Construct, Merge, Solve and Adapt: Application to the repetition-free longest common subsequence problem

In this paper we present the application of a recently proposed, general, algorithm for combinatorial optimization to the repetition-free longest common subsequence problem. The applied algorithm, which is labelled Construct, Merge, Solve & Adapt, generates sub-instances based on merging the solution components found in randomly constructed solutions. These sub-instances are subsequently solved by means of an exact solver. Moreover, the considered sub-instances are dynamically changing due to adding new solution components at each iteration, and removing existing solution components on the basis of indicators about their usefulness. The results of applying this algorithm to the repetition-free longest common subsequence problem show that the algorithm generally outperforms competing approaches from the literature. Moreover, they show that the algorithm is competitive with CPLEX for small and medium size problem instances, whereas it outperforms CPLEX for larger problem instances.Peer ReviewedPostprint (author's final draft

Recently Integrated Alu Elements In Capuchin Monkeys: A Resource For Cebus/Sapajus Genomics

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships

Sustainability of Mahogany Production in Plantations: Does Resource Availability Influence Susceptibility of Young Mahogany Plantation Stands to Hypsipyla robusta Infestation?

Hypsipyla robusta Moore (Lepidoptera: Pyralidae), like many other moth species, shows selectivity when choosing host plants for its eggs. Four Meliaceae species (Khaya grandifoliola, K. ivorensis, Swietenia macrophyla, and Entandrophragma cylindricum) were established in a moist semideciduous forest in Ghana to study this selectivity at 12 and 21 months after planting. The analysis of variance (ANOVA) at a P-value of 0.05 was used to test the significance of differences in infestation by H. robusta between the species. H. robusta attacks were recorded by month 12 after planting in the field, and only Khaya spp. was attacked, with attacks evident on 15.5% of K grandifoliola and 6.6% K. ivorensis. Saplings in blocks closer to an older H. robusta infested K. grandifoliola stand had more infestation compared to saplings further away. The mean percentage of K. grandifoliola attacked was 38.9%, 38.9%, 13.3%, and 7.4% in 4 different plots located increasingly further away from the older infested plantation. A similar trend was found in K. ivorensis with 28.4%, 7.1%, 0.0%, and 0.0% in the plots located increasingly further away from the infested stand. These results indicate a higher number of shoot borer attacks at the edge of the plantation and in proximity to other infested plantations. After 21 months, the fastest-growing species and the fastest-growing individuals within the species were the most infested. K. grandifoliola recorded the fastest growth and most attacks followed by K. ivorensis and S. macrophylla. E. cylindricum recorded the least growth and no H. robusta infestation. After 21 months, the mean percentages of trees attacked were 59.1%, 23.7%, 5.6%, and 0.0% for K. grandifoliola, K. ivorensis, S. macrophylla, and E. cylindricum, respectively. Within species, the fastest-growing saplings experienced the most attacks. A positive correlation was observed between the plant size and H. robusta attacks (R2 = 0.76). Attacks resulted in the death of the apical shoot and the proliferation of multiple shoots in only the Khaya spp., with K. ivorensis recording a lower number of shoots than K. grandifoliola. These proliferated shoots were also attacked, and a positive correlation was observed between the number of proliferated shoots and H. robusta attacks (R2 = 0.84). These findings will assist plantation developers, forest managers, and investors in mahogany plantations to devise integrated pest management strategies to reduce the impact of Hypsipyla attacks on their plantations

On the Inability of Markov Models to Capture Criticality in Human Mobility

We examine the non-Markovian nature of human mobility by exposing the inability of Markov models to capture criticality in human mobility. In particular, the assumed Markovian nature of mobility was used to establish a theoretical upper bound on the predictability of human mobility (expressed as a minimum error probability limit), based on temporally correlated entropy. Since its inception, this bound has been widely used and empirically validated using Markov chains. We show that recurrent-neural architectures can achieve significantly higher predictability, surpassing this widely used upper bound. In order to explain this anomaly, we shed light on several underlying assumptions in previous research works that has resulted in this bias. By evaluating the mobility predictability on real-world datasets, we show that human mobility exhibits scale-invariant long-range correlations, bearing similarity to a power-law decay. This is in contrast to the initial assumption that human mobility follows an exponential decay. This assumption of exponential decay coupled with Lempel-Ziv compression in computing Fano's inequality has led to an inaccurate estimation of the predictability upper bound. We show that this approach inflates the entropy, consequently lowering the upper bound on human mobility predictability. We finally highlight that this approach tends to overlook long-range correlations in human mobility. This explains why recurrent-neural architectures that are designed to handle long-range structural correlations surpass the previously computed upper bound on mobility predictability

Recently Integrated \u3cem\u3eAlu\u3c/em\u3e Elements in Capuchin Monkeys: A Resource for \u3cem\u3eCebus\u3c/em\u3e/\u3cem\u3eSapajus\u3c/em\u3e Genomics

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae fam-ily. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phy-logenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. There are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships

Secretion of functional papain precursor from insect cells. Requirement for N-glycosylation of the pro-region.

The synthetic gene coding for the precursor of the cysteine protease papain (EC 3.4.22.2) has been expressed using the baculovirus/insect cell system. The prepropapain gene was cloned into the transfer vector IpDC125 behind the polyhedrin promoter. The recombinant construct was then incorporated by homologous recombination into the Autographa californiaca nuclear polyhedrosis virus genome. The host Spodoptera frugiperda Sf9 cells infected with the recombinant baculovirus secrete an enzymatically inactive N-glycosylated papain precursor. This zymogen could be activated in vitro to yield about 400 nmol of active papain per liter of culture. The recombinant active mature papain was enzymatically indistinguishable from natural papain but the precursor was not processed to the same amino acid residue. The insect cells also accumulated prepropapain and glycosylated propapain intracellularly. This accumulation was an indication that there are rate-limiting steps in the secretion of proteins from insect cells in this expression system. Characterization of mutants of the precursor has shown that entry into the secretory pathway and addition of carbohydrate are prerequisite conditions for the production and secretion of functional propapain