Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. We first describe an algorithm that detects rows that belong to Minimal Conflicting Sets. This algorithm has a polynomial time complexity when the number of 1's in each row of the considered matrix is bounded by a constant. Next, we show that the problem of computing all Minimal Conflicting Sets can be reduced to the joint generation of all minimal true clauses and maximal false clauses for some monotone boolean function. We use these methods on simulated data related to ancestral genome reconstruction to show that computing Minimal Conflicting Set is useful in discriminating between true positive and false positive ancestral syntenies. We also study a dataset of yeast genomes and address the reliability of an ancestral genome proposal of the Saccahromycetaceae yeasts.Comment: 20 pages, 3 figure

Comparison of Northern Bobwhite Chick Fecal and Crop Analyses

Impacts of modem agriculture on gamebird brood ecology have been studied in a number of species. One common factor cited has been the decline in available invertebrate food available to foraging chicks. In the United Kingdom, assessment of chick diet has been accomplished mainly through fecal analysis of wild chicks, whereas in North America crop analysis of human-imprinted chicks has become a commonly applied technique. We compared results of both techniques on groups of human-imprinted northern bobwhite (Colinus virginianus) chicks to determine if these different techniques provide similar results. Chicks were allowed to forage in groups of 6-8 in cotton fields with various cover crops. We euthanized half the chicks for crop analysis and isolated the other half of the chicks for 12 hours to collect feces. We found a positive relationship between total number of invertebrates/chick in crops and feces (P = 0.01, R2 = 0.51). However, among important chick-food Orders the relationship varied greatly: Coleoptera (P = 0.10, R2 = 0.34), Homoptera (P \u3c 0.001, R2 = 0.41), and Hymenoptera (P = 0.81, R2 = 0.05). Our results suggest that there is a positive relationship between the 2 techniques, but that composition of the diet relative to what foods might be available in a particular site could be biased. We suggest more detailed research on technique development and standardization of techniques for assessing this important component of bobwhite life history

Photoexcitation of valley-orbit currents in (111)-oriented silicon metal-oxide-semiconductor field-effect transistors

We demonstrate the injection of pure valley-orbit currents in multivalley semiconductors and present the phenomenological theory of this effect. We studied photoinduced transport in (111)-oriented silicon metaloxide-semiconductor field effect transistors at room temperature. By shining circularly polarized light on exact oriented structures with six equivalent valleys, nonzero electron fluxes within each valley are generated, which compensate each other and do not yield a net electric current. By disturbing the balance between the valley fluxes, we demonstrate that the pure valley-orbit currents can be converted into a measurable electric current

Temporal criticality in socio-technical systems

Socio-technical systems, where technological and human elements interact in a goal-oriented manner, provide important, functional support to our societies. We draw specific attention to the concept of timeliness that has been ubiquitously and integrally adopted as a quality standard in the {\it modus operandi\/} of socio-technical systems, but remains an underappreciated aspect. We point out that a variety of incentives, often reinforced by competitive pressures, prompt system operators to myopically optimize for cost- and time-efficiencies, running the risk of inadvertently pushing the systems towards the proverbial `edge of a cliff'. Invoking a stylized model for operational delays, we argue that this cliff edge is a true critical point -- identified as {\it temporal criticality\/} -- implying that system efficiency and robustness to perturbation are in tension with each other. Specifically for firm-to-firm production networks, we suggest that the proximity to temporal criticality is a possible route for solving the fundamental ``excess volatility puzzle'' in economics. Further, in generality for optimizing socio-technical systems, we propose that system operators incorporate a measure of resilience in their welfare functions.Comment: 9 pages, 3 figures, perspective paper, corrected copy-paste error in the abstrac

Exciton dynamics in solid-state green fluorescent protein

We study the decay characteristics of Frenkel excitons in solid-state enhanced green fluorescent protein (eGFP) dried from solution. We further monitor the changes of the radiative exciton decay over time by crossing the phase transition from the solved to the solid state. Complex interactions between protonated and deprotonated states in solid-state eGFP can be identified from temperature-dependent and time-resolved fluorescence experiments that further allow the determination of activation energies for each identified process.PostprintPeer reviewe

Temporal criticality

In complex systems, external parameters often determine the phase in which the system operates, i.e., its macroscopic behavior. For nearly a century, statistical physics has extensively studied systems' transitions across phases, (universal) critical exponents, and related dynamical properties. Here we consider the functionality of systems, notably operations in socio-technical ones, production in economic ones and possibly information-processing in biological ones, where timing is of crucial importance. We introduce a stylized model on temporal networks with the magnitude of delay-mitigating buffers as the control parameter. The model exhibits {\it temporal criticality}, a novel form of critical behavior {\it in time}. We characterize fluctuations near criticality, commonly referred to as ``avalanches'', and identify the corresponding critical exponents. We show that real-world temporal networks, too, exhibit temporal criticality. We also explore potential connections with the Mode-Coupling Theory of glasses and the directed polymer problem.Comment: 11 pages of main paper, 11 figures, 9 pages of supplementary informatio

Crossover between Equilibrium and Shear-controlled Dynamics in Sheared Liquids

We present a numerical simulation study of a simple monatomic Lennard-Jones liquid under shear flow, as a function of both temperature and shear rate. By investigating different observables we find that i) It exists a line in the (temperature-shear) plane that sharply marks the boarder between an ``equilibrium'' and a ``shear-controlled'' region for both the dynamic and the thermodynamic quantities; and ii) Along this line the structural relaxation time, is proportional to the inverse shear rate, i.e. to the typical time-scale introduced by the shear flow. Above the line the liquid dynamics is unaffected by the shear flow, while below it both temperature and shear rate control the particle motion.Comment: 14 pages, 5 figure

Connected Health User Willingness to Share Personal Health Data: Questionnaire Study

Abstract Background: Connected health has created opportunities for leveraging health data to deliver preventive and personalized health care services. The increasing number of personal devices and advances in measurement technologies contribute to an exponential growth in digital health data. The practices for sharing data across the health ecosystem are evolving as there are more opportunities for using such data to deliver responsive health services. Objective: The objective of this study was to explore user attitudes toward sharing personal health data (PHD). The study was executed within the first year after the implementation of the new General Data Protection Regulation (GDPR) legal framework. Methods: The authors analyzed the results of an online questionnaire survey to explore the willingness of 8004 people using connected health services across four European countries to share their PHD and the conditions under which they would be willing to do so. Results: Our findings indicate that the majority of users are willing to share their personal PHD for scientific research (1811/8004, 22.63%). Age, education level, and occupation of the participants, in addition to the level of digitalization in their country were found to be associated with data sharing attitudes. Conclusions: Positive attitudes toward data sharing for scientific research can be perceived as an indication of trust established between users and academia. Nevertheless, the interpretation of data sharing attitudes is a complex process, related to and influenced by various factors