Age grading \u3cem\u3eAn. gambiae\u3c/em\u3e and \u3cem\u3eAn. arabiensis\u3c/em\u3e using near infrared spectra and artificial neural networks

Background Near infrared spectroscopy (NIRS) is currently complementing techniques to age-grade mosquitoes. NIRS classifies lab-reared and semi-field raised mosquitoes into \u3c or ≥ 7 days old with an average accuracy of 80%, achieved by training a regression model using partial least squares (PLS) and interpreted as a binary classifier. Methods and findings We explore whether using an artificial neural network (ANN) analysis instead of PLS regression improves the current accuracy of NIRS models for age-grading malaria transmitting mosquitoes. We also explore if directly training a binary classifier instead of training a regression model and interpreting it as a binary classifier improves the accuracy. A total of 786 and 870 NIR spectra collected from laboratory reared An. gambiae and An. arabiensis, respectively, were used and pre-processed according to previously published protocols. The ANN regression model scored root mean squared error (RMSE) of 1.6 ± 0.2 for An. gambiae and 2.8 ± 0.2 for An. arabiensis; whereas the PLS regression model scored RMSE of 3.7 ± 0.2 for An. gambiae, and 4.5 ± 0.1 for An. arabiensis. When we interpreted regression models as binary classifiers, the accuracy of the ANN regression model was 93.7 ± 1.0% for An. gambiae, and 90.2 ± 1.7% for An. arabiensis; while PLS regression model scored the accuracy of 83.9 ± 2.3% for An. gambiae, and 80.3 ± 2.1% for An. arabiensis. We also find that a directly trained binary classifier yields higher age estimation accuracy than a regression model interpreted as a binary classifier. A directly trained ANN binary classifier scored an accuracy of 99.4 ± 1.0 for An. gambiae and 99.0 ± 0.6% for An. arabiensis; while a directly trained PLS binary classifier scored 93.6 ± 1.2% for An. gambiae and 88.7 ± 1.1% for An. arabiensis. We further tested the reproducibility of these results on different independent mosquito datasets. ANNs scored higher estimation accuracies than when the same age models are trained using PLS. Regardless of the model architecture, directly trained binary classifiers scored higher accuracies on classifying age of mosquitoes than regression models translated as binary classifiers. Conclusion We recommend training models to estimate age of An. arabiensis and An. gambiae using ANN model architectures (especially for datasets with at least 70 mosquitoes per age group) and direct training of binary classifier instead of training a regression model and interpreting it as a binary classifier

Modal Rayleigh-like streaming in layered acoustofluidic devices

Classical Rayleigh streaming is well known and can be modelled using Nyborg’s limiting velocity method as driven by fluid velocities adjacent to the walls parallel to the axis of the main acoustic resonance. We have demonstrated previously the existence and the mechanism of four-quadrant transducer plane streaming patterns in thin-layered acoustofluidic devices which are driven by the limiting velocities on the walls perpendicular to the axis of the main acoustic propagation. We have recently found experimentally that there is a third case which resembles Rayleigh streaming but is a more complex pattern related to three-dimensional cavity modes of an enclosure. This streaming has vortex sizes related to the effective wavelength in each cavity axis of the modes which can be much larger than those found in the one-dimensional case with Rayleigh streaming. We will call this here modal Rayleigh-like streaming and show that it can be important in layered acoustofluidic manipulation devices. This paper seeks to establish the conditions under which each of these is dominant and shows how the limiting velocity field for each relates to different parts of the complex acoustic intensity patterns at the driving boundaries

ISO LWS Spectroscopy of M82: A Unified Evolutionary Model

We present the first complete far-infrared spectrum (43 to 197 um) of M82, the brightest infrared galaxy in the sky, taken with the Long Wavelength Spectrometer of the Infrared Space Observatory (ISO). We detected seven fine structure emission lines, [OI] 63 and 145 um, [OIII] 52 and 88 um, [NII] 122 um, [NIII] 57 um and [CII] 158 um, and fit their ratios to a combination starburst and photo-dissociation region (PDR) model. The best fit is obtained with HII regions with n = 250 cm^{-3} and an ionization parameter of 10^{-3.5} and PDRs with n = 10^{3.3} cm^{-3} and a far-ultraviolet flux of G_o = 10^{2.8}. We applied both continuous and instantaneous starburst models, with our best fit being a 3-5 Myr old instantaneous burst model with a 100 M_o cut-off. We also detected the ground state rotational line of OH in absorption at 119.4 um. No excited level OH transitions are apparent, indicating that the OH is almost entirely in its ground state with a column density ~ 4x10^{14} cm^{-2}. The spectral energy distribution over the LWS wavelength range is well fit with a 48 K dust temperature and an optical depth, tau_{Dust} proportional to lambda^{-1}.Comment: 23 pages, 4 figures, accepted by ApJ, Feb. 1, 199

Reversal of infall in SgrB2(M) revealed by Herschel/HIFI observations of HCN lines at THz frequencies

To investigate the accretion and feedback processes in massive star formation, we analyze the shapes of emission lines from hot molecular cores, whose asymmetries trace infall and expansion motions. The high-mass star forming region SgrB2(M) was observed with Herschel/HIFI (HEXOS key project) in various lines of HCN and its isotopologues, complemented by APEX data. The observations are compared to spherically symmetric, centrally heated models with density power-law gradient and different velocity fields (infall or infall+expansion), using the radiative transfer code RATRAN. The HCN line profiles are asymmetric, with the emission peak shifting from blue to red with increasing J and decreasing line opacity (HCN to H$^{13}$CN). This is most evident in the HCN 12--11 line at 1062 GHz. These line shapes are reproduced by a model whose velocity field changes from infall in the outer part to expansion in the inner part. The qualitative reproduction of the HCN lines suggests that infall dominates in the colder, outer regions, but expansion dominates in the warmer, inner regions. We are thus witnessing the onset of feedback in massive star formation, starting to reverse the infall and finally disrupting the whole molecular cloud. To obtain our result, the THz lines uniquely covered by HIFI were critically important.Comment: A&A, HIFI special issue, accepte

Diffuse-interface model for rapid phase transformations in nonequilibrium systems

A thermodynamic approach to rapid phase transformations within a diffuse interface in a binary system is developed. Assuming an extended set of independent thermodynamic variables formed by the union of the classic set of slow variables and the space of fast variables, we introduce finiteness of the heat and solute diffusive propagation at the finite speed of the interface advancing. To describe the transformation within the diffuse interface, we use the phase-field model which allows us to follow the steep but smooth change of phases within the width of diffuse interface. The governing equations of the phase-field model are derived for the hyperbolic model, model with memory, and for a model of nonlinear evolution of transformation within the diffuse-interface. The consistency of the model is proved by the condition of positive entropy production and by the outcomes of the fluctuation-dissipation theorem. A comparison with the existing sharp-interface and diffuse-interface versions of the model is given.Comment: 15 pages, regular article submitted to Physical Review

C5 Palsy After Cervical Spine Surgery: A Multicenter Retrospective Review of 59 Cases.

STUDY DESIGN: A multicenter, retrospective review of C5 palsy after cervical spine surgery. OBJECTIVE: Postoperative C5 palsy is a known complication of cervical decompressive spinal surgery. The goal of this study was to review the incidence, patient characteristics, and outcome of C5 palsy in patients undergoing cervical spine surgery. METHODS: We conducted a multicenter, retrospective review of 13 946 patients across 21 centers who received cervical spine surgery (levels C2 to C7) between January 1, 2005, and December 31, 2011, inclusive. P values were calculated using 2-sample t test for continuous variables and χ(2) tests or Fisher exact tests for categorical variables. RESULTS: Of the 13 946 cases reviewed, 59 patients experienced a postoperative C5 palsy. The incidence rate across the 21 sites ranged from 0% to 2.5%. At most recent follow-up, 32 patients reported complete resolution of symptoms (54.2%), 15 had symptoms resolve with residual effects (25.4%), 10 patients did not recover (17.0%), and 2 were lost to follow-up (3.4%). CONCLUSION: C5 palsy occurred in all surgical approaches and across a variety of diagnoses. The majority of patients had full recovery or recovery with residual effects. This study represents the largest series of North American patients reviewed to date

Training of Instrumentalists and Development of New Technologies on SOFIA

This white paper is submitted to the Astronomy and Astrophysics 2010 Decadal Survey (Astro2010)1 Committee on the State of the Profession to emphasize the potential of the Stratospheric Observatory for Infrared Astronomy (SOFIA) to contribute to the training of instrumentalists and observers, and to related technology developments. This potential goes beyond the primary mission of SOFIA, which is to carry out unique, high priority astronomical research. SOFIA is a Boeing 747SP aircraft with a 2.5 meter telescope. It will enable astronomical observations anywhere, any time, and at most wavelengths between 0.3 microns and 1.6 mm not accessible from ground-based observatories. These attributes, accruing from the mobility and flight altitude of SOFIA, guarantee a wealth of scientific return. Its instrument teams (nine in the first generation) and guest investigators will do suborbital astronomy in a shirt-sleeve environment. The project will invest $10M per year in science instrument development over a lifetime of 20 years. This, frequent flight opportunities, and operation that enables rapid changes of science instruments and hands-on in-flight access to the instruments, assure a unique and extensive potential - both for training young instrumentalists and for encouraging and deploying nascent technologies. Novel instruments covering optical, infrared, and submillimeter bands can be developed for and tested on SOFIA by their developers (including apprentices) for their own observations and for those of guest observers, to validate technologies and maximize observational effectiveness.Comment: 10 pages, no figures, White Paper for Astro 2010 Survey Committee on State of the Professio

Exact score distribution computation for ontological similarity searches

<p>Abstract</p> <p>Background</p> <p>Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., finding functionally related proteins with the Gene Ontology or phenotypically similar diseases with the Human Phenotype Ontology (HPO). We have recently shown that the performance of semantic similarity searches can be improved by ranking results according to the probability of obtaining a given score at random rather than by the scores themselves. However, to date, there are no algorithms for computing the exact distribution of semantic similarity scores, which is necessary for computing the exact <it>P</it>-value of a given score.</p> <p>Results</p> <p>In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a <it>P</it>-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik's definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the HPO. It is shown that exact <it>P</it>-value calculation improves clinical diagnosis using the HPO compared to approaches based on sampling.</p> <p>Conclusions</p> <p>The new algorithm enables for the first time exact <it>P</it>-value calculation via exact score distribution computation for ontology similarity searches. The approach is applicable to any ontology for which the annotation-propagation rule holds and can improve any bioinformatic method that makes only use of the raw similarity scores. The algorithm was implemented in Java, supports any ontology in OBO format, and is available for non-commercial and academic usage under: <url>https://compbio.charite.de/svn/hpo/trunk/src/tools/significance/</url></p