Sample size and classification error for Bayesian change-point models with unlabelled sub-groups and incomplete follow-up

Many medical (and ecological) processes involve the change of shape, whereby one trajectory changes into another trajectory at a specific time point. There has been little investigation into the study design needed to investigate these models. We consider the class of fixed effect change-point models with an underlying shape comprised two joined linear segments, also known as broken-stick models. We extend this model to include two sub-groups with different trajectories at the change-point, a change and no change class, and also include a missingness model to account for individuals with incomplete follow-up. Through a simulation study, we consider the relationship of sample size to the estimates of the underlying shape, the existence of a change-point, and the classification-error of sub-group labels. We use a Bayesian framework to account for the missing labels, and the analysis of each simulation is performed using standard Markov chain Monte Carlo techniques. Our simulation study is inspired by cognitive decline as measured by the Mini-Mental State Examination, where our extended model is appropriate due to the commonly observed mixture of individuals within studies who do or do not exhibit accelerated decline. We find that even for studies of modest size ( n = 500, with 50 individuals observed past the change-point) in the fixed effect setting, a change-point can be detected and reliably estimated across a range of observation-errors. </jats:p

Photoacid-Modified Nafion Membrane Morphology Determined by Resonant X-ray Scattering and Spectroscopy

Covalent attachment of photoacid dye molecules to perfluorinated sulfonic acid membranes is a promising route to enable active light-driven ion pumps, but the complex relationship between chemical modification and morphology is not well understood in this class of functional materials. In this study we demonstrate the effect of bound photoacid dyes on phase-segregated membrane morphology. Resonant X-ray scattering near the sulfur K-edge reveals that introduction of photoacid dyes to the end of the ionomer side chains enhances phase segregation among ionomer domains, and the ionomer domain spacing increases with increasing amount of bound dye. Furthermore, relative crystallinity is marginally enhanced within semicrystalline domains composed of the perfluorinated backbone. X-ray absorption spectroscopy coupled with first-principles density functional theory calculations suggest that above a critical concentration, the multiple hydrophilic groups on the attached photoacid dye may help increase residual water content and promote hydration of adjacent sulfonic acid side chains under dry or ambient conditions

Motivated proteins: a web application for studying small three-dimensional protein motifs

&lt;b&gt;BACKGROUND:&lt;/b&gt; Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. &lt;b&gt;DESCRIPTION:&lt;/b&gt; The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. &lt;b&gt;CONCLUSION:&lt;/b&gt; Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

Systematic review of mathematical models exploring the epidemiological impact of future TB vaccines

Mathematical models are useful for assessing the potential epidemiological impact of future tuberculosis (TB) vaccines. We conducted a systematic review of mathematical models estimating the epidemiological impact of future human TB vaccines. PubMed, Embase and WHO Global Health Library were searched, 3-stage manual sifted, and citation- and reference-tracked, identifying 23 papers. An adapted quality assessment tool was developed, with a resulting median study quality score of 20/28. The literature remains divided as to whether vaccines effective pre- or post-infection would provide greatest epidemiological impact. However, all-age or adolescent/adult targeted prevention of disease vaccines achieve greater and more rapid impact than neonatal vaccines. Mass campaigns alongside routine neonatal vaccination can have profound additional impact. Economic evaluations found TB vaccines overwhelmingly cost-effective, particularly when targeted to adolescents/adults. The variability of impact by setting, age group and vaccine characteristics must be accounted for in the development and delivery of future TB vaccines

Synchronized dynamics of cortical neurons with time-delay feedback

The dynamics of three mutually coupled cortical neurons with time delays in the coupling are explored numerically and analytically. The neurons are coupled in a line, with the middle neuron sending a somewhat stronger projection to the outer neurons than the feedback it receives, to model for instance the relay of a signal from primary to higher cortical areas. For a given coupling architecture, the delays introduce correlations in the time series at the time-scale of the delay. It was found that the middle neuron leads the outer ones by the delay time, while the outer neurons are synchronized with zero lag times. Synchronization is found to be highly dependent on the synaptic time constant, with faster synapses increasing both the degree of synchronization and the firing rate. Analysis shows that presynaptic input during the interspike interval stabilizes the synchronous state, even for arbitrarily weak coupling, and independent of the initial phase. The finding may be of significance to synchronization of large groups of cells in the cortex that are spatially distanced from each other.Comment: 21 pages, 11 figure

Autonomous decision-making against induced seismicity in deep fluid injections

The rise in the frequency of anthropogenic earthquakes due to deep fluid injections is posing serious economic, societal, and legal challenges to geo-energy and waste-disposal projects. We propose an actuarial approach to mitigate this risk, first by defining an autonomous decision-making process based on an adaptive traffic light system (ATLS) to stop risky injections, and second by quantifying a "cost of public safety" based on the probability of an injection-well being abandoned. The ATLS underlying statistical model is first confirmed to be representative of injection-induced seismicity, with examples taken from past reservoir stimulation experiments (mostly from Enhanced Geothermal Systems, EGS). Then the decision strategy is formalized: Being integrable, the model yields a closed-form ATLS solution that maps a risk-based safety standard or norm to an earthquake magnitude not to exceed during stimulation. Finally, the EGS levelized cost of electricity (LCOE) is reformulated in terms of null expectation, with the cost of abandoned injection-well implemented. We find that the price increase to mitigate the increased seismic risk in populated areas can counterbalance the heat credit. However this "public safety cost" disappears if buildings are based on earthquake-resistant designs or if a more relaxed risk safety standard or norm is chosen.Comment: 8 pages, 4 figures, conference (International Symposium on Energy Geotechnics, 26-28 September 2018, Lausanne, Switzerland

Progression of Clinical Features in Lewy Body Dementia Can Be Detected Over 6 Months

Copyright \ua9 2021 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.OBJECTIVE: This study aimed to quantify the trajectory and magnitude of change of the key clinical features and corresponding symptom domains of dementia with Lewy bodies (DLB) and Parkinson disease dementia (PDD), including global cognition, parkinsonism, recurrent visual hallucinations, cognitive fluctuations, and sleep disturbance. METHODS: One hundred sixteen patients with Lewy body dementia (DLB = 72, PDD = 44) underwent assessment at baseline and 3 and 6 months as part of a prospective multicenter randomized controlled trial. Linear mixed models were constructed for core outcome measures using the Mini-Mental State Examination (MMSE), motor section of the Unified Parkinson\u27s Disease Rating Scale (UPDRS-III), Dementia Cognitive Fluctuations Scale (DCFS), and Neuropsychiatric Inventory (NPI). RESULTS: Within the time frame of our study (6 months), we were able to identify a significant cognitive decline of 1.3 points on the MMSE (p = 0.002) and significant worsening of motor parkinsonism with an increase in UPDRS-III score of 3.2 points (p = 0.018). Fluctuation severity also increased using the DCFS with a 6-month change in score of 1.3 points (p = 0.001). Uniquely, a signal for increased severity of sleep symptoms of 1.2 points (NPI-sleep) was also detectable (p = 0.04). Significant changes in neuropsychiatric symptoms were not detected. There was no difference in rates of change of scores between DLB and PDD. DISCUSSION: Clinically significant rates of change in core clinical features can be detected and quantified in Lewy body dementia over a relatively short period (6 months) using common clinical instruments and thus may be useful as clinical endpoints for therapeutic trials of disease-modifying and symptomatic agents

Measuring measurement

Measurement connects the world of quantum phenomena to the world of classical events. It plays both a passive role, observing quantum systems, and an active one, preparing quantum states and controlling them. Surprisingly - in the light of the central status of measurement in quantum mechanics - there is no general recipe for designing a detector that measures a given observable. Compounding this, the characterization of existing detectors is typically based on partial calibrations or elaborate models. Thus, experimental specification (i.e. tomography) of a detector is of fundamental and practical importance. Here, we present the realization of quantum detector tomography: we identify the optimal positive-operator-valued measure describing the detector, with no ancillary assumptions. This result completes the triad, state, process, and detector tomography, required to fully specify an experiment. We characterize an avalanche photodiode and a photon number resolving detector capable of detecting up to eight photons. This creates a new set of tools for accurately detecting and preparing non-classical light.Comment: 6 pages, 4 figures,see video abstract at http://www.quantiki.org/video_abstracts/0807244

Blame, Symbolic Stigma and HIV Misconceptions are Associated with Support for Coercive Measures in Urban India

This study was designed to examine the prevalence of stigma and its underlying factors in two large Indian cities. Cross-sectional interview data were collected from 1,076 non-HIV patients in multiple healthcare settings in Mumbai and Bengaluru, India. The vast majority of participants supported mandatory testing for marginalized groups and coercive family policies for PLHA, stating that they “deserved” their infections and “didn’t care” about infecting others. Most participants did not want to be treated at the same clinic or use the same utensils as PLHA and transmission misconceptions were common. Multiple linear regression showed that blame, transmission misconceptions, symbolic stigma and negative feelings toward PLHA were significantly associated with both stigma and discrimination. The results indicate an urgent need for continued stigma reduction efforts to reduce the suffering of PLHA and barriers to prevention and treatment. Given the high levels of blame and endorsement of coercive policies, it is crucial that such programs are shaped within a human rights framework