3-D uncertainty-based topographic change detection with structure-from-motion photogrammetry: precision maps for ground control and directly georeferenced surveys

Structure-from-motion (SfM) photogrammetry is revolutionising the collection of detailed topographic data, but insight into geomorphological processes is currently restricted by our limited understanding of SfM survey uncertainties. Here, we present an approach that, for the first time, specifically accounts for the spatially variable precision inherent to photo-based surveys, and enables confidence-bounded quantification of 3-D topographic change. The method uses novel 3-D precision maps that describe the 3-D photogrammetric and georeferencing uncertainty, and determines change through an adapted state-of-the-art fully 3-D point-cloud comparison (M3C2; Lague, et al., 2013), which is particularly valuable for complex topography. We introduce this method by: (1) using simulated UAV surveys, processed in photogrammetric software, to illustrate the spatial variability of precision and the relative influences of photogrammetric (e.g. image network geometry, tie point quality) and georeferencing (e.g. control measurement) considerations; (2) we then present a new Monte Carlo procedure for deriving this information using standard SfM software and integrate it into confidence-bounded change detection; before (3) demonstrating geomorphological application in which we use benchmark TLS data for validation and then estimate sediment budgets through differencing annual SfM surveys of an eroding badland. We show how 3-D precision maps enable more probable erosion patterns to be identified than existing analyses, and how a similar overall survey precision could have been achieved with direct survey georeferencing for camera position data with precision half as good as the GCPs’. Where precision is limited by weak georeferencing (e.g. camera positions with multi-metre precision, such as from a consumer UAV), then overall survey precision can scale as n-½ of the control precision (n = number of images). Our method also provides variance-covariance information for all parameters. Thus, we now open the door for SfM practitioners to use the comprehensive analyses that have underpinned rigorous photogrammetric approaches over the last half-century

Determining Training Needs for Cloud Infrastructure Investigations using I-STRIDE

As more businesses and users adopt cloud computing services, security vulnerabilities will be increasingly found and exploited. There are many technological and political challenges where investigation of potentially criminal incidents in the cloud are concerned. Security experts, however, must still be able to acquire and analyze data in a methodical, rigorous and forensically sound manner. This work applies the STRIDE asset-based risk assessment method to cloud computing infrastructure for the purpose of identifying and assessing an organization's ability to respond to and investigate breaches in cloud computing environments. An extension to the STRIDE risk assessment model is proposed to help organizations quickly respond to incidents while ensuring acquisition and integrity of the largest amount of digital evidence possible. Further, the proposed model allows organizations to assess the needs and capacity of their incident responders before an incident occurs.Comment: 13 pages, 3 figures, 3 tables, 5th International Conference on Digital Forensics and Cyber Crime; Digital Forensics and Cyber Crime, pp. 223-236, 201

The incidence and clinical burden of respiratory syncytial virus disease identified through hospital outpatient presentations in Kenyan children

There is little information that describe the burden of respiratory syncytial virus (RSV) associated disease in the tropical African outpatient setting. Methods We studied a systematic sample of children aged <5 years presenting to a rural district hospital in Kenya with acute respiratory infection (ARI) between May 2002 and April 2004. We collected clinical data and screened nasal wash samples for RSV antigen by immunofluorescence. We used a linked demographic surveillance system to estimate disease incidence. Results Among 2143 children tested, 166 (8%) were RSV positive (6% among children with upper respiratory tract infection and 12% among children with lower respiratory tract infection (LRTI). RSV was more likely in LRTI than URTI (p<0.001). 51% of RSV cases were aged 1 year or over. RSV cases represented 3.4% of hospital outpatient presentations. Relative to RSV negative cases, RSV positive cases were more likely to have crackles (RR = 1.63; 95% CI 1.34–1.97), nasal flaring (RR = 2.66; 95% CI 1.40–5.04), in-drawing (RR = 2.24; 95% CI 1.47–3.40), fast breathing for age (RR = 1.34; 95% CI 1.03–1.75) and fever (RR = 1.54; 95% CI 1.33–1.80). The estimated incidence of RSV-ARI and RSV-LRTI, per 100,000 child years, among those aged <5 years was 767 and 283, respectively. Conclusion The burden of childhood RSV-associated URTI and LRTI presenting to outpatients in this setting is considerable. The clinical features of cases associated with an RSV infection were more severe than cases without an RSV diagnosis

Pseudomonas aeruginosa Enhances Production of a Non-Alginate Exopolysaccharide during Long-Term Colonization of the Cystic Fibrosis Lung

The gram-negative opportunistic pathogen Pseudomonas aeruginosa is the primary cause of chronic respiratory infections in individuals with the heritable disease cystic fibrosis (CF). These infections can last for decades, during which time P. aeruginosa has been proposed to acquire beneficial traits via adaptive evolution. Because CF lacks an animal model that can acquire chronic P. aeruginosa infections, identifying genes important for long-term in vivo fitness remains difficult. However, since clonal, chronological samples can be obtained from chronically infected individuals, traits undergoing adaptive evolution can be identified. Recently we identified 24 P. aeruginosa gene expression traits undergoing parallel evolution in vivo in multiple individuals, suggesting they are beneficial to the bacterium. The goal of this study was to determine if these genes impact P. aeruginosa phenotypes important for survival in the CF lung. By using a gain-of-function genetic screen, we found that 4 genes and 2 operons undergoing parallel evolution in vivo promote P. aeruginosa biofilm formation. These genes/operons promote biofilm formation by increasing levels of the non-alginate exopolysaccharide Psl. One of these genes, phaF, enhances Psl production via a post-transcriptional mechanism, while the other 5 genes/operons do not act on either psl transcription or translation. Together, these data demonstrate that P. aeruginosa has evolved at least two pathways to over-produce a non-alginate exopolysaccharide during long-term colonization of the CF lung. More broadly, this approach allowed us to attribute a biological significance to genes with unknown function, demonstrating the power of using evolution as a guide for targeted genetic studies.open6

Review of "Proteins of the Cerebrospinal Fluid" (2(nd )Edition) by Edward J. Thompson

This book on cerebrospinal fluid (CSF) proteins is primarily focused on immunoglobulins. The book was written as an extension of a meeting on multiple sclerosis to provide a more extensive consideration of the CSF

Utility of palliative EUS-guided biliary drainage using lumen-apposing metal stents: a prospective multicenter feasibility study (with video)

BACKGROUND AND AIMS: Biliary drainage with ERCP is successful in only 80% to 90% of extrahepatic cholangiocarcinoma and pancreatic cancer. We present the results of a multicenter prospective study assessing the safety, feasibility, and quality of life of patients after EUS-guided biliary drainage (EUS-BD) with lumen-apposing metal stents (LAMSs), after failed ERCP. METHODS: All consecutive adults with a dilated common bile duct (CBD) ≥14 mm secondary to inoperable malignant distal common bile duct (CBD) stricture and failed ERCP biliary drainage were screened and recruited from 3 tertiary U.K. centers. Technical success of EUS-BD using LAMSs was the primary endpoint. Improvement in serum bilirubin, 30-day mortality, procedure-related adverse events, and quality of life were secondary endpoints. The quality of life improvement was measured using a validated questionnaire (EORTC QLQ-BIL21). RESULTS: Twenty patients were included in analysis. EUS-BD was technically successful in all patients and the clinical success was 95% (19/20) at day 7 (>50% reduction in bilirubin) and 92.3% (12/13) at day 30 (bilirubin <50 μmol/L). There were significant improvements in overall quality of life score (49 vs 42, p=0.03) at day 30. All cause 30-day mortality was 20% and the moderate adverse event rate was 10% (1 cholangitis and 1 stent migration). CONCLUSION: EUS-BD has acceptable technical success and safety as a second line palliative treatment for inoperable malignant distal CBD strictures. Randomized controlled studies comparing EUS-BD with percutaneous transhepatic biliary drainage (PTBD) are needed to determine their effectiveness in clinical practice

A regularisation approach to causality theory for C^{1,1}Lorentzian metrics

We show that many standard results of Lorentzian causality theory remain valid if the regularity of the metric is reduced to C^{1,1}. Our approach is based on regularisations of the metric adapted to the causal structure

Conformational adaptation of Asian macaque TRIMCyp directs lineage specific antiviral activity

TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates. All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5α but they have distinct lentiviral specificities, conferring HIV-1 restriction in New World owl monkeys and HIV-2 restriction in Old World rhesus macaques. Here we provide evidence that Asian macaque TRIMCyps have acquired changes that switch restriction specificity between different lentiviral lineages, resulting in species-specific alleles that target different viruses. Structural, thermodynamic and viral restriction analysis suggests that a single mutation in the Cyp domain, R69H, occurred early in macaque TRIMCyp evolution, expanding restriction specificity to the lentiviral lineages found in African green monkeys, sooty mangabeys and chimpanzees. Subsequent mutations have enhanced restriction to particular viruses but at the cost of broad specificity. We reveal how specificity is altered by a scaffold mutation, E143K, that modifies surface electrostatics and propagates conformational changes into the active site. Our results suggest that lentiviruses may have been important pathogens in Asian macaques despite the fact that there are no reported lentiviral infections in current macaque populations

Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces

TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5αrh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5αrh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction. © 2011 Zhao et al