Anveshak - A Groundtruth Generation Tool for Foreground Regions of Document Images

We propose a graphical user interface based groundtruth generation tool in this paper. Here, annotation of an input document image is done based on the foreground pixels. Foreground pixels are grouped together with user interaction to form labeling units. These units are then labeled by the user with the user defined labels. The output produced by the tool is an image with an XML file containing its metadata information. This annotated data can be further used in different applications of document image analysis.Comment: Accepted in DAR 201

A proposed method to investigate reliability throughout a questionnaire

<p>Abstract</p> <p>Background</p> <p>Questionnaires are used extensively in medical and health care research and depend on validity and reliability. However, participants may differ in interest and awareness throughout long questionnaires, which can affect reliability of their answers. A method is proposed for "screening" of systematic change in random error, which could assess changed reliability of answers.</p> <p>Methods</p> <p>A simulation study was conducted to explore whether systematic change in reliability, expressed as changed random error, could be assessed using unsupervised classification of subjects by cluster analysis (CA) and estimation of intraclass correlation coefficient (ICC). The method was also applied on a clinical dataset from 753 cardiac patients using the Jalowiec Coping Scale.</p> <p>Results</p> <p>The simulation study showed a relationship between the systematic change in random error throughout a questionnaire and the slope between the estimated ICC for subjects classified by CA and successive items in a questionnaire. This slope was proposed as an awareness measure - to assessing if respondents provide only a random answer or one based on a substantial cognitive effort. Scales from different factor structures of Jalowiec Coping Scale had different effect on this awareness measure.</p> <p>Conclusions</p> <p>Even though assumptions in the simulation study might be limited compared to real datasets, the approach is promising for assessing systematic change in reliability throughout long questionnaires. Results from a clinical dataset indicated that the awareness measure differed between scales.</p

Effectiveness and cost of radiofrequency ablation and stereotactic body radiotherapy for treatment of early‐stage hepatocellular carcinoma: An analysis of SEER‐medicare

IntroductionFor early‐stage hepatocellular carcinoma (HCC) patients, ablative strategies are potentially curative treatment options. Stereotactic body radiotherapy (SBRT) has emerged as a promising ablative therapy, although its comparison with radiofrequency ablation (RFA) remains confined to a single institution retrospective review. We sought to characterize the comparative outcomes and cost between the two treatment strategies.MethodsWe conducted a secondary analysis of the Surveillance, Epidemiology, and End Results (SEER)‐Medicare linked database (2004–2011) and identified adult patients with stage I or II HCC and treated with RFA or SBRT as the initial treatment within 6 months of diagnosis. Survival analysis was conducted using Kaplan–Meier curves and multivariate Cox proportional hazard analysis. Factors associated with overall survival and 90‐day hospital admission post‐treatment were identified using propensity score (PS) adjusted multivariate analysis. We performed costs analysis and calculated incremental cost‐effectiveness ratios (ICER).ResultsFour hundred and forty patients were identified, 408 treated with RFA and 32 SBRT. In the overall cohort, 90‐day hospitalization and 1‐year mortality were similar between groups but RFA patients had better overall survival (P < 0.001). Multivariate analysis showed advanced age, higher stage, decompensated cirrhosis, and treatment with SBRT (HR 1.80; 95%CI: 1.15–2.82) was associated with worse survival, but in the PS adjusted analysis, survival and costs were similar between the two groups.ConclusionIn a national cohort of early stage HCC patients, treatment with RFA vs SBRT resulted in no significant difference in survival, 90‐day hospitalization, or costs. These data highlight the need for a randomized clinical trial comparing these two modalities.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146355/1/jmiro12754_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146355/2/jmiro12754.pd

Occurrence of Didymella ascospores in western and southern Poland in 2004–2006

The concentration of airborne Didymella spores has been investigated at two monitoring sites situated along the west–south transect in Poland (Szczecin, Kraków), i.e. from a height of 100 to 219 m, respectively, above sea level. The aerobiological monitoring of fungal spores was performed by means of two Lanzoni volumetric spore traps. The high Didymella spore numbers were observed at both cities in June, July and August. Statistically significant correlations have been found mainly between the Didymella spore concentrations in the air and the minimum air temperature and relative air humidity. The spore count of Didymella is determined by the diversity of local flora and weather conditions, especially by the relative air humidity. The identification of factors that influence and shape spore concentrations may significantly improve the current methods of allergy prevention

Spatio-temporal Models of Lymphangiogenesis in Wound Healing

Several studies suggest that one possible cause of impaired wound healing is failed or insufficient lymphangiogenesis, that is the formation of new lymphatic capillaries. Although many mathematical models have been developed to describe the formation of blood capillaries (angiogenesis), very few have been proposed for the regeneration of the lymphatic network. Lymphangiogenesis is a markedly different process from angiogenesis, occurring at different times and in response to different chemical stimuli. Two main hypotheses have been proposed: 1) lymphatic capillaries sprout from existing interrupted ones at the edge of the wound in analogy to the blood angiogenesis case; 2) lymphatic endothelial cells first pool in the wound region following the lymph flow and then, once sufficiently populated, start to form a network. Here we present two PDE models describing lymphangiogenesis according to these two different hypotheses. Further, we include the effect of advection due to interstitial flow and lymph flow coming from open capillaries. The variables represent different cell densities and growth factor concentrations, and where possible the parameters are estimated from biological data. The models are then solved numerically and the results are compared with the available biological literature.Comment: 29 pages, 9 Figures, 6 Tables (39 figure files in total

Crystal Structure Analysis Reveals Functional Flexibility in the Selenocysteine-Specific tRNA from Mouse

Selenocysteine tRNAs (tRNA(Sec)) exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec)-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec). tRNA(Sec) lacking the single-stranded 3'-acceptor end ((ΔGCCA)RNA(Sec)) yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCA)RNA(Sec) resembles the structure of human tRNA(Sec) determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec) used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Sec)in vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+)-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec).We provide the most highly resolved structure of a tRNA(Sec) molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec) support its interaction with proteins

Parent of origin genetic effects on methylation in humans are common and influence complex trait variation

Parent-of-origin effects (POE) are observed when there are different effects from alleles inherited from the two parents on phenotypic measures. Here, Zeng et al. study POE on DNA methylation in 5,101 individuals and identify genetic variants that associate with methylation variation via POE and their potential phenotypic consequences

18F-fluoro-deoxy-glucose focal uptake in very small pulmonary nodules: fact or artifact? Case reports

ABSTRACT: BACKGROUND: F-fluoro-deoxy-glucose (18F-FDG) positron emission tomography integrated/combined with computed tomography (PET-CT) provides the best diagnostic results in the metabolic characterization of undetermined solid pulmonary nodules. The diagnostic performance of 18F-FDG is similar for nodules measuring at least 1 cm and for larger masses, but few data exist for nodules smaller than 1 cm. CASE PRESENTATION: We report five cases of oncologic patients showing focal lung 18F-FDG uptake on PET-CT in nodules smaller than 1 cm. We also discuss the most common causes of 18F-FDG false-positive and false-negative results in the pulmonary parenchyma. In patient 1, contrast-enhanced CT performed 10 days before PET-CT did not show any abnormality in the site of uptake; in patient 2, high-resolution CT performed 1 month after PET showed a bronchiole filled with dense material interpreted as a mucoid impaction; in patient 3, contrast-enhanced CT performed 15 days before PET-CT did not identify any nodules; in patients 4 and 5, contrast-enhanced CT revealed a nodule smaller than 1 cm which could not be characterized. The 18F-FDG uptake at follow-up confirmed the malignant nature of pulmonary nodules smaller than 1 cm which were undetectable, misinterpreted, not recognized or undetermined at contrast-enhanced CT. CONCLUSION: In all five oncologic patients, 18F-FDG was able to metabolically characterize as malignant those nodules smaller than 1 cm, underlining that: 18F-FDG uptake is not only a function of tumor size but it is strongly related to the tumor biology; functional alterations may precede morphologic abnormalities. In the oncologic population, especially in higher-risk patients, PET can be performed even when the nodules are smaller than 1 cm, because it might give an earlier characterization and, sometimes, could guide in the identification of alterations missed on CT

Calibration and Characterization of the IceCube Photomultiplier Tube

Over 5,000 PMTs are being deployed at the South Pole to compose the IceCube neutrino observatory. Many are placed deep in the ice to detect Cherenkov light emitted by the products of high-energy neutrino interactions, and others are frozen into tanks on the surface to detect particles from atmospheric cosmic ray showers. IceCube is using the 10-inch diameter R7081-02 made by Hamamatsu Photonics. This paper describes the laboratory characterization and calibration of these PMTs before deployment. PMTs were illuminated with pulses ranging from single photons to saturation level. Parameterizations are given for the single photoelectron charge spectrum and the saturation behavior. Time resolution, late pulses and afterpulses are characterized. Because the PMTs are relatively large, the cathode sensitivity uniformity was measured. The absolute photon detection efficiency was calibrated using Rayleigh-scattered photons from a nitrogen laser. Measured characteristics are discussed in the context of their relevance to IceCube event reconstruction and simulation efforts.Comment: 40 pages, 12 figure

Limits on WWZ and WW\gamma couplings from p\bar{p}\to e\nu jj X events at \sqrt{s} = 1.8 TeV

We present limits on anomalous WWZ and WW-gamma couplings from a search for WW and WZ production in p-bar p collisions at sqrt(s)=1.8 TeV. We use p-bar p -> e-nu jjX events recorded with the D0 detector at the Fermilab Tevatron Collider during the 1992-1995 run. The data sample corresponds to an integrated luminosity of 96.0+-5.1 pb^(-1). Assuming identical WWZ and WW-gamma coupling parameters, the 95% CL limits on the CP-conserving couplings are -0.33<lambda<0.36 (Delta-kappa=0) and -0.43<Delta-kappa<0.59 (lambda=0), for a form factor scale Lambda = 2.0 TeV. Limits based on other assumptions are also presented.Comment: 11 pages, 2 figures, 2 table