On the segmentation and classification of hand radiographs

This research is part of a wider project to build predictive models of bone age using hand radiograph images. We examine ways of finding the outline of a hand from an X-ray as the first stage in segmenting the image into constituent bones. We assess a variety of algorithms including contouring, which has not previously been used in this context. We introduce a novel ensemble algorithm for combining outlines using two voting schemes, a likelihood ratio test and dynamic time warping (DTW). Our goal is to minimize the human intervention required, hence we investigate alternative ways of training a classifier to determine whether an outline is in fact correct or not. We evaluate outlining and classification on a set of 1370 images. We conclude that ensembling with DTW improves performance of all outlining algorithms, that the contouring algorithm used with the DTW ensemble performs the best of those assessed, and that the most effective classifier of hand outlines assessed is a random forest applied to outlines transformed into principal components

Particle interactions and lattice dynamics: Scenarios for efficient bidirectional stochastic transport?

Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We explore the possibility to have efficient transport in these systems. One possibility would be to have appropriate interactions between the various motors' species, so as to form lanes. However, we show that the lane formation mechanism based on modified attachment/detachment rates as it was proposed previously is not necessarily connected to an efficient transport state and is suppressed when the diffusivity of unbound particles is finite. We propose another interaction mechanism based on obstacle avoidance that allows to have lane formation for limited diffusion. Besides, we had shown in a separate paper that the dynamics of the lattice itself could be a key ingredient for the efficiency of bidirectional transport. Here we show that lattice dynamics and interactions can both contribute in a cooperative way to the efficiency of transport. In particular, lattice dynamics can decrease the interaction threshold beyond which lanes form. Lattice dynamics may also enhance the transport capacity of the system even when lane formation is suppressed.Comment: 25 pages, 17 figures, 2 table

Effect of Thiamine Status on Probability of Lake Ontario Chinook Salmon Spawning in the Upper and Lower Sections of Salmon River, New York

Consumption of thiaminase-containing forage fishes reduces egg and muscle thiamine content and impairs the spawning migration of Cayuga Lake (New York) rainbow trout Oncorhynchus mykiss. Because some Chinook salmon O. tshawytscha from Lake Ontario have been shown to produce eggs low in thiamine, we examined the relationship between the migration of Chinook salmon and the thiamine content of their eggs spawned in the lower and upper sections of the Salmon River, a major tributary to Lake Ontario, in 2003–2006. Eggs from the upper section of the river were collected from 79 salmon returning to the state hatchery 25 river kilometers from the mouth. Eggs from 25 salmon in the lower section were collected from redds or females angled on redds approximately 1–3 km from the mouth. For all years combined, we found the mean thiamine concentration in eggs spawned in the lower section to be significantly lower than that for eggs spawned in the upper section; however, the annual differences in thiamine content of eggs between the upper and lower sections were significant only in 2003 and 2006. Binary logistic regression showed that the odds of spawning in the upper section was increased by 96% (95% confidence interval, 21–217%) for every nanomole of increase in the thiamine content of eggs. Therefore, the migratory achievement of Chinook salmon was significantly dependent on their thiamine status

Optical and EPR spectroscopy of Er3+ in lithium yttrium borate, Li6Y(BO3)3:Er single crystals

The energy levels of Er3+ ions have been determined in lithium yttrium borate (Li6Y(BO3)3) single crystals in a wide spectral range between 6000 and 40000 cm-1 together with an analysis of the ground state, using optical and EPR spectroscopy. The crystal field splittings of the 4I15/2 ground state and those of nearly all excited states up to the 4D7/2 manifold have been obtained at low temperature from luminescence (T = 5 K) and absorption (T = 9 K) measurements, respectively. The numbers of experimentally observed Stark sublevels agree well with those expected theoretically for Er3+ ions occupying a single low symmetry (C1) site. A full set of g- and 167Er hyperfine tensor parameters are presented for the ground state characterized by EPR; the measured Orbach-type spin-relaxation rates viz. the involved activation energies correspond to the optically derived lowest excited sublevels

Modeling genomic diversity and tumor dependency in malignant melanoma

The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and "druggable" effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative "driver" events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors

Suitability versus fidelity for rating single-photon guns

The creation of specified quantum states is important for most, if not all, applications in quantum computation and communication. The quality of the state preparation is therefore an essential ingredient in any assessment of a quantum-state gun. We show that the fidelity, under the standard definitions is not sufficient to assess quantum sources, and we propose a new measure of suitability that necessarily depends on the application for the source. We consider the performance of single-photon guns in the context of quantum key distribution (QKD) and linear optical quantum computation. Single-photon sources for QKD need radically different properties than sources for quantum computing. Furthermore, the suitability for single-photon guns is discussed explicitly in terms of experimentally accessible criteria.Comment: 4 pages, 2 figures Revised per referee suggestion

Effect of Thiamine Status on Probability of Lake Ontario Chinook Salmon Spawning in the Upper or Lower Sections of Salmon River, New York

Consumption of thiaminase‐containing forage fishes reduces egg and muscle thiamine content and impairs the spawning migration of Cayuga Lake (New York) rainbow trout Oncorhynchus mykiss. Because some Chinook salmon O. tshawytscha from Lake Ontario have been shown to produce eggs low in thiamine, we examined the relationship between the migration of Chinook salmon and the thiamine content of their eggs spawned in the lower and upper sections of the Salmon River, a major tributary to Lake Ontario, in 2003–2006. Eggs from the upper section of the river were collected from 79 salmon returning to the state hatchery 25 river kilometers from the mouth. Eggs from 25 salmon in the lower section were collected from redds or females angled on redds approximately 1–3 km from the mouth. For all years combined, we found the mean thiamine concentration in eggs spawned in the lower section to be significantly lower than that for eggs spawned in the upper section; however, the annual differences in thiamine content of eggs between the upper and lower sections were significant only in 2003 and 2006. Binary logistic regression showed that the odds of spawning in the upper section was increased by 96% (95% confidence interval, 21–217%) for every nanomole of increase in the thiamine content of eggs. Therefore, the migratory achievement of Chinook salmon was significantly dependent on their thiamine status.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142217/1/nafm0895.pd

Mean field treatment of exclusion processes with random-force disorder

The asymmetric simple exclusion process with random-force disorder is studied within the mean field approximation. The stationary current through a domain with reversed bias is analyzed and the results are found to be in accordance with earlier intuitive assumptions. On the grounds of these results, a phenomenological random barrier model is applied in order to describe quantitatively the coarsening phenomena. Predictions of the theory are compared with numerical results obtained by integrating the mean field evolution equations.Comment: 21 pages, 14 figure

Evaluating the Dimensionality of First-Grade Written Composition

Purpose—We examined dimensions of written composition using multiple evaluative approaches such as an adapted 6+1 trait scoring, syntactic complexity measures, and productivity measures. We further examined unique relations of oral language and literacy skills to the identified dimensions of written composition. Method—A large sample of first grade students (N = 527) was assessed on their language, reading, spelling, letter writing automaticity, and writing in the spring. Data were analyzed using a latent variable approach including confirmatory factor analysis and structural equation modeling. Results—The seven traits in the 6+1 trait system were best described as two constructs: substantive quality, and spelling and writing conventions. When the other evaluation procedures such as productivity and syntactic complexity indicators were included, four dimensions emerged: substantive quality, productivity, syntactic complexity, and spelling and writing conventions. Language and literacy predictors were differentially related to each dimension in written composition. Conclusions—These four dimensions may be a useful guideline for evaluating developing beginning writer’s compositions

Sensitivity of epidermal growth factor receptor and ErbB2 exon 20 insertion mutants to Hsp90 inhibition

The mature epidermal growth factor receptor (EGFR) neither associates with nor requires the molecular chaperone heat-shock protein 90 (Hsp90). Mutations in EGFR exons 18, 19, and 21 confer Hsp90 chaperone dependence. In non-small cell lung cancer (NSCLC), these mutations are associated with enhanced sensitivity to EGFR inhibitors in vitro and with clinical response in vivo. Although less prevalent, insertions in EGFR exon 20 have also been described in NSCLC. These mutations, however, confer resistance to EGFR inhibitors. In NSCLC, exon 20 insertions have also been identified in the EGFR family member ErbB2. Here, we examined the sensitivity of exon 20 insertion mutants to an Hsp90 inhibitor currently in the clinic. Our data demonstrate that both EGFR and ErbB2 exon 20 insertion mutants retain dependence on Hsp90 for stability and downstream-signalling capability, and remain highly sensitive to Hsp90 inhibition. Use of Hsp90 inhibitors should be considered in NSCLC harbouring exon 20 insertions in either EGFR or ErbB2