Genome-wide comparative analysis of the codon usage patterns in plants

Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons.     

Early Indicators of Fatal Leptospirosis during the 2010 Epidemic in Puerto Rico

Background

Leptospirosis is a potentially fatal bacterial zoonosis that is endemic throughout the tropics and may be misdiagnosed as dengue. Delayed hospital admission of leptospirosis patients is associated with increased mortality.

Methodology/Principal Findings

During a concurrent dengue/leptospirosis epidemic in Puerto Rico in 2010, suspected dengue patients that tested dengue-negative were tested for leptospirosis. Fatal and non-fatal hospitalized leptospirosis patients were matched 1:1–3 by age. Records from all medical visits were evaluated for factors associated with fatal outcome. Among 175 leptospirosis patients identified (4.7 per 100,000 residents), 26 (15%) were fatal. Most patients were older males and had illness onset during the rainy season. Fatal case patients first sought medical care earlier than non-fatal control patients (2.5 vs. 5 days post-illness onset [DPO], p < 0.01), but less frequently first sought care at a hospital (52.4% vs. 92.2%, p < 0.01). Although fatal cases were more often diagnosed with leptospirosis at first medical visit (43.9% vs. 9.6%, p = 0.01), they were admitted to the hospital no earlier than non-fatal controls (4.5 vs. 6 DPO, p = 0.31). Cases less often developed fever (p = 0.03), but more often developed jaundice, edema, leg pain, hemoptysis, and had a seizure (p ≤ 0.03). Multivariable analysis of laboratory values from first medical visit associated with fatal outcome included increased white blood cell (WBC) count with increased creatinine (p = 0.001), and decreased bicarbonate with either increased WBC count, increased creatinine, or decreased platelet count (p < 0.001).

Conclusions/Significance

Patients with fatal leptospirosis sought care earlier, but were not admitted for care any earlier than non-fatal patients. Combinations of routine laboratory values predictive of fatal outcome should be considered in admission decision-making for patients with suspected leptospirosis.     

Inertia weight control strategies for particle swarm optimization

Particle swarm optimization (PSO) is a population-based, stochastic optimization technique inspired by the social dynamics of birds. The PSO algorithm is rather sensitive to the control parameters, and thus, there has been a significant amount of research effort devoted to the dynamic adaptation of these parameters. The focus of the adaptive approaches has largely revolved around adapting the inertia weight as it exhibits the clearest relationship with the exploration/exploitation balance of the PSO algorithm. However, despite the significant amount of research efforts, many inertia weight control strategies have not been thoroughly examined analytically nor empirically. Thus, there are a plethora of choices when selecting an inertia weight control strategy, but no study has been comprehensive enough to definitively guide the selection. This paper addresses these issues by first providing an overview of 18 inertia weight control strategies. Secondly, conditions required for the strategies to exhibit convergent behaviour are derived. Finally, the inertia weight control strategies are empirically examined on a suite of 60 benchmark problems. Results of the empirical investigation show that none of the examined strategies, with the exception of a randomly selected inertia weight, even perform on par with a constant inertia weight.     

Turing learning: a metric-free approach to inferring behavior and its application to swarms

We propose Turing Learning, a novel system identification method for inferring the behavior of natural or artificial systems. Turing Learning simultaneously optimizes two populations of computer programs, one representing models of the behavior of the system under investigation, and the other representing classifiers. By observing the behavior of the system as well as the behaviors produced by the models, two sets of data samples are obtained. The classifiers are rewarded for discriminating between these two sets, that is, for correctly categorizing data samples as either genuine or counterfeit. Conversely, the models are rewarded for ‘tricking’ the classifiers into categorizing their data samples as genuine. Unlike other methods for system identification, Turing Learning does not require predefined metrics to quantify the difference between the system and its models. We present two case studies with swarms of simulated robots and prove that the underlying behaviors cannot be inferred by a metric-based system identification method. By contrast, Turing Learning infers the behaviors with high accuracy. It also produces a useful by-product—the classifiers—that can be used to detect abnormal behavior in the swarm. Moreover, we show that Turing Learning also successfully infers the behavior of physical robot swarms. The results show that collective behaviors can be directly inferred from motion trajectories of individuals in the swarm, which may have significant implications for the study of animal collectives. Furthermore, Turing Learning could prove useful whenever a behavior is not easily characterizable using metrics, making it suitable for a wide range of applications.     

Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin (Pontoporia blainvillei)

The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F‐statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex‐biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long‐term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.