A New Tool Improves Diagnostic Test Performance for Transmission EM Evaluation of Axonemal Dynein Arms

Diagnosis of primary ciliary dyskinesia (PCD) by identification of dynein arm loss in transmission electron microscopy (TEM) images can be confounded by high background noise due to random electron-dense material within the ciliary matrix, leading to diagnostic uncertainty even for experienced morphologists. We developed a novel image analysis tool to average the axonemal peripheral microtubular doublets, thereby increasing microtubular signal and reducing random background noise. In a randomized, double-blinded study that compared two experienced morphologists and three different diagnostic approaches, we found that use of this tool led to improvement in diagnostic TEM test performance

Inter-species variation in colour perception

Inter-species variation in colour perception poses a serious problem for the view that colours are mind-independent properties. Given that colour perception varies so drastically across species, which species perceives colours as they really are? In this paper, I argue that all do. Specifically, I argue that members of different species perceive properties that are determinates of different, mutually compatible, determinables. This is an instance of a general selectionist strategy for dealing with cases of perceptual variation. According to selectionist views, objects simultaneously instantiate a plurality of colours, all of them genuinely mind-independent, and subjects select from amongst this plurality which colours they perceive. I contrast selectionist views with relationalist views that deny the mind-independence of colour, and consider some general objections to this strategy

Exclusion Limits on the WIMP-Nucleon Cross-Section from the First Run of the Cryogenic Dark Matter Search in the Soudan Underground Lab

The Cryogenic Dark Matter Search (CDMS-II) employs low-temperature Ge and Si detectors to seek Weakly Interacting Massive Particles (WIMPs) via their elastic scattering interactions with nuclei. Simultaneous measurements of both ionization and phonon energy provide discrimination against interactions of background particles. For recoil energies above 10 keV, events due to background photons are rejected with >99.99% efficiency. Electromagnetic events very near the detector surface can mimic nuclear recoils because of reduced charge collection, but these surface events are rejected with >96% efficiency by using additional information from the phonon pulse shape. Efficient use of active and passive shielding, combined with the the 2090 m.w.e. overburden at the experimental site in the Soudan mine, makes the background from neutrons negligible for this first exposure. All cuts are determined in a blind manner from in situ calibrations with external radioactive sources without any prior knowledge of the event distribution in the signal region. Resulting efficiencies are known to ~10%. A single event with a recoil of 64 keV passes all of the cuts and is consistent with the expected misidentification rate of surface-electron recoils. Under the assumptions for a standard dark matter halo, these data exclude previously unexplored parameter space for both spin-independent and spin-dependent WIMP-nucleon elastic scattering. The resulting limit on the spin-independent WIMP-nucleon elastic-scattering cross-section has a minimum of 4x10^-43 cm^2 at a WIMP mass of 60 GeV/c^2. The minimum of the limit for the spin-dependent WIMP-neutron elastic-scattering cross-section is 2x10^-37 cm^2 at a WIMP mass of 50 GeV/c^2.Comment: 37 pages, 42 figure

A population-modulated bibliometric measure with an application in the field of statistics

We use confirmatory factor analysis to derive a unifying measure of comparison of scientists based on bibliometric measurements, by utilizing the h-index, some similar h-type indices as well as other common measures of scientific performance. We use a real data example from nine well-known departments of statistics to demonstrate our approach and argue that our combined measure results in a better overall evaluation of a researchers' scientific work

Different cellular p16INK4a localisation may signal different survival outcomes in head and neck cancer

Background:Recently, the management of head and neck squamous cell carcinoma (HNSCC) has focused considerable attention on biomarkers, which may influence outcomes. Tests for human papilloma infection, including direct assessment of the virus as well as an associated tumour suppressor gene p16, are considered reproducible. Tumours from familial melanoma syndromes have suggested that nuclear localisation of p16 might have a further role in risk stratification. We hypothesised p16 staining that considered nuclear localisation might be informative for predicting outcomes in a broader set of HNSCC tumours not limited to the oropharynx, human papilloma virus (HPV) status or by smoking status.Methods:Patients treated for HNSCC from 2002 to 2006 at UNC (University of North Carolina at Chapel Hill) hospitals that had banked tissue available were eligible for this study. Tissue microarrays (TMA) were generated in triplicate. Immunohistochemical (IHC) staining for p16 was performed and scored separately for nuclear and cytoplasmic staining. Human papilloma virus staining was also carried out using monoclonal antibody E6H4. p16 expression, HPV status and other clinical features were correlated with progression-free (PFS) and overall survival (OS).Results:A total of 135 patients had sufficient sample for this analysis. Median age at diagnosis was 57 years (range 20–82), with 68.9% males, 8.9% never smokers and 32.6% never drinkers. Three-year OS rate and PFS rate was 63.0% and 54.1%, respectively. Based on the p16 staining score, patients were divided into three groups: high nuclear, high cytoplasmic staining group (HN), low nuclear, low cytoplasmic staining group (LS) and high cytoplasmic, low nuclear staining group (HC). The HN and the LS groups had significantly better OS than the HC group with hazard ratios of 0.10 and 0.37, respectively, after controlling for other factors, including HPV status. These two groups also had significantly better PFS than the HC staining group. This finding was consistent for sites outside the oropharynx and did not require adjustment for smoking status.Conclusion:Different p16 protein localisation suggested different survival outcomes in a manner that does not require limiting the biomarker to the oropharynx and does not require assessment of smoking status

Fast character modeling with sketch-based PDE surfaces

© 2020, The Author(s). Virtual characters are 3D geometric models of characters. They have a lot of applications in multimedia. In this paper, we propose a new physics-based deformation method and efficient character modelling framework for creation of detailed 3D virtual character models. Our proposed physics-based deformation method uses PDE surfaces. Here PDE is the abbreviation of Partial Differential Equation, and PDE surfaces are defined as sculpting force-driven shape representations of interpolation surfaces. Interpolation surfaces are obtained by interpolating key cross-section profile curves and the sculpting force-driven shape representation uses an analytical solution to a vector-valued partial differential equation involving sculpting forces to quickly obtain deformed shapes. Our proposed character modelling framework consists of global modeling and local modeling. The global modeling is also called model building, which is a process of creating a whole character model quickly with sketch-guided and template-based modeling techniques. The local modeling produces local details efficiently to improve the realism of the created character model with four shape manipulation techniques. The sketch-guided global modeling generates a character model from three different levels of sketched profile curves called primary, secondary and key cross-section curves in three orthographic views. The template-based global modeling obtains a new character model by deforming a template model to match the three different levels of profile curves. Four shape manipulation techniques for local modeling are investigated and integrated into the new modelling framework. They include: partial differential equation-based shape manipulation, generalized elliptic curve-driven shape manipulation, sketch assisted shape manipulation, and template-based shape manipulation. These new local modeling techniques have both global and local shape control functions and are efficient in local shape manipulation. The final character models are represented with a collection of surfaces, which are modeled with two types of geometric entities: generalized elliptic curves (GECs) and partial differential equation-based surfaces. Our experiments indicate that the proposed modeling approach can build detailed and realistic character models easily and quickly

IDSS: deformation invariant signatures for molecular shape comparison

<p>Abstract</p> <p>Background</p> <p>Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC) treat them as rigid bodies, which may lead to incorrect measure of the shape similarity of flexible molecules.</p> <p>Results</p> <p>To address the issue we introduce a new shape descriptor, called Inner Distance Shape Signature (IDSS), for describing the 3D shapes of flexible molecules. The inner distance is defined as the length of the shortest path between landmark points within the molecular shape, and it reflects well the molecular structure and deformation without explicit decomposition. Our IDSS is stored as a histogram which is a probability distribution of inner distances between all sample point pairs on the molecular surface. We show that IDSS is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. Our approach reduces the 3D shape comparison problem of flexible molecules to the comparison of IDSS histograms.</p> <p>Conclusion</p> <p>The proposed algorithm is robust and does not require any prior knowledge of the flexible regions. We demonstrate the effectiveness of IDSS within a molecular search engine application for a benchmark containing abundant conformational changes of molecules. Such comparisons in several thousands per second can be carried out. The presented IDSS method can be considered as an alternative and complementary tool for the existing methods for rigid MSC. The binary executable program for Windows platform and database are available from <url>https://engineering.purdue.edu/PRECISE/IDSS</url>.</p