Histogram-based models on non-thin section chest CT predict invasiveness of primary lung adenocarcinoma subsolid nodules.

109 pathologically proven subsolid nodules (SSN) were segmented by 2 readers on non-thin section chest CT with a lung nodule analysis software followed by extraction of CT attenuation histogram and geometric features. Functional data analysis of histograms provided data driven features (FPC1,2,3) used in further model building. Nodules were classified as pre-invasive (P1, atypical adenomatous hyperplasia and adenocarcinoma in situ), minimally invasive (P2) and invasive adenocarcinomas (P3). P1 and P2 were grouped together (T1) versus P3 (T2). Various combinations of features were compared in predictive models for binary nodule classification (T1/T2), using multiple logistic regression and non-linear classifiers. Area under ROC curve (AUC) was used as diagnostic performance criteria. Inter-reader variability was assessed using Cohen's Kappa and intra-class coefficient (ICC). Three models predicting invasiveness of SSN were selected based on AUC. First model included 87.5 percentile of CT lesion attenuation (Q.875), interquartile range (IQR), volume and maximum/minimum diameter ratio (AUC:0.89, 95%CI:[0.75 1]). Second model included FPC1, volume and diameter ratio (AUC:0.91, 95%CI:[0.77 1]). Third model included FPC1, FPC2 and volume (AUC:0.89, 95%CI:[0.73 1]). Inter-reader variability was excellent (Kappa:0.95, ICC:0.98). Parsimonious models using histogram and geometric features differentiated invasive from minimally invasive/pre-invasive SSN with good predictive performance in non-thin section CT

Yield and Production Costs for Three Potential Dedicated Energy Crops in Mississippi and Oklahoma Environments

The objective of this paper is to determine production costs of switchgrass, eastern gammagrass, and giant miscanthus using Mississippi and Oklahoma data. Production costs were computed using a standard enterprise budgeting approach by species and method of harvest. Results indicate cost difference across species and method of harvest.Yield and Cost, biomass species, Crop Production/Industries, Resource /Energy Economics and Policy,

An Observational Test of Two-field Inflation

We study adiabatic and isocurvature perturbation spectra produced by a period of cosmological inflation driven by two scalar fields. We show that there exists a model-independent consistency condition for all two-field models of slow-roll inflation, despite allowing for model-dependent linear processing of curvature and isocurvature perturbations during and after inflation on super-horizon scales. The scale-dependence of all spectra are determined solely in terms of slow-roll parameters during inflation and the dimensionless cross-correlation between curvature and isocurvature perturbations. We present additional model-dependent consistency relations that may be derived in specific two-field models, such as the curvaton scenario.Comment: 6 pages, latex with revtex, no figures; v2, minor changes, to appear in Physical Review

Ancillary Testing in Lung Cancer Diagnosis

The pathologic diagnosis of lung cancer historically has relied primarily on morphologic features of tumors in histologic sections. With the emergence of new targeted therapies, the pathologist is called upon increasingly to provide not only accurate typing of lung cancers, but also to provide prognostic and predictive information, based on a growing number of ancillary tests, that may have significant impact on patient management. This review provides an overview of ancillary tests currently used in the pathologic diagnosis of lung cancer, with a focus on immunohistochemistry and molecular diagnostics

Tim54p connects inner membrane assembly and proteolytic pathways in the mitochondrion

Tim54p, a component of the inner membrane TIM22 complex, does not directly mediate the import of inner membrane substrates but is required for assembly/stability of the 300-kD TIM22 complex. In addition, Δtim54 yeast exhibit a petite-negative phenotype (also observed in yeast harboring mutations in the F1Fo ATPase, the ADP/ATP carrier, mitochondrial morphology components, or the i–AAA protease, Yme1p). Interestingly, other import mutants in our strain background are not petite-negative. We report that Tim54p is not involved in maintenance of mitochondrial DNA or mitochondrial morphology. Rather, Tim54p mediates assembly of an active Yme1p complex, after Yme1p is imported via the TIM23 pathway. Defective Yme1p assembly is likely the major contributing factor for the petite-negativity in strains lacking functional Tim54p. Thus, Tim54p has two independent functions: scaffolding/stability for the TIM22 membrane complex and assembly of Yme1p into a proteolytically active complex. As such, Tim54p links protein import, assembly, and turnover pathways in the mitochondrion

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad

New pterosaur tracks (Pteraichnidae) from the Late Cretaceous Uhangri Formation, southwestern Korea

This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Numerous footprints of dinosaurs, pterosaurs and birds, together with arthropod tracks, have been discovered in the upper Cretaceous Uhangri Formation which crops out along the south-western coastline of South Korea. This ichnofauna contains the first pterosaur tracks reported from Asia. The digitigrade tridactyl manus impressions exhibit features of a typical pterosaur hand print. The pes impressions, however, show features that are different from pterosaur footprints reported previously: there is no visible trace of impressions of individual digits, and the toes are triangular or rounded in shape distally without distinct claw impressions. As these features clearly distinguish the Uhangri tracks from Pteraichnus and Purbeckopus, we assign them to a new genus, Haenamichnus which accommodates the new ichnospecies, Haenamichnus uhangriensis. The prints are five to six times larger than those of Pteraichnus, and are currently the largest pterosaur ichnites known. They show virtually no trace of the 5th phalange of the pes, indicating that they were made by pterodactyloids; moreover, features of the tracks suggest that they can be attributed to azhdarchids, the commonest pterosaur of the Late Cretaceous. The longest pterosaur trackway yet known from any track site (length 7.3 m) and consisting of 14 pairs of foot impressions, was also found in the Uhangri Formation and suggests that azhdarchids, at least, were competent terrestrial locomotors. The fossil track site at Uhangri represents the first occurrence of the tracks of pterosaurs, dinosaurs and web-footed birds all on the same level. This demonstrates that pterosaurs and birds visited the same habitat, but the large size disparity suggests that they occupied different ecological niches.Peer Reviewe

Remote oil spill detection and monitoring beneath sea ice

The spillage of oil in Polar Regions is particularly serious due to the threat to the environment and the difficulties in detecting and tracking the full extent of the oil seepage beneath the sea ice. Development of fast and reliable sensing techniques is highly desirable. In this paper hyperspectral imaging combined with signal processing and classification techniques are proposed as a potential tool to detect the presence of oil beneath the sea ice. A small sample, lab based experiment, serving as a proof of concept, resulted in the successful identification of oil presence beneath the thin ice layer as opposed to the other sample with ice only. The paper demonstrates the results of this experiment that granted a financial support to execute full feasibility study of this technology for oil spill detection beneath the sea ice