Approximating k-Forest with Resource Augmentation: A Primal-Dual Approach

In this paper, we study the $k$-forest problem in the model of resource augmentation. In the $k$-forest problem, given an edge-weighted graph $G(V,E)$, a parameter $k$, and a set of $m$ demand pairs $\subseteq V \times V$, the objective is to construct a minimum-cost subgraph that connects at least $k$ demands. The problem is hard to approximate---the best-known approximation ratio is $O(\min\{\sqrt{n}, \sqrt{k}\})$. Furthermore, $k$-forest is as hard to approximate as the notoriously-hard densest $k$-subgraph problem. While the $k$-forest problem is hard to approximate in the worst-case, we show that with the use of resource augmentation, we can efficiently approximate it up to a constant factor. First, we restate the problem in terms of the number of demands that are {\em not} connected. In particular, the objective of the $k$-forest problem can be viewed as to remove at most $m-k$ demands and find a minimum-cost subgraph that connects the remaining demands. We use this perspective of the problem to explain the performance of our algorithm (in terms of the augmentation) in a more intuitive way. Specifically, we present a polynomial-time algorithm for the $k$-forest problem that, for every $\epsilon>0$, removes at most $m-k$ demands and has cost no more than $O(1/\epsilon^{2})$ times the cost of an optimal algorithm that removes at most $(1-\epsilon)(m-k)$ demands

A numerical modelling and simulation of core-scale sandstone acidizing process: a study on the effect of temperature

A wide and comprehensive understanding of the chemical reactions and mechanisms of HBF4 is crucial as it significantly influences its performance in stimulating a sandstone formation. In general, it is well-known that HBF4 is able to provide a deeper penetration into the sandstone matrix before being spent due to its uniquely slow hydrolysis ability to produce HF. In the present study, a 3D numerical modelling and simulation were conducted to examine the capability of HBF4 in enhancing the porosity and permeability of the sandstone matrix. The model is built in COMSOL® Multiphysics commercial software of computational fluid dynamics (CFD) to simulate the acid core flooding process on sandstone core. The model had been validated against the experimental data in the literature. The results matched with the measured plot data very well. The effect of temperature on the performance HBF4 sandstone acidizing is evaluated in this study. The simulation results indicated that at low temperature of 25 °C, HBF4 is not very effective, as justified in its poor porosity and permeability increments of only 1.07 and 1.23, respectively. However, at elevated temperatures, the porosity and permeability enhancement also become increasingly more significant, which showed 1.26 and 2.06, respectively, at 65 °C; and 1.67 and 7.06, respectively, at 105 °C. Therefore, one can conclude that HBF4 acid treatment performed better at elevated temperatures due to increased hydrolysis rate, which is a governing function in HBF4 sandstone acidizing. Overall, this model had provided a reliable alternative to optimize various other parameters of HBF4 acid treatment

Escherichia coli induces apoptosis and proliferation of mammary cells

Mammary cell apoptosis and proliferation were assessed after injection of Escherichia coli into the left mammary quarters of six cows. Bacteriological analysis of foremilk samples revealed coliform infection in the injected quarters of four cows. Milk somatic cell counts increased in these quarters and peaked at 24 h after bacterial injection. Body temperature also increased, peaking at 12 h postinjection, The number of apoptotic cells was significantly higher in the mastitic tissue than in the uninfected control. Expression of Bax and interleukin-1 beta converting enzyme increased in the mastitic tissue at 24 h and 72 h postinfection, whereas Bcl-2 expression decreased at 24 h but did not differ significantly from the control at 72 h postinfection, Induction of matrix metalloproteinase-g, stromelysin-1 and urokinase-type plasminogen activator was also observed in the mastitic tissue. Moreover, cell proliferation increased in the infected tissue, These results demonstrate that Escherichia coli-induced mastitis promotes apoptosis and cell proliferation

An Analysis of Solution Properties of the Graph Coloring Problem

This paper concerns the analysis of solution properties of the Graph Coloring Problem. For this purpose, we introduce a property based on the notion of representative sets which are sets of vertices that are always colored the same in a set of solutions. Experimental results on well-studied DIMACS graphs show that many of them contain such sets and give interesting information about the diversity of the solutions. We also show how such an analysis may be used to improve a tabu search algorithm

Diagnostic accuracy of consensus diagnostic criteria for frontotemporal dementia in a memory clinic population

Background/Aims: The goal of the present study was to evaluate the diagnostic accuracy of the core diagnostic criteria for frontotemporal dementia (FTD) [Neary D, et al: Neurology 1998;51:1546-1554] within a memory clinic population. Methods: The 5 core diagnostic criteria for FTD were operationalised in an informant-based written questionnaire. For a diagnosis of FTD the total clinical picture was weighted with findings on additional investigations and possible exclusion criteria, with follow-up of at least 1 year. Results: The operationalised core criteria for FTD had a sensitivity of 79% (95% CI = 57-92) and a specificity of 90% (95% CI = 85-94). Conclusion: The core diagnostic criteria for FTD applied in a caregiver questionnaire have good diagnostic accuracy among subjects without advanced dementia attending a memory clinic. This stresses the importance of the informant-based history in the differential diagnosis of dementia. Copyrigh

A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome

Expression of Toll-like Receptor 9 in nose, peripheral blood and bone marrow during symptomatic allergic rhinitis

BACKGROUND: Allergic rhinitis is an inflammatory disease of the upper airway mucosa that also affects leukocytes in bone marrow and peripheral blood. Toll-like receptor 9 (TLR9) is a receptor for unmethylated CpG dinucleotides found in bacterial and viral DNA. The present study was designed to examine the expression of TLR9 in the nasal mucosa and in leukocytes derived from different cellular compartments during symptomatic allergic rhinitis. METHODS: The study was based on 32 patients with seasonal allergic rhinitis and 18 healthy subjects, serving as controls. Nasal biopsies were obtained before and after allergen challenge. Bone marrow, peripheral blood and nasal lavage fluid were sampled outside and during pollen season. The expression of TLR9 in tissues and cells was analyzed using immunohistochemistry and flow cytometry, respectively. RESULTS: TLR9 was found in several cell types in the nasal mucosa and in different leukocyte subpopulations derived from bone marrow, peripheral blood and nasal lavage fluid. The leukocyte expression was generally higher in bone marrow than in peripheral blood, and not affected by symptomatic allergic rhinitis. CONCLUSION: The widespread expression of TLR9 in the nasal mucosa along with its rich representation in leukocytes in different compartments, demonstrate the possibility for cells involved in allergic airway inflammation to directly interact with bacterial and viral DNA

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

<p>Abstract</p> <p>Background</p> <p>Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles.</p> <p>Results</p> <p>The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors.</p> <p>Conclusion</p> <p>The SMM-align method was shown to outperform other state of the art MHC class II prediction methods. The method predicts quantitative peptide:MHC binding affinity values, making it ideally suited for rational epitope discovery. The method has been trained and evaluated on the, to our knowledge, largest benchmark data set publicly available and covers the nine HLA-DR supertypes suggested as well as three mouse H2-IA allele. Both the peptide benchmark data set, and SMM-align prediction method (<it>NetMHCII</it>) are made publicly available.</p