ORCAE-AOCC : a centralized portal for the annotation of African orphan crop genomes

ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to “public” or “restricted” mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user- friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops

Methylphenidate Use and Infectious Diseases in Children With Attention Deficit and Hyperactivity Disorder:A Population-Based Study

Objective: Children with attention deficit hyperactivity disorder (ADHD) have more visits to the emergency department (ED) due to injuries than those without ADHD. However, no study has investigated whether children with ADHD have more ED visits or hospitalizations due to infectious diseases (IDs) and whether methylphenidate (MPH) treatment may reduce the risk. Method: The incidence of ID-related ED visits or hospitalizations was defined as the main outcome. The Cox regression and conditional Poisson regression models were calculated to estimate hazard ratios (HRs) in the population level and relative risks for the self-controlled case series design, respectively. Results: Children with ADHD had higher rates of emergency visits (HR = 1.25, 95% CI: 1.23~1.27) and hospitalizations (HR = 1.28, 95% CI: 1.26~1.31) due to IDs than those without ADHD. In the ADHD subgroup, those who received MPH treatment have a reduced risk of emergency visits (HR = 0.10, 95% CI: 0.09~0.10) and hospitalizations (HR = 0.73, 95% CI: 0.71~0.75), compared to those without treatment. The risk of ID-related emergency visits decreased to 0.21 (95% CI: 0.21~0.22); and hospitalizations decreased to 0.71 (95% CI: 0.69~0.73). Within self-controlled analysis, it is demonstrated that compared with non-MPH exposed period, children with ADHD had significantly decreased risks for infection-related emergency visits (RR = 0.73, 95% CI: 0.68~0.78) or hospitalizations (RR = 0.19, 95% CI: 0.17~0.21) during MPH-exposed periods. Conclusions and Relevance: This is the first study that reported an increased risk of ID-related healthcare utilizations in children with ADHD compared to those without, and that such risks may be significantly reduced in ADHD children that received MPH treatment.</p

Draft genomes of two Artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis)

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism

The relationship of muscular endurance and coordination and dexterity with behavioral and neuroelectric indices of attention in preschool children

This study investigated the associations of non-aerobic fitness (NAF) and motor competence (MC) with attention in 4–6 year-old preschoolers. The allocation of attentional resources and speed of stimulus categorization were examined using the amplitude and latency of P3 of event-related potentials respectively, while cortical activation related to general attention and task-specific discriminative processes were examined using event-related desynchronization (ERD) at lower (8–10 Hz) and upper (10–12 Hz) alpha frequencies, respectively. Seventy-six preschoolers completed NAF (muscular power, muscular endurance, flexibility, balance) and MC (coordination and dexterity, ball skills, agility and balance) test batteries. Electroencephalogram was recorded while participants performed an auditory oddball task. After controlling for age and MC, muscular endurance was positively related to P3 amplitude. MC and its coordination and dexterity sub-component were positively related to task performance, with higher levels of coordination and dexterity showing an additional association with greater upper alpha ERD between 700 and 1000 ms following stimulus onset after controlling for age and NAF. These findings suggest relationships of NAF and MC with early childhood neurocognitive function. Specifically, muscular endurance is related to the neuroinhibition in facilitating effective allocation of attentional resources to stimulus evaluation while coordination and dexterity are related to cortical activation underlying strategic attentional preparation for subsequent stimulus evaluation

Emerged HA and NA Mutants of the Pandemic Influenza H1N1 Viruses with Increasing Epidemiological Significance in Taipei and Kaohsiung, Taiwan, 2009–10

The 2009 influenza pandemic provided an opportunity to observe dynamic changes of the hemagglutinin (HA) and neuraminidase (NA) of pH1N1 strains that spread in two metropolitan areas -Taipei and Kaohsiung. We observed cumulative increases of amino acid substitutions of both HA and NA that were higher in the post–peak than in the pre-peak period of the epidemic. About 14.94% and 3.44% of 174 isolates had one and two amino acids changes, respective, in the four antigenic sites. One unique adaptive mutation of HA2 (E374K) was first detected three weeks before the epidemic peak. This mutation evolved through the epidemic, and finally emerged as the major circulated strain, with significantly higher frequency in the post-peak period than in the pre-peak (64.65% vs 9.28%, p<0.0001). E374K persisted until ten months post-nationwide vaccination without further antigenic changes (e.g. prior to the highest selective pressure). In public health measures, the epidemic peaked at seven weeks after oseltamivir treatment was initiated. The emerging E374K mutants spread before the first peak of school class suspension, extended their survival in high-density population areas before vaccination, dominated in the second wave of class suspension, and were fixed as herd immunity developed. The tempo-spatial spreading of E374K mutants was more concentrated during the post–peak (p = 0.000004) in seven districts with higher spatial clusters (p<0.001). This is the first study examining viral changes during the naïve phase of a pandemic of influenza through integrated virological/serological/clinical surveillance, tempo-spatial analysis, and intervention policies. The vaccination increased the percentage of E374K mutants (22.86% vs 72.34%, p<0.001) and significantly elevated the frequency of mutations in Sa antigenic site (2.36% vs 23.40%, p<0.001). Future pre-vaccination public health efforts should monitor amino acids of HA and NA of pandemic influenza viruses isolated at exponential and peak phases in areas with high cluster cases

The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

Lepton Dipole Moments and Rare Decays in the CP-violating MSSM with Nonuniversal Soft-Supersymmetry Breaking

We investigate the muon anomalous magnetic dipole moment (MDM), the muon electric dipole moment (EDM) and the lepton-flavour-violating decays of the $\tau-$lepton, $\tau \to \mu \gamma$ and $\tau\to 3\mu$, in the CP-violating Minimal Supersymmetric Standard Model (MSSM) with nonuniversal soft-supersymmetry breaking. We evaluate numerically the muon EDM and the branching ratios $B(\tau \to \mu\gamma)$ and $B(\tau \to 3\mu)$, after taking into account the experimental constraints from the electron EDM and muon MDM. Upon imposition of the experimental limits on our theoretical predictions for the aforementioned branching ratios and the muon MDM, we obtain an upper bound of about $10^{-23} e\cdot cm$ on the muon EDM which lies well within the explorable reach of the proposed experiment at BNL.Comment: Latex, 26 pages, 8 figures, accepted for publication in Phys. Rev.