Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and Physical Interactions Between Yeast RGRl and SZN4 in Chromatin Organization and Transcriptional Regulation

The SIN4 and RGRl genes of Saccharomyces cerevisiae were identified by mutations in quite different genetic screens. We have shown that the SIN4 gene product is required for proper transcriptional regulation of many genes and that a sin4 mutation can affect either activation or repression of specific genes. We have suggested that this dual nature of SIN4 in transcriptional regulation is due to its involvement in chromatin organization. We now report that the role of RGRl in gene regulation is similar to that of SIN4. SIN4 and RGRl both function as negative transcriptional regulators of HO and IMEl, and mutations in either gene lead to decreased expression of other genes including CTSl. Strains with sin4 or rgrl mutations both have phenotypes similar to those caused by histone mutations, including suppression of 6 insertion into promoters (Spt- phenotype), activation of promoters lacking UAS elements, and decreased superhelical density of plasmid DNA molecules. Overexpression of RGRl suppresses the temperature sensitivity due to a sin4 mutation. Finally, we use yeast strains expressing GST fusion proteins to demonstrate that the Sin4p and Rgrlp proteins are physically associated in vivo. These results indicate that Sin4p and Rgrlp act together in vivo to organize chromatin structure and thus regulate transcription.
Traffic Engineering Enhancement by Progressive Migration to SDN

Software-defined networking (SDN) provides an unprecedented opportunity to enhance the traffic engineering in IP networks. This emerges from the fine-grained centralized control over routing, which enables an immediate response to network dynamics. However, due to the high operational and performance costs of the migration, network operators prefer a multi-period planning approach for the deployment of SDN-enabled devices. In this letter, we present and evaluate an efficient algorithm to seek a beneficial upgrade policy for a network considering the budget constraints. Our proposed algorithm outperforms the most recent work, particularly for large-scale topologies and an increased number of time periods.
SNR Estimation Based on Metric Normalization Frequency in Viterbi Decoder

Signal-to-noise (SNR) estimation plays an important role in modern wireless communication systems because an accurate SNR value can aid the improvement of transmission performance in various aspects. In this letter, we propose a estimation method of noise variance based on the normalization frequency of path metric in Viterbi decoder, and the channel gains are evaluated by the least squares estimation and the energy estimator. Then, we derive the SNR from the ratio of the estimated channel gain to the estimated noise variance. The simulation results show that the proposed algorithm can estimate SNR more accurately than previously published SNR estimators.
Participatory Disease Surveillance and Response in Indonesia: Strengthening Veterinary Services and Empowering Communities to Prevent and Control Highly Pathogenic Avian Influenza

Abstract The participatory disease surveillance and response (PDSR) approach to highly pathogenic avian influenza (HPAI) in Indonesia has evolved significantly from the participatory disease surveillance (PDS) system developed for rinderpest eradication in Africa and Pakistan. The first phase of the PDSR project emphasized the detection and control of HPAI by separate PDS and participatory disease response teams primarily in sector 4 poultry at the household level. Lessons learned during the first phase were taken into account in the design of the second phase of the project, which has sought to further strengthen management of disease prevention and control activities by improving technical approaches, increasing active participation of key stakeholders, including local and central governments, and focusing on the village level. The ongoing evolution of the PDSR program aims to establish a sustainable community-based program within provincial and district livestock services that enhances the prevention and control of not only HPAI, but also other zoonotic and priority animal diseases.
Modulated expression of human peripheral blood microRNAs from infancy to adulthood and its role in aging

Accumulating evidence suggests a role for microRNAs (miRNAs) in regulating various processes of mammalian postnatal development and aging. To investigate the changes in blood‐based miRNA expression from preterm infants to adulthood, we compared 365 miRNA expression profiles in a screening set of preterm infants and adults. Approximately one‐third of the miRNAs were constantly expressed from postnatal development to adulthood, another one‐third were differentially expressed between preterm infants and adults, and the remaining one‐third were not detectable in these two groups. Based on their expression in infants and adults, the miRNAs were categorized into five classes, and six of the seven miRNAs chosen from each class except one with age‐constant expression were confirmed in a validation set containing infants, children, and adults. Comparing the chromosomal locations of the different miRNA classes revealed two hot spots: the miRNA cluster on 14q32.31 exhibited age‐constant expression, and the one on 9q22.21 exhibited up‐regulation in adults. Furthermore, six miRNAs detectable in adults were down‐regulated in older adults, and four chosen for individual quantification were verified in the validation set. Analysis of the network functions revealed that differentially regulated miRNAs between infants and adults and miRNAs that decreased during aging shared two network functions: inflammatory disease and inflammatory response. Four expression patterns existed in the 11 miRNAs from infancy to adulthood, with a significant transition in ages 9–20 years. Our results provide an overview on the regulation pattern of blood miRNAs throughout life and the possible biological functions performed by different classes of miRNAs.
Physical activity and resting metabolic rate

The direct effects of physical activity interventions on energy expenditure are relatively small when placed in the context of total daily energy demands. Hence, the suggestion has been made that exercise produces energetic benefits in other components of the daily energy budget, thus generating a net effect on energy balance much greater than the direct energy cost of the exercise alone. Resting metabolic rate (RMR) is the largest component of the daily energy budget in most human societies and, therefore, any increases in RMR in response to exercise interventions are potentially of great importance. Animal studies have generally shown that single exercise events and longer-term training produce increases in RMR. This effect is observed in longer-term interventions despite parallel decreases in body mass and fat mass. Flight is an exception, as both single flights and long-term flight training induce reductions in RMR. Studies in animals that measure the effect of voluntary exercise regimens on RMR are less commonly performed and do not show the same response as that to forced exercise. In particular, they indicate that exercise does not induce elevations in RMR. Many studies of human subjects indicate a short-term elevation in RMR in response to single exercise events (generally termed the excess post-exercise O2 consumption; EPOC). This EPOC appears to have two phases, one lasting 2 h and a smaller much more prolonged effect lasting up to 48 h. Many studies have shown that long-term training increases RMR, but many other studies have failed to find such effects. Data concerning long-term effects of training are potentially confounded by some studies not leaving sufficient time after the last exercise bout for the termination of the long-term EPOC. Long-term effects of training include increases in RMR due to increases in lean muscle mass. Extreme interventions, however, may induce reductions in RMR, in spite of the increased lean tissue mass, similar to the changes observed in animals in response to flight.
SANTaClass: A Self Adaptive Network Traffic Classification system

A critical aspect of network management from an operator's perspective is the ability to understand or classify all traffic that traverses the network. The failure of port based traffic classification technique triggered an interest in discovering signatures based on packet content. However, this approach involves manually reverse engineering all the applications/protocols that need to be identified. This suffers from the problem of scalability; keeping up with the new applications that come up everyday is very challenging and time-consuming. Moreover, traditional approach of developing signatures once and using them in different networks suffers from low coverage. In this work, we present a novel fully automated packet payload content (PPC) based network traffic classification system that addresses the above shortcomings. Our system learns new application signatures in the network where classification is desired. Further more, our system adapts the signatures as the traffic for an application changes. Based on real traces from several service providers, we show that our system is capable of detecting (1) tunneled or wrapped applications, (2) applications that use random ports, and (3) new applications. Moreover, it is robust to routing asymmetry, an important requirement in large ISPs, and has a very high (>99.5%) detection rate. Finally, our system is easy to deploy and setup and performs classification in real-time.
Axiom A polynomial skew products of ℂ2 and their postcritical sets

Abstract A polynomial skew product of ℂ2 is a map of the form f(z,w)=(p(z),q(z,w)), where p and q are polynomials, such that f extends holomorphically to an endomorphism of ℙ2 of degree at least two. For polynomial maps of ℂ, hyperbolicity is equivalent to the condition that the closure of the postcritical set is disjoint from the Julia set; further, critical points either iterate to an attracting cycle or infinity. For polynomial skew products, Jonsson [Dynamics of polynomial skew products on C2. Math. Ann. 314(3) (1999), 403–447] established that f is Axiom A if and only if the closure of the postcritical set is disjoint from the right analog of the Julia set. Here we present an analogous conclusion: critical orbits either escape to infinity or accumulate on an attracting set. In addition, we construct new examples of Axiom A maps demonstrating various postcritical behaviors.
A Compositional Modelling Approach for Large Sensor Networks Design

Sensor Networks are required to be properly designed in order to avoid resource waste and optimize their lifetime. Large monitoring applications require proper methodologies and tools supporting the design, when multiple solutions increase the complexity of this task. Indeed, different parameters affect the performance of a solution, as node distribution, sensing coverage, battery usage, etc. A compositional modelling approach can provide early measures, allowing to evaluate and compare different solutions since the design phase. The main contribution of the paper is the definition of a general modelling framework to integrate simple models representing the main components and features of sensor networks. A library for specific sensor devices have been developed, using the Stochastic Activity Network (SAN) formalism. This approach is shown to be compositional since the creation of complex networks can be accomplished by simple subcomponents aggregation. With this approach, obtained models can analyse the dynamic evolution of the overall network, even if complex. First experimental results are also reported and discussed.
Mammalian cellular culture models of Trypanosoma cruzi infection: a review of the published literature

Cellular culture infection with Trypanosoma cruzi is a tool used to dissect the biological mechanisms behind Chagas disease as well as to screen potential trypanocidal compounds. Data on these models are highly heterogeneous, which represents a challenge when attempting to compare different studies. The purpose of this review is to provide an overview of the cell culture infectivity assays performed to date. Scientific journal databases were searched for articles in which cultured cells were infected with any Trypanosoma cruzi strain or isolate regardless of the study’s goal. From these articles the cell type, parasite genotype, culture conditions and infectivity results were extracted. This review represents an initial step toward the unification of infectivity model data. Important differences were detected when comparing the pathophysiology of Chagas disease with the experimental conditions used in the analyzed studies. While Trypanosoma cruzi preferentially infects stromal cells in vivo, most of the assays employ epithelial cell lines. Furthermore, the most commonly used parasite strain (Tulahuen-TcVI) is associated with chagasic cardiomyopathy only in the Southern Cone of South America. Suggestions to overcome these discrepancies include the use of stromal cell lines and parasite genotypes associated with the known characteristics of the natural history of Chagas disease.
An Algebraic Graphical Model for Decision with Uncertainties, Feasibilities, and Utilities

Numerous formalisms and dedicated algorithms have been designed in the last decades to model and solve decision making problems. Some formalisms, such as constraint networks, can express "simple" decision problems, while others are designed to take into account uncertainties, unfeasible decisions, and utilities. Even in a single formalism, several variants are often proposed to model different types of uncertainty (probability, possibility.) or utility (additive or not). In this article, we introduce an algebraic graphical model that encompasses a large number of such formalisms: (1) we first adapt previous structures from Friedman, Chu and Halpern for representing uncertainty, utility, and expected utility in order to deal with generic forms of sequential decision making; (2) on these structures, we then introduce composite graphical models that express information via variables linked by "local" functions, thanks to conditional independence; (3) on these graphical models, we finally define a simple class of queries which can represent various scenarios in terms of observabilities and controllabilities. A natural decision-tree semantics for such queries is completed by an equivalent operational semantics, which induces generic algorithms. The proposed framework, called the Plausibility-Feasibility-Utility (PFU) framework, not only provides a better understanding of the links between existing formalisms, but it also covers yet unpublished frameworks (such as possibilistic influence diagrams) and unifies formalisms such as quantified boolean formulas and influence diagrams. Our backtrack and variable elimination generic algorithms are a first step towards unified algorithms.
Insulin regulates the expression of several metabolism-related genes in the liver and primary hepatocytes of rainbow trout (Oncorhynchus mykiss)

SUMMARY Rainbow trout have a limited ability to use dietary carbohydrates efficiently and are considered to be glucose intolerant. Administration of carbohydrates results in persistent hyperglycemia and impairs post-prandial down regulation of gluconeogenesis despite normal insulin secretion. Since gluconeogenic genes are mainly under insulin control, we put forward the hypothesis that the transcriptional function of insulin as a whole may be impaired in the trout liver. In order to test this hypothesis, we performed intraperitoneal administration of bovine insulin to fasted rainbow trout and also subjected rainbow trout primary hepatocytes to insulin and/or glucose stimulation. We demonstrate that insulin was able to activate Akt, a key element in the insulin signaling pathway, and to regulate hepatic metabolism-related target genes both in vivo and in vitro. In the same way as in mammals, insulin decreased mRNA expression of gluconeogenic genes, including glucose 6-phosphatase (G6Pase), fructose 1,6-bisphosphatase (FBPase) and phosphoenolpyruvate carboxykinase (PEPCK). Insulin also limited the expression of carnitine palmitoyltransferase 1 (CPT1), a limiting enzyme of fatty acid β-oxidation. In vitro studies revealed that, as in mammals, glucose is an important regulator of some insulin target genes such as the glycolytic enzyme pyruvate kinase (PK) and the lipogenic enzyme fatty acid synthase (FAS). Interestingly, glucose also stimulates expression of glucokinase (GK), which has no equivalent in mammals. This study demonstrates that insulin possesses the intrinsic ability to regulate hepatic gene expression in rainbow trout, suggesting that other hormonal or metabolic factors may counteract some of the post-prandial actions of insulin.
1.52-GHz micromechanical extensional wine-glass mode ring resonators

Vibrating polysilicon micromechanical ring resonators, using a unique extensional wine-glass-mode shape to achieve lower impedance than previous UHF resonators, have been demonstrated at frequencies as high as 1.2 GHz with a Q of 3,700, and 1.52 GHz with a Q of 2,800. The 1.2-GHz resonator exhibits a measured motional resistance of 1 MOmega with a dc-bias voltage of 20 V, which is 2.2 times lower than the resistance measured on radial contour- mode disk counterparts at the same frequency. The use of larger rings offers a path toward even lower impedance, provided the spurious modes that become more troublesome as ring size increases can be properly suppressed using methods described herein. With spurious modes suppressed, the high-Q and low-impedance advantages, together with the multiple frequency on-chip integration advantages afforded by capacitively transduced mumechanical resonators, make this device an attractive candidate for use in the front-end RF filtering and frequency generation functions needed by wireless communication devices.
Generation in Awake and Sleeping Cat Cortex Inhibition Determines Membrane Potential Dynamics and Controls Action

[PDF] [Full Text] [Abstract] , June 1, 2006; 21 (3): 197-207. Physiology J.-M. Goaillard and E. Marder Dynamic Clamp Analyses of Cardiac, Endocrine, and Neural Function [PDF] [Full Text] [Abstract] , November 22, 2006; 26 (47): 12206-12218. J. Neurosci. M. R. DeWeese and A. M. Zador Auditory Cortex. Non-Gaussian Membrane Potential Dynamics Imply Sparse, Synchronous Activity in [PDF] [Full Text] [Abstract] , January 1, 2007; 97 (1): 159-177. J Neurophysiol S. P. Peron, H. G. Krapp and F. Gabbiani Properties of a Collision-Detecting Neuron Influence of Electrotonic Structure and Synaptic Mapping on the Receptive Field [PDF] [Full Text] [Abstract] , March 1, 2007; 97 (3): 2544-2552. J Neurophysiol M. Pospischil, Z. Piwkowska, M. Rudolph, T. Bal and A. Destexhe Potential Calculating Event-Triggered Average Synaptic Conductances From the Membrane [PDF] [Full Text] [Abstract] , May 16, 2007; 27 (20): 5280-5290. J. Neurosci. M. Rudolph, M. Pospischil, I. Timofeev and A. Destexhe Generation in Awake and Sleeping Cat Cortex Inhibition Determines Membrane Potential Dynamics and Controls Action Potential
Transposon Insertions of magellan-4 That Impair Social Gliding Motility in Myxococcus xanthus

Myxococcus xanthus has two different mechanisms of motility, adventurous (A) motility, which permits individual cells to glide over solid surfaces, and social (S) motility, which permits groups of cells to glide. To identify the genes involved in S-gliding motility, we mutagenized a ΔaglU (A−) strain with the defective transposon, magellan-4, and screened for S− mutants that form nonmotile colonies. Sequence analysis of the sites of the magellan-4 insertions in these mutants and the alignment of these sites with the M. xanthus genome sequence show that two-thirds of these insertions lie within 27 of the 37 nonessential genes known to be required for social motility, including those necessary for the biogenesis of type IV pili, exopolysaccharide, and lipopolysaccharide. The remaining insertions also identify 31 new, nonessential genes predicted to encode both structural and regulatory determinants of S motility. These include three tetratricopeptide repeat proteins, several regulators of transcription that may control the expression of genes involved in pilus extension and retraction, and additional enzymes involved in polysaccharide metabolism. Three insertions that abolish S motility lie within genes predicted to encode glycolytic enzymes, suggesting that the signal for pilus retraction may be a simple product of exopolysaccharide catabolism.
KCNE1 and KCNE3 Stabilize and/or Slow Voltage Sensing S4 Segment of KCNQ1 Channel

KCNQ1 is a voltage-dependent K+ channel whose gating properties are dramatically altered by association with auxiliary KCNE proteins. For example, KCNE1, which is mainly expressed in heart and inner ear, markedly slows the activation kinetics of KCNQ1. Whether the voltage-sensing S4 segment moves differently in the presence of KCNE1 is not yet known, however. To address that question, we systematically introduced cysteine mutations, one at a time, into the first half of the S4 segment of human KCNQ1. A226C was found out as the most suited mutant for a methanethiosulfonate (MTS) accessibility analysis because it is located at the N-terminal end of S4 segment and its current was stable with repetitive stimuli in the absence of MTS reagent. MTS accessibility analysis revealed that the apparent second order rate constant for modification of the A226C mutant was state dependent, with faster modification during depolarization, and was 13 times slower in the presence of KCNE1 than in its absence. In the presence of KCNE3, on the other hand, the second order rate constant for modification was not state dependent, indicating that the C226 residue was always exposed to the extracellular milieu, even at the resting membrane potential. Taken together, these results suggest that KCNE1 stabilizes the S4 segment in the resting state and slows the rate of transition to the active state, while KCNE3 stabilizes the S4 segment in the active state. These results offer new insight into the mechanism of KCNQ1 channel modulation by KCNE1 and KCNE3.