Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient transcription and replication of simian immunodeficiency virus in the absence of NF-kappaB and Sp1 binding elements

Ten mutants of the simian immunodeficiency virus (SIV) SIVmac239 bearing deletions (delta) or substitutions (subst) in the NF-kappaB and/or Sp1 binding elements were created, and the replicative capacities of the mutants were analyzed. All mutants, including one extensively mutagenized strain entirely missing the NF-kappaB and four Spl binding elements, replicated with wild-type kinetics and to a wild-type level in peripheral blood mononuclear cell cultures in 50 to 100% of the experiments. One group of mutants replicated very similarly to SIVmac239 in kinetics and yield in CEMxl74 cells (2xNFKappaB > or = SlVmac239 approximately deltaNFkappaB approximately deltaSpl234 approximately substNFkappaB approximately substSpl2 approximately substSp23), while a second group replicated with delayed or slightly delayed kinetics in CEMxl74 cells (SIVmac239 > substSp34 > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSp1 > substSpl234). Reversions or additional mutations were not detected in the U3 and R regions of proviral DNA from CEMxl74 cells infected with the SIVmac239 mutants. Similar results were obtained when mutants of SIVmacMER (a macrophage-competent derivative of SIVmac239) were tested in peripheral blood mononuclear cell and CEMx174 cultures. However, the growth of most mutated viruses was suppressed in primary rhesus monkey alveolar macrophages (SIVmacMER approximately 2xNFkappaB approximately substNFkappaB > deltaNFkappaB > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSpl > deltaSpl234 approximately substSpl2 > substSp23 approximately substSp34 approximately substSpl234 > or = SIVmac239). Thus, changes in the Sp1 binding sites had the most dramatic effects on SIVmac replication in primary macrophage cultures. Analysis of long terminal repeat-driven secreted alkaline phosphatase activity in transient assays showed that, unlike human immunodeficiency virus type 1, the SIV long terminal repeat possesses an enhancer region just upstream of the NF-kappaB element which maintains significant levels of basal transcription in the absence of NF-kappaB and Sp1 sites. This region is responsive to transactivation by Tat. In addition, the SIV TATA box was shown to be stronger than that of human immunodeficiency virus type 1. Therefore, the surprisingly high replicative capacity of NF-kappaB and Sp1 binding site mutants of SIVmac is due to unique features or the enhancer/promoter region.
Analysis of Helical Slow-Wave Structures for Modeling Helix Thickness Using an Improved Helical-Harmonics Approximation—Part I: Theory

In this two-part paper, an improved helical-harmonics approximation (HHA) is presented, and subsequently validated by applying it to the analysis of cold (beam-absent) helix slow-wave structures (SWSs) with smoothed rods. The first part presents the theory and relevant formulations. By starting from Maxwell's equations, we obtain an improved form of supporting equations for field components in the so-called helical coordinate system with the help of which the effect of helix pitch angle on the validity of HHA is revealed. By evaluating the error in solutions caused by small changes in the pitch angle across the tape thickness, we show that HHA holds to be valid in a region whose radial thickness is a fraction of actual helix tape thickness. Furthermore, field components of a helix SWS and its dispersion relation are determined using this modified approximation. Moreover, all helical armonics that are necessary for the convergence of the results are incorporated in our analysis. The present improved HHA-based analysis of helical SWS yields a more accurate modeling of the tape thickness than the analysis based on the conventional HHA as well as that by the tape-helix model.
An accurate extended Kalman filter scheme for the reduction of the flux angle tracking error in sensorless induction motor drives

The paper deals with extended Kalman filters for the estimation of rotor flux and angular velocity in induction motors. It investigates the impact of discretization errors on the performance of extended Kalman filters in sensorless induction motor drives. It shows that first order Euler approximation and second order approximations may lead to insufficient flux angular accuracy when the sampling frequency is low or the stator frequency is high. It proposes to use an extended Kalman filter that estimates and compensates the discretization error. It shows that this solution allows to substantially reduce the flux angular error below what can be obtained with first and second order approximations. The scheme is verified experimentally.
Revising the Role of the Pneumococcal vex-vncRS Locus in Vancomycin Tolerance

ABSTRACT Vancomycin is used increasingly to treat invasive infections caused by multidrug-resistant Streptococcus pneumoniae. Although no vancomycin-resistant strains have been isolated to date, tolerant strains that fail to die rapidly and that cause relapsing disease have been described. The vex123-pep27-vncRS locus, consisting of an ABC transporter, a presumed signaling peptide, and a two-component system, respectively, has been implicated in vancomycin tolerance. Recent findings, however, challenged this model. The data presented here indicate that erythromycin in the growth medium induces a vancomycin-tolerant phenotype and that loss of function of Pep27 or VncRS does not alter autolysis. However, a role for the ABC transporter encoded by the vex123 genes in tolerance was confirmed. A vex3 mutant was considerably more tolerant to vancomycin treatment than the wild-type strain T4, and the strength of the phenotype depended on the orientation of the resistance cassette used to construct the mutant. Microarray results suggested a number of genes that might be involved in tolerance in the vex3 mutant. Although the exact function and regulation of the vex123-pep27-vncRS locus remains to be determined, several factors influence the autolysis behavior of S. pneumoniae, including the bacterial capsule, erythromycin, and the lytA and vex3 gene products.
Toll‐like receptor‐4‐mediated macrophage activation is differentially regulated by progesterone via the glucocorticoid and progesterone receptors

Macrophage function has been demonstrated to be subject to modulation by progesterone. However, as this steroid hormone can act through the glucocorticoid receptor as well as the progesterone receptor, the mechanism of action has not been precisely characterized. To determine the mode of action, we compared the ability of progesterone, norgestrel (a synthetic progesterone‐receptor‐specific agonist) and dexamethasone (a synthetic glucocorticoid receptor agonist) to modulate macrophage function following stimulation of the Toll‐like receptor‐4 (TLR‐4) ligand lipopolysaccharide (LPS). The results demonstrate that following stimulation of TLR‐4 with LPS and cotreatment with either progesterone or dexamethasone, but not norgestrel, there is a significant reduction in nitric oxide (NO) production, indicating that this progesterone‐mediated effect is through ligation of the glucocorticoid receptor. In contrast, LPS‐induced interleukin‐12 (IL‐12) production could be downregulated by all three steroids, indicating that ligation by progesterone of either the glucocorticoid or the progesterone receptors or both could mediate this effect. While progesterone downmodulated NO‐mediated killing of Leishmania donovani by activated macrophages in vitro, most probably via the glucocorticoid receptor, it had little effect on Toxoplasma gondii growth in these cells. This would suggest that progesterone‐mediated increased susceptibility to T. gondii during pregnancy is more likely to be related to the ability of the hormone to downregulate IL‐12 production and a type‐1 response utilizing the progesterone as well as the glucocorticoid receptors.
GTSE1 tunes microtubule stability for chromosome alignment and segregation through MCAK inhibition

The dynamic regulation of microtubules during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore microtubules have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The microtubule depolymerase MCAK can influence CIN through its impact on microtubule stability, but how its potent activity is controlled in cells remains unclear. Here we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumours, regulates microtubule stability during mitosis by inhibiting MCAK microtubule depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning due to microtubule instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, while artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus GTSE1 inhibition of MCAK activity regulates the balance of microtubule stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability.
Culture, Technology, Cultural Techniques – Moving Beyond Text1

Originally published in 2003, this article presents one of the first attempts to provide a systematic summary of the new concept of cultural technique. It is, in essence, an extended checklist aimed at overcoming the textualist bias of traditional cultural theory by highlighting what is elided by this bias. On the one hand, to speak of cultural techniques redirects our attention to material and physical practices that all too often assume the shape of inconspicuous quotidian practices resistant to accustomed investigations of meaning. On the other hand, cultural techniques also comprise sign systems such as musical notation or arithmetical formulas located outside the domain of the hegemony of alphabetical literacy. The rise of the latter in particular is indebted to the impact of the digital – both as a domain of technology and a source of theoretical reorientation. Together, these aspects require a paradigmatic change that challenges and supersedes the traditional ‘discursivism’ of cultural theory.
Cryptanalysis on Privacy-aware two-factor Authentication Protocol for Wireless Sensor Networks

Das first proposed two-factor authentication combining the smart card and password to resolve the security problems of wireless sensor networks (WSNs). After that, various researchers studied two-factor authentication suitable for WSNs. In user authentication protocols based on the symmetric key approach, a number of elliptic curve cryptography (ECC)-based authentication protocols have been proposed. To resolve the security and efficiency problems of ECC-based two-factor authentication protocols, Jiang et al . proposed a privacy-aware two-factor authentication protocol based on ECC for WSNs. However, this paper performs a vulnerability analysis on Jiang et al . ’s authentication protocol and shows that it has security problems, such as a lack of mutual authentication, a risk of SID modification and DoS attacks, a lack of sensor anonymity, and weak ID anonymity.
Input Contract Testing of Graphical User Interfaces

User inputs are critical for the security, safety, and reliability of software systems. This paper proposes a new concept called user input contracts, which is an integral part of a design-by-contract supplemented development process, and a model-based testing approach to detect violations of user input contracts. The approach generates test cases from an input contract integrated with graph-based model of user interface specification and applies them to the system under consideration. The paper presents a proof-of-concept tool that has been developed and used to validate the approach by experiments. The experiments are conducted on a web-based system for marketing tourist services to analyze input robustness of system under consideration with respect to user input contracts.
Antigenic heterogeneity of outer membrane proteins of nontypable Haemophilus influenzae is a basis for a serotyping system

A serotyping system for nontypable Haemophilus influenzae (NTHI) was developed by using isolated outer membrane protein (OMP) preparations and rabbit antisera. OMPs of 23 strains were isolated by molecular sieve chromatography of outer membranes in 1.5% sodium deoxycholate buffer. These OMP preparations were relatively free of lipopolysaccharide as determined by silver staining of sodium dodecyl sulfate gels and by dot assay with a monoclonal antibody which is specific for the lipid A of H. influenzae. Three antisera raised to whole organisms were used to serotype 21 of 23 strains with a kinetic enzyme-linked immunosorbent assay. Digestion of OMP preparations with proteinase K removed greater than 90% of the antigenic reactivity, indicating that the system is based on OMP antigens. Marked antigenic heterogeneity of OMPs exists among strains of NTHI. By determining the pattern of serological reactivity of OMPs with the three antisera, isolates were divided into groups based on antigenic differences. Six serotypes were identified. This OMP serotyping system is based on multiple antigenic determinants. Future studies will focus on identifying serotype-specific epitopes to further refine this serological classification scheme for NTHI.
Forced expression of RDH10 gene retards growth of HepG2 cells

The constitutive over-expression of the retinol dehydrogenase 10 (RDH10) gene, involved in retinoic acid (RA) biosynthesis, produced in HepG2 cells a significant antiproliferative response, but not signs of apoptosis. An indirect assay based on the Chloramphenicol AcetylTransferase (CAT) reporter gene driven by a retinoic acid responsive elements (RARE) suggests in genetically modified HepG2 cells an increase of the endogenous RA concentration. Furthermore, the growth arrest of HepG2 cells over-expressing the RDH10 gene was associated with the up-regulation and down-regulation of, respectively, RARβ/p21Cip1 and CycE/CdK2 mRNAs. These results indicated that forced expression of RDH10 produces antiproliferative effects highly comparable to those achieved by retinoids treatment and thus the development of a gene therapy, finalized at the restoration of the enzymatic and receptorial machinery of the RA pathway, could be a possible curative strategy for hepatocellular carcinoma (HCC).
Do Labor Market Networks Have an Important Spatial Dimension?

We test for evidence of spatial, residence-based labor market networks. Turnover is lower for workers more connected to their neighbors generally and more connected to neighbors of the same race or ethnic group. Both results are consistent with networks producing better job matches, while the latter could also reflect preferences for working with neighbors of the same race or ethnicity. For earnings, we find a robust positive effect of the overall residence-based network measure, whereas we usually find a negative effect of the same-group measure, suggesting that the overall network measure reflects productivity-enhancing positive network effects, while the same-group measure may capture a non-wage amenity.
Balancing strategy differences in bilateral knee osteoarthritis patients

Knee osteoarthritis (OA) is one of the most widespread orthopedic disease that affects the elderly. The present study aims to evaluate the biomechanical effects of bilateral osteoarthritis on elderly patients compared to a control group using stabilometry parameters. The used parameters were center of pressure (CoP) 95% confidence ellipse area, CoP path length and maximum path velocity, CoP range ratio and spectral power ratio in anteroposterior (AP) and mediolateral (ML) directions, load distribution between legs, largest amplitudes in AP and ML direction during a 30s bilateral quite standing trial on a Zebris FDM-S force distribution plate. Significant differences to the control group in path length, ML largest amplitude and spectral power ratio showed that bilaterally involved OA degrades postural stability as reported earlier, but new finding is that more intense CoP motions can be observed in ML direction in case of bilateral knee osteoarthritis.
Residential perspectives: the value of Floodplain‐ buyout open space*

This mixed‐methods case study identifies how floodplain property acquisition—a buyout—impacts an urban environment at the neighborhood scale while considering the role of individual residents in formal and informal land‐use decision making. In floodplain buyouts, the reopening of urban space is enabled by federal structural drivers, primarily Federal Emergency Management Agency (FEMA), but it is repurposed as a cultural landscape constructed and produced by individuals. This research explores how residents perceive and ascribe values to the buyout landscape in Lexington, Kentucky. Enabled by federal funds, but left largely to their own devices, residents in Lexington adopted uses, ascribed values, and produced their own land‐use norms in each buyout neighborhood.
A Decision-Making Tool to Design a Flexible Liquefied Natural Gas System under Uncertainty

We formulate an integrated design and evaluation mechanism applying techniques in the field of flexible engineering design and real options analysis to build a liquefied natural gas production and fueling system for a Singapore oil & gas company. The proposed methodology consists of four main steps: 1) design and evaluation under deterministic demand, 2) uncertainty characterization and performance re-evaluation under different uncertainty realization scenarios, 3) optimization under uncertainty, 4) post-optimality sensitivity analysis. Among the highlights of this work are applications of a metaheuristic method to more efficiently search for optimal flexible designs as well as extensive one-way and two-way sensitivity analyses to generate valuable insights. The final results show strong value in adding flexibility in this production and fueling system.
Improving approximate 1D Bloch analysis through simulation of truncated periodic structures

In this paper a simple method is presented to remove any ambiguity arising in the phase constant of Bloch modes in 1D-periodic structures recovered from simulations of a finite number of unit cells. Two reference structures are analyzed through a commercial software and their dispersive properties are correctly reconstructed as predicted from the theoretical background presented.
Bacterial Cell Wall-Induced Arthritis: Chemical Composition and Tissue Distribution of Four Lactobacillus Strains

ABSTRACT To study what determines the arthritogenicity of bacterial cell walls, cell wall-induced arthritis in the rat was applied, using four strains of Lactobacillus. Three of the strains used proved to induce chronic arthritis in the rat; all were Lactobacillus casei. The cell wall of Lactobacillus fermentum did not induce chronic arthritis. All arthritogenic bacterial cell walls had the same peptidoglycan structure, whereas that of L. fermentum was different. Likewise, all arthritogenic cell walls were resistant to lysozyme degradation, whereas the L. fermentum cell wall was lysozyme sensitive. Muramic acid was observed in the liver, spleen, and lymph nodes in considerably larger amounts after injection of an arthritogenicL. casei cell wall than following injection of a nonarthritogenic L. fermentum cell wall. The L. casei cell wall also persisted in the tissues longer than theL. fermentum cell wall. The present results, taken together with those published previously, underline the possibility that the chemical structure of peptidoglycan is important in determining the arthritogenicity of the bacterial cell wall.
Cooperative AUV motion planning using terrain information

There is widespread interest in the deployment of fleets of marine robots with the potential to roam the oceans freely and collect data at an unprecedented scale. This calls for the development of efficient algorithms for multiple vehicle motion planning that can take directly into account the capabilities of each vehicle as well as the environmental conditions and lend themselves to seamless integration with control and navigation systems. The latter connection is for the most part eschewed in the literature, in spite of the obvious fact that in order for the vehicles to execute the planned motions they must at a later stage navigate with great accuracy and follow the trajectories using control algorithms that take explicitly into account the dynamical constraints of the vehicles involved. Among the methods available for underwater vehicle navigation, terrain-based techniques have recently come to the fore. These techniques avoid the use of overly expensive inertial-like motion sensor units and hold considerable promise for the development of a new breed of affordable long range navigation systems. Motivated by these considerations, we tackle in the present paper the problem of multiple vehicle motion planning by taking explicitly into consideration inter-vehicle collision avoidance, together with a number of criteria that may include simultaneous times of arrival at assigned target points, energy minimization, acoustic communication constraints, and the maximization of terrain information along the vehicle paths (as measured by some appropriate criterion) for terrain-based navigation purposes.
Etnoarqueologia dos Grafismos \'Kaingang\': um modelo para a compreensão das sociedades Proto-Jê meridionais.

This study establishes a relation between archaeological record of the so called “local ceramic traditions” of the south of Brazil (Taquara, Itararé and Casa de Pedra), which I consider as southern Proto-Jê, and ethnographical, ethnohistorical, and linguistic records of southern Jê societies (Kaingang and Xokleng) aiming at a deeper and more sophisticated understanding of those southern Proto-Jê populations. Archaeological record left by those groups were analysed from the standpoint of their symbolic dimension mainly when it could be identified as part of a system of visual representations (graphic representations). Thus, an ethnoarchaeology of Kaingang graphic representations was undertaken in which the archaeological, ethnographical, ethnohistorical and linguistic records were related by mean of a cognitive approach which favours and interprets the production of meanings by southern Proto-Jê populations, especially their representations about social life, about natural and supernatural domains, and about death, based on ethnological studies of Kaingang society. O B S E R V A Ç Õ E S Grafou-se com trema as vogais “i”, “e”, “u” e “y” do idioma Kaingang (e das demais línguas indígenas que aparecem no texto), quando o correto seria fazê-lo com til, o que o editor de textos usado não permitiu. Exceto quando indicado expressamente, as fotografias são do autor desta tese.
Performance of diversity reception for QPSK with cochannel interference in a flat Rayleigh fading channel [mobile radio]

The performances of maximum-ratio (MRC) and optimum diversity combining schemes in the presence of ISI due to cochannel interference (CCI) in flat Rayleigh fading channels are analyzed and compared. In flat fading environments, ISI can be generated by co-channel interferers due to the random symbol and phase offsets between the desired signal and the cochannel interferers. With these two random-valued offsets, the CCI is shown as a wide-sense stationary process (WSS) and then an optimal diversity can be applied. Several fading conditions experienced by desired and interfering signals are considered. The performance using the Gaussian interference model is also provided for comparison. An accurate error rate is obtained by using the moment method for each time-varying channel in Monte-Carlo simulations.