Grounding agricultural research in resource-poor farmers' needs: a comparative analysis of diagnostic studies in Ghana and Benin

Eight researchers from Ghana and Benin, with different backgrounds but all co-operating within the Convergence of Sciences project, conducted diagnostic studies as a first step of their research aimed at developing technologies together with resource-poor farmers. The purpose of including diagnostic studies was to increase the likelihood that the resulting technologies would be grounded in the needs and opportunities of these farmers. To better understand the potential of diagnostic studies for improving the contribution of agricultural research to farmers’ livelihoods, a comparative study was conducted of the diagnostic studies carried out by the eight researchers. This research on agricultural research was participatory in that its results were arrived at in consultation with the eight researchers. The comparison revealed that diagnostic studies identified and established forums of stakeholders, especially of farmers, who were to play key roles in the co-construction of knowledge during the field experimental phase that followed the diagnostic studies. The diagnostic studies gave farmers a say in the design and conduct of the experimental phase which allowed them to influence the research process in the direction of developing and testing technologies that work in their circumstances and that satisfy their needs and priorities. In addition, the diagnostic studies have led to transparent choices with respect to the selection of sites, farmers and experiments. Furthermore, the conditions for negotiation were created. Finally, the diagnostic studies played a crucial role in making the partners within the Convergence of Sciences project aware of the importance of contextual framework conditions in determining the relevance of the project

Spotting Trees with Few Leaves

We show two results related to the Hamiltonicity and $k$-Path algorithms in undirected graphs by Bj\"orklund [FOCS'10], and Bj\"orklund et al., [arXiv'10]. First, we demonstrate that the technique used can be generalized to finding some $k$-vertex tree with $l$ leaves in an $n$-vertex undirected graph in $O^*(1.657^k2^{l/2})$ time. It can be applied as a subroutine to solve the $k$-Internal Spanning Tree ($k$-IST) problem in $O^*(\min(3.455^k, 1.946^n))$ time using polynomial space, improving upon previous algorithms for this problem. In particular, for the first time we break the natural barrier of $O^*(2^n)$. Second, we show that the iterated random bipartition employed by the algorithm can be improved whenever the host graph admits a vertex coloring with few colors; it can be an ordinary proper vertex coloring, a fractional vertex coloring, or a vector coloring. In effect, we show improved bounds for $k$-Path and Hamiltonicity in any graph of maximum degree $\Delta=4,\ldots,12$ or with vector chromatic number at most 8

Polynomial Kernels for Weighted Problems

Kernelization is a formalization of efficient preprocessing for NP-hard problems using the framework of parameterized complexity. Among open problems in kernelization it has been asked many times whether there are deterministic polynomial kernelizations for Subset Sum and Knapsack when parameterized by the number $n$ of items. We answer both questions affirmatively by using an algorithm for compressing numbers due to Frank and Tardos (Combinatorica 1987). This result had been first used by Marx and V\'egh (ICALP 2013) in the context of kernelization. We further illustrate its applicability by giving polynomial kernels also for weighted versions of several well-studied parameterized problems. Furthermore, when parameterized by the different item sizes we obtain a polynomial kernelization for Subset Sum and an exponential kernelization for Knapsack. Finally, we also obtain kernelization results for polynomial integer programs

Finding and counting vertex-colored subtrees

The problems studied in this article originate from the Graph Motif problem introduced by Lacroix et al. in the context of biological networks. The problem is to decide if a vertex-colored graph has a connected subgraph whose colors equal a given multiset of colors $M$. It is a graph pattern-matching problem variant, where the structure of the occurrence of the pattern is not of interest but the only requirement is the connectedness. Using an algebraic framework recently introduced by Koutis et al., we obtain new FPT algorithms for Graph Motif and variants, with improved running times. We also obtain results on the counting versions of this problem, proving that the counting problem is FPT if M is a set, but becomes W[1]-hard if M is a multiset with two colors. Finally, we present an experimental evaluation of this approach on real datasets, showing that its performance compares favorably with existing software.Comment: Conference version in International Symposium on Mathematical Foundations of Computer Science (MFCS), Brno : Czech Republic (2010) Journal Version in Algorithmic

A strategy for the characterization of minute chromosome rearrangements using multiple color fluorescence in situ hybridization with chromosome-specific DNA libraries and YAC clones

The identification of marker chromosomes in clinical and tumor cytogenetics by chromosome banding analysis can create problems. In this study, we present a strategy to define minute chromosomal rearrangements by multicolor fluorescence in situ hybridization (FISH) with whole chromosome painting probes derived from chromosome-specific DNA libraries and Alu-polymerase chain reaction (PCR) products of various region-specific yeast artificial chromosome (YAC) clones. To demonstrate the usefulness of this strategy for the characterization of chromosome rearrangements unidentifiable by banding techniques, an 8p+ marker chromosome with two extra bands present in the karyotype of a child with multiple anomalies, malformations, and severe mental retardation was investigated. A series of seven-color FISH experiments with sets of fluorochrome-labeled DNA library probes from flow-sorted chromosomes demonstrated that the additional segment on 8p+ was derived from chromosome 6. For a more detailed characterization of the marker chromosome, three-color FISH experiments with library probes specific to chromosomes 6 and 8 were performed in combination with newly established telomeric and subtelomeric YAC clones from 6q25, 6p23, and 8p23. These experiments demonstrated a trisomy 6pter6p22 and a monosomy 8pter8p23 in the patient. The present limitations for a broad application of this strategy and its possible improvements are discusse