Multicolored Dynamos on Toroidal Meshes

Detecting on a graph the presence of the minimum number of nodes (target set) that will be able to "activate" a prescribed number of vertices in the graph is called the target set selection problem (TSS) proposed by Kempe, Kleinberg, and Tardos. In TSS's settings, nodes have two possible states (active or non-active) and the threshold triggering the activation of a node is given by the number of its active neighbors. Dealing with fault tolerance in a majority based system the two possible states are used to denote faulty or non-faulty nodes, and the threshold is given by the state of the majority of neighbors. Here, the major effort was in determining the distribution of initial faults leading the entire system to a faulty behavior. Such an activation pattern, also known as dynamic monopoly (or shortly dynamo), was introduced by Peleg in 1996. In this paper we extend the TSS problem's settings by representing nodes' states with a "multicolored" set. The extended version of the problem can be described as follows: let G be a simple connected graph where every node is assigned a color from a finite ordered set C = {1, . . ., k} of colors. At each local time step, each node can recolor itself, depending on the local configurations, with the color held by the majority of its neighbors. Given G, we study the initial distributions of colors leading the system to a k monochromatic configuration in toroidal meshes, focusing on the minimum number of initial k-colored nodes. We find upper and lower bounds to the size of a dynamo, and then special classes of dynamos, outlined by means of a new approach based on recoloring patterns, are characterized

Dynamic Monopolies in Colored Tori

The {\em information diffusion} has been modeled as the spread of an information within a group through a process of social influence, where the diffusion is driven by the so called {\em influential network}. Such a process, which has been intensively studied under the name of {\em viral marketing}, has the goal to select an initial good set of individuals that will promote a new idea (or message) by spreading the "rumor" within the entire social network through the word-of-mouth. Several studies used the {\em linear threshold model} where the group is represented by a graph, nodes have two possible states (active, non-active), and the threshold triggering the adoption (activation) of a new idea to a node is given by the number of the active neighbors. The problem of detecting in a graph the presence of the minimal number of nodes that will be able to activate the entire network is called {\em target set selection} (TSS). In this paper we extend TSS by allowing nodes to have more than two colors. The multicolored version of the TSS can be described as follows: let $G$ be a torus where every node is assigned a color from a finite set of colors. At each local time step, each node can recolor itself, depending on the local configurations, with the color held by the majority of its neighbors. We study the initial distributions of colors leading the system to a monochromatic configuration of color $k$, focusing on the minimum number of initial $k$-colored nodes. We conclude the paper by providing the time complexity to achieve the monochromatic configuration

Castle and Stairs to Learn Iteration: Co-Designing a UMC Learning Module with Teachers

This experience report presents a participatory process that involved primary school teachers and computer science education researchers. The objective of the process was to co-design a learning module to teach iteration to second graders using a visual programming environment and based on the Use-Modify-Create methodology. The co-designed learning module was piloted with three second-grade classes. We experienced that sharing and reconciling the different perspectives of researchers and teachers was doubly effective. On the one hand, it improved the quality of the resulting learning module; on the other hand, it constituted a very significant professional development opportunity for both teachers and researchers. We describe the co-designed learning module, discuss the most significant hinges in the process that led to such a product, and reflect on the lessons learned

PARPST: a PARallel algorithm to find peptide sequence tags

Background: Protein identification is one of the most challenging problems in proteomics. Tandem mass spectrometry provides an important tool to handle the protein identification problem. Results: We developed a work-efficient parallel algorithm for the peptide sequence tag problem. The algorithm runs on the concurrent-read, exclusive-write PRAM in O(n) time using log n processors, where n is the number of mass peaks in the spectrum. The algorithm is able to find all the sequence tags having score greater than a parameter or all the sequence tags of maximum length. Our tests on 1507 spectra in the Open Proteomics Database shown that our algorithm is efficient and effective since achieves comparable results to other methods. Conclusions: The proposed algorithm can be used to speed up the database searching or to identify post-translational modifications, comparing the homology of the sequence tags found with the sequences in the biological database

A parallel algorithm for de novo peptide sequencing

Protein identification is a main problem in proteomics,the large-scale analysis of proteins. Tandem mass spec-trometry (MS/MS) provides an important tool to handleprotein identification problem. Indeed the spectrometeris capable of ionizing a mixture of peptides, essentiallyseveral copies of the same unknown peptide, dissociatingevery molecule into two fragments called complementaryions, and measuring the mass/charge ratios of the pep-tides and of their fragments. These measures are visualizedas mass peaks in a mass spectrum.There are two fundamental approaches to interpret thespectra. The first approach is to search in a database tofind the peptides that match the MS/MS spectra. This data-base search approach is effective for known proteins, butdoes not permit to detect novel proteins. This second taskcan be dealt with the de novo sequencing that computesthe amino acid sequence of the peptides directly fromtheir MS/MS spectra.In the de novo sequencing problem one knows the pep-tide mas

Structuring functional groups of aquatic insects along the resistance/resilience axis when facing water flow changes

Understanding how differences in intensity and frequency of hydrological disturbances affect the resistance and resilience of aquatic organisms is key to manage aquatic systems in a fast-changing world. Some aquatic insects have strategies that improve the permanence (resistance), while others use strategies that favor recolonization (resilience). Therefore, we carried out a manipulative experiment to understand the influence of functional characteristics of aquatic insects in their permanence and recolonization against hydrological disturbances in streams in the biodiversity hotspot of the Cerrado of Brazil. We placed 200 artificial substrates in five streams and submitted them to changing water flow regimes that differed both in frequency and intensity, and we observed the response of the aquatic community for 39 days. We used a hierarchical Bayesian approach to estimate the probabilities of permanence and recolonization of each life strategy group (nine groups). We observed that the most intense changes in the water flow tended to affect the permanence of almost all groups, but the intensity of this effect reduced over time. On the other hand, less frequent disturbances, regardless of intensity, tended to reduce the permanence of most groups of aquatic insects over time. The different effects of disturbance intensity may have been related to a greater recolonization capacity of some groups. The results we present are worrisome in a scenario of reduced riparian vegetation around streams and with the expectation of precipitation becoming more concentrated in shorter periods of time due to climate change in the Cerrado hotspot, reducing the occurrence of many groups of aquatic insects in their habitat, particularly those with traits associated with resistance against hydrological disturbance

Detection Analysis and Study of Genomic Region Variability of JCPyV, BKPyV, MCPyV, HPyV6, HPyV7 and QPyV in the Urine and Plasma of HIV-1-Infected Patients

Since it was clearly established that HIV/AIDS predisposes to the infection, persistence or reactivation of latent viruses, the prevalence of human polyomaviruses (HPyVs) among HIV-1-infected patients and a possible correlation between HPyVs and HIV sero-status were investigated. PCR was performed to detect and quantify JCPyV, BKPyV, MCPyV, HPyV6, HPyV7 and QPyV DNA in the urine and plasma samples of 103 HIV-1-infected patients. Subsequently, NCCR, VP1 and MCPyV LT sequences were examined. In addition, for MCPyV, the expression of transcripts for the LT gene was investigated. JCPyV, BKPyV and MCPyV’s presence was reported, whereas HPyV6, HPyV7 and QPyV were not detected in any sample. Co-infection patterns of JCPyV, BKPyV and MCPyV were found. Archetype-like NCCRs were observed with some point mutations in plasma samples positive for JCPyV and BKPyV. The VP1 region was found to be highly conserved among these subjects. LT did not show mutations causing stop codons, and LT transcripts were expressed in MCPyV positive samples. A significant correlation between HPyVs’ detection and a low level of CD4+ was reported. In conclusion, HPyV6, HPyV7 and QPyV seem to not have a clinical relevance in HIV-1 patients, whereas further studies are warranted to define the clinical importance of JCPyV, BKPyV and MCPyV DNA detection in these subjects

Effectiveness of Transmitted Drug Resistance Testing Before Initiation of Antiretroviral Therapy in HIV-Positive Individuals

BACKGROUND For people living with HIV, major guidelines in high-income countries recommend testing for transmitted drug resistance (TDR) to guide the choice of first-line antiretroviral therapy (ART). However, individuals who fail a first-line regimen can now be switched to one of several effective regimens. Therefore, the virological and clinical benefit of TDR testing needs to be evaluated. METHODS We included individuals from the HIV-CAUSAL Collaboration who enrolled <6 months of HIV diagnosis between 2006 and 2015, were ART-naive, and had measured CD4 count and HIV-RNA. Follow-up started at the date when all inclusion criteria were first met (baseline). We compared 2 strategies: (1) TDR testing within 3 months of baseline versus (2) no TDR testing. We used inverse probability weighting to estimate the 5-year proportion and hazard ratios (HRs) of virological suppression (confirmed HIV-RNA <50 copies/mL), and of AIDS or death under both strategies. RESULTS Of 25,672 eligible individuals (82% males, 52% diagnosed in 2010 or later), 17,189 (67%) were tested for TDR within 3 months of baseline. Of these, 6% had intermediate- or high-level TDR to any antiretroviral drug. The estimated 5-year proportion virologically suppressed was 77% under TDR testing and 74% under no TDR testing; HR 1.06 (95% confidence interval: 1.03 to 1.19). The estimated 5-year risk of AIDS or death was 6% under both strategies; HR 1.03 (95% confidence interval: 0.95 to 1.12). CONCLUSIONS TDR prevalence was low. Although TDR testing improved virological response, we found no evidence that it reduced the incidence of AIDS or death in first 5 years after diagnosis