution of survivorship over the juvenile phase, the disease mortality rate, and the infusion of stray hatchery fish. Our results suggest that the sensitivity to the disease mortality rate of the equilibrium adult spawning abundance and resilience (asymptotic return rate toward this equilibrium following a small perturbation) varied widely and differently depending on the scenario. The resilience and coefficient of variation of adult spawning abundance following a large perturbation were consistent with each other under the scenarios investigated. We conclude that the increase in disease mortality likely has an effect on fishery yield under a fluctuating environment, not only because the mean equilibrium adult spawning abundance has likely been reduced, but also because the resilience has likely decreased and the variance in adult spawning abundance has likely increased. We also infer the importance of incorporating finer-scale spatiotemporal information into population models and demonstrate a means for doing so within a matrix population modeling framework.     

Raccoon Density and Movements After Population Reduction to Control Rabies

ABSTRACT Population reduction (PR) and trap-vaccinate-release (TVR) were used to control an outbreak of the raccoon (Procyon lotor) variant of rabies in Ontario, Canada, during 1999. Raccoon density declined significantly following PR; however, density increased significantly 9–10 months post-PR. Recolonization of PR areas with raccoons marked in TVR areas was very low with only 1.8% (32/1,759) of those raccoons dispersing into PR areas during 1999–2000. In addition, the number of raccoons dispersing from TVR areas into PR areas was not significantly greater than the number of raccoons dispersing into treatment areas where population reduction had not been implemented during 1999–2000. Raccoon movements in this study, determined by mark-recapture, averaged < 4.0 km during 1999–2000 and did not differ among treatments (with or without PR). In summary, there was not a mass exodus of raccoons from TVR areas to PR areas during 1999–2000, suggesting there was not an immediate, dramatic, vacuum effect drawing raccoons into areas devoid of raccoons due to PR. However, one year post-PR, raccoon populations were near or above pre-PR densities (due to a high reproductive rate of resident raccoons), suggesting that PR would have to be an annual event if rabies is not eliminated from an area.     

Population Sizes and Growth Pressure Responses of Intestinal Microfloras of Deep-Sea Fish Retrieved from the Abyssal Zone

The intestinal floras of seven deep-sea fish retrieved at depths of from 3,200 to 5,900 m were examined for population sizes and growth responses to pressure. Large populations of culturable bacteria, ranging from 1.1 x 10(sup6) to 3.6 x 10(sup8) cells per ml of contents, were detected when samples were incubated at conditions characteristic of those of the deep sea. Culturable cell counts at in situ pressures were greater than those at atmospheric pressure in all samples. Most of the strains isolated by the spread-plating method at atmospheric pressure later proved barophilic. Barophilic bacteria were the predominant inhabitants of the abyssal fish intestines.     

具垂直传染和连续预防接种的SIRS传染病模型的研究

研究了具有垂直传染的两类连续预防接种传染病模型,分别给出了SIRS传染病模型基本再生数并利用广义Dulac函数方法和LaSalle不变原理证明了无病平衡点和正平衡点的全局稳定性.最后对两种结果进行了比较.     

Combining Perturbations and Parameter Variation to Influence Mean First Passage Times

Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilibrium number, showing that both competition and predation rates in this model are bifurcating parameters. We then introduce a stochastic process to model the effects of population perturbations. We demonstrate how to evaluate the joint effects of perturbations and drift using the common currency of mean first passage time to transitions between stable states. Our methods and results are quite general, and for example, can relate to issues in both pest control and sustainable harvest. Our results show that parameter drift (1) does not importantly change the expected time to reach target points within a basin of attraction, but (2) can dramatically change the expected time to shift between basins of attraction, through its effects on equilibrium resilience.     

Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979–1989) and 382 modern (2000–2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a “consensus-like” founder virus, the median “background” frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were “pre-adapted” to the average host HLA profile was only ∼2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America. Intriguingly, temporal changes in protein activity of patient-derived Nef (though not Gag) sequences were observed, suggesting functional implications of population-level HIV evolution on certain viral proteins.     

Death receptor 5 promoter-enhancing compounds isolated from Catimbium speciosum and their enhancement effect on TRAIL-induced apoptosis

The TRAIL/death-receptor signaling pathway has been considered a promising target for selective cancer therapy, although some malignant tumors exhibit TRAIL resistance. We previously found that isoflavonoid enhanced TRAIL-induced apoptosis in TRAIL-resistant cells, which is achieved through up-regulation of death receptor 5 (DR5). In our screening program targeting DR5 promoter enhancement activity, activity-guided fractionations of the extract of Catimbium speciosum led to the isolation of six compounds. Of the isolates, cardamomin (6), the most potent compound, enhanced the expressions of DR5 and DR4 and decreased the Bcl-xL level in TRAIL-resistant DLD1 cells. The combination of 6 and TRAIL synergistically enhanced TRAIL-induced apoptosis against TRAIL-resistant cells upon the activation of caspase-8, 9, and 3. In addition, enhancement of apoptosis by 6 was inhibited by human recombinant DR5/Fc and DR4/Fc chimera proteins, TRAIL-neutralizing fusion proteins, indicating that 6 sensitize TRAIL-resistant cells to TRAIL through the induction of DR5 and DR4. Also, up-regulation of DR5 by 6 paralleled that of CCAAT/enhancer-binding protein-homologous protein (CHOP).     

Non-Invasive Genetic Mark-Recapture as a Means to Study Population Sizes and Marking Behaviour of the Elusive Eurasian Otter (Lutra lutra)

Quantifying population status is a key objective in many ecological studies, but is often difficult to achieve for cryptic or elusive species. Here, non-invasive genetic capture-mark-recapture (CMR) methods have become a very important tool to estimate population parameters, such as population size and sex ratio. The Eurasian otter (Lutra lutra) is such an elusive species of management concern and is increasingly studied using faecal-based genetic sampling. For unbiased sex ratios or population size estimates, the marking behaviour of otters has to be taken into account. Using 2132 otter faeces of a wild otter population in Upper Lusatia (Saxony, Germany) collected over six years (2006–2012), we studied the marking behaviour and applied closed population CMR models accounting for genetic misidentification to estimate population sizes and sex ratios. We detected a sex difference in the marking behaviour of otters with jelly samples being more often defecated by males and placed actively exposed on frequently used marking sites. Since jelly samples are of higher DNA quality, it is important to not only concentrate on this kind of samples or marking sites and to invest in sufficiently high numbers of repetitions of non-jelly samples to ensure an unbiased sex ratio. Furthermore, otters seemed to increase marking intensity due to the handling of their spraints, hence accounting for this behavioural response could be important. We provided the first precise population size estimate with confidence intervals for Upper Lusatia (for 2012: N^ = 20 ± 2.1, 95% CI = 16–25) and showed that spraint densities are not a reliable index for abundances. We further demonstrated that when minks live in sympatry with otters and have comparably high densities, a non-negligible number of supposed otter samples are actually of mink origin. This could severely bias results of otter monitoring if samples are not genetically identified.     

Analysis on Factors Related to Rabies Epidemic in China from 2007-2011

To analyze features of the rabies epidemic in China between 2007 and 2011,identify factors influencing the epidemic and to provide a scientific basis for further control and prevention of rabies,Descri...     

Combining Site Occupancy,Breeding Population Sizes and Reproductive Success to Calculate Time-Averaged Reproductive Output of Different Habitat Types: An Application to Tricolored Blackbirds

In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor) has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005–2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent investigation. The method we employ should be useful in other metapopulation studies for calculating time-averaged reproductive output for different sites.     

The Ability of Diphenylpiperazines to Prevent Neuronal Death in Dorsal Root Ganglion Neurons In Vitro After Nerve Growth Factor Deprivation and In Vivo After Axotomy

Abstract: The mechanism of neuroprotection by the calcium channel antagonist flunarizine against neuronal death is unknown. We investigated the ability of other calcium channel antagonists (cinnarizine, nimodipine, nicardipine, diltiazem, and verapamil), calmodulin antagonists, and calpain inhibitors to prevent neuronal death in rat dorsal root ganglion neurons in vitro after nerve growth factor (NGF) deprivation and the ability of cinnarizine and diltiazem to protect in vivo after axotomy. In vitro, only neurons treated with cinnarizine or flunarizine were protected from death after withdrawal. In vivo, cinnarizine, but not diltiazem, protected dorsal root ganglion neurons in rats after unilateral sciatic nerve crush. Intracellular calcium concentration ([Ca²⁺],) was evaluated with fura 2 after NGF deprivation In vitro. Neurons "committed to die" 24 h after NGF deprivation displayed a decline in [Ca^a+], before visible morphological deterioration consistent with cell death. The influx of extracellular calcium was not necessary to produce neuronal death. Neurons deprived of NGF gradually lost the ability to respond to elevated external potassium with an increase in [Ca²⁺], during the first 24 h after trophic factor deprivation. After 24 h, neurons deprived of NGF could not be rescued by readministration of NGF. Neurons protected from cell death with diphenylpiperazines maintained their response to high external potassium, suggesting continued membrane integrity. We speculate that diphenylpiperazines may protect sensory neurons via an unknown mechanism that stabilizes cell membranes.     

Influence of Flight and Colour Morph on Susceptibility of Sitobion avenae to Infection by Erynia neoaphidis

The influence of clone and morph on the infection of Sitobion avenae with Erynia neoaphidis was examined in laboratory assays. The LC 50 -values were low; green alates: 0.8-1.8, green apterae: 2.9, brown alates: 1.5 and brown apterae: 2.6-3.6 conidia mm -2 . Within each of the two inoculation occasions, alates of both clones were significantly more susceptible than apterae, while there was no difference between the two clones. The LT 50 -values at 18°C varied between 6.4 and 7.5 days and there was no significant difference in LT 50 -values between either the two different coloured clones or between alates and apterae.