Chromatin proteins have expanded the mammalian synthetic biology toolbox by enabling control of active and silenced states at endogenous genes. Others have reported synthetic proteins that bind DNA and regulate genes by altering chromatin marks, such as histone modifications. Previously, we reported the first synthetic transcriptional activator, the “Polycomb-based transcription factor” (PcTF) that reads histone modifications through a protein–protein interaction between the polycomb chromodomain motif and trimethylated lysine 27 of histone H3 (H3K27me3). Here, we describe the genome-wide behavior of the polycomb-based transcription factor fusion protein. Transcriptome and chromatin profiling revealed several polycomb-based transcription factor-sensitive promoter regions marked by distal H3K27me3 and proximal fusion protein binding. These results illuminate a mechanism in which polycomb-based transcription factor interactions bridge epigenomic marks with the transcription initiation complex at target genes. In three cancer-derived human cell lines tested here, some target genes encode developmental regulators and tumor suppressors. Thus, the polycomb-based transcription factor represents a powerful new fusion protein-based method for cancer research and treatment where silencing marks are translated into direct gene activation.

Evolutionary games model a common type of interactions in a variety of complex, networked, natural systems and social systems. Given such a system, uncovering the interacting structure of the underlying network is key to understanding its collective dynamics. Based on compressive sensing, we develop an efficient approach to reconstructing complex networks under game-based interactions from small amounts of data. The method is validated by using a variety of model networks and by conducting an actual experiment to reconstruct a social network. While most existing methods in this area assume oscillator networks that generate continuous-time data, our work successfully demonstrates that the extremely challenging problem of reverse engineering of complex networks can also be addressed even when the underlying dynamical processes are governed by realistic, evolutionary-game type of interactions in discrete time.

Various biologically inspired flow field designs of the gas distributor (interconnector) have been designed and simulated. Their performance using Nafion-212 with humidified H₂ and Air at 80 °C with the ANSYS Fluent Fuel Cell module software was evaluated. Novel interdigitated designs were optimized by obeying biologically inspired branching rules. These rules allow for more mathematically formal descriptions of flow field designs, enabling relatively simple optimization. The channel to land ratio was kept equivalent between designs with typical values between 0.8 and 1.0. The pressure drop and the current density distribution were monitored for each design on both anode and cathode sides. The most promising designs are expected to exhibit lower pressure drop however, low pressure drop can also be an indication of potential water flooding at higher operating current density. A biologically inspired interdigitated design with 9 inlet channels exhibited reduced pressure drop and improved current density distribution compared to all other interdigitated designs evaluated in this study. The simulated fuel cell performance data at ambient pressure with humidified H₂ and air compares well with the experimental data using a single serpentine flow field design.

Background: The efficacy of deep brain stimulation (DBS) in Parkinson’s disease has been convincingly demonstrated in studies comparing motor performance with and without stimulation, but characterization of the stimulation dose-response curves has been limited.

Methods: In a series of case studies, eight subjects with Parkinson’s disease and bilateral DBS systems were evaluated at their clinically determined stimulation (CDS) and at three reduced amplitudes, ie, approximately 70%, 30%, and 0% of the CDS (MOD, LOW, and OFF, respectively). Performance was assessed using the motor section of the Unified Parkinson’s Disease Rating Scale (UPDRS-III), which includes subscores for tremor, bradykinesia, gait, posture, and tapping. Data at the reduced settings were analyzed to determine if individual subjects demonstrated a threshold-like response, which was defined as a dose-response curve in which one decrement in stimulation accounted for ≥70% of the maximum change observed. Day-to-day variability was assessed using the CDS data from the three different days.

Results: In the dose-response curves, two subjects exhibited a threshold-like response, four exhibited a graded change, and two did not exhibit substantial changes. For some subjects, variability in CDS performance across the three days exceeded the change observed when reducing amplitude to the MOD setting. Comparisons across this set of eight subjects demonstrated that the mean UPDRS-III and all but one subscore significantly increased (performance degraded) when amplitude was reduced from CDS to the LOW and OFF conditions, but there were no significant changes when amplitude was reduced from CDS to the MOD condition.

Conclusion: Individual differences in the DBS dose-response curves may provide opportunities to optimize clinical performance. Day-to-day variability in motor performance cautions against the use of a single UPDRS measurement in clinical selection of DBS settings.

Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics.

Increasing penetration of energy efficiency programs and distributed renewable energy generation has imposed significant challenges for utilities to recoup their large upfront costs. There is a heated debate on what surcharges should be implemented to help the utilities recover their fixed costs; however, very few studies focus on consumers’ attitudes regarding this topic. This study surveys about 190 residential consumers throughout the United States in November 2015, investigating their preferences and attitudes towards extra demand charges and volumetric energy price increases. We apply probit models and regress consumers’ attitudes on selected socio-demographic and behavioral variables. The results indicate the homeowners are more likely to prefer demand charges when compared to renters. The demographic and behavioral factors impact consumers’ perception of bill savings from energy efficiency programs or solar panel installation and also influence how consumers perceive the fairness of utilities recovering revenue losses by increasing volumetric energy price. In this paper, we demonstrate there is preference heterogeneity among consumers and that policy makers should be aware of such preference heterogeneity and apply policy targeting based on the identified demographics and behavioral factors impacting consumer preferences.

We study the low efficiency droop characteristics of semipolar InGaN light-emitting diodes (LEDs) using modified rate equation incoporating the phase-space filling (PSF) effect where the results on c-plane LEDs are also obtained and compared. Internal quantum efficiency (IQE) of LEDs was simulated using a modified ABC model with different PSF filling (n[subscript 0]), Shockley-Read-Hall (A), radiative (B), Auger (C) coefficients and different active layer thickness (d), where the PSF effect showed a strong impact on the simulated LED efficiency results. A weaker PSF effect was found for low-droop semipolar LEDs possibly due to small quantum confined Stark effect, short carrier lifetime, and small average carrier density. A very good agreement between experimental data and the theoretical modeling was obtained for low-droop semipolar LEDs with weak PSF effect. These results suggest the low droop performance may be explained by different mechanisms for semipolar LEDs.

InGaN semiconductors are promising candidates for high-efficiency next-generation thin film solar cells. In this work, we study the photovoltaic performance of single-junction and two-junction InGaN solar cells using a semi-analytical model. We analyze the major loss mechanisms in InGaN solar cell including transmission loss, thermalization loss, spatial relaxation loss, and recombination loss. We find that transmission loss plays a major role for InGaN solar cells due to the large bandgaps of III-nitride materials. Among the recombination losses, Shockley-Read-Hall recombination loss is the dominant process. Compared to other III-V photovoltaic materials, we discovered that the emittance of InGaN solar cells is strongly impacted by Urbach tail energy. For two- and multi-junction InGaN solar cells, we discover that the current matching condition results in a limited range of top-junction bandgaps. This theoretical work provides detailed guidance for the design of high-performance InGaN solar cells.

Antibody detection and accurate diagnosis of tropical diseases is essential to help prevent the spread of disease. However, most detection methods lack cost-effectiveness and field portability, which are essential features for achieving diagnosis in a timely manner. To address this, 3D-printed oblate spheroid sample chambers were fabricated to measure green light scattering of gold nanoparticles using an optical caustic focus to detect antibodies. Scattering signals of 20–200 nm gold nanoparticles using a green laser were compared to green light emitting diode (LED) light source signals and to Mie theory. The change in signal from 60 to 120 nm decreased in the order of Mie Theory > optical caustic scattering > 90° scattering. These results suggested that conjugating 60 nm gold nanoparticles and using an optical caustic system to detect plasmonic light scattering, would result in a sensitive test for detecting human antibodies in serum. Therefore, we studied the light scattering response of conjugated gold nanoparticles exposed to different concentrations of anti-protein E antibody, and a feasibility study of 10 human serum samples using dot blot and a handheld optical caustic-based sensor device. The overall agreement between detection methods suggests that the new sensor concept shows promise to detect gold nanoparticle aggregation in a homogeneous assay. Further testing and protocol optimization is needed to draw conclusions on the positive and negative predictive values for this new testing system.

Video encoding for multimedia services over communication networks has significantly advanced in recent years with the development of the highly efficient and flexible H.264/AVC video coding standard and its SVC extension. The emerging H.265/HEVC video coding standard as well as 3D video coding further advance video coding for multimedia communications. This paper first gives an overview of these new video coding standards and then examines their implications for multimedia communications by studying the traffic characteristics of long videos encoded with the new coding standards. We review video coding advances from MPEG-2 and MPEG-4 Part 2 to H.264/AVC and its SVC and MVC extensions as well as H.265/HEVC. For single-layer (nonscalable) video, we compare H.265/HEVC and H.264/AVC in terms of video traffic and statistical multiplexing characteristics. Our study is the first to examine the H.265/HEVC traffic variability for long videos. We also illustrate the video traffic characteristics and statistical multiplexing of scalable video encoded with the SVC extension of H.264/AVC as well as 3D video encoded with the MVC extension of H.264/AVC.