On the complexity of the multiple stack TSP, kSTSP

The multiple Stack Travelling Salesman Problem, STSP, deals with the collect and the deliverance of n commodities in two distinct cities. The two cities are represented by means of two edge-valued graphs (G1,d2) and (G2,d2). During the pick-up tour, the commodities are stored into a container whose rows are subject to LIFO constraints. As a generalisation of standard TSP, the problem obviously is NP-hard; nevertheless, one could wonder about what combinatorial structure of STSP does the most impact its complexity: the arrangement of the commodities into the container, or the tours themselves? The answer is not clear. First, given a pair (T1,T2) of pick-up and delivery tours, it is polynomial to decide whether these tours are or not compatible. Second, for a given arrangement of the commodities into the k rows of the container, the optimum pick-up and delivery tours w.r.t. this arrangement can be computed within a time that is polynomial in n, but exponential in k. Finally, we provide instances on which a tour that is optimum for one of three distances d1, d2 or d1+d2 lead to solutions of STSP that are arbitrarily far to the optimum STSP

Bridging gap between standard and differential polynomial approximation: The case of bin-packing

AbstractThe purpose of this paper is mainly to prove the following theorem: for every polynomial time algorithm running in time T(n) and guaranteeing standard-approximation ratio ϱ for bin-packing, there exists an algorithm running in time O(nT(n)) and achieving differential-approximation ratio 2 − ϱ for BP. This theorem has two main impacts. The first one is “operational”, deriving a polynomial time differential-approximation schema for bin-packing. The second one is structural, establishing a kind of reduction (to our knowledge not existing until now) between standard approximation and differential one

Labeled Traveling Salesman Problems: Complexity and approximation

We consider labeled Traveling Salesman Problems, defined upon a complete graph of n vertices with colored edges. The objective is to find a tour of maximum or minimum number of colors. We derive results regarding hardness of approximation and analyze approximation algorithms, for both versions of the problem. For the maximization version we give a $1/2$-approximation algorithm based on local improvements and show that the problem is APX-hard. For the minimization version, we show that it is not approximable within $n^{1-\epsilon}$ for any fixed $\epsilon>0$. When every color appears in the graph at most $r$ times and $r$ is an increasing function of $n$, the problem is shown not to be approximable within factor $O(r^{1-\epsilon})$. For fixed constant $r$ we analyze a polynomial-time $(r +H_r)/2$ approximation algorithm, where $H_r$ is the $r$-th harmonic number, and prove APX-hardness for $r = 2$. For all of the analyzed algorithms we exhibit tightness of their analysis by provision of appropriate worst-case instances

Optimal Reallocation under Additive and Ordinal Preferences

Reallocating resources to get mutually beneficial outcomes is a fundamental problem in various multi-agent settings. In the first part of the paper we focus on the setting in which agents express additive cardinal utilities over objects. We present computational hardness results as well as polynomial-time algorithms for testing Pareto optimality under different restrictions such as two utility values or lexicographic utilities. In the second part of the paper we assume that agents express only their (ordinal) preferences over single objects, and that their preferences are additively separable. In this setting, we present characterizations and polynomial-time algorithms for possible and necessary Pareto optimality.nonouirechercheInternationa

The complexity of the Pk partition problem and related problems in bipartite graphs

International audienceIn this paper, we continue the investigation made in [MT05] about the approximability of Pk partition problems, but focusing here on their complexity. Precisely, we aim at designing the frontier between polynomial and NP-complete versions of the Pk partition problem in bipartite graphs, according to both the constant k and the maximum degree of the input graph. We actually extend the obtained results to more general classes of problems, namely, the minimum k-path partition problem and the maximum Pk packing problem. Moreover, we propose some simple approximation algorithms for those problems

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis. For deleterious heteroplasmies, a severe bottleneck may abruptly transform a benign (low) frequency in a mother into a disease-causing (high) frequency in her child. Here we present a high-resolution study of heteroplasmy transmission conducted on blood and buccal mtDNA of 39 healthy mother–child pairs of European ancestry (a total of 156 samples, each sequenced at ∼20,000× per site). On average, each individual carried one heteroplasmy, and one in eight individuals carried a disease-associated heteroplasmy, with minor allele frequency ≥1%. We observed frequent drastic heteroplasmy frequency shifts between generations and estimated the effective size of the germ-line mtDNA bottleneck at only ∼30–35 (interquartile range from 9 to 141). Accounting for heteroplasmies, we estimated the mtDNA germ-line mutation rate at 1.3 × 10−8 (interquartile range from 4.2 × 10−9 to 4.1 × 10−8) mutations per site per year, an order of magnitude higher than for nuclear DNA. Notably, we found a positive association between the number of heteroplasmies in a child and maternal age at fertilization, likely attributable to oocyte aging. This study also took advantage of droplet digital PCR (ddPCR) to validate heteroplasmies and confirm a de novo mutation. Our results can be used to predict the transmission of disease-causing mtDNA variants and illuminate evolutionary dynamics of the mitochondrial genome

The Diversity of Religious Diversity. Using Census and NCS Methodology in Order to Map and Assess the Religious Diversity of a Whole Country

Religious diversity is often captured in “mapping studies” that use mostly qualitative methods in order to map and assess the religious communities in a given area. While these studies are useful, they often present weaknesses in that they treat only limited geographic regions, provide limited possibilities for comparing across religious groups and cannot test theories. In this article, we show how a census and a quantitative national congregations study (NCS) methodology can be combined in order to map and assess the religious diversity of a whole country (Switzerland), overcoming the problems mentioned above. We outline the methodological steps and selected results concerning organizational, geographic, structural, and cultural diversity

Unprocessed Viral DNA Could Be the Primary Target of the HIV-1 Integrase Inhibitor Raltegravir

Integration of HIV DNA into host chromosome requires a 3′-processing (3′-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3′-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5′C4pA33′ step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance

Gene Expression Analysis of Zebrafish Heart Regeneration

Mammalian hearts cannot regenerate. In contrast, zebrafish hearts regenerate even when up to 20% of the ventricle is amputated. The mechanism of zebrafish heart regeneration is not understood. To systematically characterize this process at the molecular level, we generated transcriptional profiles of zebrafish cardiac regeneration by microarray analyses. Distinct gene clusters were identified based on temporal expression patterns. Genes coding for wound response/inflammatory factors, secreted molecules, and matrix metalloproteinases are expressed in regenerating heart in sequential patterns. Comparisons of gene expression profiles between heart and fin regeneration revealed a set of regeneration core molecules as well as tissue-specific factors. The expression patterns of several secreted molecules around the wound suggest that they play important roles in heart regeneration. We found that both platelet-derived growth factor-a and -b (pdgf-a and pdgf-b) are upregulated in regenerating zebrafish hearts. PDGF-B homodimers induce DNA synthesis in adult zebrafish cardiomyocytes. In addition, we demonstrate that a chemical inhibitor of PDGF receptor decreases DNA synthesis of cardiomyocytes both in vitro and in vivo during regeneration. Our data indicate that zebrafish heart regeneration is associated with sequentially upregulated wound healing genes and growth factors and suggest that PDGF signaling is required