Solving Hard Computational Problems Efficiently: Asymptotic Parametric Complexity 3-Coloring Algorithm

Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular biology, e.g., genome sequencing; global alignment of multiple genomes; identifying siblings or discovery of dysregulated pathways.In almost all of these problems, there is the need for proving a hypothesis about certain property of an object that can be present only when it adopts some particular admissible structure (an NP-certificate) or be absent (no admissible structure), however, none of the standard approaches can discard the hypothesis when no solution can be found, since none can provide a proof that there is no admissible structure. This article presents an algorithm that introduces a novel type of solution method to "efficiently" solve the graph 3-coloring problem; an NP-complete problem. The proposed method provides certificates (proofs) in both cases: present or absent, so it is possible to accept or reject the hypothesis on the basis of a rigorous proof. It provides exact solutions and is polynomial-time (i.e., efficient) however parametric. The only requirement is sufficient computational power, which is controlled by the parameter $\alpha\in\mathbb{N}$. Nevertheless, here it is proved that the probability of requiring a value of $\alpha>k$ to obtain a solution for a random graph decreases exponentially: $P(\alpha>k) \leq 2^{-(k+1)}$, making tractable almost all problem instances. Thorough experimental analyses were performed. The algorithm was tested on random graphs, planar graphs and 4-regular planar graphs. The obtained experimental results are in accordance with the theoretical expected results.Comment: Working pape

The Diboson Excess: Experimental Situation and Classification of Explanations; A Les Houches Pre-Proceeding

We examine the `diboson' excess at $\sim 2$ TeV seen by the LHC experiments in various channels. We provide a comparison of the excess significances as a function of the mass of the tentative resonance and give the signal cross sections needed to explain the excesses. We also present a survey of available theoretical explanations of the resonance, classified in three main approaches. Beyond that, we discuss methods to verify the anomaly, determining the major properties of the various surpluses and exploring how different models can be discriminated. Finally, we give a tabular summary of the numerous explanations, presenting their main phenomenological features.Comment: 37 pages, 9 Figures, 1 Tabl

The prelude to industrial whaling:Identifying the targets of ancient European whaling using zooarchaeology and collagen mass-peptide fingerprinting

Taxonomic identification of whale bones found during archaeological excavations is problematic due to their typically fragmented state. This difficulty limits understanding of both the past spatio-temporal distributions of whale populations and of possible early whaling activities. To overcome this challenge, we performed zooarchaeology by mass spectrometry on an unprecedented 719 archaeological and palaeontological specimens of probable whale bone from Atlantic European contexts, predominantly dating from ca 3500 BCE to the eighteenth century CE. The results show high numbers of Balaenidae (many probably North Atlantic right whale (Eubalaena glacialis)) and grey whale (Eschrichtius robustus) specimens, two taxa no longer present in the eastern North Atlantic. This discovery matches expectations regarding the past utilization of North Atlantic right whales, but was unanticipated for grey whales, which have hitherto rarely been identified in the European zooarchaeological record. Many of these specimens derive from contexts associated with mediaeval cultures frequently linked to whaling: the Basques, northern Spaniards, Normans, Flemish, Frisians, Anglo-Saxons and Scandinavians. This association raises the likelihood that early whaling impacted these taxa, contributing to their extirpation and extinction. Much lower numbers of other large cetacean taxa were identified, suggesting that what are now the most depleted whales were once those most frequently used.</p

A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Introduction: A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy.&lt;p&gt;&lt;/p&gt; Methods: Sixty-six non-HLA SNPs showing a P value &#60;10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results: We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis.&lt;p&gt;&lt;/p&gt; Conclusion: Our results suggest a role of PPARG gene in the development of SSc

Influence of urban pollution on the production of organic particulate matter from isoprene epoxydiols in central Amazonia

The atmospheric chemistry of isoprene contributes to the production of a substantial mass fraction of the particulate matter (PM) over tropical forests. Isoprene epoxydiols (IEPOX) produced in the gas phase by the oxidation of isoprene under HO2-dominant conditions are subsequently taken up by particles, thereby leading to production of secondary organic PM. The present study investigates possible perturbations to this pathway by urban pollution. The measurement site in central Amazonia was located 4 to 6 h downwind of Manaus, Brazil. Measurements took place from February through March 2014 of the wet season, as part of the GoAmazon2014/5 experiment. Mass spectra of organic PM collected with an Aerodyne Aerosol Mass Spectrometer were analyzed by positive-matrix factorization. One resolved statistical factor (IEPOX-SOA factor) was associated with PM production by the IEPOX pathway. The IEPOX-SOA factor loadings correlated with independently measured mass concentrations of tracers of IEPOX-derived PM, namely C5-alkene triols and 2-methyltetrols (R = 0. 96 and 0.78, respectively). The factor loading, as well as the ratio f of the loading to organic PM mass concentration, decreased under polluted compared to background conditions. For an increase in NOy concentration from 0.5 to 2 ppb, the factor loading and f decreased by two to three fold. Overall, sulfate concentration explained 37 % of the variability in the factor loading. After segregation of factor loading into subsets based on NOy concentration, the sulfate concentration explained up to 75 % of the variability. Considering both factors, the data sets show that the suppressing effects of increased NO concentrations dominated over the enhancing effects of higher sulfate concentrations. The pollution from Manaus elevated NOy concentrations more significantly than sulfate concentrations relative to background conditions. In this light, increased emissions of nitrogen oxides, as anticipated for some scenarios of Amazonian economic development, could significantly alter pathways of PM production that presently prevail over the tropical forest, implying changes to air quality and regional climate.</html