Miracle-dz/UniFAR-FTUs huggingface dataset:
Listeria monocytogenes Flagella Are Used for Motility, Not as Adhesins, To Increase Host Cell Invasion

ABSTRACT Flagellar structures contribute to the virulence of multiple gastrointestinal pathogens either as the effectors of motility, as adhesins, or as a secretion apparatus for virulence factors. Listeria monocytogenes is a food-borne, gram-positive pathogen that uses flagella to increase the efficiency of epithelial cell invasion (A. Bigot, H. Pagniez, E. Botton, C. Frehel, I. Dubail, C. Jacquet, A. Charbit, and C. Raynaud, Infect. Immun. 73:5530-5539, 2005; L. Dons, E. Eriksson, Y. Jin, M. E. Rottenberg, K. Kristensson, C. N. Larsen, J. Bresciani, and J. E. Olsen, Infect. Immun. 72:3237-3244, 2004). In this study, we aimed to elucidate the mechanism by which flagella contribute to L. monocytogenes invasion. To examine the role of flagella as adhesins, invasion and adhesion assays were performed with flagellated motile and nonmotile bacteria and nonflagellated bacteria. We observed that flagellated but nonmotile bacteria do not adhere to or invade human epithelial cells more efficiently than nonflagellated bacteria. These results indicated that flagella do not function as adhesins to enhance the adhesion of L. monocytogenes to targeted host cells. Instead, it appears that motility is important for tissue culture invasion. Furthermore, we tested whether motility contributes to early colonization of the gastrointestinal tract using a competitive index assay in which mice were infected orally with motile and nonmotile bacteria in a 1:1 ratio. Differential bacterial counts demonstrated that motile bacteria outcompete nonmotile bacteria in the colonization of the intestines at early time points postinfection. This difference is also reflected in invasion of the liver 12 h later, suggesting that flagellum-mediated motility enhances L. monocytogenes infectivity soon after bacterial ingestion in vivo.
DETERMINANTS OF INFLATION IN PAKISTAN: AN ECONOMETRIC ANALYSIS USING JOHANSEN CO-INTEGRATION APPROACH

Inflation is regarded as regressive taxation against the poor. The most visible impact of inflation in recent times is its effect on real output, relative prices, taxes and interest rates. The study focuses to examine demand side and supply side determinants of inflation in Pakistan on economic and econometric criterion and also to investigate causal relationships among some macroeconomic variables. For that purpose, study has undertaken time series data for the period from 1972 to 2010. Long run and short run estimates have been investigated using Johansen Co-integration and Vector Error Correction approached. Causal relationships have been observed using Granger causality test. Data on macroeconomic variables have been selected from Handbook on Statistics of Pakistan 2010. The findings of the study reveal that in the long run consumer price index has found to be positively influenced by money supply, gross domestic product, imports and government expenditures on the other side government revenue is reducing overall price level in Pakistan. Long run elasticities of Price level with respect to money supply, gross domestic product, government expenditures, government revenue and imports are 0.61, 0.73, 0.32, -1.37 and 0.41 respectively. In the short run, last year consumer price index and two years before government revenue are directly involved in enhancing consumer price index of current year. Improvement in gross domestic product and government expenditures is necessary but it is suggested that there should be optimal level for all of them so that price level should be stable.
Assessing Water Quality with Submersed Aquatic Vegetation Habitat requirements as barometers of Chesapeake Bay health

Worldwide, estuaries are experiencing water quality problems as a result of human population growth in coastal areas. Chesapeake Bay, one of the world's largest estuaries, has experienced deterioration of water quality from nutrient enrichment, sediment inputs, and high levels of contaminants, resulting in anoxic or hypoxic conditions and declines in living resources (Horton and Eichbaum 1991). A mechanism for relating anthropogenic inputs to the health of Chesapeake Bay is through determination of relationships among water quality and various living resources. In particular, the establishment of habitat requirements and restoration goals for critical species living in Chesapeake Bay is a way in which scientists, resource managers, politicians and the
On Active Networking and Congestion Samrat Bhattacharjee

Active networking o ers a change in the usual network paradigm: from passive carrier of bits to a more general computation engine. The implementation of such a change is likely to enable radical new applications that cannot be foreseen today. Large-scale deployment, however, involves signi cant challenges in interoperability and security. Less clear, perhaps, are the \immediate" bene ts of such a paradigm shift, and how they might be used to justify migration towards active networking. In this paper, we focus on the bene ts of active networking with respect to a problem that is unlikely to disappear in the near future: network congestion. In particular, we consider application-speci c processing of user data within the network at congested nodes. Given an architecture in which applications can specify intra-network processing, the bandwidth allocated to each application's packets can be reduced in a manner that is tailored to the application, rather than being applied generically. We consider a range of schemes for processing application data during congestion, including \unit" level dropping (a generalization of packet dropping), media transformation, and multi-stream interaction. We also present some architectural considerations for a simple approach, in which packets are labeled to indicate permitted manipulations. Our results suggest that congestion control makes a good case for active networking, enabling schemes that are not possible within the conventional view of the network. College of Computing Georgia Institute of Technology Atlanta, Georgia 30332{0280
A High Fraction of Mergers in the cluster MS1054-03 at z=0.83

We used the Hubble Space Telescope to take a wide field, multicolor image of the high redshift cluster MS1054-03 at z=0.83. The Keck telescope was used to take 200 redshifts in the field. We have a total of 81 spectroscopically confirmed cluster members with deep WFPC2 imaging. A surprisingly large number of these cluster members are mergers: 13 out of 77 galaxies are classified as merger remnants, or mergers in progress. Most of these are red, and massive. Their restframe B luminosities are amongst the brightest in the cluster: we find that 5 out of the brightest 16 are mergers. No such bright mergers were found in a lower redshift cluster with similar wide field coverage. The mergers in MS1054-03 are preferentially found in the outskirts of the cluster. The distribution of pairs in the outskirts of the cluster shows an excess of galaxies with separation < 10 h^-1 kpc, which is independent confirmation of the enhanced interaction rate. The fraction of mergers (17 %) is comparable to the fraction of ellipticals (22 %). Hence up to 50 % of low redshift ellipticals may have formed through mergers since z=1. There is no evidence for strong star formation in most of the mergers. The mean stellar ages of the mergers may therefore be much older than the ``assembly age'', i.e., the age since the time the system was put together. These new results are qualitatively consistent with predictions from hierarchical galaxy formation, and are inconsistent with an early collapse for all early type galaxies.
Prohibitin 2 Regulates the Proliferation and Lineage-Specific Differentiation of Mouse Embryonic Stem Cells in Mitochondria

Background The pluripotent state of embryonic stem (ES) cells is controlled by a network of specific transcription factors. Recent studies also suggested the significant contribution of mitochondria on the regulation of pluripotent stem cells. However, the molecules involved in these regulations are still unknown. Methodology/Principal Findings In this study, we found that prohibitin 2 (PHB2), a pleiotrophic factor mainly localized in mitochondria, is a crucial regulatory factor for the homeostasis and differentiation of ES cells. PHB2 was highly expressed in undifferentiated mouse ES cells, and the expression was decreased during the differentiation of ES cells. Knockdown of PHB2 induced significant apoptosis in pluripotent ES cells, whereas enhanced expression of PHB2 contributed to the proliferation of ES cells. However, enhanced expression of PHB2 strongly inhibited ES cell differentiation into neuronal and endodermal cells. Interestingly, only PHB2 with intact mitochondrial targeting signal showed these specific effects on ES cells. Moreover, overexpression of PHB2 enhanced the processing of a dynamin-like GTPase (OPA1) that regulates mitochondrial fusion and cristae remodeling, which could induce partial dysfunction of mitochondria. Conclusions/Significance Our results suggest that PHB2 is a crucial mitochondrial regulator for homeostasis and lineage-specific differentiation of ES cells.
Analytical modeling and evaluation of network-on-chip architectures

Network-on-chip (NoC) architectures adopted for System-on-Chip (SoC) are characterized by different trade-offs between latency, throughput, communication load, energy consumption, and silicon area requirements. Evaluating NoC architectures is usually performed using simulations which provide little insight on how different design parameters affect the actual NoC performance metrics. Analytical models that allow rapid trade-off investigations of NoC parameters and accelerate the estimation of main metrics are required. In this paper, a Network Calculus-based methodology is presented to analyze and evaluate the performance metrics such as the latency and the cost metrics such as the energy consumption of NoC-based architectures. The WK-recursive on-chip interconnect is analyzed and results are compared against those produced using simulations. The values obtained by simulations and by analysis show the same increasing/decreasing trends in the same order of magnitude.
An interactive VLSI CAD tool for yield estimation

The yield of a VLSI chip depends on the sensitivity of the chip to defects occurring during the fabrication process, among other factors. To predict this sensitivity, one usually needs to compute the so-called critical area (A/sub c/), which reflects how many and how large the defects must be in order to result in a circuit failure. The main computational problem in yield estimation is to calculate A/sub c/ efficiently for complicated, irregular layouts. A novel approach is suggested for this problem that results in an algorithm that will solve it efficiently. This paper provides an interactive, accurate, and fast method for the evaluation of critical area as a design tool; the tool utilizes good visual feedback to allow layout improvement for higher yield. The algorithm is compared to other yield-prediction methods, which use either the Monte Carlo approach (VLASIC) or a deterministic approach (SCA); the algorithm is shown to be faster. It also has the advantage that it can graphically show a detailed 'defect sensitivity map' that can assist a chip designer in improving the yield of his/her layout. >
The lookahead in a user-transparent conservative parallel simulator

One of the difficulties inherent to conservative parallel discrete event simulation (PDES) is the need for extraction and explicit specification of the lookahead. In this paper we propose a simulator design which allows users to build simulation models with lookahead transparently. This is based on the cooperation between PDES experts and the users, and on the reusability of model components. We introduce the principal design of the simulator and give the results related to its lookahead.
Experimental Investigation of Flow Condensation in Microgravity

Future manned missions to Mars are expected to greatly increase the space vehicle’s size, weight, and heat dissipation requirements. An effective means to reducing both size and weight is to replace single-phase thermal management systems with two-phase counterparts that capitalize upon both latent and sensible heat of the coolant rather than sensible heat alone. This shift is expected to yield orders of magnitude enhancements in flow boiling and condensation heat transfer coefficients. A major challenge to this shift is a lack of reliable tools for accurate prediction of two-phase pressure drop and heat transfer coefficient in reduced gravity. Developing such tools will require a sophisticated experimental facility to enable investigators to perform both flow boiling and condensation experiments in microgravity in pursuit of reliable databases. This study will discuss the development of the Flow Boiling and Condensation Experiment (FBCE) for the International Space Station (ISS), which was initiated in 2012 in collaboration between Purdue University and NASA Glenn Research Center. This facility was recently tested in parabolic flight to acquire condensation data for FC-72 in microgravity, aided by high-speed video analysis of interfacial structure of the condensation film. The condensation is achieved by rejecting heat to a counter flow of water, and experiments were performed at different mass velocities of FC-72 and water and different FC-72 inlet qualities. It is shown that the film flow varies from smooth-laminar to wavy-laminar and ultimately turbulent with increasing FC-72 mass velocity. The heat transfer coefficient is highest near the inlet of the condensation tube, where the film is thinnest, and decreases monotonically along the tube, except for high FC-72 mass velocities, where the heat transfer coefficient is enhanced downstream. This enhancement is attributed to both turbulence and increased interfacial waviness. One-ge correlations are shown to predict the average condensation heat transfer coefficient with varying degrees of success, and a recent correlation is identified for its superior predictive capability, evidenced by a mean absolute error of 21.7%. Copyright © 2013 by ASME
Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc. , 126, 16 405–16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc. , in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93–102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.
Is there service in computing service learning?

A variety of researchers have advocated for service learning projects in post-secondary computing programs. While these projects can achieve important disciplinary outcomes for the students, what has been under examined is the benefit that these projects have for the service recipients and their community. This paper argues that since service learning projects are meant to benefit both student donors and community recipients, we must examine much more carefully how computing service projects interact with all the social actors affected by the projects. Taking such an approach will require recognizing that ICT by itself will not improve or increase democracy, equality, social inclusion, or any other social good. Analogous to the experience of foreign aid recipients in the developing world, some service learning projects may actually do more harm than good. The paper concludes by providing some sample computer learning projects that are oriented more strongly towards achieving true service for the recipients.
School Meals: A Nutritional and Environmental Perspective

In light of the rise in childhood obesity rates and the influence of the food system on fossil fuel use, this article analyzes current school meals in Baltimore and makes suggestions for school meal reform based on both childhood nutrition and environmental resource use. The nutrient content and estimated energy costs of a typical school lunch are compared with a proposed alternate meal. The study indicates that healthier meals can significantly limit fossil fuel energy inputs for harvesting, production, processing, packaging, and transportation. The authors also provide strategies for developing menus that are both more nutritious and more energy efficient.
An Improved Model for Live Migration in Data Centre Simulators

Due to the difficulty of employing real data centres' infrastructure for assessing the effectiveness of energy-aware algorithms, many researchers resort to use simulation tools. These tools require precise and detailed models for virtualized data centres in order to deliver accurate results. In recent years, many models have been proposed, but most of them either do not consider energy consumption related to virtual machine (VM) migration or do not investigate some of the energy impacting components (e.g. CPU, network, storage). We propose a new model for data centre energy consumption that takes into account the previously omitted components and provides more accurate energy consumption predictions compared to other state-of-the-art solutions. We evaluate our model's accuracy in a comprehensive set of scenarios implemented in the combined GroudSim/DISSECT-CF simulator. With the use of these scenarios, we present a comparative analysis of our model with a similar state-of-the-art simulator. Our analysis revealed a significant improvement in accuracy (up to 42.5%) in the modelled energy consumption compared to a similar state-of-the-art simulator.
Long-Wavelength Approximation Theory of Light Reflection from Nanoscale Anisotropic Layered Media

The reflection of linearly polarized light from an N-layer system of anisotropic nanometer-size insulating films is investigated in the long-wavelength limit. The approximate expressions for the reflection characteristics of s- and ppolarized light for multilayer systems of anisotropic films are derived. All analytical results are supported by computer-aided analysis made on the basis of general wave propagation theory for anisotropic layered media. It is show that the accuracy of the long-wavelength approximation for nanoscopic anisotropic layered systems is quite satisfactory: if the thickness of a multilayer divided by the wavelength comprises only a few hundredths, then the error of approximate expressions will be of the order of several percent. The most useful feature of obtained formulas is that they are simply invertible, allowing a direct calculation of the parameters of nanoscale layers.
Interaction between Flavivirus and Cytoskeleton during Virus Replication

Flaviviruses are potentially human pathogens that cause major epidemics worldwide. Flavivirus interacts with host cell factors to form a favourable virus replication site. Cell cytoskeletons have been observed to have close contact with flaviviruses, which expands the understanding of cytoskeleton functions during virus replication, although many detailed mechanisms are still unclear. The interactions between the virus and host cytoskeletons such as actin filaments, microtubules, and intermediate filaments have provided insight into molecular alterations during the virus infection, such as viral entry, in-cell transport, scaffold assembly, and egress. This review article focuses on the utilization of cytoskeleton by Flavivirus and the respective functions during virus replication.
Synthesis of vowels and tones in Thai language by articulatory modeling

We propose a way of synthesizing Thai vowels, monophthong and diphthong which consist of nine short-long vowel pairs and three short-long vowel pairs respectively. By adjusting the fundamental frequency or pitch contour, the five tonal of these vowels can be synthesized, leading to a total of 120 phonemes. We evaluate the synthesized monophthongs by comparing the first and second formants to standard in terms of different percentages, which result in 9.89% and 7.44% respectively. For the synthesis of diphthongs, we slide from one vocal-tract vowel to another using linear, logarithmic, or exponential functions.
Improving the retrieval performance by using distance-based bigram

In this paper, we discussed a new scheme of forming and weighing a term called a distance- based bigram. In this scheme, the distance between two words is considered for a new term and a new weighting. This new scheme is applied to the vector formation in the process of the vector space model with other standard term forming schemes: unigram and bigram. The tested domains are English and Thai medical corpora. The results show that our proposed method performs well for the Thai corpus under the condition that only a few returned documents are needed. Within the first ten percent of recall, our method improves the precision over the standard unigram by nearly 30%.
A 21.8–27.5GHz PLL in 32nm SOI using Gm linearization to achieve −130dBc/Hz phase noise at 10MHz offset from a 22GHz carrier

This paper describes a new approach to low phase noise LC VCO design based on transconductance linearization of the active devices. A prototype 25GHz VCO based on this approach is integrated in a dual loop PLL and achieves superior performance compared to the state of the art. The design is implemented in the 32nm SOI deep sub-micron CMOS technology and achieves a phase noise of -130dBc/Hz at 10MHz offset from a 22GHz carrier. Additionally, the paper introduces a new layout approach for switched capacitor arrays that enables a wide tuning range of 23%. More than 500 measurements across PVT variations validate the proposed PLL design: phase noise variation across 46 dies for 3 different frequencies is σ <; 0.6dB, across supply variation over 0.7-1.5V is 2dB and across 80°C temperature variation is 2dB. At the 25GHz center frequency, the VCO FOMT is 188dBc/Hz.