On the expressive power of read-once determinants

We introduce and study the notion of read-$k$ projections of the determinant: a polynomial $f \in \mathbb{F}[x_1, \ldots, x_n]$ is called a {\it read-$k$ projection of determinant} if $f=det(M)$, where entries of matrix $M$ are either field elements or variables such that each variable appears at most $k$ times in $M$. A monomial set $S$ is said to be expressible as read-$k$ projection of determinant if there is a read-$k$ projection of determinant $f$ such that the monomial set of $f$ is equal to $S$. We obtain basic results relating read-$k$ determinantal projections to the well-studied notion of determinantal complexity. We show that for sufficiently large $n$, the $n \times n$ permanent polynomial $Perm_n$ and the elementary symmetric polynomials of degree $d$ on $n$ variables $S_n^d$ for $2 \leq d \leq n-2$ are not expressible as read-once projection of determinant, whereas $mon(Perm_n)$ and $mon(S_n^d)$ are expressible as read-once projections of determinant. We also give examples of monomial sets which are not expressible as read-once projections of determinant

Semidefinite Representation of the kk-Ellipse

The $k$-ellipse is the plane algebraic curve consisting of all points whose sum of distances from $k$ given points is a fixed number. The polynomial equation defining the $k$-ellipse has degree $2^k$ if $k$ is odd and degree $2^k{-}\binom{k}{k/2}$ if $k$ is even. We express this polynomial equation as the determinant of a symmetric matrix of linear polynomials. Our representation extends to weighted $k$-ellipses and $k$-ellipsoids in arbitrary dimensions, and it leads to new geometric applications of semidefinite programming.Comment: 16 pages, 5 figure

Negotiations of minority ethnic rugby league players in the Cathar country of France

This article is based on new empirical, qualitative research with minority ethnic rugby league players in the southwest of France. Drawing on similar research on rugby league in the north and the south of England, the article examines how rugby league, traditionally viewed as a white, working-class male game (Collins, 2006; Denham, 2004; Spracklen, 1995, 2001) has had to re-imagine its symbolic boundaries as they are constituted globally and locally to accommodate the needs of players from minority ethnic backgrounds. In particular, the article examines the sense in which experiences of minority ethnic rugby league players in France compare with those of their counterparts in England (Spracklen, 2001, 2007), how rugby league is used in France to construct identity, and in what sense the norms associated with the imaginary community of rugby league are replicated or challenged by the involvement of minority ethnic rugby league players in France. Questions about what it means to be (provincial, national) French (Kumar, 2006) are posed, questions that relate to the role of sport in the construction of Frenchness, and in particular the role of rugby league (and union). © Copyright ISSA and SAGE Publications

Leukaemogenic effects of Ptpn11 activating mutations in the stem cell microenvironment

Germline activating mutations of the protein tyrosine phosphatase SHP2 (encoded by PTPN11), a positive regulator of the RAS signalling pathway, are found in 50% of patients with Noonan syndrome. These patients have an increased risk of developing leukaemia, especially juvenile myelomonocytic leukaemia (JMML), a childhood myeloproliferative neoplasm (MPN). Previous studies have demonstrated that mutations in Ptpn11 induce a JMML-like MPN through cell-autonomous mechanisms that are dependent on Shp2 catalytic activity. However, the effect of these mutations in the bone marrow microenvironment remains unclear. Here we report that Ptpn11 activating mutations in the mouse bone marrow microenvironment promote the development and progression of MPN through profound detrimental effects on haematopoietic stem cells (HSCs). Ptpn11 mutations in mesenchymal stem/progenitor cells and osteoprogenitors, but not in differentiated osteoblasts or endothelial cells, cause excessive production of the CC chemokine CCL3 (also known as MIP-1α), which recruits monocytes to the area in which HSCs also reside. Consequently, HSCs are hyperactivated by interleukin-1β and possibly other proinflammatory cytokines produced by monocytes, leading to exacerbated MPN and to donor-cell-derived MPN following stem cell transplantation. Remarkably, administration of CCL3 receptor antagonists effectively reverses MPN development induced by the Ptpn11-mutated bone marrow microenvironment. This study reveals the critical contribution of Ptpn11 mutations in the bone marrow microenvironment to leukaemogenesis and identifies CCL3 as a potential therapeutic target for controlling leukaemic progression in Noonan syndrome and for improving stem cell transplantation therapy in Noonan-syndrome-associated leukaemias

A new approach to local hardness

The applicability of the local hardness as defined by the derivative of the chemical potential with respect to the electron density is undermined by an essential ambiguity arising from this definition. Further, the local quantity defined in this way does not integrate to the (global) hardness - in contrast with the local softness, which integrates to the softness. It has also been shown recently that with the conventional formulae, the largest values of local hardness do not necessarily correspond to the hardest regions of a molecule. Here, in an attempt to fix these drawbacks, we propose a new approach to define and evaluate the local hardness. We define a local chemical potential, utilizing the fact that the chemical potential emerges as the additive constant term in the number-conserving functional derivative of the energy density functional. Then, differentiation of this local chemical potential with respect to the number of electrons leads to a local hardness that integrates to the hardness, and possesses a favourable property; namely, within any given electron system, it is in a local inverse relation with the Fukui function, which is known to be a proper indicator of local softness in the case of soft systems. Numerical tests for a few selected molecules and a detailed analysis, comparing the new definition of local hardness with the previous ones, show promising results.Comment: 30 pages (including 6 figures, 1 table

Bubbles and denaturation in DNA

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular dynamics studies, were premature. This could either imply that the present PBD should be improved or that biological activity can only be predicted in a more complex frame work that involves interactions with proteins and super helical stresses. In this article, we give detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as function of position and bubble size and the so-called $l$-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG 200

Spin Gaps in High Temperature Superconductors

The phenomenology and theory of spin gap effects in high temperature superconductors is summarized. It is argued that the spin gap behavior can only be explained by a model of charge 0 spin 1/2 fermions which become paired into singlets and that there are both theoretical and experimental reasons for believing that the pairing is greatly enhanced in the bilayer structure of the $YBa_2Cu_3O_{6+x}$ system. This article will appear in the Proceedings of the Stanford Conference on Spectroscopies in Novel Superconductors. To obtain postscript files containing the figures send mail to [email protected]: 9 pages, revtex. To obtain figures contact [email protected]

RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.

Dermatophytes are the most common agents of superficial mycoses in humans and animals. The aim of the present investigation was to systematically identify the extracellular, possibly secreted, proteins that are putative virulence factors and antigenic molecules of dermatophytes. A complete gene expression profile of Arthroderma benhamiae was obtained during infection of its natural host (guinea pig) using RNA sequencing (RNA-seq) technology. This profile was completed with those of the fungus cultivated in vitro in two media containing either keratin or soy meal protein as the sole source of nitrogen and in Sabouraud medium. More than 60% of transcripts deduced from RNA-seq data differ from those previously deposited for A. benhamiae. Using these RNA-seq data along with an automatic gene annotation procedure, followed by manual curation, we produced a new annotation of the A. benhamiae genome. This annotation comprised 7,405 coding sequences (CDSs), among which only 2,662 were identical to the currently available annotation, 383 were newly identified, and 15 secreted proteins were manually corrected. The expression profile of genes encoding proteins with a signal peptide in infected guinea pigs was found to be very different from that during in vitro growth when using keratin as the substrate. Especially, the sets of the 12 most highly expressed genes encoding proteases with a signal sequence had only the putative vacuolar aspartic protease gene PEP2 in common, during infection and in keratin medium. The most upregulated gene encoding a secreted protease during infection was that encoding subtilisin SUB6, which is a known major allergen in the related dermatophyte Trichophyton rubrum. IMPORTANCE Dermatophytoses (ringworm, jock itch, athlete's foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing annotation for A. benhamiae. Comparing gene expression during infection on guinea pigs with keratin degradation in vitro, which is supposed to mimic the host environment, revealed the critical importance of using real in vivo conditions for investigating virulence mechanisms. The analysis of genes expressed in vivo, encoding cell surface and secreted proteins, particularly proteases, led to the identification of new allergen and virulence factor candidates

Metabolic Effects of Acute Thiamine Depletion Are Reversed by Rapamycin in Breast and Leukemia Cells

Thiamine-dependent enzymes (TDEs) control metabolic pathways that are frequently altered in cancer and therefore present cancer-relevant targets. We have previously shown that the recombinant enzyme thiaminase cleaves and depletes intracellular thiamine, has growth inhibitory activity against leukemia and breast cancer cell lines, and that its growth inhibitory effects were reversed in leukemia cell lines by rapamycin. Now, we first show further evidence of thiaminase therapeutic potential by demonstrating its activity against breast and leukemia xenografts, and against a primary leukemia xenograft. We therefore further explored the metabolic effects of thiaminase in combination with rapamycin in leukemia and breast cell lines. Thiaminase decreased oxygen consumption rate and increased extracellular acidification rate, consistent with the inhibitory effect of acute thiamine depletion on the activity of the TDEs pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes; these effects were reversed by rapamycin. Metabolomic studies demonstrated intracellular thiamine depletion and the presence of the thiazole cleavage product in thiaminase-treated cells, providing validation of the experimental procedures. Accumulation of ribose and ribulose in both cell lines support the thiaminase-mediated suppression of the TDE transketolase. Interestingly, thiaminase suppression of another TDE, branched chain amino ketoacid dehydrogenase (BCKDH), showed very different patterns in the two cell lines: in RS4 leukemia cells it led to an increase in BCKDH substrates, and in MCF-7 breast cancer cells it led to a decrease in BCKDH products. Immunoblot analyses showed corresponding differences in expression of BCKDH pathway enzymes, and partial protection of thiaminase growth inhibition by gabapentin indicated that BCKDH inhibition may be a mechanism of thiaminase-mediated toxicity. Surprisingly, most of thiaminase-mediated metabolomic effects were also reversed by rapamycin. Thus, these studies demonstrate that acute intracellular thiamine depletion by recombinant thiaminase results in metabolic changes in thiamine-dependent metabolism, and demonstrate a previously unrecognized role of mTOR signaling in the regulation of thiamine-dependent metabolism

Australian clinical practice guidelines for the diagnosis and management of Barrett's esophagus and early esophageal adenocarcinoma

Author version made available following 12 month embargo from date of publication according to publisher copyright policy.Barrett's esophagus (BE), a common condition, is the only known precursor to esophageal adenocarcinoma (EAC). There is uncertainty about the best way to manage BE as most people with BE never develop EAC and most patients diagnosed with EAC have no preceding diagnosis of BE. Moreover, there have been recent advances in knowledge and practice about the management of BE and early EAC. To aid clinical decision making in this rapidly moving field, Cancer Council Australia convened an expert working party to identify pertinent clinical questions. The questions covered a wide range of topics including endoscopic and histological definitions of BE and early EAC; prevalence, incidence, natural history, and risk factors for BE; and methods for managing BE and early EAC. The latter considered modification of lifestyle factors; screening and surveillance strategies; and medical, endoscopic, and surgical interventions. To answer each question, the working party systematically reviewed the literature and developed a set of recommendations through consensus. Evidence underpinning each recommendation was rated according to quality and applicability