Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Genome Sequence Analysis of the Naturally Competent Acinetobacter baumannii Clinical Isolate A118

Recent studies have demonstrated a high genomic plasticity in Acinetobacter baumannii, which may explain its high capacity to acquire multiple antibiotic resistance determinants and to survive in the hospital environment. Acinetobacter baumannii strain A118 (Ab A118) was isolated in the year 1995 from a blood culture of an intensive care unit patient. As this particular strain showed some peculiar characteristic such as being naturally competent and susceptible to numerous antibiotics, we performed whole-genome comparison (WGC) studies to gain insights into the nature and extent of the genomic differences. The Ab A118 genome is approximately 3,824 kb long with a 38.4% GC content and contains 3,520 coding sequences. WGC studies showed that the Ab A118 genome has 98% average nucleotide identity with that of A. baumannii ATCC 17978, and 96% average nucleotide identity with that of strains AYE and ACICU. At least 12 inversions, 275 insertions, and 626 deletions were identified when the Ab A118 genome was compared with those of strains ATCC 17978, AYE, and ACICU using MAUVE WGC. Multiple gene order arrangements were observed among the analyzed strains. MAUVE WGC analysis identified 19 conserved segments, known as locally colinear blocks. The number of single nucleotide polymorphisms found when comparing the Ab A118 genome with that of strains ATCC 17978, AYE, and ACICU was 43,784 (1.1496%), 44,130 (1.158%), and 43,914 (1.153%), respectively. Genes comEA, pilQ, pilD, pilF, comL, pilA, comEC, pilI, pilH, pilO, pilN, pilY1(comC), pilE, pilR, and comM, potentially involved in natural competence were found in the Ab A118 genome. In particular, unlike in most strains where comM is interrupted by an insertion of a resistance island (AbaR), in strain Ab A118 it is uninterrupted.
A Descriptive in vitro Electron Microscopic Study of Acidic Fluoride-Treated Enamel: Potential Anti-Erosion Effects

This study aimed to investigate the surface zones of acidic fluoride-treated enamel. Human teeth were each divided into three or four enamel specimens that were treated for 10 min with solutions of 0.2 and 0.4% HF (pH 3.09 and 2.94), 1.74% SnF2 (pH 2.9), 0.68% TiF4 (pH 1.6) and 0.84% NaF (pH 4.5). Untreated specimens functioned as negative controls. The microstructure and elemental composition of the surface zones were studied by scanning electron microscopy/energy-dispersive X-ray (EDX) analysis, transmission electron microscopy (TEM) and nanospot-EDX following cross-sectional preparation using focused ion beam technology. TEM/EDX analyses of NaF-treated specimens showed a 500-nm-thick closed surface film containing 20-40 at% (atomic percent) F. HF-treated specimens had a distinct surface film 200-600 nm thick (dense, not globular) containing 45-47 at% F. TiF4-treated specimens had a surface film of 200-300 nm in thickness containing 8-11 at% Ti but no detectable fluoride. SnF2-treated specimens had a modified surface enamel layer varying in thickness from 200 to 800 nm with an inhomogeneous distribution of Sn. Local spots were detected with as high as 8 at% Sn (30 wt%, weight percent). The results suggest that the reaction mechanisms of SnF2 and TiF4 solutions with dental enamel differ from those occurring after enamel exposure to acidulated NaF and HF solutions. While the HF and NaF treatments resulted in the formation of CaF2-like material as shown by EDX, no significant surface fluoridation was found for SnF2 and TiF4 solutions within the TEM/EDX detection limits. These results suggest that the erosion-protective mechanisms of these latter compounds probably relate more to the formation of hardly soluble and acid-resistant reaction surface films and less to surface fluoride incorporation.
Vector analysis and control of advanced static VAr compensators

The advanced static VAr compensator (ASVC) is based on the principle that a self-commutating static inverter can be connected between three-phase AC power lines and an energy-storage device, such as an inductor or capacitor, and controlled to draw mainly reactive current from the lines. This capability is analogous to that of the rotating synchronous condenser and it can be used in a similar way for the dynamic compensation of power transmission systems, providing voltage support, increased transient stability, and improved damping. The authors present a simplified mathematical model of the ASVC that has made it possible to derive the transfer functions needed for control system synthesis. The resulting control system designs are briefly outlined and further analysis is presented to show the behaviour of the ASVC when the line voltage is unbalanced or distorted. The analysis is based on a vectorial transformation of variables, first described by R.H. Park (1928) for AC machine analysis, and later, using complex numbers, by W.V. Lyon (1954) in the theory of instantaneous symmetrical components.
CSTR 2009-02 Image-Based Exploration of Massive Online Environments

This paper presents a system for interactive exploration of massive, detailed virtual environments over a broadband network. We build upon the hierarchical image-based framework pioneered by Shade et al. [1996] and Schaufler and Stürzlinger [1996], introducing key adaptations for scalability. A cluster of servers maintain a hierarchy of depth images of bounded regions of the scene. A client displays the scene using a logarithmic set of depth images that can be maintained under constant bandwidth independent of scene size. We report on techniques used to overcome the daunting visual quality issues encountered with image-based rendering of general unstructured scenes with billions of polygons on commodity hardware over a wide-area network. Experimental results are reported on scenes that exemplify the extreme demands of large-scale online worlds. CR Categories: I.3. 2 [Computer Graphics]: Graphics Systems— Distributed/network graphics;
The Transforming Rho Family GTPase Wrch-1 Disrupts Epithelial Cell Tight Junctions and Epithelial Morphogenesis

ABSTRACT Wrch-1, an atypical and transforming Rho GTPase, regulates cellular activities including proliferation and actin organization, but its functions and effectors remain poorly characterized. We show here that Wrch-1 distributes along the apical and basolateral membranes in MDCK cells and binds the cell polarity protein Par6 in a GTP-dependent manner. Activated Wrch-1 negatively regulates the kinetics of tight junction (TJ) assembly during epithelial cell polarization but has no detectable effect on overall cell polarity in confluent monolayers. It also causes a dramatic cytoskeletal reorganization and multilayering in cells grown in two-dimensional culture and disrupts cystogenesis of cells grown in three-dimensional (3D) culture. Similarly, short hairpin RNA-mediated knockdown of Wrch-1 perturbs cystogenesis in 3D culture, suggesting that tight regulation of Wrch-1 activity is necessary for normal epithelial morphogenesis. A weakly transforming effector domain mutant of activated Wrch-1 that inhibits Par6 binding abrogates the ability of Wrch-1 to disrupt TJ formation, actin organization, and epithelial morphogenesis. We hypothesize that Wrch-1-induced morphological and growth transformation may occur in part through Par6-mediated disruption of TJs and actin organization.
Paradox-free Formal Foundation of Vector Space Model

In the Vector Space Model (VSM) of Information Retrieval (IR), the documents and queries are conceived as vectors of weights belonging to the same linear space, and retrieval is based on similarity measures. This view yields paradoxes and problems as regards concepts of fundamental importance to IR (s imilarity, term independence, preference, linearity). In the present paper, a different view is proposed: the VSM of IR may be conceived as a probability space that decreases the amount of the Shannon information associated to the selection of documents as answers to queries. This view can serve as another formal foundation of the VSM that is paradox-free and, at the same time, preserves the computational practice developed thus far. Experiments are also reported to reflect this view in practice. Key Word s Information Retrieval, Vector Space Model, Probability Space,
Peace is in Movement: A Dynamical Systems Perspective on the Emergence of Peace in Mozambique

The Mozambique peace process is one of the most promising cases of an intervention strategy that transformed a protracted, intractable conflict into a resilient social system of sustainable peace. After 16 years of extremely violent civil war, a series of semi-official interventions led to a successful transition to peace in 1992, much to the surprise of the international community. This article uses the dynamical systems perspective to explore how the escalation, maintenance, and transformation of the Mozambican conflict may be understood and systematized. First, this article analyzes how the social system lost its adaptability after the country had gained independence, and illustrates how a strong enmity system was created and maintained in the country. This article discusses how various counterintuitive conflict transformation initiatives changed the political landscape and promoted the re-establishment of adaptive functions of the social system, moving Mozambique from war toward peace. This article an.
Filarial Nematode Parasites Secrete a Homologue of the Human Cytokine Macrophage Migration Inhibitory Factor

ABSTRACT Filarial nematode parasites establish long-term chronic infections in the context of an antiparasite immunity that is strongly biased toward a Th2 response. The mechanisms that lead to this Th2 bias toward filarial antigens are not clear, but one possibility is that the parasites produce molecules that have the capacity to proactively modify their immunological environment. Here we report that filarial parasites of humans secrete a homologue of the human proinflammatory cytokine macrophage migration inhibitory factor (MIF) that has the capability of modifying the activity of human monocytes/macrophages. A cDNA clone isolated from a Brugia malayi infective-stage larva expression library encoded a 12.5-kDa protein product (Bm-MIF) with 42% identity to human and murine MIF. MIF homologues were also found to be expressed in the related filarial species Wuchereria bancrofti and Onchocerca volvulus. Bm-mif was transcribed by adult and larval parasites, and the protein product was found in somatic extracts and in the parasite’s excretory-secretory products. Immunohistocytochemistry revealed that Bm-MIF was localized to cells of the hypodermis/lateral chord, the uterine wall, and larvae developing in utero. Unexpectedly, the activities of recombinant Bm-MIF and human MIF on human monocytes/macrophages were found to be similar. When placed with monocytes/macrophages in a cell migration assay,Bm-MIF inhibited random migration. When placed away from cells, Bm-MIF induced an increase in monocyte/macrophage migration that was specifically inhibited by neutralizing anti-Bm-MIF antibodies. Bm-MIF is the first demonstration that helminth parasites produce cytokine homologues that have the potential to modify host immune responses to promote parasite survival.
Improved Inapproximability Results for the Shortest Superstring and Related Problems

We develop a new method for proving explicit approximation lower bounds for the Shortest Superstring problem, the Maximum Compression problem, the Maximum Asymmetric TSP problem, the (1, 2)--ATSP problem and the (1, 2)--TSP problem improving on the best known approximation lower bounds for those problems.
Adaptive Concentration Inequalities for Sequential Decision Problems

A key challenge in sequential decision problems is to determine how many samples are needed for an agent to make reliable decisions with good probabilistic guarantees. We introduce Hoeffding-like concentration inequalities that hold for a random, adaptively chosen number of samples. Our inequalities are tight under natural assumptions and can greatly simplify the analysis of common sequential decision problems. In particular, we apply them to sequential hypothesis testing, best arm identification, and sorting. The resulting algorithms rival or exceed the state of the art both theoretically and empirically.
Small molecule regulators of postnatal Nkx2.5 cardiomyoblast proliferation and differentiation

•Introduction to postnatal cardiac progenitor cells •Methods to examine postnatal CPCs with small molecules ‐Transgenic mice ‐Cell culture ‐Measurement of cell proliferation ‐Flow cytometry ‐Immunofluorescence ‐Chemical reagents •Results and discussion of small molecule effects on CPCs ‐Modulation of TGF‐β but not activin A or BMP2 signalling affects smooth muscle cell differentiation of neonatal Nkx2.5+ cardiomyoblasts ‐Small molecule inhibition of Alk receptors induces an expansion of neonatal Nkx2.5‐eGFP+ cells
Experimental diffuse brain injury results in regional alteration of gross vascular morphology independent of neuropathology

Abstract Primary objective: A dynamic relationship exists between diffuse traumatic brain injury and changes to the neurovascular unit. The purpose of this study was to evaluate vascular changes during the first week following diffuse TBI. It was hypothesized that pathology is associated with modification of the vasculature. Methods: Male Sprague-Dawley rats underwent either midline fluid percussion injury or sham-injury. Brain tissue was collected 1, 2 or 7 days post-injury or sham-injury (n = 3/time point). Tissue was collected and stained by de Olmos amino-cupric silver technique to visualize neuropathology or animals were perfused with AltaBlue casting resin before high-resolution vascular imaging. The average volume, surface area, radius, branching and tortuosity of the vessels were evaluated across three regions of interest. Results: In M2, average vessel volume (p < 0.01) and surface area (p < 0.05) were significantly larger at 1 day relative to 2 days, 7 days and sham. In S1BF and VPM, no significant differences in the average vessel volume or surface area at any of the post-injury time points were observed. No significant changes in average radius, branching or tortuosity were observed. Conclusions: Preliminary findings suggest gross morphological changes within the vascular network likely represent an acute response to mechanical forces of injury, rather than delayed or chronic pathological processes.
INHIBITION OF FOCAL ADHESION KINASE EXPRESSION CORRELATES WITH CHANGES IN THE CYTOSKELETON BUT NOT APOPTOSIS IN PRIMARY CULTURES OF CHICK EMBRYO CELLS

Cell adhesion to the extracellular matrix through integrin receptors can activate signaling cascades within the cell. Focal adhesion kinase (FAK) is a protein tyrosine kinase activated by integrin adhesion. The role of FAK within the cell is not clear, although evidence suggests roles in cell motility or the regulation of adhesion‐dependent cell survival. We have treated primary cultures of chick embryo cells with antisense oligonucleotides to FAK to reduce the level of FAK protein expression. Levels of the related protein, proline‐rich tyrosine kinase 2 (Pyk2) and the FAK substrate paxillin, were unaffected by the addition of oligonucleotides, whereas FAK expression was reduced by 70%. Levels of apoptotic cell death did not significantly increase after the addition of oligonucleotides. However, there was a change in the distribution of focal adhesion sites from a uniformly distributed pattern to a mainly peripheral pattern. This was accompanied by a loss of stress fibers and an increase in the peripheral actin cytoskeleton, as the cells became rounded. These results suggest that in these early embryonic cells, FAK expression regulates the arrangement of focal adhesions and the cytoskeleton that result in a motile phenotype, but that FAK does not appear to regulate apoptosis.
Managing information cycles for intra-organisational coordination of humanitarian logistics

As the humanitarian aid sector is expanding, the need for enhancing coordination capabilities increases as well. This holds especially for the area of logistics, because humanitarian operations typically take place in unstable and risky environments, where infrastructure is poor, while staff turnover is high. The effectiveness of humanitarian logistics critically depends on the availability and quality of logistics support information, but data is often scarce and ICT support to remote areas is limited. The challenges caused by these constraints call for conceptual insight into the intra-organisational coordination process in humanitarian aid. In order to assess current practice of intra-organisational logistics information management for humanitarian aid, we combine humanitarian logistics and organisational literatures to develop a model that ties in information cycles with activity cycles that ultimately should lead to value creation. The model serves as a basis to analyse coordination practice at the Dutch filial of Medecins Sans Frontieres (MSF-Holland) and develop implications for research and practice.
Executive function in girls with turner's syndrome

Turner's syndrome (TS), a genetic disorder affecting girls, has a well‐described neurocognitive profile including difficulty with visuospatial processing and attention skills. The goal of this study was to investigate executive function and attention abilities in girls with TS. Executive skills include the ability to plan, organize, monitor, and execute multistep problem‐solving processes. Measures of attention and executive function were analyzed from 105 girls with TS and from 153 female controls matched for age, IQ, and socioeconomic status. Three age groups were evaluated in order to assess developmental patterns in executive skills. The TS group (all ages) performed significantly less well than did controls on measures of attention, including the Freedom From Distractibility factor of the Wechsler Intelligence Scale for Children‐Revised and the Test of Variables of Attention. In the executive function domain, girls with TS performed at levels comparable to controls on the Wisconsin Card Sort Test and.
A noncanonical WD‐repeat protein from the cyanobacterium Synechocystis PCC6803: Structural and functional study

Synechocystis PCC6803 possesses several open reading frames encoding putative WD‐repeat proteins. One, the Hat protein, is involved in the control of a high‐affinity transport system for inorganic carbon that is active when the cells are grown under a limiting concentration of this carbon substrate. The protein is composed of two major domains separated by a hydrophobic linker region of 20 amino acid residues. The N‐terminal domain of Hat has no homolog in standard databases and does not display any particular structural features. Eleven WD repeats have been identified in the C‐terminal moiety. The region encompassing the four terminal WD repeats is essential for growth under a limiting inorganic carbon regime. The region encompassing the two most terminal WD repeats is required for the activity of the high‐affinity transport system. However, because the Hat protein is located in the thylakoids, it should not be itself an element of the transport system. The structural organization of the WD‐containing domain of Hat was modeled from the crystal structure of the G protein β subunit (with seven WD repeats) and of hemopexin (a structural analog with four blades). Functional and structural data argue in favor of an organization of the Hat WD moiety in two subdomains of seven and four WD repeats. The C‐terminal 4‐mer subdomain might interact with another, yet unknown, protein/peptide. This interaction could be essential in modulating the stability of the 4‐mer structure and, thus, the accessibility of this subdomain, or at least of the region encompassing the last two WD repeats.
Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations

The association of hemagglutinin (HA) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A. Lipid rafts are thought to be small, fluctuating patches of membrane enriched in saturated phospholipids, sphingolipids, cholesterol and certain types of protein. However, raft-associating transmembrane (TM) proteins generally partition into Ld domains in model membranes, which are enriched in unsaturated lipids and depleted in saturated lipids and cholesterol. The reason for this apparent disparity in behavior is unclear, but model membranes differ from the plasma membrane in a number of ways. In particular, the higher protein concentration in the plasma membrane may influence the partitioning of membrane proteins for rafts. To investigate the effect of high local protein concentration, we have conducted coarse-grained molecular dynamics (CG MD) simulations of HA clusters in domain-forming bilayers. During the simulations, we observed a continuous increase in the proportion of raft-type lipids (saturated phospholipids and cholesterol) within the area of membrane spanned by the protein cluster. Lateral diffusion of unsaturated lipids was significantly attenuated within the cluster, while saturated lipids were relatively unaffected. On this basis, we suggest a possible explanation for the change in lipid distribution, namely that steric crowding by the slow-diffusing proteins increases the chemical potential for unsaturated lipids within the cluster region. We therefore suggest that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids. This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes.
Brief announcement: anonymity and trust in distributed systems

In this paper, we present a framework for achieving anonymity and trust, two seemingly contradictory properties, in distributed systems. Our approach builds on webs of trust, a well-established and widely deployed decentralized infrastructure for establishing the authenticity of the binding between public keys and users, and more generally, trust relationships among users. We introduce the concept of anonymous webs of trust - an extension of webs of trust where users can authenticate messages and determine each other's trust level without compromising their anonymity. Our framework comprises novel cryptographic protocols based on zero-knowledge proofs for achieving anonymity in webs of trust and a prototype implementation based on GnuPG. We conduct an automated analysis to formally verify the security of our protocol and an experimental evaluation to demonstrate the effectiveness of our approach.
A Levenberg-Marquardt method for large nonlinear least squares problems with noisy functions and gradients

In this paper we consider large scale nonlinear least squares problems with noisy function and gradient and propose a Levenberg-Marquardt method for solving such problems. More precisely, we consider that the exact function to optimize is not available or its evaluation is computationally demanding, but that approximations of it are available at any prescribed accuracy level. The proposed method relies on a control of the accuracy level, and requires an improvement of function approximations when the accuracy is detected to be too low to proceed with the optimization process. We prove global and local convergence and complexity of our procedure and show encouraging numerical results on test problems arising in data assimilation and machine learning.