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Mapping the distribution of malaria: current approaches and future directions
Mapping the distribution of malaria has received substantial attention because the disease is a major source of illness and mortality in humans, especially in developing countries. It also has a defined temporal and spatial distribution. The distribution of malaria is most influenced by its mosquito vector, which is sensitive to extrinsic environmental factors such as rainfall and temperature. Temperature also affects the development rate of the malaria parasite in the mosquito. Here, we review the range of approaches used to model the distribution of malaria, from spatially explicit to implicit, mechanistic to correlative. Although current methods have significantly improved our understanding of the factors influencing malaria transmission, significant gaps remain, particularly in incorporating nonlinear responses to temperature and temperature variability. We highlight new methods to tackle these gaps and to integrate new data with models.
Avian Influenza spread and transmission dynamics
The spread of highly pathogenic avian influenza (HPAI) viruses of type A of subtype H5N1 has been a serious threat to global public health. Understanding the roles of various (migratory, wild, poultry) bird species in the transmission of these viruses is critical for designing and implementing effective control and intervention measures. Developing appropriate models and mathematical techniques to understand these roles and to evaluate the effectiveness of mitigation strategies have been a challenge. Recent development of the global health surveillance (especially satellite tracking and GIS techniques) and the mathematical theory of dynamical systems combined have gradually shown the promise of some cutting-edge methodologies and techniques in mathematical biology to meet this challenge.
Measuring spatial patterns in floodplains: A step towards understanding the complexity of floodplain ecosystems: Chapter 6
Floodplains can be viewed as complex adaptive systems (Levin, 1998) because they are comprised of many different biophysical components, such as morphological features, soil groups and vegetation communities as well as being sites of key biogeochemical processing (Stanford et al., 2005). Interactions and feedbacks among the biophysical components often result in additional phenomena occuring over a range of scales, often in the absence of any controlling factors (sensu Hallet, 1990). This emergence of new biophysical features and rates of processing can lead to alternative stable states which feed back into floodplain adaptive cycles (cf. Hughes, 1997; Stanford et al., 2005). Interactions between different biophysical components, feedbacks, self emergence and scale are all key properties of complex adaptive systems (Levin, 1998; Phillips, 2003; Murray et al., 2014) and therefore will influence the manner in which we study and view spatial patterns. Measuring the spatial patterns of floodplain biophysical components is a prerequisite to examining and understanding these ecosystems as complex adaptive systems. Elucidating relationships between pattern and process, which are intrinsically linked within floodplains (Ward et al., 2002), is dependent upon an understanding of spatial pattern. This knowledge can help river scientists determine the major drivers, controllers and responses of floodplain structure and function, as well as the consequences of altering those drivers and controllers (Hughes and Cass, 1997; Whited et al., 2007). Interactions and feedbacks between physical, chemical and biological components of floodplain ecosystems create and maintain a structurally diverse and dynamic template (Stanford et al., 2005). This template influences subsequent interactions between components that consequently affect system trajectories within floodplains (sensu Bak et al., 1988). Constructing and evaluating models used to predict floodplain ecosystem responses to natural and anthropogenic disturbances therefore require quantification of spatial pattern (Asselman and Middelkoop, 1995; Walling and He, 1998). Quantifying these patterns also provides insights into the spatial and temporal domains of structuring processes as well as enabling the detection of self-emergent phenomena, environmental constraints or anthropogenic interference (Turner et al., 1990; Holling, 1992; De Jager and Rohweder, 2012). Thus, quantifying spatial pattern is an important building block on which to examine floodplains as complex adaptive systems (Levin, 1998). Approaches to measuring spatial pattern in floodplains must be cognisant of scale, self-emergent phenomena, spatial organisation, and location. Fundamental problems may arise when patterns observed at a site or transect scale are scaled-up to infer processes and patterns over entire floodplain surfaces (Wiens, 2002; Thorp et al., 2008). Likewise, patterns observed over the entire spatial extent of a landscape can mask important variation and detail at finer scales (Riitters et al., 2002). Indeed, different patterns often emerge at different scales (Turner et al., 1990) because of hierarchical structuring processes (O'Neill et al., 1991). Categorising data into discrete, homogeneous and predefined spatial units at a particular scale (e.g. polygons) creates issues and errors associated with scale and subjective classification (McGarigal et al., 2009; Cushman et al., 2010). These include, loss of information within classified ‘patches’, as well as the ability to detect the emergence of new features that do not fit the original classification scheme. Many of these issues arise because floodplains are highly heterogeneous and have complex spatial organizations (Carbonneau et al., 2012; Legleiter, 2013). As a result, the scale and location at which measurements are made can influence the observed spatial patterns; and patterns may not be scale independent or applicable in different geomorp
Vegetation as a tool in the interpretation of fluvial geomorphic processes and landforms
This chapter exemplifies that vegetation can be used as a tool for geomorphic interpretation in several major ways. It presents a general overview: through dendrogeomorphic analysis (tree rings) to estimate the timing of important geomorphic events including floods and mass wasting and to estimate rates of erosion and sedimentation; through the documentation and interpretation of species distributional patterns that are established in response to prevailing hydrogeomorphic conditions; and through the role that it plays, depending on size, shape and growth form, in flow rates and subsequent erosion and deposition processes. Floods, from prolonged inundation characteristic of relatively large, low-gradient basins to high-gradient and short-period destructive events, are the most important extrinsic factor in bottomland systems. Vegetation organization, composition and plant community dynamics on river floodplains are controlled by disturbance type and scale, and biological characteristics of plants linked to resistance to disturbance, resilience and competitive ability.
Modeling flow, sediment transport and morphodynamics in rivers
Predicting the response of natural or man-made channels to imposed supplies of water and sediment is one of the difficult practical problems commonly addressed by fluvial geomorphologists. This problem typically arises in three situations. In the first situation, geomorphologists are attempting to understand why a channel or class of channels has a certain general form; in a sense, this is the central goal of fluvial geomorphology. In the second situation, geomorphologists are trying to understand and explain how and why a specific channel will evolve or has evolved in response to altered or unusual sediment and water supplies to that channel. For example, this would include explaining the short-term response of a channel to an unusually large flood or predicting the response of a channel to long-term changes in flow or sediment supply due to various human activities such as damming or diversions. Finally, geomorphologists may be called upon to design or assess the design of proposed man-made channels that must carry a certain range of flows and sediment loads in a stable or at least quasi-stable manner. In each of these three situations, the problem is really the same: geomorphologists must understand and predict the interaction of the flow field in the channel, the sediment movement in the channel and the geometry of the channel bed and banks. In general, the flow field, the movement of sediment making up the bed and the morphology of the bed are intricately linked; the flow moves the sediment, the bed is altered by erosion and deposition of sediment and the shape of the bed is critically important for predicting the flow. This complex linkage is precisely what makes understanding channel form and process such a difficult and interesting challenge.
Surficial geological tools in fluvial geomorphology: Chapter 2
Increasingly, environmental scientists are being asked to develop an understanding of how rivers and streams have been altered by environmental stresses, whether rivers are subject to physical or chemical hazards, how they can be restored, and how they will respond to future environmental change. These questions present substantive challenges to the discipline of fluvial geomorphology, especially since decades of geomorphologic research have demonstrated the general complexity of fluvial systems. It follows from the concept of complex response that synoptic and short-term historical views of rivers will often give misleading understanding of future behavior. Nevertheless, broadly trained geomorphologists can address questions involving complex natural systems by drawing from a tool box that commonly includes the principles and methods of geology, hydrology, hydraulics, engineering, and ecology.
When worlds collide: challenges and opportunities for conservation of biodiversity in the Hawaiian Islands
This chapter identifies four key challenges and opportunities for long-term conservation of biodiversity in the Hawaii's Islands. Following are the challenges that need to be resolved for remaining species of native forest birds to survive into the next century: invasive species, landscape processes, social factors, and climate change. These challenges are also relevant to other threatened terrestrial taxonomic groups (i.e., plants and invertebrates) in the Hawaiian Islands. Such threats are familiar to conservation biologists the world over, but rarely do they act as synergistically as they do in the Hawaiian Islands. The chapter reviews conservation successes and failures in Hawaii, and provides an example of the possible future course of conservation in other island communities.
Soils as relative-age dating tools
Soils develop at the earth's surface via multiple processes that act through time. Precluding burial or disturbance, soil genetic horizons form progressively and reflect the balance among formation processes, surface age, and original substrate composition. Soil morphology provides a key link between process and time (soil age), enabling soils to serve as both relative and numerical dating tools for geomorphic studies and landscape evolution. Five major factors define the contemporary state of all soils: climate, organisms, topography, parent material, and time. Soils developed on similar landforms and parent materials within a given landscape comprise what we term a soil/landform/substrate complex. Soils on such complexes that differ in development as a function of time represent a soil chronosequence. In a soil chronosequence, time constitutes the only independent formation factor; the other factors act through time. Time dictates the variations in soil development or properties (field or laboratory measured) on a soil/landform/substrate complex. Using a dataset within the chronosequence model, we can also formulate various soil development indices based upon one or a combination of soil properties, either for individual soil horizons or for an entire profile. When we evaluate soil data or soil indices mathematically, the resulting equation creates a chronofunction. Chronofunctions help quantify processes and mechanisms involved in soil development, and relate them mathematically to time. These rigorous kinds of comparisons among and within soil/landform complexes constitute an important tool for relative-age dating. After determining one or more absolute ages for a soil/landform complex, we can calculate quantitative soil formation, and or landform-development rates. Multiple dates for several complexes allow rate calculations for soil/landform-chronosequence development and soil-chronofunction calibration.
Great Apes
Anesthesia of great apes is often necessary to conduct diagnostic analysis, provide therapeutics, facilitate surgical procedures, and enable transport and translocation for conservation purposes. Due to the stress of remote delivery injection of anesthetic agents, recent studies have focused on oral delivery and/or transmucosal absorption of preanesthetic and anesthetic agents. Maintenance of the airway and provision of oxygen is an important aspect of anesthesia in great ape species. The provision of analgesia is an important aspect of the anesthesia protocol for any procedure involving painful stimuli. Opioids and nonsteroidal anti-inflammatory drugs (NSAIDs) are often administered alone, or in combination to provide multi-modal analgesia. There is increasing conservation management of in situ great ape populations, which has resulted in the development of field anesthesia techniques for free-living great apes for the purposes of translocation, reintroduction into the wild, and clinical interventions.
Change detection using vegetation indices and multiplatform satellite imagery at multiple temporal and spatial scales
This chapter describes emerging methods for using satellite imagery across temporal and spatial scales using a case study approach to illustrate some of the opportunities now available for combining observations across scales. It explores the use of multiplatform sensor systems to characterize ecological change, as exemplified by efforts to scale the effects of a biocontrol insect (the leaf beetle Diorhabda carinulata ) on the phenology and water use of Tamarix shrubs (Tamarix ramosissima and related species and hybrids) targeted for removal on western U.S. rivers, from the level of individual leaves to the regional level of measurement. Finally, the chapter summarizes the lessons learned and emphasize the need for ground data to calibrate and validate remote sensing data and the types of errors inherent in scaling point data over wide areas, illustrated with research on evapotranspiration (ET) of Tamarix using a wide range of ground measurement and remote sensing methods.
Vaccination against bacterial kidney disease
Bacterial kidney disease (BKD) of salmonid fishes, caused by Renibacterium salmoninarum , has been recognized as a serious disease in salmonid fishes since the 1930s. This chapter discusses the occurrence and significance, etiology, and pathogenesis of BKD. It then describes the different vaccination procedures and the effects and side-effects of vaccination. Despite years of research, however, only a single vaccine has been licensed for prevention of BKD, and has demonstrated variable efficacy. Therefore, in addition to a presentation of the current status of BKD vaccination, a discussion of potential future directions for BKD vaccine development is included in the chapter. This discussion is focused on the unique characteristics of R. salmoninarum and its biology, as well as aspects of the salmonid immune system that might be explored specifically to develop more effective vaccines for BKD prevention.
Contrasting volcanism in Hawaiʻi and the Galápagos
The archipelagos of Hawai‘i and the Galápagos originated at mantle hotspots, yet the volcanoes that make up the island chains differ in most respects. Some of the most important differences include the dynamics of magma supply, characteristics of magma storage and transport, morphology, and compositional and structural evolution. Of particular significance in the Galápagos is the lack of well-developed rift zones, which may be related to higher rates of pre-eruptive inflation compared to Hawai‘i, and the absence of widespread flank instability—a common feature of Hawai‘i's volcanoes. The close proximity of the Galápagos to a mid-ocean-ridge system may account for many of the differences between Hawaiian and Galápagos volcanoes. The Galápagos archipelago is built on young, thin oceanic crust, which might allow for contemporaneous growth of numerous volcanoes, and its volcanoes are fed by a mix of plume and asthenospheric melt sources. Hawaiian volcanoes, in contrast, grew in the middle of the Pacific Plate on older, thicker crust, where localized changes in mantle and lithosphere structure and composition did not exert dominant control over volcano evolution.
The geology and geochemistry of Isla Floreana, Galápagos: A different type of late-stage ocean island volcanism
Isla Floreana, the southernmost volcano in the Galápagos Archipelago, has erupted a diverse suite of alkaline basalts continually since 1.5 Ma. Because these basalts have different compositions than xenoliths and older lavas from the deep submarine sector of the volcano, Floreana is interpreted as being in a rejuvenescent or late-stage phase of volcanism. Most lavas contain xenoliths, or their disaggregated remains. The xenolithic debris and large ranges in composition, including during single eruptions, indicate that the magmas do not reside in crustal magma chambers, unlike magmas in the western Galápagos. Floreana lavas have distinctive trace element compositions that are rich in fluid-immobile elements (e.g., Ta, Nb, Th, Zr) and even richer in fluid-mobile elements (e.g., Ba, Sr, Pb). Rare earth element (REE) patterns are light REE-enriched and distinctively concave-up. Neodymium isotopic ratios are comparable to those from Fernandina, at the core of the Galápagos plume, but Floreana has the most radiogenic Sr and Pb isotopic ratios in the archipelago. These trace element patterns and isotopic ratios are attributed to a mixed source originating within the Galápagos plume, which includes depleted upper mantle, plume material rich in TITAN elements (Ti, Ta, Nb), and recycled oceanic crust that has undergone partial dehydration in an ancient subduction zone. Because Floreana lies at the periphery of the Galápagos plume, melting occurs mostly in the spinel zone, and enriched components dominate; the Floreana recycled mantle component influence is detectable in volcanoes along the entire southern periphery of the archipelago as well. Floreana is the only Galápagos volcano known to have undergone late-stage volcanism. Here, however, the secondary stage activity is more compositionally enriched than the shield-building phase, in contrast to what is observed in Hawai‘i, suggesting that the mechanism driving late-stage volcanism may vary among ocean island provinces.
Episodic deflation-inflation events at Kīlauea Volcano and implications for the shallow magma system
Episodic variations in magma pressures and flow rates at Kīlauea Volcano, defined by a characteristic temporal evolution and termed deflation-inflation (DI) events, have been observed since at least the 1990s. DI events consist of transient, days-long deflations and subsequent reinflations of the summit region, accompanied since 2008 by fluctuations in the surface height of Kīlauea's summit lava lake. After a delay of minutes to hours, these events also often appear along the volcano's East Rift Zone in ground deformation data and as temporary reductions in eruption rate (sometimes followed by brief surges). Notable pauses in DI activity have preceded many eruptive events at Kīlauea. We analyzed more than 500 DI events recorded by borehole tiltmeters at the summit during 2000–2013. Inverse modeling suggests that DI-related ground deformation at the summit is generated by pressure transients in a shallow magma reservoir located beneath the east margin of Halema‘uma‘u Crater and that this reservoir has remained remarkably stable for more than a decade. Utilizing tilt data and variation in the level of the summit lava lake during a large DI event, we estimate a reservoir volume of approximately 1 km 3 (0.2–5.5 km 3 at 95% confidence).
Crustal stress and structure at Kīlauea Volcano inferred from seismic anisotropy
Seismic anisotropy, measured through shear wave splitting (SWS) analysis, can be indicative of the state of stress in Earth's crust. Changes in SWS at Kīlauea Volcano, Hawai‘i, associated with the onset of summit eruptive activity in 2008 hint at the potential of the technique for tracking volcanic activity. To use SWS observations as a monitoring tool, however, it is important to understand the cause of seismic anisotropy at the volcano throughout the eruptive cycle. To address this need, we analyzed SWS results from across Kīlauea in combination with macroscopic surface structures (mapped fractures, faults, and fissures) and stress orientations inferred from fault plane solutions. Seismic anisotropy seems to be due to pervasive aligned structures in most regions of the volcano. The upper East and Southwest Rift Zones, however, show a bimodality in stress and SWS, suggesting a stress discontinuity with depth, perhaps related to magma conduits that trend obliquely to the dominant structure. Other areas in and around Kīlauea Caldera display principal stresses of similar magnitudes, indicating that small stress perturbations can rotate the maximum horizontal compressive stress direction by up to 90 ° . In these locations, static structures generally control SWS, but dynamic conditions due to magmatic activity can override the structural control. Monitoring of SWS may therefore provide important signs of impending volcanism.
Delicate balance of magmatic-tectonic interaction at Kilauea Volcano, Hawai`i, revealed from slow slip events: Chapter 13
Eleven slow slip events (SSEs) have occurred on the southern flank of Kilauea Volcano, Hawai’i, since 1997 through 2014. We analyze this series of SSEs in the context of Kilauea’s magma system to assess whether or not there are interactions between these tectonic events and eruptive/intrusive activity. Over time, SSEs have increased in magnitude and become more regular, with interevent times averaging 2.44 ± 0.15 years since 2003. Two notable SSEs that impacted both the flank and the magmatic system occurred in 2007, when an intrusion and small eruption on the East Rift Zone were part of a feedback with a SSE and 2012, when slow slip induced 2.5 cm of East Rift Zone opening (but without any change in eruptive activity). A summit inflation event and surge in East Rift Zone lava effusion was associated with a SSE in 2005, but the inferred triggering relation is not clear due to a poorly constrained slip onset time. Our results demonstrate that slow slip along Kilauea’s décollement has the potential to trigger and be triggered by activity within the volcano’s magma system. Since only three of the SSEs have been associated with changes in magmatic activity within the summit and rift zones, both the décollement and magma system must be close to failure for triggering to occur.
Reticulite‐producing fountains from ring fractures in Kīlauea Caldera ca. 1500 CE
A widely dispersed reticulite bed occurs close to the base of the Keanakākoʻi Tephra at Kīlauea Volcano. It can be divided into six subunits in the northern sector of the volcano; the reticulite also occurs in the southern sector, but outcrops are sparse owing to penecontemporaneous erosion and burial. Multilobate isopachs for each subunit and the total deposit suggest that multiple fountaining vents were distributed in the northern half of the caldera, possibly along ring fractures for the newly formed caldera. Isopach maps also show a sharp decline in thickness along the dispersal axis of each lobe, which could be explained by remobilization of tephra and/or inclined fountains. Despite such isopach characteristics, thinning rates calculated from the isopach data indicate that the fountains were among the most intense and powerful of all studied Kīlauea fountains. Density analyses of the pyroclasts suggest that fountaining was high (>600m) yet complex, possibly due to lava ponding and reentrainment. The calculated volume of the reticulite deposited around the caldera rim is approximately 0.2km 3 , more voluminous than the deposits of the 1959 Kīlauea Iki eruption; this volume is a minimum, however, as the low-density tephra is easily remobilized, and 600m high caldera walls probably trapped tephra within the caldera, which is deeply buried today and not accounted for in the volume calculations. The duration of this eruption was most likely at least a few days to weeks, based on the calculated volume and estimated discharge rates as seen during the Kīlauea Iki 1959 eruption.