A remote sensing method for resolving depth and subpixel composition of aquatic benthos

The problem of subpixel heterogeneity in cover types has been addressed in terrestrial environments by the application of linear spectral unmixing techniques. However, in aquatic systems the interceding depth of water causes the apparent reflectance of the substrate to diverge from a linear model, and if depth is unknown these methods cannot be applied. A new technique is presented in which the conventional spectral unmixing method has been modified to calculate depth at each pixel in addition to the proportions of substrate type. The technique requires knowledge of the reflectance spectra of m pure substrata in n (n > m) spectral bands at depth 0 and the water diffuse attenuation coefficients for the site in the same bands. Depth, z, can be entirely unknown. The method is comparable to "classical" spectral unmixing and proceeds by performing a Gaussian elimination for endmember quantities and then solving the remaining nonlinear function of z for f(z) = 0 by successive approximation. Computer-based models are used to test the technique with realistic water diffuse attenuation coefficients and random spectra and actual spectra of coral reef substrata. The robustness of the technique is assessed against three forms of introduced error: measurement errors on the spectra to be unmixed, differences between the true endmember spectra and those used in the analysis, and measurement error on the water diffuse attenuation coefficients. The results of these tests imply the technique is sufficiently robust for use on real data. Furthermore, spectral unmixing of aquatic systems appears to be relatively insensitive to inaccuracies in depth estimation and offers great utility for benthic mapping

Structural complexity governs seagrass acclimatization to depth with relevant consequences for meadow production, macrophyte diversity and habitat carbon storage capacity

Analyses of the integrated seagrass response to depth support the previously documented low plasticity and consistent shade-adapted leaf physiology of a habitat-builder that dominates well-illuminated reef environments. Two structural responses, "canopy-opening" and "below-ground-mass-depletion", govern the photoacclimatory response and facilitate, respectively, light penetration within the canopy and functional adjustments in whole-plant carbon balances. Conversely, "canopy-closing" may also explain dense canopies formed close to the waterline, as they provide shade and photoprotection to a susceptible leaf physiology under high-light. Canopy light attenuation is primarily regulated by the leaf area index (LAI), which is governed by changes in shoot size and density. Shoot density diminishes non-linearly with depth, while shoot size increases to a maximum followed by a decline. The initial increase in shoot size, which resembles a self-thinning response, increases LAI and meadow production in shallow depths. These seagrass structural adjustments have relevant ecological implications. Canopy-thinning allows macrophyte diversity to increase with depth, while seagrass production and carbon storage diminish exponentially, and are maximal only in a shallow coastal fringe. The results support the universality of plant self-thinning, from phytoplankton to complex canopies, likely the consequence of simple physical laws related to light limitation and pigment self-shading within photosynthetic structures and communities

Seagrass Canopy Photosynthetic Response Is a Function of Canopy Density and Light Environment: A Model for Amphibolis griffithii

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments

The Oregon Promise Barley Population: A tool for understanding the genetic basis of traits fundamental for barley production, malting, brewing, and distilling

The simultaneous availability of unique germplasm resources and cost-effective high-throughput genotyping allows for accelerated genome exploration and gene discovery. Our germplasm -the Oregon Promise population- is an array of 200 barley doubled haploids developed from the cross of Full Pint x Golden Promise. The spring 2-row parents have contrasting alleles at two of the dwarfing genes deployed in current varieties. The four homozygous combinations of these plant height alleles lead to contrasting phenotypes and each allele has pleiotropic effects on a range of other traits. Golden Promise is an iconic variety for malting, brewing, and distilling; Full Pint is a contributor to the craft brew Renaissance. Accordingly, the Oregon Promise will provide a valuable resource for extending current knowledge of malting and brewing genes to the frontiers of sensory assessment. The population shows transgressive segregation for adult plant resistance to stripe rust. As this disease is likely to become increasingly prevalent as a consequence of climate change, expanding the catalog of genes conferring durable resistance to this pathogen is an essential defensive breeding step. The availability of a quick-turnaround and cost effective SNP genotyping service (400+ markers) at Eureka Genomics (developed in collaboration with the James Hutton Institute) allows accelerated linkage map construction, QTL detection, and unraveling of gene interactions and pleiotropic effects based on the multi-environment, multi-trait phenotyping of the Oregon Promise population. This project is possible thanks to the tools and knowledge generated by the USDA-NIFA T-CAP project.Peer Reviewe

An unusual case of a microscopic alveolar adenoma coexisting with lung carcinoma: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Alveolar adenomas are extremely rare, benign, primary lung tumors of unknown histogenesis that are characterized by proliferative type II alveolar epithelium and septal mesenchyma. Mostly incidental, they are clinically important as they can imitate benign primary and secondary malignant tumors and at times are difficult to differentiate from early-stage lung cancer. We describe the case of a 59-year-old man with an incidental microscopic alveolar adenoma coexisting with poorly differentiated lung carcinoma.</p> <p>Case presentation</p> <p>A 59-year-old Caucasian man with a medical history of smoking and chronic obstructive pulmonary disease was incidentally found to have a right upper lobe mass while undergoing a computed tomographic chest scan as part of a chronic obstructive pulmonary disease clinical trial. Our patient underwent a right upper lobectomy after a bronchoscopic biopsy of the mass revealed the mass to be a carcinoma. A pathological examination revealed an incidental, small, 0.2 cm, well circumscribed lesion on the staple line margin of the lobectomy in addition to the carcinoma. Histopathological and immunohistochemical examinations revealed the lesion to be an alveolar adenoma.</p> <p>Conclusions</p> <p>We report the rare presentation of a microscopic alveolar adenoma coexisting with lung carcinoma. Alveolar adenoma is an entirely benign incidental neoplasm that can be precisely diagnosed using immunohistochemical analysis in addition to its unique histopathological characteristics.</p

MYC regulates fatty acid metabolism through a multigenic program in claudin-low triple negative breast cancer

Background: Recent studies have suggested that fatty acid oxidation (FAO) is a key metabolic pathway for the growth of triple negative breast cancers (TNBCs), particularly those that have high expression of MYC. However, the underlying mechanism by which MYC promotes FAO remains poorly understood. Methods: We used a combination of metabolomics, transcriptomics, bioinformatics, and microscopy to elucidate a potential mechanism by which MYC regulates FAO in TNBC. Results: We propose that MYC induces a multigenic program that involves changes in intracellular calcium signalling and fatty acid metabolism. We determined key roles for fatty acid transporters (CD36), lipases (LPL), and kinases (PDGFRB, CAMKK2, and AMPK) that each contribute to promoting FAO in human mammary epithelial cells that express oncogenic levels of MYC. Bioinformatic analysis further showed that this multigenic program is highly expressed and predicts poor survival in the claudin-low molecular subtype of TNBC, but not other subtypes of TNBCs, suggesting that efforts to target FAO in the clinic may best serve claudin-low TNBC patients. Conclusion: We identified critical pieces of the FAO machinery that have the potential to be targeted for improved treatment of patients with TNBC, especially the claudin-low molecular subtype

Supranuclear eye movements and nystagmus in children: A review of the literature and guide to clinical examination, interpretation of findings and age-appropriate norms.

Abnormal eye movements in children present a significant challenge to Ophthalmologists and other healthcare professionals. Similarly, examination of supra-nuclear eye movements in children and interpretation of any resulting clinical signs can seem very complex. A structured assessment is often lacking although in many cases, simple clinical observations, combined with a basic understanding of the underlying neurology, can hold the key to clinical diagnosis. As the range of underlying diagnoses for children with abnormal eye movements is broad, recognising clinical patterns and understanding their neurological basis is also imperative for ongoing management. Here we present a review and best practice guide for a structured, methodical clinical examination of supranuclear eye movements in children, a guide to clinical interpretation and age-appropriate norms. We also detail the more common specific clinical findings and how they should be interpreted and used to guide further management. In summary, this review will encourage clinicians to combine a structured assessment and a logical interpretation of the resulting clinical signs, in order to recognise patterns of presentation and avoid unnecessary investigations and protracted delays in diagnosis and clinical care

BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration

BRF1 is a rate-limiting factor for RNA Polymerase III-mediated transcription and is elevated in numerous cancers. Here, we report that elevated levels of BRF1 associate with poor prognosis in human prostate cancer. In vitro studies in human prostate cancer cell lines demonstrated that transient overexpression of BRF1 increased cell proliferation whereas the transient downregulation of BRF1 reduced proliferation and mediated cell cycle arrest. Consistent with our clinical observations, BRF1 overexpression in a Pten-deficient mouse (Pten BRF1 ) prostate cancer model accelerated prostate carcinogenesis and shortened survival. In Pten BRF1 tumours, immune and inflammatory processes were altered, with reduced tumoral infiltration of neutrophils and CD4 positive T cells, which can be explained by decreased levels of complement factor D (CFD) and C7 components of the complement cascade, an innate immune pathway that influences the adaptive immune response. We tested if the secretome was involved in BRF1-driven tumorigenesis. Unbiased proteomic analysis on BRF1-overexpresing PC3 cells confirmed reduced levels of CFD in the secretome, implicating the complement system in prostate carcinogenesis. We further identify that expression of C7 significantly correlates with expression of CD4 and has the potential to alter clinical outcome in human prostate cancer, where low levels of C7 associate with poorer prognosis

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy