Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly oscillatory, data for different gene networks. However, the regulation of gene expression at the level of an individual cell involves reactions between finite numbers of molecules, and this can result in inherent randomness in expression dynamics, which blurs the boundaries between aperiodic fluctuations and noisy oscillators. Thus, there is an acute need for an objective statistical method for classifying whether an experimentally derived noisy time series is periodic. Here we present a new data analysis method that combines mechanistic stochastic modelling with the powerful methods of non-parametric regression with Gaussian processes. Our method can distinguish oscillatory gene expression from random fluctuations of non-oscillatory expression in single-cell time series, despite peak-to-peak variability in period and amplitude of single-cell oscillations. We show that our method outperforms the Lomb-Scargle periodogram in successfully classifying cells as oscillatory or non-oscillatory in data simulated from a simple genetic oscillator model and in experimental data. Analysis of bioluminescent live cell imaging shows a significantly greater number of oscillatory cells when luciferase is driven by a {\it Hes1} promoter (10/19), which has previously been reported to oscillate, than the constitutive MoMuLV 5' LTR (MMLV) promoter (0/25). The method can be applied to data from any gene network to both quantify the proportion of oscillating cells within a population and to measure the period and quality of oscillations. It is publicly available as a MATLAB package.Comment: 36 pages, 17 figure

H.B. 600: Ohio\u27s Bill of Rights for Nursing Home Patients

Nursing home residents are among the most helpless individuals in our society; their dependence on institutions for food, shelter, and personal care has cost them control over their own lives. “Because of the vulnerability of the aged population of the nursing home and the fact that most of them will reside in these homes for the rest of their lives, society bears a special obligation to ensure that the quality of their care is satisfactory and their treatment humane.” Ohio has responded to this obligation by enacting H.B. 600, which is directed at improving the care of Ohio nursing home residents. Acclaimed as model legislation, H.B. 600 “[e]numerates thirty rights of nursing home patients concerning safety, treatment, privacy, civil rights, restraints, smoking and drinking, information, financial affairs, transfer and discharge, [and] grievances …” H.B. 600 was necessary because federal and state regulations have heretofore largely failed to ensure humane treatment9 of all nursing home residents, whose special needs and rights have often been sacrificed to administrative convenience, efficiency, and economy. Consequently, residents have suffered abuses, neglect, and crass commercialism, which have been widely publicized and documented. The Patients’ Bill of Rights was enacted after considerable debate and revision. Upon ratification, this legislation enumerated thirty specific rights guaranteed to Ohio nursing home residents as well as concrete implementation and enforcement provisions

The Influence of Georgia’s Quality Rated System on School Readiness in Pre-School Children

Background: Georgia rates the quality of early childcare learning centers using a tiered quality improvement system. Georgia’s Quality Rated system (QR) designates a star level, (one star, two stars or three stars) to each center based on a portfolio of QR standards and an onsite assessment by Georgia Department of Early Care and Learning (DECAL). Childcare centers applying for QR status first submit a portfolio documenting how their practices align with QR standards centered on staff qualifications; child health, nutrition and physical activity; family engagement; holistic curricula and teacher-to-student ratios. Subsequently, an on-site assessment of the center is performed by DECAL using the Early Childhood Environment Rating Scale– Revised (ECERS-R). Methods: The Bracken School Readiness Assessment-3rd Edition (BSRA-3) was administered to children in various one-star (N=2), two-star (N=4) and three-star (N=6) childcare learning centers in Georgia. Children’s height and weight were recorded and BMI assessments were conducted. Results: Significant differences were found in school readiness scores based on quality rating with two and three star centers scoring higher than one star centers. Children in childcare centers at the one-star level (Mean = 95.00, SD = 16.80) performed lower than children in childcare centers at the two-star level (Mean = 103.67, SD = 16.55) and three-star level (Mean = 100.42, SD = 14.35). Multiple comparison tests did not reveal differences between two-star and three-star level centers. Conclusions: Higher levels of quality in QR childcare centers displayed more school readiness than centers with lower levels of quality. Future studies should examine differences in higher quality centers to further explore the influence of QR programs on school readiness

Supporting Job-Seekers Experiencing Homelessness: Best Practices for CoC & Workforce Board Engagement

The slides are from a presentation given at the Michigan Summit to End Homelessness in September 2016

COVID-19 in the United States: Insights from Healthcare Systems

During this COCA Call, presenters will discuss the current impact of the COVID-19 pandemic on healthcare systems in the U.S., including key successes and challenges from the hospital response perspective

Self Disclosure: Beneficial for Cohesion in Demographically Diverse Work Groups?

Many organizational efforts to improve co-worker relationships entail inducing employees to bring their “whole selves” into the workplace, which for employees often means disclosing personal experiences at work. Several psychological theories suggest that increased self-disclosure will lead to better relationships in organizational work groups. However, this chapter considers the factors impacting self-disclosure in demographically diverse settings. We posit that although self-disclosure has led to closer relationships in past research, it may not increase cohesion for employees in demographically diverse work groups, or those who are demographically dissimilar from the majority of their co-workers

Revealing nascent proteomics in signaling pathways and cell differentiation.

Regulation of gene expression at the level of protein synthesis is a crucial element in driving how the genetic landscape is expressed. However, we are still limited in technologies that can quantitatively capture the immediate proteomic changes that allow cells to respond to specific stimuli. Here, we present a method to capture and identify nascent proteomes in situ across different cell types without disturbing normal growth conditions, using O-propargyl-puromycin (OPP). Cell-permeable OPP rapidly labels nascent elongating polypeptides, which are subsequently conjugated to biotin-azide, using click chemistry, and captured with streptavidin beads, followed by digestion and analysis, using liquid chromatography-tandem mass spectrometry. Our technique of OPP-mediated identification (OPP-ID) allows detection of widespread proteomic changes within a short 2-hour pulse of OPP. We illustrate our technique by recapitulating alterations of proteomic networks induced by a potent mammalian target of rapamycin inhibitor, MLN128. In addition, by employing OPP-ID, we identify more than 2,100 proteins and uncover distinct protein networks underlying early erythroid progenitor and differentiation states not amenable to alternative approaches such as amino acid analog labeling. We present OPP-ID as a method to quantitatively identify nascent proteomes across an array of biological contexts while preserving the subtleties directing signaling in the native cellular environment