Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust circadian clocks from coupled protein-modification and transcription–translation cycles

The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription–translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to analyze how these cycles interact to generate stable rhythms in growing, dividing cells. We find that a protein phosphorylation cycle by itself is robust when protein turnover is low. For high decay or dilution rates (and compensating synthesis rates), however, the phosphorylation-based oscillator loses its integrity. Circadian rhythms thus cannot be generated with a phosphorylation cycle alone when the growth rate, and consequently the rate of protein dilution, is high enough; in practice, a purely posttranslational clock ceases to function well when the cell doubling time drops below the 24-h clock period. At higher growth rates, a transcription–translation cycle becomes essential for generating robust circadian rhythms. Interestingly, although a transcription–translation cycle is necessary to sustain a phosphorylation cycle at high growth rates, a phosphorylation cycle can dramatically enhance the robustness of a transcription–translation cycle at lower protein decay or dilution rates. In fact, the full oscillator built from these two tightly intertwined cycles far outperforms not just each of its two components individually, but also a hypothetical system in which the two parts are coupled as in textbook models of coupled phase oscillators. Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.
Design & Development of a Computational Model using Virtualization and Multi-tenancy Technologies for Cloud Computing Architecture

Cloud computing has arrived as a solution to reduce costs in organizations and at the same time offer on-demand resources and computation without requiring to create an IT infrastructure. Services, such as Amazon Web Services (AWS) or Microsoft Azure provide a means for organizations to instantly provision and de-provision virtual machines (VM) depending on their needs, just paying for what they use. In order to make the necessary environment, cloud service providers (CSP) make use of virtualization technologies to maximize the value of their systems. Servers have always needed to run alone in physical machines to avoid other services to interfere with them; but the downside of this was the waste of resources. Virtualization enables the use of all the resources in a physical host by sharing them between the guest operating systems (OS). Many organizations have already deployed private clouds on their own infrastructures or through third parties. However, Public Clouds provide an additional advantage that makes it extremely attractive, cost savings. The resources for a cloud consumer seem to be unlimited by sharing all the host machines between different organizations. At the same time, the CSPs can easily maximize the use of each physical machine. Multi-tenancy is the name that receives this computational model. However, there is a drawback on multi-tenancy and public clouds. Host systems are shared between multiple tenants with different owners and one of them could potentially be a malicious attacker or even a competitor. Now someone trying to compromise an organization‟s business processes or data will not need to break through their traditional lines of defense. The traditional perimeter in their networks no longer exists. Now an organization‟s systems coexist shoulder to shoulder with unknown tenants with potential malicious intentions. The virtualization layer adds a new attack surface to be compromised where the hypervisor and the resident VMs can be the target. The alarms have been triggered, stopping many organizations on their path to the Cloud. This research paper aims to provide an overview of the security issues that this new computational model arises. The problem will be aboard from the general cloud computing term, through multi-tenancy, down to virtualization. The main goal is to explore and analyze the different threats that virtualization and multi-tenancy combined bring to the Cloud. More specifically, the venues to compromise a VM or a hypervisor in a physical machine will be analyzed and recommendations will be given on how to mitigate the risks.
Secure Communications with Untrusted Secondary Nodes in Cognitive Radio Networks

We consider a cooperation scenario between primary users and untrusted secondary users in cognitive radio networks. The secondary users are willing to help the primary users to relay the primary users' messages in reward for being allowed to share the primary users' spectrum bands. However, the primary users might be reluctant to accept this help, since the secondary users are untrustworthy and may try unauthorized decoding of the primary users' messages. This paper will answer the question: when is this cooperation mutually beneficial for primary and secondary users? Taking an approach of information-theoretic secrecy, such as coding techniques for wiretap channels, the primary users can allow the secondary users to sense and relay the message, while ensuring that the secondary users are ignorant of the primary users' messages. We characterize an achievable secrecy rate of primary users with a rate of the secondary users' communication. From the derived rate pairs, an optimization problem is formulated such that the secondary transmitter distributes its transmit power to maximize its data rate while providing a higher secrecy rate to the primary users. We demonstrate that this cooperation can provide a positive secrecy rate, even when a non-cooperative scheme achieves a zero secrecy rate.
Optogenetic Activation of Basal Forebrain Cholinergic Neurons Modulates Neuronal Excitability and Sensory Responses in the Main Olfactory Bulb

The main olfactory bulb (MOB) in mammals receives massive centrifugal input from cholinergic neurons in the horizontal limb of the diagonal band of Broca (HDB) in the basal forebrain, the activity of which is thought to be correlated with animal behaving states, such as attention. Cholinergic signals in the bulb facilitate olfactory discrimination and learning, but it has remained controversial how the activity of HDB cholinergic neurons modulates neuronal excitability and olfactory responses in the MOB. In this study, we used an optogenetic approach to selectively activate HDB cholinergic neurons and recorded the effect of this activation on the spontaneous firing activity and odor-evoked responses of mouse MOB neurons. Cells were juxtacellularly labeled and their specific types were morphologically determined. We find that light stimulation of HDB cholinergic neurons inhibits the spontaneous firing activity of all major cell types, including mitral/tufted (M/T) cells, periglomerular (PG) cells, and GABAergic granule cells. Inhibitions are significantly produced by stimulation at 10 Hz and further enhanced at higher frequencies. In addition, cholinergic activation sharpens the olfactory tuning curves of a majority of M/T cells but broadly potentiates odor-evoked responses of PG cells and granule cells. These results demonstrate strong effects of the basal forebrain cholinergic system on modulating neuronal excitability in the MOB and support the hypothesis that cholinergic activity increases olfactory discrimination capability.
Penultimate Draft-final Version Forthcoming in Philosophical Psychology

The Phenomenological Mind is part of a recent initiative to show that phenomenology contributes something important to cognitive science. (For other examples, see the References section.) Phenomenology, of course, has been a part of cognitive science for a long time. It implicitly informs the works of Andy Clark (e.g., 1997) and John Haugeland (e.g., 1998), and Hubert Dreyfus explicitly uses it (e.g., 1992). But where the former use phenomenology in the background as broad context and Dreyfus uses it primarily (though not exclusively) as a critique of conventional artificial intelligence, Gallagher and Zahavi indicate a positive and constructive place for it. They do not recommend that we simply accept pronouncements of thinkers like Husserl, Heidegger, Sartre and Merleau-Ponty and apply them to questions of cognition, but that we use revised forms of phenomenology to illuminate dimensions of cognitive experience that are missing in current research. After an introductory chapter that places phenomenology in the context of other approaches, the book lays out the traditional tenets of the phenomenological method and some potential surprises, namely, attempts to " naturalize " phenomenology, a few attempts to formalize it, and the emergence of " neurophenomenology. " Each of these is a surprise because Husserl was a critic of naturalism, seeing transcendental phenomenology as an alternative to the empirical study of consciousness. He was also skeptical about the possibilities of mathematizing it. Gallagher and Zahavi acknowledge these points, but since they are not repeating history or undertaking exegesis, adherence to canonical phenomenology is not required. " Naturalizing " phenomenology means recognizing that " the phenomena it studies are part of nature and are therefore also open to empirical investigation " (p. 32) and that scientific investigation and phenomenology should mutually inform each other. They are corroborative, rather than competitive, though how this is best understood remains " contentious " (p. 30). " Formalizing " phenomenology is a matter of codifying " the formal structure of experience " (p. 30) in order to translate " data from phenomenological and naturalistic realms into a common language " (p. 32). The benefits of doing so are clear upon reflection, though the book does not offer detail. If we can find a way to code descriptions of experience in a language recognizable to science, we might go a long way toward finding scientific explanations for it—at least this seems to be the hope. Along similar lines, " neurophenomenology …
Secure wireless multicasting through multi-cellular MIMO networks with linear equalization

In this paper, we consider a confidential communication through multi-cellular co-located multiple-input multiple-output (C-MIMO) and distributed MIMO (D-MIMO) networks in the presence of an eavesdropper. The base station (BS) of each cell sends a common stream of information to a group of receivers within the cell and an eavesdropper observes their communications. We are interested to protect these information from eavesdropping, so that no eavesdropper can decode any information. Moreover, we investigate the performance of maximal ratio combining (MRC), zero-forcing (ZF) and minimum mean-square error (MMSE) detectors in enhancing security in multi-cellular MIMO networks considering their presence at the receivers and eavesdropper. Our results show that although the D-MIMO system is more sensitive to interference than C-MIMO system but in the high interference region, the effect of interference on both the MIMO models are almost same. The increase in transmit antennas enhances security and the MRC and MMSE detectors perform better than the ZF detector when the number of transmit antennas is very small.
Constraint Query Languages

We investigate the relationship between programming with constraints and database query languages. We show that efficient, declarative database programming can be combined with efficient constraint solving. The key intuition is that the generalization of a ground fact, or tuple, is a conjunction of constraints over a small number of variables. We describe the basic constraint query language design principles and illustrate them with four classes of constraints: real polynomial inequalities, dense linear order inequalities, equalities over an infinite domain, and boolean equalities. For the analysis, we use quantifier elimination techniques from logic and the concept of data complexity from database theory. This framework is applicable to managing spatial data and can be combined with existing multi-dimensional searching algorithms and data structures. KEYWORDS: database queries, spatial databases, data complexity, quantifier elimination, constraint logic programming, relational calculus, Datalog.
A general probability model for the inheritance of binary traits

In the era of genomics, large scale trait mapping studies are conducted. These experiments involve hundreds of markers and increasingly frequently they focus on complex traits. Complex traits are interesting because of the inherent multigenic nature of the traits, and the possible interaction between genes on the phenotype. Binary traits, such as disease resistance, have a simple phenotype but may also be multigenic. Likelihood and regression methods for modeling genotype and phenotypic relationships rely on underlying classical transmission genetics and the ability to implement complicated models. In principle, the expansion from one to two, three and more loci is understood as is the transmission probability from an F2 to an F3. What is missing is a comprehensive, flexible notation that allows for an arbitrary number of loci and the transmission for multiple generations. In effect, the integration of theory involving mapping functions with the theory of quantitative inheritance. We used classical genetics theory to construct a probability model for the joint distribution of marker genotypes, trait genotypes and trait values for any number of marker and trait loci, and develop the corresponding likelihood. This framework is described in detail for a binary trait where the trait probabilities are parameterized in terms of a penetrance function. The transmission portion of the probability model is completely general and will apply regardless of the model employed for the trait values. We provide Maple code that generates the marginal distributions as well as the joint distribution. The explicit mathematical formulation described here will assist in implementing different models for the behavior of the complex trait and provides a common set of useful notation that can be used regardless of the trait model employed.
Peak-End Effects for Subjective Mental Workload Ratings

The present study examines the possible impact of the peak-end rule as it applies to the measurement of subjective workload. Researchers presented participants with the same three tasks presented in a different order and asked participants to rate the workload of the entire session using a single item rating scale and the NASA-TLX. One of the three tasks was designed to be more challenging than the other two as confirmed by a manipulation check. When the challenging task was presented last in the session, there were significantly higher ratings on the TLX-mental demand and TLX-effort subscales. The overall NASA-TLX and the single item rating scale both produced scores that were higher when this challenging task was last but did not reach statistical significance. Future research regarding subjective mental workload should be careful to consider these end-effects as a potential source of bias.
A helper initiated distributed cooperative Medium Access Control (MAC) protocol for wireless networks

Spatial diversity for wireless transmission requires more than one antenna at the transmitter. However, mobile devices are usually limited by size, so installation of multiple antennas increases the hardware complexity significantly. Due to the omnidirectional nature of wireless signal, a data transmission between a source node and a destination node can be overheard by many other neighbor nodes. By exploiting this characteristic, a number of recent research activities on cooperative Medium Access Control (MAC) have been devised where low data rate stations are assisted by the high data rate stations in forwarding data traffics. Therefore, wireless devices with a single antenna can effectively form a virtual array of antennas by sharing each other's' antennas in a multiuser environment. To facilitate cooperative communication in the data link layer requires a great deal of attention. In designing a cooperative MAC, selection of relay stations is the most important criterion. In this paper, we propose a distributed cooperative MAC protocol where a potential relay node initiates itself to participate in the cooperation by calculating supported data transmission rate between source to relay and relay to destination links. A mathematical analysis of our proposed scheme is derived and throughput of the proposed scheme is then compared with that of the existing IEEE 802.11 DCF MAC. Numerical results show that our proposed scheme can increase the throughput of any IEEE 802.11 low data rate station comprehensively.
A Distributed Monitoring Approach for Trust Assessment Based on Formal Testing

Communications systems are growing in use and in popularity. While their interactions are becoming more numerous, trust those interactions now becomes a priority. In this paper, we focus on trust management systems based on observations of trustee behaviors. Based on a formal testing methodology, we propose a formal distributed network monitoring approach to analyze the packets exchanged between the trust or, trustee and other points of observation in order to prove the trustee is acting in a trustworthy manner. Based on formal "trust properties", the monitored systems behaviors provide a verdict of trust by analyzing and testing those properties. Finally, our methodology is applied to a real industrial DNS use case scenario.
Task Partitioning and Platform Synthesis for Energy Efficiency

Energy-efficient and power-aware designs have played important roles in modern computing systems to reduce the power bills for server systems or prolong the lifetime of embedded devices. Moreover, systems with multiple heterogeneous processing units have been widely adopted to enhance the computing capability or reduce the power consumption. This work explores how to synthesize a heterogeneous multiprocessor platform or select processing units with the partitioning of real-time tasks so that the energy consumption is minimized. Given a set of processing unit types, characterized by the power consumption for maintaining activeness and executing jobs, this paper proposes an efficient and effective algorithm to allocate processing units with energy-efficient task partitioning. We show that the algorithm is with a $(1+\ln n)$-approximation factor, in worst cases, for processing unit types with a variety of power consumption models, where $n$ is the number of tasks. The approximation factor is asymptotically optimal for polynomial-time approximation algorithms unless ${\cal P}={\cal NP}$. Experimental results show that the proposed algorithm is effective for energy consumption minimization.
Conflict Avoidance Scheduling Using Grouping List for Transactional Memory

Conventional Transactional Memory (TM) systems may experience performance degradation in applications with high contention, given the fact that execution of transaction will frequently restart due to conflicts. The restarting of transaction essentially requires rollback that is a wasteful operation. To address this point, we developed a system to reduce the overhead caused by high contention. In this paper, we present a method called Conflict Avoidance Scheduling (CAS), which prevents the conflicts in high contention by use of conflict characteristic. In CAS, threads that execute transactions which have high probability of conflicts are grouped together. Based on the group information, concurrent execution of threads in the same group is restricted. Therefore, threads that may cause conflict are serially executed. We evaluate the performance of the proposed design by comparing it with Log TM-SE. The simulation results show that our system improves the performance by 23% on an average in applications with high contention, as compared with the conventional Log TM-SE.
Bundle protocol mail convergence layer: leveraging legacy internet infrastructure for DTNs

In the past many research prototypes employed a DTN to provide mail services to remote areas. This work proposes the opposite: Using SMTP and IMAP to transport the Bundle Protocol (BP). Despite the obvious feasibility of such a scheme, we will show that the Mail Convergence Layer (MCL) provides advantages over other Convergence Layers and can qualitatively enhance the capabilities of a DTN. Each DTN node has an associated mailbox that can be used to deposit bundles, if the node is absent. In this case a mail server effectively acts as an intermediate always-on DTN node without the need to deploy a BP router. We will present the motivation and the concept of the MCL as well as an open-source implementation.
Three-phase soft-switching PWM inverter for brushless DC motor

The brushless direct current motor (BLDCM) has high torque, compact size, and high efficiency. Therefore, BLDCM is widely used in computers, household and industrial products, and automobiles. It is usually driven by a hard-switching pulse width modulation (PWM) inverter, which has low switching frequency, high switching loss, high electro-magnetic interference (EMI) and acoustic noise, etc. To solve the drawbacks of the voltage source-type hard switching inverter, a novel zero voltage transition (ZVT) three-phase soft-switching voltage source inverter (VSI) is proposed for BLDCM drive systems. The proposed ZVT-VSI consists of three switches, six diodes, three capacitors and an inductor. Soft switching operation of all switching devices in inverter is realized by adding auxiliary resonant unit to DC link of conventional one. Auxiliary switches are also operated under zero current switching (ZCS) or zero voltage switching (ZVS). The proposed inverter is suitable for PWM operation. The soft-switching operation of the ZVT -VSI is explained in terms of modes. The validity of the topology is verified by experimental results.
Quantitative molecular monitoring of human immunodeficiency virus type 1 activity during therapy with specific antiretroviral compounds

Methods for the absolute quantitation of nucleic acids present in small amounts in biological samples (competitive PCR and competitive reverse transcription PCR) were applied to the direct monitoring of specific anti-human immunodeficiency virus type 1 (HIV-1) therapy. With these techniques, different parameters of HIV-1 activity (including genomic RNA copy numbers in plasma, proviral and late transcript copy numbers in peripheral blood lymphocytes, and mean transcriptional activity per each HIV-1 provirus) were monitored during therapy with azidothymidine or ddI. In most of these treated patients, a direct response to the antiretroviral compounds employed was detected during the first few weeks of treatment, as documented by a fast decrease of all molecular indexes of HIV-1 activity. However, residual viral replication (albeit at minimal levels) was documented during therapy in all subjects monitored in this study. In a minority of the patients under study (3 of 12), the drug-dependent viral inhibition was maintained throughout the observation time (213 to 791 days), but in 9 patients a rebound in viremia level was detected during therapy with competitive reverse transcription PCR. Sequencing analysis of a portion of the HIV-1 gene pol from cell-free virions showed that circulating viral variants bearing at least two mutations compatible with azidothymidine or ddI resistance were detectable in the patients who exhibited a rebound in cell-free HIV-1 genomic RNA copy numbers in plasma but not in one patient who maintained (for 455 days) lowered levels of viral load during ddI treatment.