Miracle-dz/UniFAR-FTUs huggingface dataset:
Using noise to probe and characterize gene circuits

Stochastic fluctuations (or “noise”) in the single-cell populations of molecular species are shaped by the structure and biokinetic rates of the underlying gene circuit. The structure of the noise is summarized by its autocorrelation function. In this article, we introduce the noise regulatory vector as a generalized framework for making inferences concerning the structure and biokinetic rates of a gene circuit from its noise autocorrelation function. Although most previous studies have focused primarily on the magnitude component of the noise (given by the zero-lag autocorrelation function), our approach also considers the correlation component, which encodes additional information concerning the circuit. Theoretical analyses and simulations of various gene circuits show that the noise regulatory vector is characteristic of the composition of the circuit. Although a particular noise regulatory vector does not map uniquely to a single underlying circuit, it does suggest possible candidate circuits, while excluding others, thereby demonstrating the probative value of noise in gene circuit analysis.
Solving the Mystery of Dengue in Iran; Are We Close to an Answer?

Today around half of the world’s population live in areas where there is a risk of dengue virus (DENV) infection. It is known that at least 100 countries in Asia, the Pacific, the Americas, Africa, and the Caribbean are endemic for DENV. It is estimated that approximately 400 million infections occur annually, including 2 million severe dengue disease cases and 21,000 deaths. However, no approved antiviral therapies or vaccines are available against DENV (1). There are 4 different serotypes DENV (DENV1-4), all classified within the family Flaviviridae, genus Flavivirus. Although the serotypes have cross reactivity in serological tests they do not produce cross immunity. The main route of virus transmission to humans is the bite of infected Aedes mosquitoes, however, there are other non-vector-borne modes of transmission, which include mothers to fetus transmission, transfusion-related transmission and laboratory mishandle of blood specimen. The incubation period is 5 to 7 days on average but could range from 3 to 12 days. The DENV infection is usually asymptomatic or causes mild dengue fever (DF); nevertheless, it may lead to a life threatening dengue hemorrhagic fever (DHF)
Plasminogen activation and cancer

Summary Breakdown of the extracellular matrix is crucial for cancer invasion and metastasis. It is accomplished by the concerted action of several proteases, including the serine protease plasmin and a number of matrix metalloproteases. The activity of each of these proteases is regulated by an array of activators, inhibitors and cellular receptors. Thus, the generation of plasmin involves the pro-enzyme plasminogen, the urokinase type plasminogen activator uPA and its pro-enzyme pro-uPA, the uPA inhibitor PAI-1, the cell surface uPA receptor uPAR, and the plasmin inhibitor α2-antiplasmin. Furthermore, the regulation of extracellular proteolysis in cancer involves a complex interplay between cancer cells and non-malignant stromal cells in the expression of the molecular components involved. For some types of cancer, this cellular interplay mimics that observed in the tissue of origin during non-neoplastic tissue remodelling processes. We propose that cancer invasion can be considered as uncontrolled tissue remodelling. Inhibition of extracellular proteases is an attractive approach to cancer therapy. Because proteases have many different functions in the normal organism, efficient inhibition will have toxic side effects. In cancer invasion, like in normal tissue remodelling processes, there appears to be a functional overlap between different extracellular proteases. This redundancy means that combinations of protease inhibitors must be used. Such combination therapy, however, is also likely to increase toxicity. Therefore for each type of cancer, a combination of protease inhibitors that is optimised with respect to both maximal therapeutic effect and minimal toxic side effects need to be identified.
Synthesis and stochastic assessment of schedules for lacquer production

The Modest modeling language pairs modeling features from stochastic process algebra and from timed and probabilistic automata with light-weight notations such as exception handling. It is supported by the Motor tool, which facilitates the execution and evaluation of Modest specifications by means of the discrete event simulation engine of the Mobius tool. This paper describes the application of Modest, Motor and Mobius to a highly nontrivial case. We investigate the effect of faulty behavior on a hard real-time scheduling problem from the domain of lacquer production. The scheduling problem is first solved using the timed model-checker Uppaal. The resulting schedules are then embedded in a Modest failure model of the lacquer production line, and analyzed with the discrete event simulator of Mobius. This approach allows one to assess the quality of the schedules with respect to timeliness, utilization of resources, and sensitivity to different assumptions about the reliability of the production line.
Phage Delivery Strategies for Biocontrolling Human, Animal, and Plant Bacterial Infections: State of the Art

This review aims at presenting the main strategies that are currently available for the delivery of bacteriophages to combat bacterial infections in humans, animals, and plants. It can be seen that the main routes for phage delivery are topical, oral, systemic, and airways for humans. In animals, the topical and oral routes are the most used. To combat infections in plant species, spraying the plant’s phyllosphere or drenching the soil are the most commonly used methods. In both phage therapy and biocontrol using phages, very promising results have been obtained so far. However, more experiments are needed to establish forms of treatment and phage doses, among other parameters. Furthermore, in general, there is a lack of specific standards for the use of phages to combat bacterial infections.
Biomechanical analysis of two change-of-direction maneuvers while running.

Many research efforts focus on unidirectional gait. However, few functional activities are exclusively linear: people regularly change directions to evade obstructions. Directional changes have been identified as particularly hazardous, but rarely studied. The purpose of this study was to examine the kinetics of abrupt changes of direction while running. Twelve adult volunteers performed 10 trials each for 45 degrees and 90 degrees change-of-direction conditions. Orthogonal force and moment (torque) records were obtained using a computer-interfaced force platform system. Vertical, braking, and propulsive force and applied torque variables were extracted for statistical analysis. Significant force differences (p < .01) were identified between conditions. Applied torques were highly variable and not significantly different. Functionally, these data suggest that applied forces serve as the principal impetus of directional change.
A Technique for Constructing Developable Surfaces

Paper, sheet metal, and many other materials are approximately unstretchable. The surfaces obtained by bending these materials can be flattened onto a plane without stretching or tearing. More precisely, there exists a transformation that maps the surface onto the plane,after which the length of any curve drawn on the surface remains the same. Such surfaces, when sufficiently regular, are well known to mathematicians as developable surfaces. While developable surfaces have been widely used in engineering, design and manufacture, they have been less popular in computer graphics, despite the fact that their isometric properties make them ideal primitives for texture mapping, some kinds of surface modelling, and computer animation. Unfortunately, their constrained isometric behaviour cuts across common surface formulations. We formulate a new developable surface representation technique suitable for use in interactive computer graphics. The feasibility of our model is demonstrated by applying it to the modelling of a hanging scarf and ribbons and bows. Possible extensions and interesting areas of further research are discussed.
A QoS-Aware Data Reconstruction Strategy for a Data Fault-Tolerant Storage System

Recently, many applications and users rely on cloud storage services, such as Google drive, Dropbox, iCloud and Sky drive, to store private files and system data, and cloud storage services must thus be reliable and secure. To increase reliability, previous studies have proposed a variety of erasure coding algorithms for data fault tolerance for use in storage systems. Although these data fault tolerance mechanisms increase data reliability, implementation also increases storage system costs and energy consumption due to data redundancy. However, to date energy-efficient schemes have only been developed based on a RAID architecture, and none have been implemented using an erasure coding algorithm. To address this issue, this study proposes an energy-aware I/O framework with a quality-of-service (QoS) aware data reconstruction scheduler for erasure coding algorithms, called the EEC-scheme. This approach reduces storage system energy consumption and decreases response times for user requests when the system restores failed disks. A series of experiments show that the proposed scheme can significantly reduce power consumption in storage systems.
Micron-Sized Thiol-Functional Polysilsesquioxane Microspheres with Open and Interconnected Macropores: Preparation, Characterization and Formation Mechanism

Polysilsesquioxane (PSQ) microspheres have shown promise in many fields, but previous studies about porous PSQ microspheres are scarce. Herein, we fabricated novel micron-sized thiol-functional polysilsesquioxane (TMPSQ) microspheres with open and interconnected macropores by combining inverse suspension polymerization with two-step sol–gel and polymerization-induced phase separation processes, without using phase-separation-promoting additives or sacrificial templates. The chemical composition of the TMPSQ microspheres was confirmed using FTIR and Raman spectroscopy. The morphology of the TMPSQ microspheres was characterized using SEM and TEM. TGA was employed to test the thermal stability of the TMPSQ microspheres. Mercury intrusion porosimetry and nitrogen adsorption–desorption tests were performed to investigate the pore structure of the TMPSQ microspheres. The results showed that the TMPSQ microspheres had open and interconnected macropores with a pore size of 839 nm, and the total porosity and intraparticle porosity reached 70.54% and 43.21%, respectively. The mechanism of porous generation was proposed based on the morphological evolution observed using optical microscopy. The macropores were formed through the following four steps: phase separation (spinodal decomposition), coarsening, gelation, and evaporation of the solvent. The macropores can facilitate the rapid mass transfer between the outer and inner spaces of the TMPSQ microspheres. The TMPSQ microspheres are promising in various fields, such as catalyst supports and adsorbents.
Childhood and Adolescent Diabetes

A new comprehensive textbook on childhood and adolescent diabetes has been long overdue and Dr Chris Kelnar and his many coauthors have produced what must approach the definitive text for 1995. The text and clinical appoach is predominantly British with 35 of the 46 chapters written by UK authors. The contributor list is impressive and lengthy, totalling 70 different contributors, 46 UK based and 24 prominent investigators and clinicians from the United States, Australia, Denmark, and Israel. Contributions come not only from scientists and clinicians but also from the ranks ofhighly experienced specialist nurses, dietitians, and those involved in the general welfare of the child with diabetes. Diabetes has for a long time been the Cinderella of paediatric endocrinology, looked upon by the endocrine scientists as too clinically based to be interesting. This book serves to redress the balance and puts paediatric diabetes on a firm scientific base. It achieves a good balance between the hard endocrine 'science' (the deranged metabolism of diabetes, the immunogenetic aetiopathogenesis, and the pharmacology) and the 'art' of diabetes management (the family/child/clinician interaction, the psychology, the practical aspects of care and support). The book is divided into six sessions though each is without a clear subheading. The first covers the basics of energy homoeostasis and important chapters on normal physical and psychological growth and development through childhood and adolescence and their relation and interaction with diabetes. The second section outlines the history and current knowledge of the aetiopathogenesis of diabetes. The third section, which is perhaps the most conventional section, brings to the reader a wealth of clinical knowledge and experience on the management of diabetes from a wide variety of experienced clinical practitioners and contains important sections on eating disorders and other psychological aspects. Clear guidelines on many management aspects are given without being too didactic and allowances made for the debate between various management options. Part four details the interaction of the child with diabetes and its family and surroundings. Parts five and six provide fascinating chapters on current knowledge on screening, prevention, complications and their avoidance, and also new strategies for future treatment and management. The book finishes with two appendices of the St Vincent and ISPAD declarations. It is an essential read for all those involved in childhood diabetes management. With such a large number of contributors, overlap* is inevitable but has been kept to a very acceptable minimum by the editor. The style is impressively uniform, easy to read, and very well referenced. Progress in the immunogenetic aspects of this disease is rapid and inevitably it will date quickly. I trust the authors are already working on the next edition. IAN G JEFFERSON Consultant paediatnician
The Impact of Mobility Models on the Performance of AODV, DSR and LAR Routing Protocols

MANETs are the collection of wireless nodes that can dynamically form a network anytime and anywhere to exchange information without using any pre-existing infrastructure. There are some challenges that make the design of mobile ad hoc network routing protocols a tough task. Firstly, in mobile ad hoc networks, node mobility causes frequent topology changes and network partitions. Secondly, because of the variable and unpredictable capacity of wireless links, packet losses may happen frequently. Moreover, the broadcast nature of wireless medium introduces the hidden terminal and exposed terminal problems. Additionally, mobile nodes have restricted power, computing and bandwidth resources and require effective routing schemes. The highly dynamic nature of MANET coupled with limited bandwidth and battery power imposes severe restrictions on routing protocols especially on achieving the routing stability. Due to all these constraints, designing of a routing protocol is still a challenging task for researchers. In this paper an attempt has been made to evaluate and compare the impact of different mobility models on the performance of three most commonly used on-demands routing protocols named as AODV, DSR and LAR. The performance of these routing protocols has been simulated using QualNet 5.0 simulator.
The Response of Denervated Muscle to Long-Term Electrical Stimulation

Adapted from: Lømo T, Westgaard RH, Hennig R, Gundersen K. The response of denervated muscle to long-term electrical stimulation, In: Carraro U, Angelini C, eds. Proceedings of the First Abano Terme Meeting on Rehabilitation, 1985 August 28-30, Abano Terme, Padova, Italy, An International Symposium, Satellite Meeting of the XIII World Congress of Neurology, Hamburg 1985. Cleup Padova 1985. pp 81–90.
A speed-up theorem for cryptosystems . ( 2000 , unpublished manuscript )

We show that any encryption/decryption system can be converted to an algorithm which uses roughly three machine operations per bit. We prove that our technique yields an encryption/decryption system which is as secure as the original system provided the plaintext has full-entropy. We then show how to remove the full-entropy assumption. Our techniques speed up software implementations of RSA by four orders of magnitude. Alternatively, our techniques can be used as a blueprint for encryption/decryption circuits which are public-key yet are as fast or faster than circuits implementing private-key cryptography.
&bgr;3-Containing Gamma-Aminobutyric AcidA Receptors Are Not Major Targets for the Amnesic and Immobilizing Actions of Isoflurane

Mice bearing an N265M point mutation in the gamma-aminobutyric acid (GABA)A receptor &bgr;3 subunit resist various anesthetic effects of propofol and etomidate. They also require a 16% larger concentration of enflurane and a 21% larger concentration of halothane to abolish the withdrawal reflex than do wild-type mice. Using a Pavlovian test, we measured whether this mutation increased the concentration of isoflurane required to impair learning and memory relative to wild-type mice. We found that the concentration was not significantly increased. We also measured MAC (the minimum alveolar concentration required to eliminate movement in response to noxious stimulation in 50% of subjects). Isoflurane MAC for mutant mice (1.93% ± 0.0.03%; mean ± se; n = 14) was 17.0% larger than MAC for wild-type mice (1.65 ± 0.04; n = 14; P < 0.001). Similarly, the cyclopropane MAC for mutant mice (27.6% ± 0.55%; n = 16) was 13.6% larger than MAC for wild-type mice (24.3 ± 0.46; n = 8; P < 0.01). The increase in MAC for cyclopropane was unexpected, because published reports find only minimal actions at &agr;1&bgr;2&ggr;2 GABAA receptors whereas isoflurane provides a large enhancement. Consistent with previous work on &agr;1&bgr;2&ggr;2 GABAA receptors, we found in Xenopus oocytes that 5 MAC cyclopropane enhanced the effect of GABA on &agr;1&bgr;2&ggr;2 GABAA receptors by only 76%, and by a nearly identical enhancement in &agr;1&bgr;3&ggr;2, and &agr;6&bgr;3&ggr;2 receptors. In contrast, a much smaller concentration of isoflurane (1 MAC) produced a 160% to 310% enhancement in these receptors. If, relative to isoflurane, cyclopropane minimally increases GABA-induced chloride currents at any GABAA receptor subtype, the present data for MAC are consistent with the notion that GABAA receptors do not mediate the immobility produced by inhaled anesthetics.
Link Analysis of Higher-Order Paths in Supervised Learning Datasets

Due to recent concerns with security and terrorism there has been an increasing focus on techniques that discover links and relations in data. Several efforts that employ “data mining” techniques have contributed to this field, but few focus on discovering patterns in sets of higher-order links, which can reveal hidden or indirect relationships in data. In this work we focus on the discovery and analysis of higher-order path patterns in a supervised learning dataset. We first analyze higher-order links in the leaf nodes of a decision tree and find evidence for distinguishing between nodes of different classes. Based on these results we next focus on the training data itself used to build the tree. Our results indicate that classes of instances in labeled training data may be separable based on the characteristics of higher-order paths. This technique has potential applications in cybersecurity and cyberforensics, as well as text mining and analytics.
Design and Implementation of Portable Outdoor Air Quality Measurement System using Arduino

Recently, there is increasing public awareness of the real time air quality due to air pollution can cause severe effects to human health and environments. The Air Pollutant Index (API) in Malaysia is measured by Department of Environment (DOE) using stationary and expensive monitoring station called Continuous Air Quality Monitoring stations (CAQMs) that are only placed in areas that have high population densities and high industrial activities. Moreover, Malaysia did not include particulate matter with the size of less than 2. 5μm (PM2.5) in the API measurement system. In this paper, we present a cost effective and portable air quality measurement system using Arduino Uno microcontroller and four low cost sensors. This device allows people to measure API in any place they want. It is capable to measure the concentration of carbon monoxide (CO), ground level ozone (O3) and particulate matters (PM10 & PM2.5) in the air and convert the readings to API value. This system has been tested by comparing the API measured from this device to the current API measured by DOE at several locations. Based on the results from the experiment, this air quality measurement system is proved to be reliable and efficient.
Draft Genome Sequence of Flavobacterium succinicans Strain DD5b

ABSTRACT We present the first 3.315-Mbp assembled draft genome sequence of Flavobacterium succinicans strain DD5b. This bacterium is a phosphite-assimilating representative of the genus Flavobacterium isolated from guts of the zooplankton Daphnia magna.
Outage Performance of Cognitive Relay Networks With Wireless Information and Power Transfer

In this paper, we consider underlay cognitive radio (CR) networks with one primary receiver, one cognitive transmitter-receiver pair, and one energy harvesting relay. The transmission power of the secondary source is opportunistically determined by its interference to the primary receiver, and the relay transmission is powered by the energy harvested from the radio-frequency observations at the relay. For the considered CR networks with simultaneous wireless information and power transfer (SWIPT), we derive analytical expressions for the outage probability, as well as their high signal-to-noise ratio (SNR) approximations in closed form. The developed analytical results demonstrate that the use of SWIPT will not cause any loss in diversity gain, but the outage probability achieved by the SWIPT-CR scheme asymptotically decays as log SNR/SNR, whereas a decaying rate of 1/SNR is achieved by a conventional CR network. Computer simulation results are also provided to demonstrate the accuracy of the presented analysis.
Abundance of Selected Lipopolysaccharide-Rich Bacteria and Levels of Toll-like Receptor 4 and Interleukin 8 Expression Are Significantly Associated with Live Attenuated Rotavirus Vaccine Shedding among South African Infants

Bacterial lipopolysaccharides (LPSs) have been shown to promote enteric viral infections. This study tested the hypothesis that elevated levels of bacterial LPS improve oral rotavirus vaccine replication in South African infants. Stool samples were collected from infants a week after rotavirus vaccination to identify vaccine virus shedders (n = 43) and non-shedders (n = 35). Quantitative real-time PCR was used to assay for selected LPS-rich bacteria, including Serratia marcescens, Pseudomonas aeruguinosa and Klebsiella pneumonia, and to measure the gene expression of bacterial LPS, host Toll-like Receptor 4 (TLR4) and Interleukin-8 (IL-8). The abundance of selected LPS-rich bacteria was significantly higher in vaccine shedders (median log 4.89 CFU/g, IQR 2.84) compared to non-shedders (median log 3.13 CFU/g, IQR 2.74), p = 0.006. The TLR4 and IL-8 gene expressions were increased four- and two-fold, respectively, in vaccine shedders versus non-shedders, but no difference was observed in the bacterial LPS expression, p = 0.09. A regression analysis indicated a significant association between the abundance of selected LPS-rich bacteria and vaccine virus shedding (Odds ratio 1.5, 95% CI = 1.10–1.89), p = 0.002. The findings suggest that harbouring higher counts of LPS-rich bacteria can increase the oral rotavirus vaccine take in infants.