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

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

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

Migration and Legal Precarity in the Time of Pandemic : Qualitative Research on the Italian Case

The COVID-19 pandemic has unequally impacted the lives of Italian subjects. The article uses evidence from forty-seven semi-structured interviews with various migrant groups to illuminate how temporalities embedded in Italy’s migration governance shape migrants’ precarious legal status and access to welfare. The authors show that whereas migrants with secure legal status or citizenship have not engaged significantly with Italian bureaucracies, they have no easy access to welfare as it is contingent on their employment and financial status. Migrants with precarious status have been the worst hit by the pandemic’s secondary effects across several fronts. These findings have implications for policy and future research

Beyond Perfect phylogeny: Multisample Phylogeny reconstruction via ILP

Most of the evolutionary history reconstruction approaches are based on the infinite site assumption which is underlying the Perfect Phylogeny model. This is one of the most used models in cancer genomics. Recent results gives a strong evidence that recurrent and back mutations are present in the evolutionary history of tumors [19], thus showing that more general models then the Perfect phylogeny are required. To address this problem we propose a framework based on the notion of Incomplete Perfect Phylogeny. Our framework incorporates losing and gaining mutations, hence including the Dollo and the Camin-Sokal models, and is described with an Integer Linear Programming (ILP) formulation. Our approach generalizes the notion of persistent phylogeny [1] and the ILP approach [14, 15] proposed to solve the corresponding phylogeny reconstruction problem on character data. The final goal of our paper is to integrate our approach into an ILP formulation of the problem of reconstructing trees on mixed populations, where the input data consists of the fraction of cells in a set of samples that have a certain mutation. This is a fundamental problem in cancer genomics, where the goal is to study the evolutionary history of a tumor. An experimental analysis shows that our ILP approach is able to explain data that do not fit the perfect phylogeny assumption, thereby allowing (1) multiple losses and gains of mutations, and (2) a number of subpopulations that is smaller than the number of input mutations

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

Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein

Citation: Londono-Renteria, B., Troupin, A., Conway, M. J., Vesely, D., Ledizet, M., Roundy, C. M., . . . Colpitts, T. M. (2015). Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein. Plos Pathogens, 11(10), 23. doi:10.1371/journal.ppat.1005202Dengue virus (DENV) is a mosquito-borne flavivirus that causes serious human disease and mortality worldwide. There is no specific antiviral therapy or vaccine for DENV infection. Alterations in gene expression during DENV infection of the mosquito and the impact of these changes on virus infection are important events to investigate in hopes of creating new treatments and vaccines. We previously identified 203 genes that were >= 5-fold differentially upregulated during flavivirus infection of the mosquito. Here, we examined the impact of silencing 100 of the most highly upregulated gene targets on DENV infection in its mosquito vector. We identified 20 genes that reduced DENV infection by at least 60% when silenced. We focused on one gene, a putative cysteine rich venom protein (SeqID AAEL000379; CRVP379), whose silencing significantly reduced DENV infection in Aedes aegypti cells. Here, we examine the requirement for CRVP379 during DENV infection of the mosquito and investigate the mechanisms surrounding this phenomenon. We also show that blocking CRVP379 protein with either RNAi or specific antisera inhibits DENV infection in Aedes aegypti. This work identifies a novel mosquito gene target for controlling DENV infection in mosquitoes that may also be used to develop broad preventative and therapeutic measures for multiple flaviviruses

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