Visual_HEA: Habitat Equivalency Analysis Software to Calculate Compensatory Restoration Following Natural Resource Injury

Habitat Equivalency Analysis (HEA) is a means to determine the amount of compensatory restoration required to provide services that are equivalent to the interim loss of natural resource services following an injury. HEA includes a discounting procedure to account for asset valuation in that the total asset value is equal to the discounted value of the future stream of all services from the natural resource or the compensatory resource. Discounting is used to include the relative valuation of loss and gain of ecological services of the resources over time. Visual_HEA is a computer program developed to calculate the amount of compensatory resource services that would be required to match those lost following an injury to natural resources. The program accepts input of parameters necessary to determine long-term service loss from the injury and long-term service gain from the desired compensatory restoration action. HEA results are highly dependent upon assumptions, and consequently it is useful to examine sensitivity of results to a range of parameter values. Visual_HEA offers an intuitive graphical interface that allows the user to input or modify input parameters and hence quickly create or alter the lost and gain service level shape functions. The ability to calculate results of many scenarios allows ready comparisons that may assist in determination of the most appropriate compensatory action

CoralXDS - Coral X-radiograph Densitometry System

The Coral X-radiograph Densitometry System (CoralXDS) is a Windows-based program which provides a tool for measurement of linear extension, density, and calcification from coral X-radiographs. These quantities are determined for high-density, low-density, and annual bands. CoralXDS operates in two modes : full mode and extension/luminance mode. Full mode measures linear extension, density, and calcification, while extension/luminance mode measures only linear extension. Extension/luminance mode requires only a coral image with scaling information. CoralXDS allows user specification of transect location and orientation on the coral image, and provides several options for automated and manual band selection. The output measurements are provided as plots and datasets

Spatial Patterns in Arabian Gulf Coral Assemblages (Jebel Ali, Dubai, U.A.E.) in Response to Temperature-Forcing

We evaluated spatial and temporal patterns using maps from Ikonos satellite imagery in combination with 8 years of line transects and photosquares and the HadISST1 sea-surface temperature data set to explain why coral assemblages in the southern Arabian Gulf (Dubai) are impoverished and mostly do not build framework reefs. Analysis of archive sea surface temperature (SST) data confirms that the area is subjected to recurrent temperature anomalies. Frequencies of anomalies might suggest at least a partial link to the El Niño Southern Oscillation possibly via the Indian Ocean Zonal Mode. The dominant driver of local temperature was oscillations in the position of the subtropical jetstream. Classification of IKONOS satellite data showed that the spatial expression of four coral assemblages was consistent with reef development on a (multi-)decadal time-scale following recurring episodes of coral mass mortality induced by severe SST anomalies. Merging a remotely sensed map of substrate distribution with a detailed bathymetric digital elevation model revealed no evidence of significant framework development, suggesting that the cycle of temperature induced mortality has been operating for a considerable time

The Statistics of Natural Shapes in Modern Coral Reef Landscapes

Spatial heterogeneity is a fundamental characteristic of modern and ancient depositional settings, and the scaling of many carbonate environments has been shown to follow power function distributions. The difficulty in obtaining information on the horizontal persistence of sedimentary lithotopes at the basin scale has, however, hampered evaluation of this fact over larger geographic areas. In recent years, large‐scale maps of reef facies derived from remotely sensed data have become widely available, allowing for an analysis of reef‐scale map products from 26 sites spread through four reef provinces, covering \u3e7000 km2 of shallow‐water habitat in the U.S. territorial Pacific. For each site, facies maps were decomposed to polygons describing the perimeter of patches of differing sedimentologic/benthic character. A suite of geospatial metrics quantifying unit shape, fractal dimension, and frequency‐area relations was applied to investigate the intra‐ and intersite variability. The spatial architecture of these reef sites displays robust fractal properties over an extended range of scales with remarkable consistency between provinces. These results indicate the possibility of extrapolating information from large to small scales in various depositional environments

A Tale of Germs, Storms, and Bombs: Geomorphology and Coral Assemblage Structure at Vieques (Puerto Rico) Compared to St. Croix (U.S. Virgin Islands)

The former U.S. Navy range at Vieques Island (Puerto Rico, United States) is now the largest national wildlife refuge in the Caribbean. We investigated the geomorphology and benthic assemblage structure to understand the status of the coral reefs. Coral assemblages were quantified at 24 sites at Vieques and at 6 sites at St. Croix, U.S. Virgin Islands. These sites were chosen to represent the major zones of reef geomorphology. Sites consisted of two or three 21-m-long photo-quadrate belt transects. The results revealed surprisingly little differentiation in the coral assemblages within and between reefs of comparable geomorphological and oceanographic setting at Vieques and St. Croix. At Vieques, the Acropora palmata zone was almost completely lost, and it was severely reduced at St. Croix, presumably primarily due to diseases and hurricane impacts since the 1970s. Subtle, but nonsignificant, differences with respect to the nature of the shelf margin (north adjacent to the bank, south adjacent to the open sea) and depth zone were observed at Vieques. At St. Croix, benthic assemblages differed more between depth zones but not between north and south. Effects of natural disturbances were severe at Vieques, outweighing impacts of past military activity— which were present but not quantitatively discernible at our scale of sampling. Germs and storms, rather than bombs (and associated naval activities), primarily seem to have taken the worst toll on corals at both Vieques and St. Croix

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution

Exoplanet Diversity in the Era of Space-based Direct Imaging Missions

This whitepaper discusses the diversity of exoplanets that could be detected by future observations, so that comparative exoplanetology can be performed in the upcoming era of large space-based flagship missions. The primary focus will be on characterizing Earth-like worlds around Sun-like stars. However, we will also be able to characterize companion planets in the system simultaneously. This will not only provide a contextual picture with regards to our Solar system, but also presents a unique opportunity to observe size dependent planetary atmospheres at different orbital distances. We propose a preliminary scheme based on chemical behavior of gases and condensates in a planet's atmosphere that classifies them with respect to planetary radius and incident stellar flux.Comment: A white paper submitted to the National Academy of Sciences Exoplanet Science Strateg

The conservation status of the world's freshwater molluscs

With the biodiversity crisis continuing unchecked, we need to establish levels and drivers of extinction risk, and reassessments over time, to effectively allocate conservation resources and track progress towards global conservation targets. Given that threat appears particularly high in freshwaters, we assessed the extinction risk of 1428 randomly selected freshwater molluscs using the IUCN Red List Categories and Criteria, as part of the Sampled Red List Index project. We show that close to one-third of species in our sample are estimated to be threatened with extinction, with highest levels of threat in the Nearctic, Palearctic and Australasia and among gastropods. Threat levels were higher in lotic than lentic systems. Pollution (chemical and physical) and the modification of natural systems (e.g. through damming and water abstraction) were the most frequently reported threats to freshwater molluscs, with some regional variation. Given that we found little spatial congruence between species richness patterns of freshwater molluscs and other freshwater taxa, apart from crayfish, new additional conservation priority areas emerged from our study. We discuss the implications of our findings for freshwater mollusc conservation, the adequacy of a sampled approach and important next steps to estimate trends in freshwater mollusc extinction risk over time

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

The human skin is a complex ecosystem that hosts a heterogeneous flora. Until recently, the diversity of the cutaneous microbiota was mainly investigated for bacteria through culture based assays subsequently confirmed by molecular techniques. There are now many evidences that viruses represent a significant part of the cutaneous flora as demonstrated by the asymptomatic carriage of beta and gamma-human papillomaviruses on the healthy skin. Furthermore, it has been recently suggested that some representatives of the Polyomavirus genus might share a similar feature. In the present study, the cutaneous virome of the surface of the normal-appearing skin from five healthy individuals and one patient with Merkel cell carcinoma was investigated through a high throughput metagenomic sequencing approach in an attempt to provide a thorough description of the cutaneous flora, with a particular focus on its viral component. The results emphasize the high diversity of the viral cutaneous flora with multiple polyomaviruses, papillomaviruses and circoviruses being detected on normal-appearing skin. Moreover, this approach resulted in the identification of new Papillomavirus and Circovirus genomes and confirmed a very low level of genetic diversity within human polyomavirus species. Although viruses are generally considered as pathogen agents, our findings support the existence of a complex viral flora present at the surface of healthy-appearing human skin in various individuals. The dynamics and anatomical variations of this skin virome and its variations according to pathological conditions remain to be further studied. The potential involvement of these viruses, alone or in combination, in skin proliferative disorders and oncogenesis is another crucial issue to be elucidated