425 research outputs found
A boosting method for maximizing the partial area under the ROC curve
<p>Abstract</p> <p>Background</p> <p>The receiver operating characteristic (ROC) curve is a fundamental tool to assess the discriminant performance for not only a single marker but also a score function combining multiple markers. The area under the ROC curve (AUC) for a score function measures the intrinsic ability for the score function to discriminate between the controls and cases. Recently, the partial AUC (pAUC) has been paid more attention than the AUC, because a suitable range of the false positive rate can be focused according to various clinical situations. However, existing pAUC-based methods only handle a few markers and do not take nonlinear combination of markers into consideration.</p> <p>Results</p> <p>We have developed a new statistical method that focuses on the pAUC based on a boosting technique. The markers are combined componentially for maximizing the pAUC in the boosting algorithm using natural cubic splines or decision stumps (single-level decision trees), according to the values of markers (continuous or discrete). We show that the resulting score plots are useful for understanding how each marker is associated with the outcome variable. We compare the performance of the proposed boosting method with those of other existing methods, and demonstrate the utility using real data sets. As a result, we have much better discrimination performances in the sense of the pAUC in both simulation studies and real data analysis.</p> <p>Conclusions</p> <p>The proposed method addresses how to combine the markers after a pAUC-based filtering procedure in high dimensional setting. Hence, it provides a consistent way of analyzing data based on the pAUC from maker selection to marker combination for discrimination problems. The method can capture not only linear but also nonlinear association between the outcome variable and the markers, about which the nonlinearity is known to be necessary in general for the maximization of the pAUC. The method also puts importance on the accuracy of classification performance as well as interpretability of the association, by offering simple and smooth resultant score plots for each marker.</p
Anxiety Disorders and Sensory Over-Responsivity in Children with Autism Spectrum Disorders: Is There a Causal Relationship?
Anxiety disorders and sensory over-responsivity (SOR) are common in children with autism spectrum disorders (ASD), and there is evidence for an association between these two conditions. Currently, it is unclear what causal mechanisms may exist between SOR and anxiety. We propose three possible theories to explain the association between anxiety and SOR: (a) SOR is caused by anxiety; (b) Anxiety is caused by SOR; or (c) SOR and anxiety are causally unrelated but are associated through a common risk factor or diagnostic overlap. In this paper, we examine support for each theory in the existing anxiety, autism, and neuroscience literature, and discuss how each theory informs choice of interventions and implications for future studies
Natural selection shaped the rise and fall of passenger pigeon genomic diversity.
The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction
Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces
We study some aspects of hydrophobic interaction between molecular rough and
flexible model surfaces. The model we use in this work is based on a model we
used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113,
13222-13228), when we studied the interaction between model patches of lipid
membranes. Our original model consisted of two graphene plates with attached
polar headgroups; the plates were immersed in a water bath. The interaction
between such plates can be considered as an example of a hydrophilic
interaction. In the present work we modify our previous model by removing the
charge from the zwitterionic headgroups. As a result of this procedure, the
plate character changes; it becomes hydrophobic. By separating the total
interaction (or potential of mean force, PMF) between plates into the direct
and the water-mediated interactions we observe that the latter changes from
repulsive to attractive, clearly emphasizing the important role of water as a
medium. We also investigate the effect of roughness and flexibility of the
headgroups on the interaction between plates and observe that roughness
enhances the character of the hydrophobic interaction. The presence of a
dewetting transition in a confined space between charge-removed plates confirms
that the interaction between plates is strongly hydrophobic. In addition, we
notice that there is a shallow local minimum in the PMF in case of
charge-removed plates. We find that this minimum is associated with the
configurational changes that flexible headgroups undergo, as the two plates are
brought together.Comment: 27 pages, 9 figure
Effects of pretreatments of Napier Grass with deionized water, sulfuric acid and sodium hydroxide on pyrolysis oil characteristics
The depletion of fossil fuel reserves has led to
increasing interest in liquid bio-fuel from renewable biomass. Biomass is a complex organic material consisting of
different degrees of cellulose, hemicellulose, lignin,
extractives and minerals. Some of the mineral elements
tend to retard conversions, yield and selectivity during
pyrolysis processing. This study is focused on the extraction of mineral retardants from Napier grass using deionized water, dilute sodium hydroxide and sulfuric acid and subsequent pyrolysis in a fixed bed reactor. The raw biomass was characterized before and after each pretreatment
following standard procedure. Pyrolysis study was conducted
in a fixed bed reactor at 600 o�C, 30 �C/min and 30 mL/min N2 flow. Pyrolysis oil (bio-oil) collected was analyzed using standard analytic techniques. The bio-oil yield and characteristics from each pretreated sample were compared with oil from the non-pretreated sample. Bio-oil
yield from the raw sample was 32.06 wt% compared to
38.71, 33.28 and 29.27 wt% oil yield recorded from the
sample pretreated with sulfuric acid, deionized water and
sodium hydroxide respectively. GC–MS analysis of the oil
samples revealed that the oil from all the pretreated biomass had more value added chemicals and less ketones and
aldehydes. Pretreatment with neutral solvent generated
valuable leachate, showed significant impact on the ash
extraction, pyrolysis oil yield, and its composition and
therefore can be regarded as more appropriate for thermochemical conversion of Napier grass
Development of a diagnostic protocol for dizziness in elderly patients in general practice: a Delphi procedure
<p>Abstract</p> <p>Background</p> <p>Dizziness in general practice is very common, especially in elderly patients. The empirical evidence for diagnostic tests in the evaluation of dizziness is scarce. Aim of our study was to determine which set of diagnostic tests should be part of a diagnostic protocol for evaluating dizziness in elderly patients in general practice.</p> <p>Methods</p> <p>We conducted a Delphi procedure with a panel of 16 national and international experts of all relevant medical specialities in the field of dizziness. A selection of 36 diagnostic tests, based on a systematic review and practice guidelines, was presented to the panel. Each test was described extensively, and data on test characteristics and methodological quality (assessed with the Quality Assessment of Diagnostic Accuracy Studies, QUADAS) were presented. The threshold for in- or exclusion of a diagnostic test was set at an agreement of 70%.</p> <p>Results</p> <p>During three rounds 21 diagnostic tests were selected, concerning patient history (4 items), physical examination (11 items), and additional tests (6 items). Five tests were excluded, although they are recommended by existing practice guidelines on dizziness. Two tests were included, although several practice guidelines question their diagnostic value. Two more tests were included that have never been recommended by practice guidelines on dizziness.</p> <p>Conclusion</p> <p>In this study we successfully combined empirical evidence with expert opinion for the development of a set of diagnostic tests for evaluating dizziness in elderly patients. This comprehensive set of tests will be evaluated in a cross-sectional diagnostic study.</p
Interaction of catechol O-methyltransferase and serotonin transporter genes modulates effective connectivity in a facial emotion-processing circuitry
Imaging genetic studies showed exaggerated blood oxygenation level-dependent response in limbic structures in carriers of low activity alleles of serotonin transporter-linked promoter region (5-HTTLPR) as well as catechol O-methyltransferase (COMT) genes. This was suggested to underlie the vulnerability to mood disorders. To better understand the mechanisms of vulnerability, it is important to investigate the genetic modulation of frontal-limbic connectivity that underlies emotional regulation and control. In this study, we have examined the interaction of 5-HTTLPR and COMT genetic markers on effective connectivity within neural circuitry for emotional facial expressions. A total of 91 healthy Caucasian adults underwent functional magnetic resonance imaging experiments with a task presenting dynamic emotional facial expressions of fear, sadness, happiness and anger. The effective connectivity within the facial processing circuitry was assessed with Granger causality method. We have demonstrated that in fear processing condition, an interaction between 5-HTTLPR (S) and COMT (met) low activity alleles was associated with reduced reciprocal connectivity within the circuitry including bilateral fusiform/inferior occipital regions, right superior temporal gyrus/superior temporal sulcus, bilateral inferior/middle prefrontal cortex and right amygdala. We suggest that the epistatic effect of reduced effective connectivity may underlie an inefficient emotion regulation that places these individuals at greater risk for depressive disorders
Correction:Brain structural abnormalities in obesity: relation to age, genetic risk, and common psychiatric disorders: Evidence through univariate and multivariate mega-analysis including 6420 participants from the ENIGMA MDD working group (Molecular Psychiatry, (2020), 10.1038/s41380-020-0774-9)
CfA3: 185 Type Ia Supernova Light Curves from the CfA
We present multi-band photometry of 185 type-Ia supernovae (SN Ia), with over
11500 observations. These were acquired between 2001 and 2008 at the F. L.
Whipple Observatory of the Harvard-Smithsonian Center for Astrophysics (CfA).
This sample contains the largest number of homogeneously-observed and reduced
nearby SN Ia (z < 0.08) published to date. It more than doubles the nearby
sample, bringing SN Ia cosmology to the point where systematic uncertainties
dominate. Our natural system photometry has a precision of 0.02 mag or better
in BVRIr'i' and roughly 0.04 mag in U for points brighter than 17.5 mag. We
also estimate a systematic uncertainty of 0.03 mag in our SN Ia standard system
BVRIr'i' photometry and 0.07 mag for U. Comparisons of our standard system
photometry with published SN Ia light curves and comparison stars, where
available for the same SN, reveal agreement at the level of a few hundredths
mag in most cases. We find that 1991bg-like SN Ia are sufficiently distinct
from other SN Ia in their color and light-curve-shape/luminosity relation that
they should be treated separately in light-curve/distance fitter training
samples. The CfA3 sample will contribute to the development of better
light-curve/distance fitters, particularly in the few dozen cases where
near-infrared photometry has been obtained and, together, can help disentangle
host-galaxy reddening from intrinsic supernova color, reducing the systematic
uncertainty in SN Ia distances due to dust.Comment: Accepted to the Astrophysical Journal. Minor changes from last
version. Light curves, comparison star photometry, and passband tables are
available at http://www.cfa.harvard.edu/supernova/CfA3
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