An incremental Knox test for the determination of the serial interval between successive cases of an infectious disease

An estimate of the interval between successive infections is essential for surveillance, control, and modeling of infectious diseases. This paper proposes a method for determining the serial interval when the location and time of onset of illness are known. The theoretical underpinning of this method is the intrinsically spatial nature of disease transmission. Successive infections tend to be closer than unrelated cases of disease and, therefore, exhibit spatial clustering. An incremental Knox type analysis of cases is introduced. Cases occurring at a range of time intervals are examined to determine the serial interval. The significance of clustering is determined using a permutation approach under the null hypothesis of space-time independence. The power of this method is evaluated using an individual level, spatially explicit epidemic simulation. The time increment Knox test is robust to multiple introductions and incomplete sampling. Finally, the increment Knox statistic is used to analyze an outbreak of dengue fever in the city of Florida, Puerto Rico during 1991. Results indicate that the likely interval between successive cases during this outbreak is at least 18–19 days.     

Using multiple scale spatio-temporal patterns for validating spatially explicit agent-based models

Spatially explicit agent-based models (ABMs) have been widely utilized to simulate the dynamics of spatial processes that involve the interactions of individual agents. The assumptions embedded in the ABMs may be responsible for uncertainty in the model outcomes. To ensure the reliability of the outcomes in terms of their space-time patterns, model validation should be performed. In this article, we propose the use of multiple scale spatio-temporal patterns for validating spatially explicit ABMs. We evaluated several specifications of vector-borne disease transmission models by comparing space-time patterns of model outcomes to observations at multiple scales via the sum of root mean square error (RMSE) measurement. The results indicate that specifications of the spatial configurations of residential area and immunity status of individual humans are of importance to reproduce observed patterns of dengue outbreaks at multiple space-time scales. Our approach to using multiple scale spatio-temporal patterns can help not only to understand the dynamic associations between model specifications and model outcomes, but also to validate spatially explicit ABMs.     

Gene structure of the novel cytochrome P4501D1 genes in stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes)

The cytochrome P450 1 (CYP1) family has expanded with the addition of the CYP1B and CYP1C subfamilies. We recently identified a new CYP1 subfamily in zebrafish, CYP1D, with a single gene, CYP1D1. Here we examined sequences found in other fish genomes, i.e., stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes), for similarities among fish CYP1D1 genes. The full-length deduced amino acid sequences for CYP1D1 in these two species averaged about 43% identity to the CYP1As, but nearly 50% when sequence alignment ambiguities were masked. CYP1D1 has seven exons, similar in size and position to the exons in CYP1D1 and CYP1A in zebrafish. However, the intronic distances were substantially smaller in the medaka and stickleback. There also were differing numbers of putative xenobiotic response elements in the CYP1D1 of the various species. Whether the stickleback or medaka genes are inducible by aryl hydrocarbon receptor (AHR) agonists is yet to be determined.     

Lunar surface electric potential changes associated with traversals through the Earth's foreshock

We report an analysis of one year of Suprathermal Ion Detector Experiment (SIDE) Total Ion Detector (TID) “resonance” events observed between January 1972 and January 1973. The study includes only those events during which upstream solar wind conditions were readily available. The analysis shows that these events are associated with lunar traversals through the dawn flank of the terrestrial magnetospheric bow shock. We propose that the events result from an increase in lunar surface electric potential effected by secondary electron emission due to primary electrons in the Earth's foreshock region (although primary ions may play a role as well). This work establishes (1) the lunar surface potential changes as the Moon moves through the terrestrial bow shock, (2) the lunar surface achieves potentials in the upstream foreshock region that differ from those in the downstream magnetosheath region, (3) these differences can be explained by the presence of energetic electron beams in the upstream foreshock region and (4) if this explanation is correct, the location of the Moon with respect to the terrestrial bow shock influences lunar surface potential.     

Geochemistry of southern Pagan Island lavas,Mariana arc: the role of subduction zone processes

New major and trace element abundances, and Pb, Sr, and Nd isotopic ratios of Quaternary lavas from two adjacent volcanoes (South Pagan and the Central Volcanic Region, or CVR) located on Pagan Island allow us to investigate the mantle source (i.e., slab components) and melting dynamics within the Mariana intra-oceanic arc. Geologic mapping reveals a pre-caldera (780–9.4 ka) and post-caldera (<9.4 ka) eruptive stage for South Pagan, whereas the eruptive history of the older CVR is poorly constrained. Crystal fractionation and magma mixing were important crustal processes for lavas from both volcanoes. Geochemical and isotopic variations indicate that South Pagan and CVR lavas, and lavas from the northern volcano on the island, Mt. Pagan, originated from compositionally distinct parental magmas due to variations in slab contributions (sediment and aqueous fluid) to the mantle wedge and the extent of mantle partial melting. A mixing model based on Pb and Nd isotopic ratios suggests that the average amount of sediment in the source of CVR (~2.1%) and South Pagan (~1.8%) lavas is slightly higher than Mt. Pagan (~1.4%) lavas. These estimates span the range of sediment-poor Guguan (~1.3%) and sediment-rich Agrigan (~2.0%) lavas for the Mariana arc. Melt modeling demonstrates that the saucer-shaped normalized rare earth element (REE) patterns observed in Pagan lavas can arise from partial melting of a mixed source of depleted mantle and enriched sediment, and do not require amphibole interaction or fractionation to depress the middle REE abundances of the lavas. The modeled degree of mantle partial melting for Agrigan (2–5%), Pagan (3–7%), and Guguan (9–15%) lavas correlates with indicators of fluid addition (e.g., Ba/Th). This relationship suggests that the fluid flux to the mantle wedge is the dominant control on the extent of partial melting beneath Mariana arc volcanoes. A decrease in the amount of fluid addition (lower Ba/Th) and extent of melting (higher Sm/Yb), and an increase in the sediment contribution (higher Th/Nb, La/Sm, and Pb isotopic ratios) from Mt. Pagan to South Pagan could reflect systematic cross-arc or irregular along-arc melting variations. These observations indicate that the length scale of compositional heterogeneity in the mantle wedge beneath Mariana arc volcanoes is small (~10 km).     

A computationally efficient method for delineating irregularly shaped spatial clusters

In this paper, we present an efficiency improvement for the algorithm called AMOEBA, A Multidirectional Optimum Ecotope-Based Algorithm, devised by Aldstadt and Getis (Geogr Anal 38(4):327?C343, 2006). AMOEBA embeds a local spatial autocorrelation statistic in an iterative procedure in order to identify spatial clusters (ecotopes) of related spatial units. We provide an analysis of the computational complexity of the original AMOEBA and develop an alternative formulation that reduces computational time without losing optimality. Empirical evidence is provided using georeferenced socio-demographic data in Accra, Ghana.     

Identification of the Bloody Creek structure,a possible impact crater in southwestern Nova Scotia,Canada

Abstract— An approximately 0.4 km diameter elliptical structure formed in Devonian granite in southwestern Nova Scotia, herein named the Bloody Creek structure (BCS), is identified as a possible impact crater. Evidence for an impact origin is based on integrated geomorphic, geophysical, and petrographic data. A near‐continuous geomorphic rim and a 10 m deep crater that is infilled with lacustrine sediments and peat define the BCS. Ground penetrating radar shows that the crater has a depressed inner floor that is sharply ringed by a 1 m high buried scarp. Heterogeneous material under the floor, interpreted as deposits from collapse of the transient cavity walls, is overlain by stratified and faulted lacustrine and wetland sediments. Alteration features found only in rim rocks include common grain comminution, polymict lithic microbreccias, kink‐banded feldspar and biotite, single and multiple sets of closely spaced planar microstructures (PMs) in quartz and feldspar, and quartz mosaicism, rare reduced mineral birefringence, and chlorite showing plastic deformation and flow microtextures. Based on their form and crystallographic orientations, the quartz PMs consist of planar deformation features that document shock‐metamorphic pressures ≤25 GPa. The age of the BCS is not determined. The low depth to diameter ratio of the crater, coupled with anomalously high shock‐metamorphic pressures recorded at its exposed rim, may be a result of significant post‐impact erosion. Alternatively, impact onto glacier ice during the waning stages of Wisconsinian deglaciation (about 12 ka BP) may have resulted in dissipation of much impact energy into the ice, resulting in the present morphology of the BCS.     

Topographic correlations with soil and regolith thickness from shallow‐seismic refraction constraints across upland hillslopes in the Valles Caldera,New Mexico

How rock is weathered physically and chemically into transportable material is a fundamental question in critical‐zone science. In addition, the distribution of weathered material (soil and intact regolith) across upland landscapes exerts a first‐order control on the hydrology of watersheds. In this paper we present the results of six shallow seismic‐refraction surveys in the Redondo Mountain region of the Valles Caldera, New Mexico. The P‐wave velocities corresponding to soil (≤ 0.6 km s^?1) were inferred from a seventh seismic survey where soil‐thickness data were determined by pit excavation. Using multivariable regression, we quantified the relationships among slope gradient, aspect, and topographic wetness index (TWI) on soil and regolith (soil plus intact regolith) thicknesses. Our results show that both soil and regolith thicknesses vary inversely with TWI in all six survey areas while varying directly with slope aspect (i.e. thicker beneath north‐facing slopes) and inversely with slope gradient (i.e. thinner beneath steep slopes) in the majority of the survey areas. An empirical model based on power‐law relationships between regolith thickness and its correlative variables can fit our inferred thicknesses with R² ‐values up to 0.880 for soil and 0.831 for regolith in areas with significant topographic variations. These results further demonstrate the efficacy of shallow seismic refraction for mapping and determining how soil and regolith variations correlate with topography across upland landscapes. Copyright © 2016 John Wiley & Sons, Ltd.