Hitting all Maximal Independent Sets of a Bipartite Graph

We prove that given a bipartite graph G with vertex set V and an integer k, deciding whether there exists a subset of V of size k hitting all maximal independent sets of G is complete for the class Sigma_2^P.Comment: v3: minor chang

On 1-factorizations of Bipartite Kneser Graphs

It is a challenging open problem to construct an explicit 1-factorization of the bipartite Kneser graph $H(v,t)$, which contains as vertices all $t$-element and $(v-t)$-element subsets of $[v]:=\{1,\ldots,v\}$ and an edge between any two vertices when one is a subset of the other. In this paper, we propose a new framework for designing such 1-factorizations, by which we solve a nontrivial case where $t=2$ and $v$ is an odd prime power. We also revisit two classic constructions for the case $v=2t+1$ --- the \emph{lexical factorization} and \emph{modular factorization}. We provide their simplified definitions and study their inner structures. As a result, an optimal algorithm is designed for computing the lexical factorizations. (An analogous algorithm for the modular factorization is trivial.)Comment: We design the first explicit 1-factorization of H(2,q), where q is a odd prime powe

Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase

Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load

Control over phase separation and nucleation using a laser-tweezing potential

Control over the nucleation of new phases is highly desirable but elusive. Even though there is a long history of crystallization engineering by varying physicochemical parameters, controlling which polymorph crystallizes or whether a molecule crystallizes or forms an amorphous precipitate is still a poorly understood practice. Although there are now numerous examples of control using laser-induced nucleation, the absence of physical understanding is preventing progress. Here we show that the proximity of a liquid–liquid critical point or the corresponding binodal line can be used by a laser-tweezing potential to induce concentration gradients. A simple theoretical model shows that the stored electromagnetic energy of the laser beam produces a free-energy potential that forces phase separation or triggers the nucleation of a new phase. Experiments in a liquid mixture using a low-power laser diode confirm the effect. Phase separation and nucleation using a laser-tweezing potential explains the physics behind non-photochemical laser-induced nucleation and suggests new ways of manipulating matter

Involving research participants in a pan-European research initiative: the EPAD participant panel experience

Abstract: Background: Including participants in patient and public involvement activities is increasingly acknowledged as a key pillar of successful research activity. Such activities can influence recruitment and retention, as well as researcher experience and contribute to decision making in research studies. However, there are few established methodologies of how to set up and manage participant involvement activities. Further, there is little discussion of how to do so when dealing with collaborative projects that run across countries and operate in multiple linguistic and regulatory contexts. Methods: In this paper we describe the set-up, running and experiences of the EPAD participant panel. The EPAD study was a pan-European cohort study with the aim to understand risks for developing Alzheimer’s disease and build a readiness cohort for Phase 2 clinical trials. Due to the longitudinal nature of this study, combined with the enrolment of healthy volunteers and those with mild cognitive impairments, the EPAD team highlighted participant involvement as crucial to the success of this project. The EPAD project employed a nested model, with local panels meeting in England, France, Scotland, Spain and The Netherlands, and feeding into a central study panel. The local panels were governed by terms of reference which were adaptable to local needs. Results: The impact of the panels has been widespread, and varies from feedback on documentation, to supporting with design of media materials and representation of the project at national and international meetings. Conclusions: The EPAD panels have contributed to the success of the project and the model established is easily transferable to other disease areas investigating healthy or at-risk populations

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

BACKGROUND: The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk. RESULTS: Although the function of disease-associated non-coding single nucleotide polymorphisms (SNPs) at 6q23 is unknown, the association is generally assigned to TNFAIP3, the closest gene. However, the DNA fragment containing the associated SNPs interacts through chromatin looping not only with TNFAIP3, but also with IL20RA, located 680 kb upstream. The risk allele of the most likely causal SNP, rs6927172, is correlated with both a higher frequency of interactions and increased expression of IL20RA, along with a stronger binding of both the NFκB transcription factor and chromatin marks characteristic of active enhancers in T-cells. CONCLUSIONS: Our results highlight the importance of gene assignment for translating GWAS findings into biologically meaningful mechanisms of disease and potential therapeutic targets; indeed, monoclonal antibody therapy targeting IL-20 is effective in the treatment of rheumatoid arthritis and psoriasis, both with strong GWAS associations to this region

Some implications of superconducting quantum interference to the application of master equations in engineering quantum technologies

In this paper we consider the modeling and simulation of open quantum systems from a device engineering perspective. We derive master equations at different levels of approximation for a superconducting quantum interference device (SQUID) ring coupled to an ohmic bath. We demonstrate that the master equations we consider produce decoherences that are qualitatively and quantitatively dependent on both the level of approximation and the ring's external flux bias. We discuss the issues raised when seeking to obtain Lindbladian dissipation and show, in this case, that the external flux (which may be considered to be a control variable in some applications) is not confined to the Hamiltonian, as often assumed in quantum control, but also appears in the Lindblad terms

Natural occurrence of Cucumber mosaic virus infecting water mint (Mentha aquatica) in Antalya and Konya, Turkey

A virus causing a disease in mint (the aromatic and culinary plant) has recently become a problem in the Taurus Mountains, a mountain range in the Mediterranean region of Turkey. To detect the virus and investigate its distribution in the region, mint leaf samples were collected from the vicinity of spring areas in the plateaus of Antalya and Konya in 2009. It was found that Cucumber mosaic virus (CMV) was detected in 27.08% of symptomatic samples tested by DAS-ELISA. To the best of our knowledge, this is the first report of CMV on mint plants in this region of Turkey

Measurements on the reality of the wavefunction

Quantum mechanics is an outstandingly successful description of nature, underpinning fields from biology through chemistry to physics. At its heart is the quantum wavefunction, the central tool for describing quantum systems. Yet it is still unclear what the wavefunction actually is: does it merely represent our limited knowledge of a system, or is it an element of reality? Recent no-go theorems argued that if there was any underlying reality to start with, the wavefunction must be real. However, that conclusion relied on debatable assumptions, without which a partial knowledge interpretation can be maintained to some extent. A different approach is to impose bounds on the degree to which knowledge interpretations can explain quantum phenomena, such as why we cannot perfectly distinguish non-orthogonal quantum states. Here we experimentally test this approach with single photons. We find that no knowledge interpretation can fully explain the indistinguishability of non-orthogonal quantum states in three and four dimensions. Assuming that some underlying reality exists, our results strengthen the view that the entire wavefunction should be real. The only alternative is to adopt more unorthodox concepts such as backwards-in-time causation, or to completely abandon any notion of objective reality.Comment: 7 pages, 4 figure

Herpes Simplex Virus Type 2, Genital Ulcers and HIV-1 Disease Progression in Postpartum Women

Co-infection with herpes simplex virus type 2 (HSV-2) has been associated with increased HIV-1 RNA levels and immune activation, two predictors of HIV-1 progression. The impact of HSV-2 on clinical outcomes among HIV-1 infected pregnant women is unclear.HIV-1 infected pregnant women in Nairobi were enrolled antenatally and HSV-2 serology was obtained. HIV-1 RNA and CD4 count were serially measured for 12-24 months postpartum. Survival analysis using endpoints of death, opportunistic infection (OI), and CD4<200 cells µL, and linear mixed models estimating rate of change of HIV-1 RNA and CD4, were used to determine associations between HSV-2 serostatus and HIV-1 progression.Among 296 women, 254 (86%) were HSV-2-seropositive. Only 30 (10%) women had prior or current genital ulcer disease (GUD); median baseline CD4 count was 422 cells µL. Adjusting for baseline CD4, women with GUD were significantly more likely to have incident OIs (adjusted hazard ratio (aHR) 2.79, 95% CI: 1.33-5.85), and there was a trend for association between HSV-2-seropositivity and incident OIs (aHR 3.83, 95% CI: 0.93-15.83). Rate of change in CD4 count and HIV-1 RNA did not differ by HSV-2 status or GUD, despite a trend toward higher baseline HIV-1 RNA in HSV-2-seropositive women (4.73 log10 copies/ml vs. 4.47 log10 copies/ml, P = 0.07).HSV-2 was highly prevalent and pregnant HIV-1 infected women with GUD were significantly more likely to have incident OIs than women without GUD, suggesting that clinically evident HSV-2 is a more important predictor of HIV-1 disease progression than asymptomatic HSV-2