Covering Pairs in Directed Acyclic Graphs

The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In this paper, we study the computational complexity of two constrained variants of Minimum Path Cover motivated by the recent introduction of next-generation sequencing technologies in bioinformatics. The first problem (MinPCRP), given a DAG and a set of pairs of vertices, asks for a minimum cardinality set of paths "covering" all the vertices such that both vertices of each pair belong to the same path. For this problem, we show that, while it is NP-hard to compute if there exists a solution consisting of at most three paths, it is possible to decide in polynomial time whether a solution consisting of at most two paths exists. The second problem (MaxRPSP), given a DAG and a set of pairs of vertices, asks for a path containing the maximum number of the given pairs of vertices. We show its NP-hardness and also its W[1]-hardness when parametrized by the number of covered pairs. On the positive side, we give a fixed-parameter algorithm when the parameter is the maximum overlapping degree, a natural parameter in the bioinformatics applications of the problem

YBCO microwave resonators for strong collective coupling with spin ensembles

Coplanar microwave resonators made of 330 nm-thick superconducting YBCO have been realized and characterized in a wide temperature ($T$, 2-100 K) and magnetic field ($B$, 0-7 T) range. The quality factor $Q_L$ exceeds 10$^4$ below 55 K and it slightly decreases for increasing fields, remaining 90$\%$ of $Q_L(B=0)$ for $B=7$ T and $T=2$ K. These features allow the coherent coupling of resonant photons with a spin ensemble at finite temperature and magnetic field. To demonstrate this, collective strong coupling was achieved by using DPPH organic radical placed at the magnetic antinode of the fundamental mode: the in-plane magnetic field is used to tune the spin frequency gap splitting across the single-mode cavity resonance at 7.75 GHz, where clear anticrossings are observed with a splitting as large as $\sim 82$ MHz at $T=2$ K. The spin-cavity collective coupling rate is shown to scale as the square root of the number of active spins in the ensemble.Comment: to appear in Appl. Phys. Let

The zero exemplar distance problem

Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that \textsc{Zero Exemplar Distance} for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this paper, we give a very simple alternative proof of this result. We also study the problem \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order, and prove the analogous result that it is also NP-hard even if each gene appears at most two times in each genome. For the positive direction, we show that both variants of \textsc{Zero Exemplar Distance} admit polynomial-time algorithms if each gene appears exactly once in one genome and at least once in the other genome. In addition, we present a polynomial-time algorithm for the related problem \textsc{Exemplar Longest Common Subsequence} in the special case that each mandatory symbol appears exactly once in one input sequence and at least once in the other input sequence. This answers an open question of Bonizzoni et al. We also show that \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order is fixed-parameter tractable if the parameter is the maximum number of chromosomes in each genome.Comment: Strengthened and reorganize

Approximating Clustering of Fingerprint Vectors with Missing Values

The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some improvements in closing the gaps between the known lower bounds and upper bounds on the approximability of some variants of the biological problem. Namely we are able to prove that the problem is APX-hard even when each fingerprint contains only two unknown position. Moreover we have studied some variants of the orginal problem, and we give two 2-approximation algorithm for the IECMV and OECMV problems when the number of unknown entries for each vector is at most a constant.Comment: 13 pages, 4 figure

Transmission Spectroscopy of Molecular Spin Ensembles in the Dispersive Regime

The readout in the dispersive regime is originally developed—and it is now largely exploited—for non-demolitive measurement of super- and semiconducting qubits. More recently it has been successfully applied to probe collective spin excitations in ferro(i)magnetic bulk samples or collections of paramagnetic spin centers embedded into microwave cavities. The use of this readout technique within a semiclassical limit of excitation is only marginally investigated although it holds for a wide class of problems, including advanced magnetic resonance techniques. In this work, the coupling between a coplanar microwave resonator and diphenyl-nitroxide organic radical diluted in a fully deuterated benzophenone single crystal is investigated. Two-tone transmission spectroscopy experiments demonstrate the possibility to reconstruct the spectrum of the spin system with little loss of sensitivity with respect to the resonant regime. Likewise, pulse sequences of detuned microwave frequency allow the measurement of the spin-lattice relaxation time (T1). The independent tunability of the probe and the drive power enables one to adjust the signal-to-noise ratio of the spectroscopy. These results suggest that electron spin dispersive spectroscopy can be used as a complementary tool of electron spin resonance to investigate the spin response

Microsatellite polymorphism in tsetse flies (Diptera: Glossinidae).

In sub-Saharan Africa, tsetse flies are the vectors of trypanosomes, the causative agents of sleeping sickness in humans and nagana in animals. Certain wild populations of the palpalis group exhibit intraspecific variation and are suspect of manifest differences in vectorial capacity. The current study reports the identification of 13 polymorphic microsatellite loci from Glossina palpalis palpalis Robinean-Desvoidy. The majority of these markers amplify corresponding loci from the related species C. p. gambiensis Vanderplank, G. f. fuscipes Newstead, and G. tachinoides Westwood. Only seven of 13 loci were amplified from G. austeni Newstead. Genetic variability was estimated in one field population of G. p. gambiensis. These results confirmed that microsatellite markers may be used to examine the subpopulation structure of tsetse flies

Ultrastrong Magnon-Photon Coupling Achieved by Magnetic Films in Contact with Superconducting Resonators

Coherent coupling between spin-wave excitations (magnons) and microwave photons in a cavity may disclose new paths to unconventional phenomena as well as novel applications. Here, we present a systematic investigation of yttrium iron garnets (YIG) films on top of coplanar waveguide resonators made of superconducting YBa2Cu3O7 (YBCO). We first show that spin-wave excitations with frequency higher than the Kittel mode can be excited by putting in direct contact a 5-pm-thick YIG film with the YBCO coplanar resonator (cavity frequency & omega;c/27r = 8.65 GHz). With this configuration, we obtain very large values of the collective coupling strength & lambda;/27r & AP; 2 GHz and cooperativity C = 5 x 104. Transmission spectra are analyzed by a modified Hopfield model for which we provide an exact solution that allows us to well reproduce spectra by introducing a limited number of free parameters. It turns out that the coupling of the dominant magnon mode with photons exceeds 0.2 times the cavity frequency, thus demonstrating the achievement of the ultrastrong-coupling regime with this architecture. Our analysis also shows a vanishing contribution of the diamagnetic term, which is a peculiarity of pure spin systems

Bimacrocyclic Effect in Anion Recognition by a Copper(II) Bicyclam Complex

The dicopper(II) complex of the bimacrocyclic ligand α,α′-bis(5,7-dimethyl-1,4,8,11-tetraazacyclotetradecan-6-yl)-o-xylene, 2, interacts with selected anions in dimethyl sulfoxide solution according to two different modes: (i) halides (Cl-, Br-, and I-) and N3- coordinate the two metal centers at the same time between the two macrocyclic subunits that face each other and (ii) anionic species that do not fit the bridging coordination mode (e.g., NCO-, SCN-, CH3COO-, NO3-, and H2PO4-) interact with copper(II) ions only at the "external" positions or their interaction is too weak to be detected. Occurrence of the bridging interaction is demonstrated by X-ray crystallographic studies performed on the adduct formed by [Cu2(2)]4+ with azide and by electron paramagnetic resonance investigation, as the anion coordination between the two copper(II) centers induces spin-spin coupling. Isothermal titration calorimetry experiments performed on [Cu2(2)]4+ and, for comparison, on [(5,7-dimethyl-6-benzyl-1,4,8,11-tetraazacyclotetradecane)copper(II)], representing the mononuclear analogue, allowed determination of thermodynamic parameters (log K, ΔH, and TΔS) associated with the considered complex/anion equilibria. Thermodynamic data showed that adducts formed by [Cu2(2)]4+ with halides and azide benefit from an extra stability that can be explained on the basis of the anion advantage of simultaneously binding the two metal centers, i.e., in terms of the bimacrocyclic effect

Structured self-monitoring of blood glucose is associated with more appropriate therapeutic interventions than unstructured self-monitoring: A novel analysis of data from the PRISMA trial

Aims: To investigate the relationship between single therapeutic interventions and indicators of glycemic control in the PRISMA trial, a large study comparing the effects of intensive structured SMBG (ISM) vs. active control (AC) in non-insulin-treated type 2 diabetes (T2D). Methods: Information was collected at four time points, corresponding to months 3, 6, 9, and 12 and visits 2, 3, 4, and 5, respectively. Data on therapeutic interventions, HbA1c levels and the number of hypoglycemic episodes at each visit were analyzed. Results: Intensification of drug therapy occurred in 20.3% vs. 15.6%, and no change in 71.8% vs. 78.7% of visits for the ISM and AC groups, respectively. On the other hand, de-intensification and redistribution of drugs and/or drug dose occurred in a similar proportion of visits. Intensification of drug therapy in both groups was associated with significant reductions in HbA1c vs. the previous visit, while de-intensification of therapy led to a significant increase in HbA1c in the AC group only. Conclusions. Our data strongly support that structured SMBG has clinical value in reducing HbA1c in non-insulin-treated T2D and suggest that this clinical benefit may be mediated by more appropriate and timely changes in drug therapy