A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Complete nucleotide sequence of pVQS1 containing a quinolone resistance determinant from Salmonella enterica serovar Virchow associated with foreign travel

Nalidixic acid-resistant Salmonella enterica serovars Kentucky (n5) and Virchow (n6) cultured from individuals were investigated for the presence of plasmid-mediated quinolone resistance (PMQR) determinants.

PMQR markers and mutations within the quinolone resistance-determining regions of the target genes were investigated by PCR followed by DNA sequencing. Conjugation, plasmid profiling and targeted PCR were performed to demonstrate the transferability of the qnrS1 gene. Subsequently, a plasmid was identified that carried a quinolone resistance marker and this was completely sequenced.

A Salmonella Virchow isolate carried a qnrS1 gene associated with an IncN incompatibility group conjugative plasmid of 40995 bp, which was designated pVQS1. The latter conferred resistance to ampicillin and nalidixic acid and showed sequence similarity in its core region to plasmid R46, whilst the resistance-encoding region was similar to pAH0376 from Shigella flexneri and pINF5 from Salmonella Infantis and contained an IS26 remnant, a complete Tn3 structure, a truncated IS2 element and a qnrS1 marker, followed by IS26. In contrast to pINF5, IS26 was identified immediately downstream of the qnrS1 gene.

This is the first known report of a qnrS1 gene in Salmonella spp. in Switzerland. Analysis of the complete nucleotide sequence of the qnrS1-containing plasmid showed a novel arrangement of this antibiotic resistance-encoding region.

Dense subgraphs on dynamic networks

In distributed networks, it is often useful for the nodes to be aware of dense subgraphs, e.g., such a dense subgraph could reveal dense substructures in otherwise sparse graphs (e.g. the World Wide Web or social networks); these might reveal community clusters or dense regions for possibly maintaining good communication infrastructure. In this work, we address the problem of self-awareness of nodes in a dynamic network with regards to graph density, i.e., we give distributed algorithms for maintaining dense subgraphs that the member nodes are aware of. The only knowledge that the nodes need is that of the dynamic diameter D, i.e., the maximum number of rounds it takes for a message to traverse the dynamic network. For our work, we consider a model where the number of nodes are fixed, but a powerful adversary can add or remove a limited number of edges from the network at each time step. The communication is by broadcast only and follows the CONGEST model. Our algorithms are continuously executed on the network, and at any time (after some initialization) each node will be aware if it is part (or not) of a particular dense subgraph. We give algorithms that (2 + e)-approximate the densest subgraph and (3 + e)-approximate the at-least-k-densest subgraph (for a given parameter k). Our algorithms work for a wide range of parameter values and run in O(D log n) time. Further, a special case of our results also gives the first fully decentralized approximation algorithms for densest and at-least-k-densest subgraph problems for static distributed graphs. © 2012 Springer-Verlag.

Brief announcement: Maintaining large dense subgraphs on dynamic networks

In distributed networks, some groups of nodes may have more inter-connections, perhaps due to their larger bandwidth availability or communication requirements. In many scenarios, it may be useful for the nodes to know if they form part of a dense subgraph, e.g., such a dense subgraph could form a high bandwidth backbone for the network. In this work, we address the problem of self-awareness of nodes in a dynamic network with regards to graph density, i.e., we give distributed algorithms for maintaining dense subgraphs (subgraphs that the member nodes are aware of). The only knowledge that the nodes need is that of the dynamic diameter D, i.e., the maximum number of rounds it takes for a message to traverse the dynamic network. For our work, we consider a model where the number of nodes are fixed, but a powerful adversary can add or remove a limited number of edges from the network at each time step. The communication is by broadcast only and follows the CONGEST model in the sense that only messages of O(log n) size are permitted, where n is the number of nodes in the network. Our algorithms are continuously executed on the network, and at any time (after some initialization) each node will be aware if it is part (or not) of a particular dense subgraph. We give algorithms that approximate both the densest subgraph, i.e., the subgraph of the highest density in the network, and the at-least-k-densest subgraph (for a given parameter k), i.e., the densest subgraph of size at least k. We give a (2 + e)-approximation algorithm for the densest subgraph problem. The at-least-k-densest subgraph is known to be NP-hard for the general case in the centralized setting and the best known algorithm gives a 2-approximation. We present an algorithm that maintains a (3+e)-approximation in our distributed, dynamic setting. Our algorithms run in O(Dlog n) time. © 2012 Authors.

Complete nucleotide sequence of φCHU: A Luz24likevirus infecting Pseudomonas aeruginosa and displaying a unique host range

A complete nucleotide sequence of the new Pseudomonas aeruginosa Luz24likevirus phiCHU was obtained. This virus was shown to have a unique host range whereby it grew poorly on the standard laboratory strain PAO1, but infected 26 of 46 clinical isolates screened, and strains harboring IncP2 plasmid pMG53. It was demonstrated that phiCHU has single strand interruptions in its genome. Analysis of the phiCHU genome also suggested that recombination event(s) participated in the evolution of the leftmost portion of the genome, presumably encoding early genes.

Complete control of high-harmonic generation for high average power applications

We present a new dual-gas multi-jet HHG source which can be perfectly controlled via phasematching of the long and short trajectory contributions and is applicable for high average power driver laser systems. © 2011 Optical Society of America.

The Complete Works of John Milton: Volume III: The Shorter Poems (826pp.)

Stephen B. Dobranski, Milton Quarterly 49.3 (October, 2015), 181-4:

'By addressing classical and neo-Latin works with which Milton's poems appear to engage, Haan has pursued something unattempted yet. Her erudite and engaging commentary on the Poemata is the most extensive and impressive that I have encountered in any edition ... Haan's discussion of Milton's Poemata - including the Testimonia, the one Italian and four Latin encomia by the poet's acquaintances published in 1645 and 1673 - is remarkably detailed and well-researched. In these sections, readers learn, for example, how Milton's Epitaphium Damonis borrows from both classical writers (Theocritus, Moschus) and contemporary models (Castiglione, Zanchi) while transcending all of them through a pattern of resurrection motifs. Or, readers can discover affinities between Milton's lament on the death of the Bishop of Ely and a poem by the Italian humanist Hieronymo Aleander, Jr., or learn about the connections between Milton's Elegia Quinta and George Buchanan's Maiae Calendae ... The Shorter Poems is a scholarly achievement of the highest order.'

Noam Reisner, Review of English Studies 65 (2014), 744-5:
‘Haan shines with her Neo-Latinist expertise by offering a vivid separate introduction to the Latin poems, which sets up Milton’s poemata specifically within the Neo-Latin contexts of the seventeenth century, thereby dispelling any remaining view of these poems as juvenilia (a view which results from reading the poems chronologically). … The present volume will instantly establish itself as the definitive resource for any reader interested in Milton’s shorter poems, and it is scarcely imaginable that it will ever be eclipsed or be in need of replacing. Its contribution is important in all areas, especially in providing for the first time in a single volume truly valuable documents which can teach us a lot more about Milton’s poetic development than simply reading the poems in chronological sequence. But perhaps, this edition’s greatest achievement is the way in which it succeeds in giving Milton’s Latin poems the pride of place they have long deserved as fully integral to Milton’s complete poetic imagination. Haan’s specific achievement in this regard is less in updating the translations than in providing a different context through which to look at the Latin poems themselves. Haan’s detailed commentaries set the Latin poems in a completely fresh light which looks beyond the obvious classical references and allusions, noted by Carey and many other editors, to Milton’s complex engagement with the Neo-Latin literary culture of his time. It is this aspect of the volume, more than anything else, which vindicates its essentialness.'

Understanding Complete Oxidation of Methane on Spinel Oxides at Molecular Level

It is crucial to develop a catalyst made of earth-abundant elements highly active for a complete oxidation of methane at a relatively low temperature. NiCo₂O₄ consisting of earth-abundant elements which can completely oxidize methane in the temperature range of 350-550 °C. Being a cost-effective catalyst, NiCo₂O₄ exhibits activity higher than precious-metal-based catalysts. Here we report that the higher catalytic activity at the relatively low temperature results from the integration of nickel cations, cobalt cations and surface lattice oxygen atoms/oxygen vacancies at the atomic scale. In situ studies of complete oxidation of methane on NiCo₂O₄ and theoretical simulations show that methane dissociates to methyl on nickel cations and then couple with surface lattice oxygen atoms to form -CH₃O with a following dehydrogenation to -CH₂O; a following oxidative dehydrogenation forms CHO; CHO is transformed to product molecules through two different sub-pathways including dehydrogenation of OCHO and CO oxidation.

EGF61 polymorphism predicts complete pathologic response to cetuximab-based chemoradiation independent of KRAS status in locally advanced rectal cancer patients

BACKGROUND: Cetuximab has shown significant clinical activity in metastatic colon cancer. However, cetuximab-containing neoadjuvant chemoradiation has not been shown to improve tumor response in locally advanced rectal cancer patients in recent phase I/II trials. We evaluated functional germline polymorphisms of genes involved in epidermal growth factor receptor pathway, angiogenesis, antibody-dependent cell-mediated cytotoxicity, DNA repair, and drug metabolism, for their potential role as molecular predictors for clinical outcome in locally advanced rectal cancer patients treated with preoperative cetuximab-based chemoradiation.

METHODS: 130 patients (74 men and 56 women) with locally advanced rectal cancer (4 with stage II, 109 with stage III, and 15 with stage IV, 2 unknown) who were enrolled in phase I/II clinical trials treated with cetuximab-based chemoradiation in European cancer centers were included. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor samples and genotyping was done by using PCR-RFLP assays. Fisher's exact test was used to examine associations between polymorphisms and complete pathologic response (pCR) that was determined by a modified Dworak classification system (grade III vs. grade IV: complete response).

RESULTS: Patients with the epidermal growth factor (EGF) 61 G/G genotype had pCR of 45% (5/11), compared with 21% (11/53) in patients heterozygous, and 2% (1/54) in patients homozygous for the A/A allele (P < 0.001). In addition, this association between EGF 61 G allele and pCR remained significant (P = 0.019) in the 59 patients with wild-type KRAS.

CONCLUSION: This study suggested EGF A+61G polymorphism to be a predictive marker for pCR, independent of KRAS mutation status, to cetuximab-based neoadjuvant chemoradiation of patients with locally advanced rectal cancer.

Spectral characterization of families of split graphs

An upper bound for the sum of the squares of the entries of the principal eigenvector corresponding to a vertex subset inducing a k-regular subgraph is introduced and applied to the determination of an upper bound on the order of such induced subgraphs. Furthermore, for some connected graphs we establish a lower bound for the sum of squares of the entries of the principal eigenvector corresponding to the vertices of an independent set. Moreover, a spectral characterization of families of split graphs, involving its index and the entries of the principal eigenvector corresponding to the vertices of the maximum independent set is given. In particular, the complete split graph case is highlighted.

Weakly spectrally complete pair of matrices

Let and be matrices over an algebraically closed field. Let be elements of such that and . We give necessary and sufficient condition for the existence of matrices and similar to and, respectively, such that has eigenvalues.