This paper presents a novel image classification scheme for benthic coral reef images that can be applied to both single image and composite mosaic datasets. The proposed method can be configured to ...the characteristics (e.g., the size of the dataset, number of classes, resolution of the samples, color information availability, class types, etc.) of individual datasets. The proposed method uses completed local binary pattern (CLBP), grey level co-occurrence matrix (GLCM), Gabor filter response, and opponent angle and hue channel color histograms as feature descriptors. For classification, either k-nearest neighbor (KNN), neural network (NN), support vector machine (SVM) or probability density weighted mean distance (PDWMD) is used. The combination of features and classifiers that attains the best results is presented together with the guidelines for selection. The accuracy and efficiency of our proposed method are compared with other state-of-the-art techniques using three benthic and three texture datasets. The proposed method achieves the highest overall classification accuracy of any of the tested methods and has moderate execution time. Finally, the proposed classification scheme is applied to a large-scale image mosaic of the Red Sea to create a completely classified thematic map of the reef benthos.
The Surface Water Ocean Topography (SWOT) satellite mission expected to launch in 2021 will offer a unique opportunity to map river discharge at an unprecedented spatial resolution globally from ...observations of water surface elevation, width, and slope. Because river discharge will not be directly observed from SWOT, a number of algorithms of varying complexity have been developed to estimate discharge from SWOT observables. Outstanding issues include the lack of accurate prior information and parameter equifinality. We developed a new data assimilation discharge algorithm that aimed to overcome these limitations by integrating a data‐driven approach to estimate priors with a model informed by hydraulic geometry relations. A comprehensive simulated dataset of 18 rivers was used to evaluate the algorithm and four different configurations (rectangular channel, generic channel, and geomorphologically classified channel with and without regularization) to assess the impact of progressively adding hydraulic geometry constraints to the estimation problem. The algorithm with the full set of constraints outperformed the other configurations with median Nash‐Sutcliffe coefficients of 0.77, compared with −0.46, 0.31 and 0.66, while other error metrics showed similar improvement. Results from this study show the promise of this hybrid data‐driven approach to estimating river discharge from SWOT observations, although a number of enhancements need to be tested to improve the operational applicability of the algorithm.
Key Points
Data assimilation of SWOT observations can retrieve large‐river discharge even with a simple steady‐state model
A data‐driven approach led to a plausible estimation of prior probability distributions of hydraulic variables
Hydraulic geometry constraints improved river discharge estimation accuracy across all metrics
Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We used integrative molecular profiling to discover and characterize molecular ...subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering showed three reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and showed that the molecular subtypes defined by gene expression showed distinct genomic changes. Tumors from the 'muscle-enriched' cluster showed significantly increased copy number changes (P=0.04). A majority of the muscle-enriched cases showed loss at 16q24, which contains Fanconi anemia, complementation group A, known to have an important role in DNA repair, and loss at 1p36, which contains PRDM16, of which loss promotes muscle differentiation. Immunohistochemistry (IHC) was performed on LMS tissue microarrays (n=377) for five markers with high levels of messenger RNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP, CFL2 and MYLK) and showed significantly correlated expression of the five proteins (all pairwise P<0.005). Expression of the five markers was associated with improved disease-specific survival in a multivariate Cox regression analysis (P<0.04). In this analysis that combined gene expression profiling, aCGH and IHC, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers.
At‐many‐stations hydraulic geometry (AMHG), while useful for estimating river discharge from satellite data, remains empirical and has yet to be reconciled with the at‐a‐station hydraulic geometry ...(AHG) from which it was originally derived. Here we present evidence, using United States Geological Survey field measurements of channel hydraulics for 155 rivers, that AMHG can be hydraulically and geomorphically reconciled with AHG. Our results indicate that AMHG is rightly understood as an expression of a river‐wide model of hydraulics driven by changes in slope imposed upon AHG physics. The explanatory power of AHG and this river‐wide model combine to determine whether AMHG exists: if both AHG and the river‐wide model adequately describe hydraulics, then we show that AMHG is a necessary mathematical consequence of these two phenomena. We also orient these findings in the context of river discharge estimation and other applications.
Plain Language Summary
Hydraulic geometry (HG) is an empirical phenomenon that predicts river width, depth, and velocity given river discharge and is fundamental to our ability to predict floods, river habitats, and water availability for human and ecosystem use. Recently, a new form of HG was discovered (at‐many‐stations HG, or AMHG), and it has been successfully deployed in a range of applications and proven to exist in a wide variety of rivers. However, the novel phenomenon of AMHG remains empirical with puzzling and seemingly contradictory links to other, traditional forms of HG, which are well understood and have been studied since the 1950s. AMHG is also not manifested in all rivers, adding to confusion as to its origin. Here, we show for the first time that we can reconcile AMHG with all other traditional variants of HG and gain a complete understanding of how and when AMHG occurs in rivers. This puts the most puzzling aspects of AMHG—why is it observed in some rivers but not others, and what causes the phenomenon—to rest. We have fundamentally changed the conception of AMHG and suggest this work as a basis for all future AMHG research.
Key Points
We derive AMHG, explain why it exists in some rivers and not others, and reconcile AMHG and AHG, validated across 155 rivers
We suggest that AMHG is a necessary consequence of any well‐fit river‐wide relationship of slope, roughness, and geometry imposed on AHG physics
We show that AMHG presence/absence is a function of the explanatory power of both AHG and a river‐wide slope roughness model
Ribosome profiling and mass spectroscopy have identified canonical and noncanonical translation initiation codons (TICs) that are upstream of the main translation initiation site and used to ...translate oncogenic proteins. There have previously been conflicting reports about the patterns of nucleotides that surround noncanonical TICs. Here, we use a Kozak Similarity Score algorithm to find that nearly all of these TICs have flanking nucleotides closely matching the Kozak sequence. Remarkably, the nucleotides flanking alternative noncanonical TICs are frequently closer to the Kozak sequence than the nucleotides flanking TICs used to translate the gene’s main protein. Of note, the 5′ untranslated region (5‘UTR) of cancer-associated genes with an upstream TIC tend to be significantly longer than the same region in genes not associated with cancer. The presence of a longer-than-typical 5′UTR increases the likelihood of ribosome binding to upstream noncanonical TICs, and may be a distinguishing feature of a number of genes overexpressed in cancer. Noncanonical TICs that are located in the 5′UTR, although thought by some to be disadvantageous and suppressed by evolution, may translate oncogenic proteins because of their flanking nucleotides.
Population distributions are affected by a variety of spatial processes, including dispersal, intraspecific dynamics and habitat selection. Within reef‐building coral communities, these processes are ...especially important during the earliest life stages when reproduction provides mobility among sessile organisms and populations experience the greatest mortality bottlenecks both before and immediately after settlement. Here, we used large‐area imaging to create photomosaics that allowed us to identify and map the location of 4681 juvenile (1–5 cm diameter) and 25 902 adult (>5 cm diameter) coral colonies from eight 100‐m2 plots across the forereef of Palmyra Atoll. Using metrics of density, percent cover and the relative location of each colony within each plot, we examined abundance and spatial relationships between juvenile and adult coral taxa. Within coral taxa, juvenile density was generally positively related to the numerical density and percent cover of adults. Nearest neighbor analyses showed aggregation of juveniles near adults of the same taxon for two of the focal taxa (Pocillopora and Fungiids), while all other taxa showed random spatial patterning relative to adults. Three taxa had clustered distributions of juveniles overall. Additionally, we found that on a colony level, juveniles for five of nine focal taxa (accounting for >98% of all identified juveniles) associated with a specific habitat type, with four of those five taxa favoring unconsolidated (e.g. rubble) over consolidated substrata. The general lack of clustering in juvenile corals contrasts with consistent clustering patterns seen in adult corals, suggesting that adult spatial patterns are largely driven by processes occurring after maturity such as partial colony mortality, including fission and fragmentation. The association of many taxa with unconsolidated habitat also suggests that corals may play an important role in colonizing natural rubble patches that could contribute to reef stabilization over time.
The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si–Br, Si–H, and Si–CH3 groups, ...respectively. The surface termination influenced the band bending, with the Si 2p3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)–Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)–H, followed by Si(111)–CH3 (whose Fermi level was positioned near midgap at the surface). Si(111)–CH3 surfaces exposed to Br2(g) yielded the lowest binding energies, with the Fermi level positioned between midgap and the valence band. The Fermi level position of Br2(g)-exposed Si(111)–CH3 was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.
Primary myoepithelial tumors of soft tissue are uncommon, and criteria for malignancy among these neoplasms have only recently been established. Of 51 myoepithelial carcinomas of soft tissue in the ...literature, 11 occurred in children, 7 of which were included in a previous series of myoepithelial tumors from our group. We have collected an additional 22 cases of myoepithelial carcinoma of soft tissue in the pediatric population, and we describe the detailed clinicopathologic features of all 29 cases herein. There were 15 girls and 14 boys; age at diagnosis ranged from newborn to 17 years (median, 9 y). Sites included extremities (14 cases), trunk (6 cases), viscera (5 cases: 3 mediastinal, 1 retroperitoneal, and 1 intracardiac), and head/neck (4 cases). Histologically, the tumors were heterogeneous, with epithelioid, clear, spindle and/or plasmacytoid cells forming nests, cords or solid sheets in a myxoid or hyalinized stroma. Epithelioid cells predominated in the majority of cases (27 of 29; 93%) and in 10 cases (34%), tumor cells focally had scant cytoplasm with round cell morphology. The mitotic rate ranged from <1 to 68 per 10 high power fields (median, 8), and tumor necrosis was present in 14 cases. At least 1 broad-spectrum cytokeratin was positive in all tumors CAM5.2 in 17 of 18 (94%), AE1/AE3 in 15 of 20 (75%), and PAN-K in 14 of 21 (67%), and EMA was positive in 19 of 29 cases (66%). Either S100 or GFAP was positive in all but 4 cases S100 in 21 of 29 (72%) and GFAP in 15 of 28 (54%). Clinical follow-up in 23 cases revealed that 9 patients had local recurrences (53% of the 17 patients who underwent complete excision with negative margins); 12 (52%) developed metastases; and 10 (43%) have died of disease so far, at a median interval of 9 months after diagnosis. Despite the relative rarity of carcinomas in the pediatric population, myoepithelial carcinoma seems to be disproportionately common among children and often has an aggressive clinical course.
Prior studies have shown that myeloma patients exhibiting either genetically defined high-risk disease or plasma cell leukemia have a poor outcome with a median overall survival (OS) of ≤3 years. ...Results of IFM 2005-01 and 02 suggest that relatively limited bortezomib-containing induction regimens did not produce a major survival benefit among these patients. However, results of recent studies suggest that combination therapy may benefit these patients when given early and again later in the treatment. We evaluated a combination maintenance/consolidation regimen (RVD) following autologous stem cell transplant (ASCT) for high-risk patients to evaluate the impact of this approach on outcome. Following initiation of RVD maintenance, 51% of patients achieved stringent complete response (sCR), with 96% achieving at least VGPR as best response. Median progression free survival (PFS) for all patients is 32 months with a 3-year OS of 93%. The regimen was well tolerated with no grade 3/4 neuropathy. Early ASCT followed by RVD maintenance is a promising strategy for high-risk myeloma patients and delivered excellent response rates, and promising PFS and OS.
Individualized, precision feeding of dairy cattle may contribute to profitable and sustainable dairy production. Feeding strategies targeted at optimizing efficiency of individual cows, rather than ...groups of animals with similar characteristics, is a logical goal of individualized precision feeding. However, algorithms designed to make feeding recommendations for specific animals are scarce. The objective of this study was to develop and test 2 algorithms designed to improve feed efficiency of individual cows by supplementing total mixed rations (TMR) with varying types and amounts of top-dressed feedstuffs. Twenty-four Holstein dairy cows were assigned to 1 of 3 treatment groups as follows: a control group fed a common TMR ad libitum, a group fed individually according to algorithm 1, and a group fed individually according to algorithm 2. Algorithm 1 used a mixed-model approach with feed efficiency as the response variable and automated measurements of production parameters and top-dress type as dependent variables. Cow was treated as a random effect, and cow by top-dress interactions were included if significant. Algorithm 2 grouped cows based on top-dress response efficiency structure using a principal components and k-means clustering. Both algorithms were trained over a 36-d experimental period immediately before testing, and were updated weekly during the 35-d testing period. Production performance responses for dry matter intake (DMI), milk yield, milk fat percentage and yield, milk protein percentage and yield, and feed efficiency were analyzed using a mixed-effects model with fixed effects for feeding algorithm, top dress, week, and the 2- and 3-way interactions among these variables. Milk protein percentage and feed efficiency were significantly affected by the 3-way interaction of top dress, algorithm, and week, and DMI tended to be affected by this 3-way interaction. Feeding algorithm did not affect milk yield, milk fat yield, or milk protein yield. However, feeding costs were reduced, and hence milk revenue increased on the algorithm-fed cows. The efficacy of feeding algorithms differed by top dress and time, and largely relied on DMI shifts to modulate feed efficiency. The net result, for the cumulative feeding groups, was that cows in the algorithm 1 and 2 groups earned over $0.45 and $0.70 more per head per day in comparison to cows on the TMR control, respectively. This study yielded 2 candidate approaches for efficiency-focused, individualized feeding recommendations. Refinement of algorithm selection, development, and training approaches are needed to maximize production parameters through individualized feeding.
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