GUI Interfacing of DICOM images including 3D Model Creation

The purpose of this project is to create a simple method for viewing DICOM images taken during a medical scan such as CT or MRI. To perform this, Matlab programming was used to create a graphical user interface. This interface shows the user the image and attached information with subsequent images accessible via a slider bar. Furthermore, the user has the option to view a three-dimensional model of the object scanned which can then be rotated and viewed at multiple angles. This modeling was achieved using custom edge detection algorithms which locate and exclude exterior edges to allow viewing of the targeted objects. For testing purposes, a DICOM set of lung images was used to reconstruct the interior lung structure

The potential impact of Ocean Thermal Energy Conversion (OTEC) on fisheries

The commercial development of ocean thermal energy conversion (OTEC) operations will involve some environmental perturbations for which there is no precedent experience. The pumping of very large volumes of warm surface water and cold deep water and its subsequent discharge will result in the impingement, entrainment, and redistribution of biota. Additional stresses to biota will be caused by biocide usage and temperature depressions. However, the artificial upwelling of nutrients associated with the pumping of cold deep water, and the artificial reef created by an OTEC plant may have positive effects on the local environment. Although more detailed information is needed to assess the net effect of an OTEC operation on fisheries, certain assumptions and calculations are made supporting the conclusion that the potential risk to fisheries is not significant enough to deter the early development of IDEe. It will be necessary to monitor a commercial-scale plant in order to remove many of the remaining uncertainties. (PDF file contains 39 pages.

Estimating the population size of the Sanje mangabey (Cercocebus sanjei) using acoustic distance sampling

The Sanje mangabey (Cercocebus sanjei) is endemic to the Udzungwa Mountains, Tanzania, and is classified as Endangered due to its putatively declining population size, habitat degradation and fragmentation. Previous population size estimates have ranged from 1,350 to 3,500 individuals, with the last direct survey being conducted 15 years before the present study. Previous estimates are now thought to have underestimated the population due to a limited knowledge of group and habitat size, nonsystematic approaches and the use of visual methods that are not suitable for surveying the Sanje mangabey with its semi‐terrestrial and elusive behaviors. We used an acoustic survey method with observers recording the distinctive “whoop‐gobble” vocalization produced by mangabeys and point transect distance sampling to model a detection function and estimate abundance. Twenty‐eight surveys were conducted throughout the two forests where Sanje mangabeys are found: Mwanihana forest in the Udzungwa Mountains National Park (n = 13), and the Uzungwa Scarp Nature Reserve (n = 15). Group density was found to be significantly lower in the relatively unprotected Uzungwa Scarp forest (0.15 groups/km2; 95% CI: 0.08–0.27) compared to the well‐protected Mwanihana forest (0.29 groups/km2; 95% CI: 0.19–0.43; p = .03). We estimate that there are 1,712 (95% CI: 1,141–2,567) individuals in Mwanihana and 1,455 (95% CI: 783–2,702) in the Uzungwa Scarp, resulting in a total population size of 3,167 (95% CI: 2,181–4,596) individuals. The difference in group density between sites is likely a result of the differing protection status and levels of enforcement between the forests, suggesting that protection of the Uzungwa Scarp should be increased to encourage recovery of the population, and reduce the threat of degradation and hunting. Our results contribute to the reassessment of the species' IUCN Red List status and informing management and conservation action planning

Predicting the northward expansion of tropical lineage Rhipicephalus sanguineus sensu lato ticks in the United States and its implications for medical and veterinary health

The tropical lineage within the Rhipicephalus sanguineus species complex is cause for growing concern in the U.S. based on its prominent role in creating and perpetuating multiple recently identified outbreaks of Rocky Mountain spotted fever in the southwestern United States and northern Mexico. This lineage is undergoing a northward range expansion in the United States, necessitating the need for enhanced surveillance for Rh. sanguineus. To inform more focused surveillance efforts we use species distribution models (SDMs) to predict current (2015–2019) and future (2021–2040) habitat for the tropical lineage. Models using the MaxEnt algorithm were informed using geolocations of ticks genetically confirmed to be of the tropical lineage, for which data on 23 climatic and ecological variables were extracted. Models predicted that suitability was optimal where temperatures are relatively warm and stable, and there is minimal precipitation. This translated into habitat being predicted along much of the coast of southern states including California, Texas, Louisiana, and Florida. Although the endophilic nature of tropical Rh. sanguineus somewhat violates the assumptions of SDMs, our models correctly predicted known locations of this tick and provide a starting point for increased surveillance efforts. Furthermore, we highlight the importance of using molecular methods to distinguish between ticks in the Rh. sanguineus species complex.EEA RafaelaFil: Pascoe, Emily L. University of California. School of Veterinary Medicine. Department of Medicine and Epidemiology; Estados UnidosFil: Pascoe, Emily L. Wageningen University & Research. Laboratory of Entomology; Países BajosFil: Nava, Santiago. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea (IDICAL); ArgentinaFil: Nava, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación de la Cadena Láctea (IDICAL); ArgentinaFil: Labruna, Marcelo. Universidade de São Paulo. Faculdade de Medicina Veterinaria e Zootecnia. Departamento de Medicina Veterinaria Preventiva e Saude Animal; BrasilFil: Paddock, Christopher D. United States Department of Health and Human Services. Centers for Disease Control and Prevention. Division of Vector-Borne Diseases. Rickettsial Zoonoses Branch; Estados UnidosFil: Levin, Michael L. United States Department of Health and Human Services. Centers for Disease Control and Prevention. Division of Vector-Borne Diseases. Rickettsial Zoonoses Branch; Estados UnidosFil: Marcantonio, Matteo. Université Catholique de Louvain. Earth & Life Institute. Evolutionary Ecology and Genetics Group; BélgicaFil: Foley, Janet E. University of California. School of Veterinary Medicine. Department of Medicine and Epidemiology; Estados Unido

Factors Determining Mortality of Adult Chaparral Shrubs in an Extreme Drought Year in California

We measured dieback and mortality in a chaparral shrub community at a chaparral/desert ecotone following four years of below-average rainfall. Ecotones are important systems in which to examine plant and community responses to extreme and prolonged drought conditions and the potential impact of global change on plant distributions and community composition. Following a particularly severe drought year, dieback and mortality were documented for seven co-dominant shrub species. We examined whether mortality was related to species ecology, leaf traits, or water relations. Dieback and mortality were greatest in two non-sprouting species. These species also had high xylem cavitation resistance and low specific leaf area compared to several sprouting species. Among two sprouting congeners, mortality was greater in the more shallowly rooted species, even though this species was more cavitation resistant. Across all species, those that were more resistant to cavitation had greater mortality. Evidently, high resistance to xylem cavitation does not prevent adult plant mortality at chaparral/desert ecotones. A series of extreme drought years could preferentially reduce or eliminate non-sprouting species from mixed chaparral populations, causing a shift in community structure and contributing to desertification

Predominance of Ehrlichia ewingii in Missouri dogs

To investigate the species distribution of Ehrlichia present in Missouri dogs, we tested 78 dogs suspected of having acute ehrlichiosis and 10 healthy dogs. Blood from each dog was screened with a broad-range 16S rRNA gene PCR assay that detects known pathogenic species of Ehrlichia and Anaplasma. The species was determined by using species-specific PCR assays and nucleotide sequencing. Ehrlichia antibody testing was performed by using an indirect immunofluorescence assay with Ehrlichia chaffeensis as the antigenic substrate. The broad-range assay detected Ehrlichia or Anaplasma DNA in 20 (26%) of the symptomatic dogs and 2 (20%) of the asymptomatic dogs. E. ewingii accounted for 20 (91%), and E. chaffeensis accounted for 1 (5%) of the positives. Anaplasma phagocytophilum DNA was detected in one dog, and the sequences of regions of the 16S rRNA gene and the groESL operon amplified from the blood of this dog matched the published sequences of this organism. Antibodies reactive with E. chaffeensis were detected in 14 (67%) of the 21 PCR-positive dogs and in 12 (19%) of the 64 PCR-negative dogs. Combining the results of PCR and serology indicated that 33 (39%) of 85 evaluable dogs had evidence of past or current Ehrlichia infection. We conclude that E. ewingii is the predominant etiologic agent of canine ehrlichiosis in the areas of Missouri included in this survey. E. canis, a widely recognized agent of canine ehrlichiosis, was not detected in any animal. The finding of E. ewingii in asymptomatic dogs suggests that dogs could be a reservoir for this Ehrlichia species

Rickettsia parkeri in Amblyomma americanum Ticks, Tennessee and Georgia, USA

To determine the geographic distribution of the newly recognized human pathogen Rickettsia parkeri, we looked for this organism in ticks from Tennessee and Georgia, USA. Using PCR and sequence analysis, we identified R. parkeri in 2 Amblyomma americanum ticks. This rickettsiosis may be underdiagnosed in the eastern United States

notes on the present distribution and conservation of the sooty mangabey (Cercocebus atys) in Guinea-Bissau, West Africa

UIDB/04038/2020 UIDP/04038/2020The West-African sooty mangabey (Cercocebus atys) is threatened by habitat loss, hunting for meat consumption, and mortality during crop-foraging events. The species’ overall demographic trend is unknown. Presence and distribution in Guinea-Bissau, a country neighbored by Senegal and Republic of Guinea, was confirmed in 1946 but the species was declared extinct in 1989 and not observed in subsequent countrywide expeditions. Narratives of its presence across southern Guinea-Bissau are scattered in reports and occurrence in the eastern part was reported in 2017, but the limits of its distribution are currently unknown. Here, we present recent geo-referenced visual and molecular-based records of the sooty mangabey for three protected areas in southern Guinea-Bissau collected as part of a region-wide survey. Individuals were observed in Cufada Lagoons Natural Park (2015) and Dulombi National Park (NP) (2016) and photographed in Boé NP (2007, 2015 and 2020). Thirty-six samples collected in Boé NP (2017) were identified as sooty mangabey using a 402 base pair fragment of the mitochondrial cytochrome b gene. Our work suggests a wider distribution in Guinea-Bissau than previously described, augments knowledge of the populations’ current habitat use and threats, and has implications for efforts to conserve the species in West Africa. Considering the sooty mangabey as the reservoir of the simian immunodeficiency virus that led to the human variant, HIV-2, confirmation that the Guinea-Bissau population is not extinct may lead to a better understanding of early viral jump to humans and consequent epidemic spread, specifically of the HIV-2 Subgroup A. We highlight the need for extra conservation measures by Guinea-Bissau authorities.publishersversionpublishe

Ehrlichia ewingii Infection in White-Tailed Deer (Odocoileus virginianus)

Two closely related zoonotic ehrlichiae, Ehrlichia chaffeensis and E. ewingii, are transmitted by Amblyomma americanum, the lone star tick. Because white-tailed deer (Odocoileus virginianus) are critical hosts for all mobile stages of A. americanum and are important vertebrate reservoirs of E. chaffeensis, we investigated whether deer may be infected with E. ewingii, a cause of granulocytotropic ehrlichiosis in humans and dogs. To test for E. ewingii infection, we used polymerase chain reaction and inoculation of fawns with whole blood from wild deer. Of 110 deer tested from 20 locations in 8 U.S. states, 6 (5.5%) were positive for E. ewingii. In addition, natural E. ewingii infection was confirmed through infection of captive fawns. These findings expand the geographic distribution of E. ewingii, along with risk for human infection, to include areas of Kentucky, Georgia, and South Carolina. These data suggest that white-tailed deer may be an important reservoir for E. ewingii

A new arenavirus in a cluster of fatal transplant-associated diseases

Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points