k-Trails: Recognition, Complexity, and Approximations

The notion of degree-constrained spanning hierarchies, also called k-trails, was recently introduced in the context of network routing problems. They describe graphs that are homomorphic images of connected graphs of degree at most k. First results highlight several interesting advantages of k-trails compared to previous routing approaches. However, so far, only little is known regarding computational aspects of k-trails. In this work we aim to fill this gap by presenting how k-trails can be analyzed using techniques from algorithmic matroid theory. Exploiting this connection, we resolve several open questions about k-trails. In particular, we show that one can recognize efficiently whether a graph is a k-trail. Furthermore, we show that deciding whether a graph contains a k-trail is NP-complete; however, every graph that contains a k-trail is a (k+1)-trail. Moreover, further leveraging the connection to matroids, we consider the problem of finding a minimum weight k-trail contained in a graph G. We show that one can efficiently find a (2k-1)-trail contained in G whose weight is no more than the cheapest k-trail contained in G, even when allowing negative weights. The above results settle several open questions raised by Molnar, Newman, and Sebo

Algorithms for outerplanar graph roots and graph roots of pathwidth at most 2

Deciding whether a given graph has a square root is a classical problem that has been studied extensively both from graph theoretic and from algorithmic perspectives. The problem is NP-complete in general, and consequently substantial effort has been dedicated to deciding whether a given graph has a square root that belongs to a particular graph class. There are both polynomial-time solvable and NP-complete cases, depending on the graph class. We contribute with new results in this direction. Given an arbitrary input graph G, we give polynomial-time algorithms to decide whether G has an outerplanar square root, and whether G has a square root that is of pathwidth at most 2

Lack of structural rearrangement in c-kit and stem cell factor genes in Hong Kong Chinese patients with myelodysplastic syndromes or acute myeloid leukaemia

Stem cell factor is a haemopoietic growth factor that interacts with the c-kit--encoded transmembrane tyrosine kinase receptor during signal transduction in haemopoietic progenitor stem cells. We have screened 127 Chinese patients with myelodysplastic syndromes or acute myeloid leukaemia for structural rearrangements in the stem cell factor and c-kit genes using Southern blot analysis. No structural rearrangements were detected in any of the bone marrow samples that were tested. It seems that structural rearrangements in the stem cell factor and c-kit genes are rare in Hong Kong patients who have a haematological malignancy.published_or_final_versio

Degree bounded matroids and submodular flows

We consider two related problems, the Minimum Bounded Degree Matroid Basis problem and the Minimum Bounded Degree Submodular Flow problem. The first problem is a generalization of the Minimum Bounded Degree Spanning Tree problem: We are given a matroid and a hypergraph on its ground set with lower and upper bounds f(e)≤g(e) for each hyperedge e. The task is to find a minimum cost basis which contains at least f(e) and at most g(e) elements from each hyperedge e. In the second problem we have a submodular flow problem, a lower bound f(v) and an upper bound g(v) for each node v, and the task is to find a minimum cost 0-1 submodular flow with the additional constraint that the sum of the incoming and outgoing flow at each node v is between f(v) and g(v). Both of these problems are NP-hard (even the feasibility problems are NP-complete), but we show that they can be approximated in the following sense. Let opt be the value of the optimal solution. For the first problem we give an algorithm that finds a basis B of cost no more than opt such that f(e)-2Δ+1≤|B∩e|≤g(e)+2Δ-1 for every hyperedge e, where Δ is the maximum degree of the hypergraph. If there are only upper bounds (or only lower bounds), then the violation can be decreased to Δ-1. For the second problem we can find a 0-1 submodular flow of cost at most opt where the sum of the incoming and outgoing flow at each node v is between f(v)-1 and g(v)+1. These results can be applied to obtain approximation algorithms for several combinatorial optimization problems with degree constraints, including the Minimum Crossing Spanning Tree problem, the Minimum Bounded Degree Spanning Tree Union problem, the Minimum Bounded Degree Directed Cut Cover problem, and the Minimum Bounded Degree Graph Orientation problem. © 2012 János Bolyai Mathematical Society and Springer-Verlag Berlin Heidelberg

Prevalence and genotypes of α- and β-thalassemia carriers in Hong Kong - Implications for population screening

Background: The thalassemias are common in southern China. We determined the prevalence of heterozygous carriers of these genetic disorders in Hong Kong and assessed the feasibility of a community-based screening program. Methods: An educational and screening program for the thalassemias was carried out in three high schools with a total of 2420 students. Seventy- five percent of the students agreed to undergo screening, which consisted of blood counts, hemoglobin electrophoresis, serum ferritin measurements, and DNA analyses. Results: Of the 1800 blood samples tested, 150 (8.3 percent) had microcytosis (mean corpuscular volume, <80 μm3). Ninety students (5.0 percent) were carriers of α-thalassemia, of whom 81 (4.5 percent) were carriers of the Southeast Asian type of deletion, in which both α-globin genes on the same chromosome 16 are deleted. Sixty-one students (3.4 percent) were carriers of either β-thalassemia or the mutation coding for hemoglobin E. Six students were carriers of both α- and β-thalassemias. On the basis of these figures, the estimated numbers of pregnancies in Hong Kong in which the fetus is at risk for homozygous α-thalassemia and β-thalassemia major or intermedia are 145 and 80 per year, respectively. In Hong Kong the actual numbers of women referred for prenatal diagnoses of these disorders are approximately 95 and 40 per year, respectively. Conclusions: Despite the availability of hospital-based screening and prenatal diagnosis for many years in Hong Kong, many women carrying fetuses at risk for thalassemia are not referred for genetic counseling. A community-based program of education, screening, and counseling is needed in Hong Kong and southern China.published_or_final_versio

Identification of diverse lipid-binding modes in the groove of zinc α2 glycoprotein reveals its functional versatility

ZAG is a multifunctional glycoprotein with a class I MHC-like protein fold and an α1-α2 lipid-binding groove. The intrinsic ZAG ligand is unknown. Our previous studies showed that ZAG binds the dansylated C11 fatty acid, DAUDA, differently to the boron dipyrromethane C16 fatty acid, C16-BODIPY. Here, the molecular basis for this difference was elucidated. Multi-wavelength analytical ultracentrifugation confirmed that DAUDA and C16-BODIPY individually bind to ZAG and compete for the same binding site. Molecular docking of lipid-binding in the structurally related CD1-proteins predicted nine conserved ligand contact residues in ZAG. Twelve mutants were accordingly created by alanine scanning site directed mutagenesis for characterisation. Mutation of Y12 caused ZAG to misfold. Mutation of K147, R157 and A158 abrogated C16-BODIPY but not DAUDA binding. L69 and T169 increased the fluorescence emission intensity of C16-BODIPY but not of DAUDA compared to wild-type ZAG and showed that C16-BODIPY binds close to T169 and L69. Distance measurements of the crystal structure revealed K147 forms a salt bridge with D83. A range of bioactive bulky lipids including phospholipids and sphingolipids displaced DAUDA from the ZAG binding site but unexpectedly did not displace C16-BODIPY. We conclude that the ZAG α1-α2 groove contains separate but overlapping sites for DAUDA and C16-BODIPY and is involved in binding to a bulkier and wider repertoire of lipids than previously reported. This work suggested that the in vivo activity of ZAG may be dictated by its lipid ligand

Modulation of human cardiac transient outward potassium current by EGFR tyrosine kinase and Src-family kinases

Aims: The human cardiac transient outward K + current Ito (encoded by Kv4.3 or KCND3) plays an important role in phase 1 rapid repolarization of cardiac action potentials in the heart. However, modulation of I to by intracellular signal transduction is not fully understood. The present study was therefore designed to determine whether/how human atrial I to and hKv4.3 channels stably expressed in HEK 293 cells are regulated by protein tyrosine kinases (PTKs). Methods and results: Whole-cell patch voltage-clamp, immunoprecipitation, western blotting, and site-directed mutagenesis approaches were employed in the present study. We found that human atrial I to was inhibited by the broad-spectrum PTK inhibitor genistein, the selective epidermal growth factor receptor (EGFR) kinase inhibitor AG556, and the Src-family kinases inhibitor PP2. The inhibitory effect was countered by the protein tyrosine phosphatase inhibitor orthovanadate. In HEK 293 cells stably expressing human KCND3, genistein, AG556, and PP2 significantly reduced the hKv4.3 current, and the reduction was antagonized by orthovanadate. Interestingly, orthovanadate also reversed the reduced tyrosine phosphorylation level of hKv4.3 channels by genistein, AG556, or PP2. Mutagenesis revealed that the hKv4.3 mutant Y136F lost the inhibitory response to AG556, while Y108F lost response to PP2. The double-mutant Y108FY136F hKv4.3 channels showed no response to either AG556 or PP2. Conclusion: Our results demonstrate that human atrial Ito and cloned hKv4.3 channels are modulated by EGFR kinase via phosphorylation of the Y136 residue and by Src-family kinases via phosphorylation of the Y108 residue; tyrosine phosphorylation of the channel may be involved in regulating cardiac electrophysiology. © The Author 2011.postprin

Using Social Media for Actionable Disease Surveillance and Outbreak Management: A Systematic Literature Review

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Upregulation of the cell-cycle regulator RGC-32 in Epstein-Barr virus-immortalized cells

Epstein-Barr virus (EBV) is implicated in the pathogenesis of multiple human tumours of lymphoid and epithelial origin. The virus infects and immortalizes B cells establishing a persistent latent infection characterized by varying patterns of EBV latent gene expression (latency 0, I, II and III). The CDK1 activator, Response Gene to Complement-32 (RGC-32, C13ORF15), is overexpressed in colon, breast and ovarian cancer tissues and we have detected selective high-level RGC-32 protein expression in EBV-immortalized latency III cells. Significantly, we show that overexpression of RGC-32 in B cells is sufficient to disrupt G2 cell-cycle arrest consistent with activation of CDK1, implicating RGC-32 in the EBV transformation process. Surprisingly, RGC-32 mRNA is expressed at high levels in latency I Burkitt's lymphoma (BL) cells and in some EBV-negative BL cell-lines, although RGC-32 protein expression is not detectable. We show that RGC-32 mRNA expression is elevated in latency I cells due to transcriptional activation by high levels of the differentially expressed RUNX1c transcription factor. We found that proteosomal degradation or blocked cytoplasmic export of the RGC-32 message were not responsible for the lack of RGC-32 protein expression in latency I cells. Significantly, analysis of the ribosomal association of the RGC-32 mRNA in latency I and latency III cells revealed that RGC-32 transcripts were associated with multiple ribosomes in both cell-types implicating post-initiation translational repression mechanisms in the block to RGC-32 protein production in latency I cells. In summary, our results are the first to demonstrate RGC-32 protein upregulation in cells transformed by a human tumour virus and to identify post-initiation translational mechanisms as an expression control point for this key cell-cycle regulator

Inorganic nitrate attenuates cardiac dysfunction: roles for xanthine oxidoreductase and nitric oxide

Nitric oxide (NO) is a vasodilator and independent modulator of cardiac remodelling. Commonly, in cardiac disease (e.g. heart failure) endothelial dysfunction (synonymous with NO-deficiency) has been implicated in increased blood pressure (BP), cardiac hypertrophy and fibrosis. Currently no effective therapies replacing NO have succeeded in the clinic. Inorganic nitrate (NO3 - ), through chemical reduction to nitrite and then NO, exerts potent BP-lowering but whether it might be useful in treating undesirable cardiac remodelling is unknown. In a nested age- and sex-matched case-control study of hypertensive patients +/- left ventricular hypertrophy (NCT03088514) we show that lower plasma nitrite concentration and vascular dysfunction accompany cardiac hypertrophy and fibrosis in patients. In mouse models of cardiac remodelling, we also show that restoration of circulating nitrite levels using dietary nitrate improves endothelial dysfunction through targeting of xanthine oxidoreductase (XOR)-driven H2 O2 and superoxide, and reduces cardiac fibrosis through NO-mediated block of SMAD-phosphorylation leading to improvements in cardiac structure and function. We show that via these mechanisms dietary nitrate offers easily translatable therapeutic options for treatment of cardiac dysfunction