Neural Networks, Logistic Regression, and Calibration: A Reply

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68566/2/10.1177_0272989X9801800414.pd

In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR

BACKGROUND: Clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. Although DNA is commonly extracted from fixed tissues and amplified by PCR, the effects of formalin fixation are relatively unknown. Formalin fixation is known to impair PCR, presumably through damage that blocks polymerase elongation, but an insidious possibility is error prone translesion synthesis across sites of damage, producing in vitro artifactual mutations during PCR. METHODS: To better understand the consequences of fixation, DNA specimens extracted from fresh or fixed tissues were amplified with Taq DNA polymerase, and their PCR products were cloned and sequenced. RESULTS: Significantly more (3- to 4-fold) mutations were observed with fixed DNA specimens. The majority of mutations were transitions, predominantly at A:T base pairs, randomly distributed along the template. CONCLUSIONS: Formalin fixation appears to cause random base damage, which can be bridged during PCR by Taq DNA polymerase through error prone translesion synthesis. Fixed DNA is a damaged but "readable" template

Profiling filaments: comparing near-infrared extinction and submillimetre data in TMC-1

Interstellar filaments are an important part of star formation. To understand the structure of filaments, cross-section profiles are often fitted with Plummer profiles. This profiling is often done with submm studies, such as Herschel. It would be convenient if filament properties could also be studied using groundbased NIR data. We compare the filament profiles obtained by NIR extinction and submm observations to find out if reliable profiles can be derived using NIR data. We use J-, H-, and K-band data of a filament north of TMC-1 to derive an extinction map from colour excesses of background stars. We compare the Plummer profiles obtained from extinction maps with Herschel dust emission maps. We present 2 methods to estimate profiles from NIR: Plummer profile fits to median Av of stars or directly to the Av of individual stars. We compare the methods by simulations. In simulations extinction maps and the new methods give correct results to within ~10-20 for modest densities. Direct fit to data on individual stars gives more accurate results than extinction map, and can work in higher density. In profile fits to real observations, values of Plummer parameters are generally similar to within a factor of ~2. Although parameter values can vary significantly, estimates of filament mass usually remain accurate to within some tens of per cent. Our results for TMC-1 are in agreement with earlier results. High resolution NIR data give more details, but 2MASS data can be used to estimate profiles. NIR extinction can be used as an alternative to submm observations to profile filaments. Direct fits of stars can also be a valuable tool. Plummer profile parameters are not always well constrained, and caution should be taken when making fits. In the evaluation of Plummer parameters, one can use the independence of dust emission and NIR data and the difference in the shapes of the confidence regions.Comment: accepted to Astronomy & Astrophysics; abstract has been shortened for astrop

Impact of prechlorination pH on Pb(II)-NOM complexation and lead release in drinking water distribution systems

The presence of Pb in drinking water resulting from corrosion of lead pipes, solder and fixtures poses a significant threat to public health and safety. Pb is a potent neurotoxin that can impair the cognitive development of children at low concentrations in the bloodstream. During the corrosion of distribution system components containing Pb, precipitate scales form on the interior surfaces of pipes in the distribution system providing a protective barrier between the bulk solution and the pipe surface; the amount of dissolved Pb²⁺ is controlled by the thermodynamics and kinetics of precipitation/dissolution of the particular Pb scales in the system. The solubility and composition of Pb scales phases residing on the pipe surfaces are a function of the background water chemistry (including pH, redox potential and ligand types and concentration). Therefore, considering the conditional stability of lead scales is crucial when making changes to water treatment processes, as alterations in water quality can significantly disrupt the stability of scales in the DWDS, leading to elevated lead concentrations. In distribution systems that employ monochloramine to provide residual disinfection, the formation of Pb(II) scales such as cerussite (PbCO₃) and hydroxyapatite are favored depending on the background water composition (e.g., phosphates added for corrosion protection or carbonate present). Utilities that chloraminate typically implement a prechlorination step in which free chlorine reacts for a specified time prior to ammonia addition to meet disinfection requirements. During the prechlorination step, free chlorine can react with natural organic matter (NOM) to promote Pb release. The formation of NOM-Pb complexes increases the total soluble Pb in distribution systems containing Pb scales. However, before NOM enters the drinking water distribution system (DWDS) oxidation or nucleophilic substitution of NOM functional groups during prechlorination can decrease the extent of Pb(II)-NOM complexation. The relative impact of these processes on Pb(II) concentrations in drinking water distribution systems must be understood for effective Pb control in DWDS’s containing NOM. In this study, the impact of Pb-NOM complexation on Pb(II) release from cerussite (PbCO₃), a Pb scale phase that can form in the DWDS, is studied in batch dissolution experiments with and without prechlorination. Prechorination of the water containing NOM for a 30-minute contact time decreased the amount of Pb released in the presence of NOM with greater reduction at lower pH. The trends in pH were consistent with the greater reactivity between free chlorine and NOM at lower pH. Additionally, excitation emission matrices (EEMs) and near edge x-ray fine structures (NEXAFS) spectroscopy confirmed that chlorination of the NOM led to destruction of electron rich aromatic moieties that function as prominent ligands in Pb(II)-NOM complexation Further, it was found that fewer in number of disinfection byproducts (DBPs) precursors were generated upon reaction of chlorine and NOM at lower pH conditions. These results demonstrate the potential for chlorination to reduce Pb(II)-NOM complexation. The concentrations of total soluble Pb observed in the batch dissolution experiments ranging from 40 ppb to 600 ppb are not representative of dissolved Pb concentrations in the water distribution system as a Pb concentration of 15 ppb necessitates the implementation of corrosion control measures. Further studies are needed to assess the relative impact of Pb(II)-NOM complexation under continuous flow conditions that more closely mimic pipe flow through conditions representative of water distribution system conditions.Environmental and Water Resources Engineerin

A multi-scale, multi-wavelength source extraction method: getsources

We present a multi-scale, multi-wavelength source extraction algorithm called getsources. Although it has been designed primarily for use in the far-infrared surveys of Galactic star-forming regions with Herschel, the method can be applied to many other astronomical images. Instead of the traditional approach of extracting sources in the observed images, the new method analyzes fine spatial decompositions of original images across a wide range of scales and across all wavebands. It cleans those single-scale images of noise and background, and constructs wavelength-independent single-scale detection images that preserve information in both spatial and wavelength dimensions. Sources are detected in the combined detection images by following the evolution of their segmentation masks across all spatial scales. Measurements of the source properties are done in the original background-subtracted images at each wavelength; the background is estimated by interpolation under the source footprints and overlapping sources are deblended in an iterative procedure. In addition to the main catalog of sources, various catalogs and images are produced that aid scientific exploitation of the extraction results. We illustrate the performance of getsources on Herschel images by extracting sources in sub-fields of the Aquila and Rosette star-forming regions. The source extraction code and validation images with a reference extraction catalog are freely available.Comment: 31 pages, 27 figures, to be published in Astronomy & Astrophysic

The initial conditions of star formation in the Ophiuchus main cloud: Kinematics of the protocluster condensations

The earliest phases of clustered star formation and the origin of the stellar initial mass function (IMF) are currently much debated. In order to constrain the origin of the IMF, we investigated the internal and relative motions of starless condensations and protostars previously detected by us in the dust continuum at 1.2mm in the L1688 protocluster of the Ophiuchus molecular cloud complex. The starless condensations have a mass spectrum resembling the IMF and are therefore likely representative of the initial stages of star formation in the protocluster. We carried out detailed molecular line observations, including some N2H+(1-0) mapping, of the Ophiuchus protocluster condensations using the IRAM 30m telescope. We measured subsonic or at most transonic levels of internal turbulence within the condensations, implying virial masses which generally agree within a factor of ~ 2 with the masses derived from the 1.2mm dust continuum. This supports the notion that most of the L1688 starless condensations are gravitationally bound and prestellar in nature. We measured a global one-dimensional velocity dispersion of less than 0.4 km/s between condensations. This small relative velocity dispersion implies that, in general, the condensations do not have time to interact with one another before evolving into pre-main sequence objects. Our observations support the view that the IMF is partly determined by cloud fragmentation at the prestellar stage. Competitive accretion is unlikely to be the dominant mechanism at the protostellar stage in the Ophiuchus protocluster, but it may possibly govern the growth of starless, self-gravitating condensations initially produced by gravoturbulent fragmentation toward an IMF, Salpeter-like mass spectrum.Comment: 17 pages, 8 figures. A&A, in press (v2: notes added to Table 3

STM observation of electronic wave interference effect in finite-sized graphite with dislocation-network structures

Superperiodic patterns near a step edge were observed by STM on several-layer-thick graphite sheets on a highly oriented pyrolitic graphite substrate, where a dislocation network is generated at the interface between the graphite overlayer and the substrate. Triangular- and rhombic-shaped periodic patterns whose periodicities are around 100 nm were observed on the upper terrace near the step edge. In contrast, only outlines of the patterns similar to those on the upper terrace were observed on the lower terrace. On the upper terrace, their geometrical patterns gradually disappeared and became similar to those on the lower terrace without any changes of their periodicity in increasing a bias voltage. By assuming a periodic scattering potential at the interface due to dislocations, the varying corrugation amplitudes of the patterns can be understood as changes in LDOS as a result of the beat of perturbed and unperturbed waves, i.e. the interference in an overlayer. The observed changes in the image depending on an overlayer height and a bias voltage can be explained by the electronic wave interference in the ultra-thin overlayer distorted under the influence of dislocation-network structures.Comment: 8 pages; 6 figures; Paper which a part of cond-mat/0311068 is disscussed in detai

Implementation of routine outcome measurement in child and adolescent mental health services in the United Kingdom: a critical perspective

The aim of this commentary is to provide an overview of clinical outcome measures that are currently recommended for use in UK Child and Adolescent Mental Health Services (CAMHS), focusing on measures that are applicable across a wide range of conditions with established validity and reliability, or innovative in their design. We also provide an overview of the barriers and drivers to the use of Routine Outcome Measurement (ROM) in clinical practice

Childhood adversity, mental ill-health and aggressive behavior in an African orphanage: Changes in response to trauma-focused therapy and the implementation of a new instructional system

<p>Abstract</p> <p>Background</p> <p>The number of orphans in Sub-Saharan Africa is constantly rising. While it is known that family or community care is preferable over institutional care of African orphans, little is known about the quality of care in orphanages and possibilities of improvement.</p> <p>Study 1</p> <p>Methods</p> <p>Exposure to traumatic stress, experiences of violence in the home, school and orphanage, as well as mental ill-health and aggression of 38 children (mean age of <it>M </it>= 8.64 years) living in an orphanage in rural Tanzania were assessed at two time points. The severity of post-traumatic stress disorder symptoms (PTSD), depressive symptoms, and internalizing and externalizing problems were used as indicators of mental ill-health.</p> <p>Results</p> <p>Violence experienced in the orphanage correlated more strongly with all indicators of mental ill-health than violence in the former home, school or neighborhood at time point 1. Additionally, violence experienced in the orphanage had a positive relationship with the aggressive behavior of the children at time point 2.</p> <p>Study 2</p> <p>Methods</p> <p>With the help of the pre-post assessment of Study 1, the implementation of a new instructional system and psychotherapeutic treatment (KIDNET) for trauma-related illness were evaluated.</p> <p>Results</p> <p>In response to both, a change in the instructional system and psychotherapeutic treatment of PTSD, a massive decline in experienced violence and in the severity of PTSD-symptoms was found, whereas depressive symptoms and internalizing and externalizing problems exhibited little change.</p> <p>Conclusions</p> <p>These studies show that violence, especially in the orphanage, can severely contribute to mental ill-health in orphans and that mental health can be improved by implementing a new instructional system and psychotherapeutic treatment in an orphanage. Moreover, the results indicate that the experience of violence in an orphanage also plays a crucial role in aggressive behavior of the orphans.</p

Disorder-induced trapping versus Anderson localization in Bose-Einstein condensates expanding in disordered potentials

We theoretically investigate the localization of an expanding Bose-Einstein condensate with repulsive atom-atom interactions in a disordered potential. We focus on the regime where the initial inter-atomic interactions dominate over the kinetic energy and the disorder. At equilibrium in a trapping potential and for small disorder, the condensate shows a Thomas-Fermi shape modified by the disorder. When the condensate is released from the trap, a strong suppression of the expansion is obtained in contrast to the situation in a periodic potential with similar characteristics. This effect crucially depends on both the momentum distribution of the expanding BEC and the strength of the disorder. For strong disorder, the suppression of the expansion results from the fragmentation of the core of the condensate and from classical reflections from large modulations of the disordered potential in the tails of the condensate. We identify the corresponding disorder-induced trapping scenario for which large atom-atom interactions and strong reflections from single modulations of the disordered potential play central roles. For weak disorder, the suppression of the expansion signals the onset of Anderson localization, which is due to multiple scattering from the modulations of the disordered potential. We compute analytically the localized density profile of the condensate and show that the localization crucially depends on the correlation function of the disorder. In particular, for speckle potentials the long-range correlations induce an effective mobility edge in 1D finite systems. Numerical calculations performed in the mean-field approximation support our analysis for both strong and weak disorder.Comment: New Journal of Physics; focus issue "Quantum Correlations in Tailored Matter - Common perspectives of mesoscopic systems and quantum gases"; 30 pages, 10 figure