Cellular heterogeneity mediates inherent sensitivity–specificity tradeoff in cancer targeting by synthetic circuits

Synthetic gene circuits are emerging as a versatile means to target cancer with enhanced specificity by combinatorial integration of multiple expression markers. Such circuits must also be tuned to be highly sensitive because escape of even a few cells might be detrimental. However, the error rates of decision-making circuits in light of cellular variability in gene expression have so far remained unexplored. Here, we measure the single-cell response function of a tunable logic AND gate acting on two promoters in heterogeneous cell populations. Our analysis reveals an inherent tradeoff between specificity and sensitivity that is controlled by the AND gate amplification gain and activation threshold. We implement a tumor-mimicking cellculture model of cancer cells emerging in a background of normal ones, and show that molecular parameters of the synthetic circuits control specificity and sensitivity in a killing assay. This suggests that, beyond the inherent tradeoff, synthetic circuits operating in a heterogeneous environment could be optimized to efficiently target malignant state with minimal loss of specificity. Keywords: synthetic gene circuits; cellular heterogeneity; cancer gene therapy; cell-state targeting; mammalian synthetic biolog

Sec-Lib: Protecting Scholarly Digital Libraries From Infected Papers Using Active Machine Learning Framework

Researchers from academia and the corporate-sector rely on scholarly digital libraries to access articles. Attackers take advantage of innocent users who consider the articles\u27 files safe and thus open PDF-files with little concern. In addition, researchers consider scholarly libraries a reliable, trusted, and untainted corpus of papers. For these reasons, scholarly digital libraries are an attractive-target and inadvertently support the proliferation of cyber-attacks launched via malicious PDF-files. In this study, we present related vulnerabilities and malware distribution approaches that exploit the vulnerabilities of scholarly digital libraries. We evaluated over two-million scholarly papers in the CiteSeerX library and found the library to be contaminated with a surprisingly large number (0.3-2%) of malicious PDF documents (over 55% were crawled from the IPs of US-universities). We developed a two layered detection framework aimed at enhancing the detection of malicious PDF documents, Sec-Lib, which offers a security solution for large digital libraries. Sec-Lib includes a deterministic layer for detecting known malware, and a machine learning based layer for detecting unknown malware. Our evaluation showed that scholarly digital libraries can detect 96.9% of malware with Sec-Lib, while minimizing the number of PDF-files requiring labeling, and thus reducing the manual inspection efforts of security-experts by 98%

Quantum-classical processing and benchmarking at the pulse-level

Towards the practical use of quantum computers in the NISQ era, as well as the realization of fault-tolerant quantum computers that utilize quantum error correction codes, pressing needs have emerged for the control hardware and software platforms. In particular, a clear demand has arisen for platforms that allow classical processing to be integrated with quantum processing. While recent works discuss the requirements for such quantum-classical processing integration that is formulated at the gate-level, pulse-level discussions are lacking and are critically important. Moreover, defining concrete performance benchmarks for the control system at the pulse-level is key to the necessary quantum-classical integration. In this work, we categorize the requirements for quantum-classical processing at the pulse-level, demonstrate these requirements with a variety of use cases, including recently published works, and propose well-defined performance benchmarks for quantum control systems. We utilize a comprehensive pulse-level language that allows embedding universal classical processing in the quantum program and hence allows for a general formulation of benchmarks. We expect the metrics defined in this work to form a solid basis to continue to push the boundaries of quantum computing via control systems, bridging the gap between low-level and application-level implementations with relevant metrics.Comment: 22 page

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human cells, limiting their use for conditional gene regulation. We present new strategies that enable expression of functional gRNAs from RNA polymerase II promoters and multiplexed production of proteins and gRNAs from a single transcript in human cells. We use multiple RNA regulatory strategies, including RNA-triple-helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing. Using these tools, we efficiently modulate endogenous promoters and implement tunable synthetic circuits, including multistage cascades and RNA-dependent networks that can be rewired with Csy4 to achieve complex behaviors. This toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for biology, therapeutic, and synthetic biology applications.United States. Defense Advanced Research Projects AgencyNational Institutes of Health (U.S.) (DP2 OD008435)National Institutes of Health (U.S.) (P50 GM098792

Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection

The integration of nanotechnology and synthetic biology could lay the framework for new classes of engineered biosensors that produce amplified readouts of disease states. As a proof-of-concept demonstration of this vision, here we present an engineered gene circuit that, in response to cancer-associated transcriptional deregulation, expresses heterologous enzyme biomarkers whose activity can be measured by nanoparticle sensors that generate amplified detection readouts. Specifically, we designed an AND-gate gene circuit that integrates the activity of two ovarian cancer-specific synthetic promoters to drive the expression of a heterologous protein output, secreted Tobacco Etch Virus (TEV) protease, exclusively from within tumor cells. Nanoparticle probes were engineered to carry a TEV-specific peptide substrate in order to measure the activity of the circuit-generated enzyme to yield amplified detection signals measurable in the urine or blood. We applied our integrated sense-and-respond system in a mouse model of disseminated ovarian cancer, where we demonstrated measurement of circuit-specific TEV protease activity both in vivo using exogenously administered nanoparticle sensors and ex vivo using quenched fluorescent probes. We envision that this work will lay the foundation for how synthetic biology and nanotechnology can be meaningfully integrated to achieve next-generation engineered biosensors

The Risk of Rectal Temperature Measurement in Neutropenia

Background: Avoiding rectal thermometry is recommended in patients with neutropenic fever. Permeability of the anal mucosa may result in a higher risk of bacteremia in these patients. Still, this recommendation is based on only a few studies. Methods: This retrospective study included all individuals admitted to our emergency department during 2014–2017 with afebrile (body temperature <38.3°C) neutropenia (neutrophil count <500 cells/microL) who were over the age of 18. Patients were stratified by the presence or absence of a rectal temperature measurement. The primary outcome was bacteremia during the first five days of index hospitalization; the secondary outcome was in-hospital mortality. Results: The study included 40 patients with rectal temperature measurements and 407 patients whose temperatures were only measured orally. Among patients with oral temperature measurements, 10.6% had bacteremia, compared to 5.1% among patients who had rectal temperature measurements. Rectal temperature measurement was not associated with bacteremia, neither in non-matched (odds ratio [OR] 0.36, 95% confidence interval [CI] 0.07–1.77) nor in matched cohort analyses (OR 0.37, 95% CI 0.04–3.29). In-hospital mortality was also similar between the groups. Conclusions: Patients with neutropenia who had their temperature taken using a rectal thermometer did not experience a higher frequency of events of documented bacteremia or increased in-hospital mortality