Parametric modeling of cellular state transitions as measured with flow cytometry

<p>Abstract</p> <p>Background</p> <p>Gradual or sudden transitions among different states as exhibited by cell populations in a biological sample under particular conditions or stimuli can be detected and profiled by flow cytometric time course data. Often such temporal profiles contain features due to transient states that present unique modeling challenges. These could range from asymmetric non-Gaussian distributions to outliers and tail subpopulations, which need to be modeled with precision and rigor.</p> <p>Results</p> <p>To ensure precision and rigor, we propose a parametric modeling framework StateProfiler based on finite mixtures of skew <it>t</it>-Normal distributions that are robust against non-Gaussian features caused by asymmetry and outliers in data. Further, we present in StateProfiler a new greedy EM algorithm for fast and optimal model selection. The parsimonious approach of our greedy algorithm allows us to detect the genuine dynamic variation in the key features as and when they appear in time course data. We also present a procedure to construct a well-fitted profile by merging any redundant model components in a way that minimizes change in entropy of the resulting model. This allows precise profiling of unusually shaped distributions and less well-separated features that may appear due to cellular heterogeneity even within clonal populations.</p> <p>Conclusions</p> <p>By modeling flow cytometric data measured over time course and marker space with StateProfiler, specific parametric characteristics of cellular states can be identified. The parameters are then tested statistically for learning global and local patterns of spatio-temporal change. We applied StateProfiler to identify the temporal features of yeast cell cycle progression based on knockout of S-phase triggering cyclins Clb5 and Clb6, and then compared the S-phase delay phenotypes due to differential regulation of the two cyclins. We also used StateProfiler to construct the temporal profile of clonal divergence underlying lineage selection in mammalian hematopoietic progenitor cells.</p

Extrasolar Planet Transits Observed at Kitt Peak National Observatory

We obtained J-, H- and JH-band photometry of known extrasolar planet transiting systems at the 2.1-m Kitt Peak National Observatory Telescope using the FLAMINGOS infrared camera between October 2008 and October 2011. From the derived lightcurves we have extracted the mid-transit times, transit depths and transit durations for these events. The precise mid-transit times obtained help improve the orbital periods and also constrain transit-time variations of the systems. For most cases the published system parameters successfully accounted for our observed lightcurves, but in some instances we derive improved planetary radii and orbital periods. We complemented our 2.1-m infrared observations using CCD z'-band and B-band photometry (plus two Hydrogen Alpha filter observations) obtained with the Kitt Peak Visitor's Center telescope, and with four H-band transits observed in October 2007 with the NSO's 1.6-m McMath-Pierce Solar Telescope. The principal highlights of our results are: 1) our ensemble of J-band planetary radii agree with optical radii, with the best-fit relation being: (Rp/R*)J = 0.0017 + 0.979 (Rp/R*)optical, 2) We observe star spot crossings during the transit of WASP-11/HAT-P-10, 3) we detect star spot crossings by HAT-P-11b (Kepler-3b), thus confirming that the magnetic evolution of the stellar active regions can be monitored even after the Kepler mission has ended, and 4) we confirm a grazing transit for HAT-P-27/WASP-40. In total we present 57 individual transits of 32 known exoplanet systems.Comment: 33 pages, 6 figures, accepted in Publications of the Astronomical Society of the Pacifi

The Local Edge Machine: inference of dynamic models of gene regulation

We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle. Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks.Department of Applied Mathematic

Cortisol as an Acute Stress Biomarker in Young Hematopoietic Cell Transplant Patients/Caregivers: Active Music Engagement Protocol

Objective: Primary aims of the proposed protocol are to determine the feasibility/acceptability of the active music engagement intervention protocol during hematopoietic stem cell transplantation (HSCT) and clinical feasibility/acceptability of the biological sample collection schedule. Design: The authors propose a single-case, alternating treatment design to compare levels of child and caregiver cortisol in blood and saliva collected on alternating days, when the dyad receives and does not receive AME sessions. Included are the scientific rationale for this design and detailed intervention and sample collection schedules based on transplant type. Setting/Location: Pediatric inpatient HSCT unit. Subjects: Eligible participants are dyads of children 3-8 years old, hospitalized for HSCT, and their caregiver. Children with malignant and nonmalignant conditions will be eligible, regardless of transplant type. Intervention: AME intervention is delivered by a board-certified music therapist who tailors music-based play experiences to encourage active engagement in, and independent use of, music play to manage the inter-related emotional distress experienced by children and their caregivers during HSCT. Dyads will receive two 45-min AME sessions each week during hospitalization. Outcome Measures: Eight collections of blood (child) and saliva (child/caregiver) will be performed for cortisol measurement. The authors will also collect self-report and caregiver proxy measures for dyad emotional distress, quality of life, and family function. At study conclusion, qualitative caregiver interviews will be conducted. Results: Planned analyses will be descriptive and evaluate the feasibility of participant recruitment, cortisol collection, planned evaluations, and AME delivery. Analysis of qualitative interviews will be used to gain an understanding about the ease/burden of biological sample collection and any perceived benefit of AME. Conclusions: Behavioral intervention studies examining biological mechanisms of action in pediatric transplant populations are rare. Findings will provide important information about the feasibility/acceptability of collecting cortisol samples during a high-intensity treatment and advance understanding about the use of active music interventions to mitigate child/caregiver distress during the transplant period

Polarity effect in electrovibration for tactile display

Abstract-Electrovibration is the tactile sensation of an alternating potential between the human body and a smooth conducing surface when the skin slides over the surface and where the current is too small to stimulate sensory nerves directly. It has been proposed as a high-density tactile display method, for example to display pictographic information to persons who are blind. Previous models for the electrovibration transduction mechanism are based on a parallel-plate capacitor in which the electrostatic force is insensitive to polarity. We present experimental data showing that electrovibratory perceptual sensitivity to positive pulses is less than that for negative or biphasic pulses and propose that this disparity may be due to the asymmetric electrical properties of human skin. We furthermore propose using negative pulses for insulated tactile displays based on electrovibration because their sensory thresholds were found to be more stable than for waveforms incorporating positive pulses

Systematic study and uncertainty evaluation of P, T-odd molecular enhancement factors in BaF

A measurement of the magnitude of the electric dipole moment of the electron (eEDM) larger than that predicted by the Standard Model (SM) of particle physics is expected to have a huge impact on the search for physics beyond the SM. Polar diatomic molecules containing heavy elements experience enhanced sensitivity to parity (P) and time-reversal (T)-violating phenomena, such as the eEDM and the scalar-pseudoscalar (S-PS) interaction between the nucleons and the electrons, and are thus promising candidates for measurements. The NL-eEDM collaboration is preparing an experiment to measure the eEDM and S-PS interaction in a slow beam of cold BaF molecules [P. Aggarwal et al., Eur. Phys. J. D 72, 197 (2018)]. Accurate knowledge of the electronic structure parameters, Wd and Ws, connecting the eEDM and the S-PS interaction to the measurable energy shifts is crucial for the interpretation of these measurements. In this work, we use the finite field relativistic coupled cluster approach to calculate the Wd and Ws parameters in the ground state of the BaF molecule. Special attention was paid to providing a reliable theoretical uncertainty estimate based on investigations of the basis set, electron correlation, relativistic effects, and geometry. Our recommended values of the two parameters, including conservative uncertainty estimates, are 3.13 ±0.12×1024Hzecm for Wd and 8.29 ± 0.12 kHz for W

B-Cyclin/CDKs Regulate Mitotic Spindle Assembly by Phosphorylating Kinesins-5 in Budding Yeast

Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes, kinesin-5 motors, and the SCFCdc4 ubiquitin ligase are required for the separation of spindle poles and assembly of a bipolar spindle. It has been suggested that, in budding yeast, B-type cyclin/CDK (Clb/Cdc28) complexes promote spindle pole separation by inhibiting the degradation of the kinesins-5 Kip1 and Cin8 by the anaphase-promoting complex (APCCdh1). We have determined, however, that the Kip1 and Cin8 proteins are present at wild-type levels in the absence of Clb/Cdc28 kinase activity. Here, we show that Kip1 and Cin8 are in vitro targets of Clb2/Cdc28 and that the mutation of conserved CDK phosphorylation sites on Kip1 inhibits spindle pole separation without affecting the protein's in vivo localization or abundance. Mass spectrometry analysis confirms that two CDK sites in the tail domain of Kip1 are phosphorylated in vivo. In addition, we have determined that Sic1, a Clb/Cdc28-specific inhibitor, is the SCFCdc4 target that inhibits spindle pole separation in cells lacking functional Cdc4. Based on these findings, we propose that Clb/Cdc28 drives spindle pole separation by direct phosphorylation of kinesin-5 motors

The impact of land use/land cover scale on modelling urban ecosystem services

Context Urbanisation places increasing stress on ecosystem services; however existing methods and data for testing relationships between service delivery and urban landscapes remain imprecise and uncertain. Unknown impacts of scale are among several factors that complicate research. This study models ecosystem services in the urban area comprising the towns of Milton Keynes, Bedford and Luton which together represent a wide range of the urban forms present in the UK. Objectives The objectives of this study were to test (1) the sensitivity of ecosystem service model outputs to the spatial resolution of input data, and (2) whether any resultant scale dependency is constant across different ecosystem services and model approaches (e.g. stock- versus flow-based). Methods Carbon storage, sediment erosion, and pollination were modelled with the InVEST framework using input data representative of common coarse (25 m) and fine (5 m) spatial resolutions. Results Fine scale analysis generated higher estimates of total carbon storage (9.32 vs. 7.17 kg m−2) and much lower potential sediment erosion estimates (6.4 vs. 18.1 Mg km−2 year−1) than analyses conducted at coarser resolutions; however coarse-scale analysis estimated more abundant pollination service provision. Conclusions Scale sensitivities depend on the type of service being modelled; stock estimates (e.g. carbon storage) are most sensitive to aggregation across scales, dynamic flow models (e.g. sediment erosion) are most sensitive to spatial resolution, and ecological process models involving both stocks and dynamics (e.g. pollination) are sensitive to both. Care must be taken to select model data appropriate to the scale of inquiry

SHIV-162P3 Infection of Rhesus Macaques Given Maraviroc Gel Vaginally Does Not Involve Resistant Viruses

Maraviroc (MVC) gels are effective at protecting rhesus macaques from vaginal SHIV transmission, but breakthrough infections can occur. To determine the effects of a vaginal MVC gel on infecting SHIV populations in a macaque model, we analyzed plasma samples from three rhesus macaques that received a MVC vaginal gel (day 0) but became infected after high-dose SHIV-162P3 vaginal challenge. Two infected macaques that received a placebo gel served as controls. The infecting SHIV-162P3 stock had an overall mean genetic distance of 0.294±0.027%; limited entropy changes were noted across the envelope (gp160). No envelope mutations were observed consistently in viruses isolated from infected macaques at days 14–21, the time of first detectable viremia, nor selected at later time points, days 42–70. No statistically significant differences in MVC susceptibilities were observed between the SHIV inoculum (50% inhibitory concentration [IC50] 1.87 nM) and virus isolated from the three MVC-treated macaques (MVC IC50 1.18 nM, 1.69 nM, and 1.53 nM, respectively). Highlighter plot analyses suggested that infection was established in each MVC-treated animal by one founder virus genotype. The expected Poisson distribution of pairwise Hamming Distance frequency counts was observed and a phylogenetic analysis did not identify infections with distinct lineages from the challenge stock. These data suggest that breakthrough infections most likely result from incomplete viral inhibition and not the selection of MVC-resistant variants