Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study

With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations

Adaptive large neighborhood search for the commodity constrained split delivery VRP

International audienceThis paper addresses the commodity constrained split delivery vehicle routing problem (C-SDVRP) where customers require multiple commodities. This problem arises when customers accept to be delivered separately. All commodities can be mixed in a vehicle as long as the vehicle capacity is satisfied. Multiple visits to a customer are allowed, but a given commodity must be delivered in one delivery. In this paper, we propose a heuristic based on the adaptive large neighborhood search (ALNS) to solve the C-SDVRP, with the objective of efficiently tackling medium and large sized instances. We take into account the distinctive features of the C-SDVRP and adapt several local search moves to improve a solution. Moreover, a mathematical programming based operator (MPO) that reassigns commodities to routes is used to improve a new global best solution. Computational experiments have been performed on benchmark instances from the literature. The results assess the efficiency of the algorithm, which can provide a large number of new best-known solutions in short computational times

Adaptive large neighborhood search for the commodity constrained split delivery VRP

International audienc

Adaptive large neighborhood search for multicommodity VRP

International audienc

Adaptive large neighborhood search for multicommodity VRP

International audienc

Submission of Evidence on Online Violence Against Women to the UN Special Rapporteur on Violence Against Women, its Causes and Consequences, Dr Dubravka Šimonović

Figure S1. B3GALNT2 levels determined by W.B. and ROC curve. a–c Relative mRNA expression of B3GALNT2 in HCC tumor tissues and normal liver tissues obtained from GSE76427, GSE36376, and TCGA-LIHC datasets. d Western blot analysis of B3GALNT2 levels in 24 pairs of HCC tissues. T HCC tumor tissue, N adjacent non-tumor tissue. e ROC curve analysis of the sensitivity and specificity for the predictive value of TNM model, B3GALNT2 expression, and the combination model. (TIFF 546 kb

A sequential approach for a multi-commodity two-echelon distribution problem

We address a Multi-Commodity two-echelon Distribution Problem (MC2DP) where three sets of stakeholders are involved: suppliers, distribution centers, and customers. Multiple commodities have to be sent from suppliers to customers, using multiple distribution centers for consolidation purposes. Commodities are collected from the suppliers and delivered to the distribution centers with direct trips, while a fleet of homogeneous vehicles distributes commodities to customers. Commodities are compatible, that is any vehicle can transport any set of commodities as long as its capacity is not exceeded. The goal is to minimize the total transportation cost from suppliers to customers. We present two sequential schemes based on the solution, in a different order, of a collection and a delivery subproblem. In both cases, the solution of the first subproblem determines the quantity of each commodity at each distribution center. The second subproblem takes this information as input. We also propose different strategies to guide the solution of the first subproblem in order to take into account the impact of its solution on the second subproblem. The proposed sequential heuristics are evaluated and compared both on randomly generated instances and on a case study related to a short and local fresh food supply chain. The results show the impact of problem characteristics on solution strategies

A multi-commodity transportation planning problem in supply chain management

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Sequential approaches to solve a multi-commodity transportation planning problem

International audienceWe address a transportation planning problem with three sets of stakeholders : suppliers, distribution centers and customers. Different commodities have to be sent from suppliers to customers, using multiple distribution centers for consolidation. Commodities are compatible and can be mixed inside the vehicles as long as the vehicle capacity is respected. Multiple visits to a customer are allowed to reduce transportation costs. However, a single commodity has to be delivered at once for the convenience of customers. The operations are as follows : suppliers transport commodities to distribution centers with direct trips, while a fleet of homogeneous vehicles distributes commodities to customers. The problem concerns both collection and delivery operations. However, the objective is to optimize these two operations jointly. Note that collection decisions (which quantity of each commodity is delivered to which center) impact delivery operations. Thus, collection and delivery must be determined jointly. In order to solve the whole problem, we consider two sequential solution approaches : first collection then delivery or first delivery then collection. In both cases, the solution of the first subproblem determines the quantity of each commodity that is required at each distribution center. The second subproblem takes this information and deals with delivery or collection accordingly. To solve the first subproblem, we propose several strategies in order to take into account the impact on the second subproblem. A case study on a fresh local vegetable supply chain is studied. Results will be presented and analyzed for two types of clients : school catering and supermarkets

Treatment of W. bancrofti (Wb) in HIV/Wb Coinfections in South India

Background: The disease course of human immunodeficiency virus (HIV) is often altered by existing or newly acquired coincident infections. Methodology/Principal Findings: To assess the influence of pre-existing Wuchereria bancrofti infection on HIV progression, we performed a case-controlled treatment study of HIV positive individuals with (FIL+) or without (FIL-) W. bancrofti infection. Twenty-eight HIV+/FIL+ and 51 matched HIV+/FIL- subjects were treated with a single dose of diethylcarbamazine and albendazole (DEC/Alb) and followed for a year at regular intervals. Sixteen of the HIV+/FIL+ subjects (54%) and 28 of the HIV+/FIL- controls (57%) were on antiretroviral therapy (ART) during the study. Following treatment, no differences were noted in clinical outcomes between the 2 groups. There also was no significant difference between the groups in the HIV viral load at 12 months as a percentage of baseline viral load (HIV+/FIL+ group had on average 0.97 times the response of the HIV+/FIL- group, 95% CI 0.88, 1.07) between the groups. Furthermore, there were no significant differences found in either the change in viral load at 1, 3, or 6 months or in the change in CD4 count at 3, 6, or 12 months between the 2 groups. Conclusions/Significance: We were unable to find a significant effect of W. bancrofti infection or its treatment on HIV clinical course or surrogate markers of HIV disease progression though we recognized that our study was limited by the smaller than predicted sample size and by the use of ART in half of the patients. Treatment of W. bancrofti coinfection in HIV positive subjects (as is usual in mass drug administration campaigns) did not represent an increased risk to the subjects, and should therefore be considered for PLWHA living in W. bancrofti endemic areas