Overview of sperm whale Physeter macrocephalus mortality events in the Adriatic Sea, 1555–2009

• 1 In the Mediterranean Sea, the sperm whale Physeter macrocephalus is one of eight regular cetacean species. Poor knowledge of its ecology and status, together with suspected decline in numbers, make studies of historical and present occurrence especially relevant. Long‐term time series of stranding events are the most reliable data to provide a scientific framework for testing hypotheses that seek to explain the mechanisms responsible for cetacean strandings.
• 2 We present a comprehensive overview of cases of sperm whale mortality and human response to such events encompassing five centuries (1555–2009) within a portion of the Mediterranean Sea that offers a wealth of historical information – the Adriatic Sea.
• 3 A total of 36 mortality events were validated, involving 68 animals. Two findings of skeletal materials are also reported. The geographic distribution of strandings within the basin clearly was uneven: 44% of records (n = 16) were clustered along a 280km portion of the western Adriatic coast. A relatively high number of mortality events occurred along gently sloping sandy beaches away from suitable sperm whale habitat.
• 4 Until the first half of the 20th century, live‐stranded animals were routinely killed: all but one cases with known human response elicited killing attempts. Starting from the 1980s, killing was replaced by efforts to rescue the animals.
• 5 Mass strandings of sperm whales have occurred since historical times in the Adriatic Sea. Mortality events involving multiple individuals accounted for at least 17% of the total sample (6 of 36 mortality events). At least 29% of live strandings (6 of 21) involved more than one individual.
• 6 This study contributes a long‐term dataset based on careful validation of historical information, suitable for hypothesis testing aimed at investigating spatial and temporal correlates of sperm whale strandings – particularly live strandings – as a clue to their causes.

     

Overproduction, purification, and biochemical characterization of the dual specificity H1 protein phosphatase encoded by variola major virus

Smallpox, a highly contagious infectious disease caused by the variola major virus, has an overall mortality rate of about 30%. Because there currently is no specific treatment for smallpox, and the only prevention is vaccination, there is an urgent need for the development of effective antiviral drugs. The dual specificity protein phosphatase encoded by the smallpox virus (H1) is essential for the production of infectious viral particles, making it a promising molecular target for antiviral therapeutics. Here, we report the molecular cloning, overproduction, purification, and initial biochemical characterization of H1 phosphatase, thereby paving the way for the discovery of small molecule inhibitors.     

Non-exponential tolerance to infection in epidemic systems--modeling, inference, and assessment

The transmission dynamics of infectious diseases have been traditionally described through a time-inhomogeneous Poisson process, thus assuming exponentially distributed levels of disease tolerance following the Sellke construction. Here we focus on a generalization using Weibull individual tolerance thresholds under the susceptible-exposed-infectious-removed class of models which is widely employed in epidemics. Applications with experimental foot-and-mouth disease and historical smallpox data are discussed, and simulation results are presented. Inference is carried out using Markov chain Monte Carlo methods following a Bayesian approach. Model evaluation is performed, where the adequacy of the models is assessed using methodology based on the properties of Bayesian latent residuals, and comparison between 2 candidate models is also considered using a latent likelihood ratio-type test that avoids problems encountered with relevant methods based on Bayes factors.     

A linear mixed model to estimate COVID-19-induced excess mortality

The Corona Virus Disease (COVID-19) pandemic has increased mortality in countries worldwide. To evaluate the impact of the pandemic on mortality, the use of excess mortality rather than reported COVID-19 deaths has been suggested. Excess mortality, however, requires estimation of mortality under nonpandemic conditions. Although many methods exist to forecast mortality, they are either complex to apply, require many sources of information, ignore serial correlation, and/or are influenced by historical excess mortality. We propose a linear mixed model that is easy to apply, requires only historical mortality data, allows for serial correlation, and down-weighs the influence of historical excess mortality. Appropriateness of the linear mixed model is evaluated with fit statistics and forecasting accuracy measures for Belgium and the Netherlands. Unlike the commonly used 5-year weekly average, the linear mixed model is forecasting the year-specific mortality, and as a result improves the estimation of excess mortality for Belgium and the Netherlands.     

Extending epidemiologic transition theory: A new stage

Abstract

The epidemiologic transition theory focuses on the changing patterns of morbidity and mortality and postulates that mortality by cause will evolve from a predominance of acute and infectious diseases to a predominance of chronic and degenerative diseases. The epidemiologic transition theory comprises three stages: the age of pestilence and famine (lasting until 1875), receding pandemics (from 1875 to 1930), and degenerative and man‐made diseases (from 1930 to the present). Recent information suggests that developed societies have entered a new stage in the transition. This fourth stage, which we term the hybristic stage, is increasingly influenced by individual behaviors and life‐styles. In this paper, we examine the epidemiologic transition theory, substantiate the need for a new stage, and discuss current cause‐specific trends in mortality and the social and demographic implications of such trends.     

Dynamics and Control of Diseases in Networks with Community Structure

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.     

Extracting key information from historical data to quantify the transmission dynamics of smallpox

Background  

Quantification of the transmission dynamics of smallpox is crucial for optimizing intervention strategies in the event of a bioterrorist attack. This article reviews basic methods and findings in mathematical and statistical studies of smallpox which estimate key transmission parameters from historical data.     

Climate–human interactions contributed to historical forest recruitment dynamics in Mediterranean subalpine ecosystems

Long‐term tree recruitment dynamics of subalpine forests mainly depend on temperature changes, but little is known about the feedbacks between historical land use and climate. Here, we analyze a southern European, millennium‐long dataset of tree recruitment from three high‐elevation pine forests located in Mediterranean mountains (Pyrenees, northeastern Spain; Pollino, southern Italy; and Mt. Smolikas, northern Greece). We identify synchronized recruitment peaks in the late 15th and early 16th centuries, following prolonged periods of societal and climate instability. Major European population crises in the 14th and 15th centuries associated with recurrent famines, the Black Death pandemic, and political turmoil are likely to have reduced the deforestation of subalpine environments and caused widespread rewilding. We suggest that a distinct cold phase in the Little Ice Age around 1450 ce could also have accelerated the cessation of grazing pressure, particularly in the Pyrenees, where the demographic crisis was less severe. Most pronounced in the Pyrenees, the enhanced pine recruitment from around 1500–1550 ce coincides with temporarily warmer temperatures associated with a positive phase of the North Atlantic Oscillation. We diagnose that a mixture of human and climate factors has influenced past forest recruitment dynamics in Mediterranean subalpine ecosystems. Our results highlight how complex human–climate interactions shaped forest dynamics during pre‐industrial times and provide historical analogies to recent rewilding.     

Environmental and social influences on emerging infectious diseases: past, present and future

During the processes of human population dispersal around the world over the past 50 000-100 000 years, along with associated cultural evolution and inter-population contact and conflict, there have been several major transitions in the relationships of Homo sapiens with the natural world, animate and inanimate. Each of these transitions has resulted in the emergence of new or unfamiliar infectious diseases.The three great historical transitions since the initial advent of agriculture and livestock herding, from ca. 10 000 years ago, occurred when: (i) early agrarian-based settlements enabled sylvatic enzootic microbes to make contact with Homo sapiens; (ii) early Eurasian civilizations (such as the Greek and Roman empires, China and south Asia) came into military and commercial contact, ca. 3000-2000 years ago, swapping their dominant infections; and (iii) European expansionism, over the past five centuries, caused the transoceanic spread of often lethal infectious diseases. This latter transition is best known in relation to the conquest of the Americas by Spanish conquistadores, when the inadvertent spread of measles, smallpox and influenza devastated the Amerindian populations.Today, we are living through the fourth of these great transitional periods. The contemporary spread and increased lability of various infectious diseases, new and old, reflect the combined and increasingly widespread impacts of demographic, environmental, behavioural, technological and other rapid changes in human ecology. Modern clinical medicine has, via blood transfusion, organ transplantation, and the use of hypodermic syringes, created new opportunities for microbes. These have contributed to the rising iatrogenic problems of hepatitis C, HIV/AIDS and several other viral infections. Meanwhile, the injudicious use of antibiotics has been a rare instance of human action actually increasing 'biodiversity'.Another aspect of this fourth transition is that modern hyper-hygienic living restricts microbial exposure in early life. This, in the 1950s, may have contributed to an epidemic of more serious, disabling, poliomyelitis, affecting older children than those affected in earlier, more endemic decades. As with previous human-microbe transitions, a new equilibrial state may lie ahead. However, it certainly will not entail a world free of infectious diseases. Any mature, sustainable, human ecology must come to terms with both the need for, and the needs of, the microbial species that help to make up the interdependent system of life on Earth. Humans and microbes are not "at war"; rather, both parties are engaged in amoral, self-interested, coevolutionary struggle. We need to understand better, and therefore anticipate, the dynamics of that process.     

Phylogeny, Life History, and Ecology Contribute to Differences in Amphibian Susceptibility to Ranaviruses

Research that identifies the potential host range of generalist pathogens as well as variation in host susceptibility is critical for understanding and predicting the dynamics of infectious diseases within ecological communities. Ranaviruses have been linked to amphibian die-off events worldwide with the greatest number of reported mortality events occurring in the United States. While reports of ranavirus-associated mortality events continue to accumulate, few data exist comparing the relative susceptibility of different species. Using a series of laboratory exposure experiments and comparative phylogenetics, we compared the susceptibilities of 19 amphibian species from two salamander families and five anurans families for two ranavirus isolates: frog virus 3 (FV3) and an FV3-like isolate from an American bullfrog culture facility. We discovered that ranaviruses were capable of infecting 17 of the 19 larval amphibian species tested with mortality ranging from 0 to 100%. Phylogenetic comparative methods demonstrated that species within the anuran family Ranidae were generally more susceptible to ranavirus infection compared to species from the other five families. We also found that susceptibility to infection was associated with species that breed in semi-permanent ponds, develop rapidly as larvae, and have limited range sizes. Collectively, these results suggest that phylogeny, life history characteristics, and habitat associations of amphibians have the potential to impact susceptibility to ranaviruses.     

The state-reproduction number for a multistate class age structured epidemic system and its application to the asymptomatic transmission model

In this paper, we develop the theory of a state-reproduction number for a multistate class age structured epidemic system and apply it to examine the asymptomatic transmission model. We formulate a renewal integral equation system to describe the invasion of infectious diseases into a multistate class age structured host population. We define the state-reproduction number for a class age structured system, which is the net reproduction number of a specific host type and which plays an analogous role to the type-reproduction number [M.G. Roberts, J.A.P. Heesterbeek, A new method for estimating the effort required to control an infectious disease, Proc. R. Soc. Lond. B 270 (2003) 1359; J.A.P. Heesterbeek, M.G. Roberts, The type-reproduction number T in models for infectious disease control, Math. Biosci. 206 (2007) 3] in discussing the critical level of public health intervention. The renewal equation formulation permits computations not only of the state-reproduction number, but also of the generation time and the intrinsic growth rate of infectious diseases.Subsequently, the basic theory is applied to capture the dynamics of a directly transmitted disease within two types of infected populations, i.e., asymptomatic and symptomatic individuals, in which the symptomatic class is observable and hence a target host of the majority of interventions. The state-reproduction number of the symptomatic host is derived and expressed as a measurable quantity, leading to discussion on the critical level of case isolation. The serial interval and other epidemiologic indices are computed, clarifying the parameters on which these indices depend. As a practical example, we illustrate the eradication threshold for case isolation of smallpox. The generation time and serial interval are comparatively examined for pandemic influenza.     

Changes in the skull morphology of the Arctic wolf, Canis lupus arctos, during the twentieth century

Measurements of a large series of skulls of the Arctic wolf, Canis lupus arctos . have shown that since 1930 there has been an overall reduction in the size of the skulls, together with widening of the cranium, shortening of the facial region, and reduction in size of the teeth. This suggests that hybridization and subsequent introgression occurred with huskies ( Canis familiaris ) during the 1930s, which is consistent with historical accounts. Since 1950 there has been a reversion in skull morphology to a more 'wolf-like' form, suggesting that hybridization is no longer occurring.
The skull of a wolf/dog hybrid is intermediate in size between the skulls of wolves and huskies but its shape is allometrically dissimilar. Skulls of wolves from the period 1930–50 are moi-e similar to the skull of this hybrid than in the other time periods.
The skull of a male canid from a carcass collected on Ellesmere Island and presented to the Natural History Museum. London, in 1986 was at first thought to be from a wolf/dog hybrid but analyses of the measurements show that it is more likely to be from an Arctic wolf with severe abnormalities to the jaws.     

Unraveling the structure of the variola topoisomerase IB-DNA complex: a possible new twist on smallpox therapy

Smallpox is a serious and highly contagious disease that is caused by the variola virus. It is one of the most severe infectious human diseases known, with mortality rates as high as 30%. A successful worldwide vaccination program led to the eradication of smallpox in 1980. However, the high transmission rate of variola virus, coupled with the deadly nature of smallpox, makes this virus a potentially devastating weapon for bioterrorism. Currently, there is no specific treatment for smallpox. However, a recent article on the structure of a variola topoisomerase IB-DNA complex provides an intriguing starting point for the rational design of drugs with potential activity against smallpox.     

Long-term growth dynamics of natural forests in Hokkaido,northern Japan

Abstract. The long-term growth dynamics of natural forest stands on the island of Hokkaido were described on the basis of an analysis of data from 38 permanent plots spanning 15–22 yr. Stand structure was characterized by basal area, stem density and tree size variability. To detect trends in stand structure, regression models for recruitment rate (per ha per yr), mortality rate and the rate of change in stem density and tree size variability were developed by a stepwise method using initial basal area, stem density, tree size variability, species composition summarized by LNMDS ordination, altitude, annual mean temperature, annual precipitation, type of understorey vegetation, topography and slope aspect as candidates for predictor variables. The same analyses were conducted for basal area increment (net growth) and its components: survivor growth = basal area gain by growth of surviving individuals and mortality = basal area loss by death of individuals. Stem density remained generally unchanged; recruitment was relatively low even in very sparse stands. Stand basal area generally increased as survivor growth was approximately double the mortality. Recruitment rate was strongly affected by the presence of dwarf bamboo (Sasa spp.) vegetation on the forest floor which inhibited tree regeneration. Mortality rate was density-dependent; dense stands had higher mortality than sparse stands. Density change rate (recruitment rate - mortality rate) was, therefore, determined by both the type of understorey vegetation and stem density. Survivor growth was high in stands with high stem density and basal area. Mortality was dependent on basal area and altitude. Net basal area increment (net growth) was dependent only on stem density with other factors that influenced survivor growth and mortality omitted. Tree size variability decreased in stands with high tree size variability whereas it increased in stands with low size variability. Based on the obtained models for density change rate and net basal area increment, trajectories of stands were illustrated on a log-log diagram of stem density and basal area. The predicted differences in trajectories as affected by the understorey vegetation type indicated the importance of dwarf bamboo vegetation for forest dynamics on Hokkaido.     

Rivers Through Time: Historical Changes in the Riparian Vegetation of the Semi-Arid,Winter Rainfall Region of South Africa in Response to Climate and Land Use

This paper examines how the riparian vegetation of perennial and ephemeral rivers systems in the semi-arid, winter rainfall region of South Africa has changed over time. Using an environmental history approach we assess the extent of change in plant cover at 32 sites using repeat photographs that cover a time span of 36–113 years. The results indicate that in the majority of sites there has been a significant increase in cover of riparian vegetation in both the channel beds and adjacent floodplain environments. The most important species to have increased in cover across the region is Acacia karroo. We interpret the findings in the context of historical changes in climate and land use practices. Damage to riparian vegetation caused by mega-herbivores probably ceased sometime during the early 19th century as did scouring events related to large floods that occurred at regular intervals from the 15th to early 20th centuries. Extensive cutting of riparian vegetation for charcoal and firewood has also declined over the last 150 years. Changes in the grazing history as well as increased abstraction and dam building along perennial rivers in the region also account for some of the changes observed in riparian vegetation during the second half of the 20th century. Predictions of climate change related to global warming anticipate increased drought events with the subsequent loss of species and habitats in the study area. The evidence presented here suggests that an awareness of the region’s historical ecology should be considered more carefully in the modelling and formulation of future climate change predictions as well as in the understanding of climate change impacts over time frames of decades and centuries.     

Effects of behavioral changes in a smallpox attack model

The impact of individual and community behavioral changes in response to an outbreak of a disease with high mortality is often not appreciated. Response strategies to a smallpox bioterrorist attack have focused on interventions such as isolation of infectives, contact tracing, quarantine of contacts, ring vaccination, and mass vaccination. We formulate and analyze a mathematical model in which some individuals lower their daily contact activity rates once an epidemic has been identified in a community. Transmission parameters are estimated from data and an expression is derived for the effective reproduction number. We use computer simulations to analyze the effects of behavior change alone and in combination with other control measures. We demonstrate that the spread of the disease is highly sensitive to how rapidly people reduce their contact activity rates and to the precautions that the population takes to reduce the transmission of the disease. Even gradual and mild behavioral changes can have a dramatic impact in slowing an epidemic. When behavioral changes are combined with other interventions, the epidemic is shortened and the number of smallpox cases is reduced. We conclude that for simulations of a smallpox outbreak to be useful, they must consider the impact of behavioral changes. This is especially true if the model predictions are being used to guide public health policy.     

The ecological history of a mediaeval man-made lake. Hickling Broad,Norfolk, United Kingdom

Changes in Hickling Broad, since its creation in the 14th or 15th centuries by the flooding of peat diggings, have been deduced from dating and analysis of a sediment core, historical information and current limnological studies. Until the 1930's there was little major change. Increased agricultural land fertilization led to markedly increased organic sedimentation from the 1930's onwards, due to increased growth of submerged macrophytes. Inorganic sedimentation increased concurrently as more powerful pumps were installed to help drain the adjacent fens and marshes.There was no evidence of increased plankton populations during this phase, but epiphytic diatom populations increased. In the mid 1960's the current period of hypereutrophication began. Epiphytic diatom numbers increased markedly and in the early 1970's the previous luxuriant macrophytes became sparse and the water became turbid with phytoplankton. These changes are attributable mainly to increases in the size of a roost of migratory black headed gulls (Larus ridibundus L.) on the lake in autumn and winter.     

Day-to-day and seasonal fluctuations of urban mortality in Houston,Texas

Mortality, exclusive of that caused by accidents, for Houston, Texas, from 1971 to 1973 was studied for temporal patterns and for associations with daily maximum and minimum temperature, relative humidity, barometric pressure, and precipitation. The sensitive and unbiased method of spectral analysis permitted the consideration of time lags between events. The findings revealed significant seasonal difference in mortality with the highest being in winter and more interestingly, strong lagged associations were found between short-term upswings in mortality and specific weather conditions, such as those characterized by low air temperature and high barometric pressure. In combination these weather features are typical of winter anticyclones. The peaks in mortality were evident after cold spells within periods of two weeks. Furthermore, episodes of elevated mortality also were observed subsequent to heat waves such as those during the summer of 1971.     

A general model for mortality in adult tsetse (Glossina spp.)

Tsetse exhibit a U-shaped age-mortality curve, with high losses after eclosion and a well-marked ageing process, which is particularly dramatic in males. A three-parameter (k(1) -k(3) ) model for age-dependent adult instantaneous mortality rates was constructed using mark-recapture data for the tsetse fly Glossina morsitans morsitans Westwood (Diptera: Glossinidae). Mortality changed linearly with k(1) over all ages; k(2) affected only losses in roughly the first week of adult life, and k(3) controlled the ageing rate. Mortality pooled over age was twice as sensitive to changes in k(3) as in k(1) . Population growth rate was, however, similarly affected by these two parameters, reflecting the disproportionate effect of k(3) on mortality in the oldest flies that contribute least to the growth rate. Pooled-age mortality and growth rate were insensitive to changes in k(2) . The same model also provided good fits to data for laboratory colonies of female G. m. morsitans and Glossina austeni Newstead and should be applicable to all tsetse of both sexes. The new model for tsetse mortality should be incorporated into models of tsetse and trypanosome population dynamics; it will also inform the estimation of adult female mortality from ovarian dissection data.