title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1732 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Occurrence of concurrent infections with multiple serotypes of dengue viruses during 2013–2015 in northern Kerala, India link: https://peerj.com/articles/2970 last-modified: 2017-03-14 description: BackgroundDengue is a global human public health threat, causing severe morbidity and mortality. The occurrence of sequential infection by more than one serotype of dengue virus (DENV) is a major contributing factor for the induction of Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS), two major medical conditions caused by DENV infection. However, there is no specific drug or vaccine available against dengue infection. There are reports indicating the increased incidence of concurrent infection of dengue in several tropical and subtropical regions. Recently, increasing number of DHF and DSS cases were reported in India indicating potential enhancement of concurrent DENV infections. Therefore, accurate determination of the occurrence of DENV serotype co-infections needs to be conducted in various DENV prone parts of India. In this context, the present study was conducted to analyse the magnitude of concurrent infection in northern Kerala, a southwest state of India, during three consecutive years from 2013 to 2015.MethodsA total of 120 serum samples were collected from the suspected dengue patients. The serum samples were diagnosed for the presence of dengue NS1 antigen followed by the isolation of dengue genome from NS1 positive samples. The isolated dengue genome was further subjected to RTPCR based molecular serotyping. The phylogenetic tree was constructed based on the sequence of PCR amplified products.ResultsOut of the total number of samples collected, 100 samples were positive for dengue specific antigen (NS1) and 26 of them contained the dengue genome. The RTPCR based molecular serotyping of the dengue genome revealed the presence of all four serotypes with different combinations. However, serotypes 1 and 3 were predominant combinations of concurrent infection. Interestingly, there were two samples with all four serotypes concurrently infected in 2013.DiscussionAll samples containing dengue genome showed the presence of more than one serotype, indicating 100% concurrent infection. However, the combination of serotypes 1 and 3 was predominant. To the best of our knowledge, this is the first report indicating the concurrent infection of dengue in the northern Kerala, India. The phylogenetic analysis of dengue serotype 1 identified in this study shows a close relationship with the strain isolated in Delhi and South Korea during the 2006 and 2015 epidemics respectively. Similarly this study indicates that the phylogeny of dengue serotype 3 of northern Kerala is more closely related to dengue isolate of Rajasthan state, India. The geographical and climatic conditions of Kerala favours the breeding of both the mosquito vectors of dengue (Aedes albopictus and Aedes aegypti), which may enhance the severity of dengue in the future. Therefore, the study provides an alarming message for the urgent need of an antiviral strategy or other health management systems to curb the spread of dengue infection. creator: Manchala Nageswar Reddy creator: Ranjeet Dungdung creator: Lathika Valliyott creator: Rajendra Pilankatta uri: https://doi.org/10.7717/peerj.2970 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Reddy et al. title: Persistent erectile dysfunction in men exposed to the 5α-reductase inhibitors, finasteride, or dutasteride link: https://peerj.com/articles/3020 last-modified: 2017-03-09 description: ImportanceCase reports describe persistent erectile dysfunction (PED) associated with exposure to 5α-reductase inhibitors (5α-RIs). Clinical trial reports and the manufacturers’ full prescribing information (FPI) for finasteride and dutasteride state that risk of sexual adverse effects is not increased by longer duration of 5α-RI exposure and that sexual adverse effects of 5α-RIs resolve in men who discontinue exposure.ObjectiveOur chief objective was to assess whether longer duration of 5α-RI exposure increases risk of PED, independent of age and other known risk factors. Men with shorter 5α-RI exposure served as a comparison control group for those with longer exposure.DesignWe used a single-group study design and classification tree analysis (CTA) to model PED (lasting ≥90 days after stopping 5α-RI). Covariates included subject attributes, diseases, and drug exposures associated with sexual dysfunction.SettingOur data source was the electronic medical record data repository for Northwestern Medicine.SubjectsThe analysis cohorts comprised all men exposed to finasteride or dutasteride or combination products containing one of these drugs, and the subgroup of men 16–42 years old and exposed to finasteride ≤1.25 mg/day.Main outcome and measuresOur main outcome measure was diagnosis of PED beginning after first 5α-RI exposure, continuing for at least 90 days after stopping 5α-RI, and with contemporaneous treatment with a phosphodiesterase-5 inhibitor (PDE5I). Other outcome measures were erectile dysfunction (ED) and low libido. PED was determined by manual review of medical narratives for all subjects with ED. Risk of an adverse effect was expressed as number needed to harm (NNH).ResultsAmong men with 5α-RI exposure, 167 of 11,909 (1.4%) developed PED (persistence median 1,348 days after stopping 5α-RI, interquartile range (IQR) 631.5–2320.5 days); the multivariable model predicting PED had four variables: prostate disease, duration of 5α-RI exposure, age, and nonsteroidal anti-inflammatory drug (NSAID) use. Of 530 men with new ED, 167 (31.5%) had new PED. Men without prostate disease who combined NSAID use with >208.5 days of 5α-RI exposure had 4.8-fold higher risk of PED than men with shorter exposure (NNH 59.8, all p < 0.002). Among men 16–42 years old and exposed to finasteride ≤1.25 mg/day, 34 of 4,284 (0.8%) developed PED (persistence median 1,534 days, IQR 651–2,351 days); the multivariable model predicting PED had one variable: duration of 5α-RI exposure. Of 103 young men with new ED, 34 (33%) had new PED. Young men with >205 days of finasteride exposure had 4.9-fold higher risk of PED (NNH 108.2, p < 0.004) than men with shorter exposure.Conclusion and relevanceRisk of PED was higher in men with longer exposure to 5α-RIs. Among young men, longer exposure to finasteride posed a greater risk of PED than all other assessed risk factors. creator: Tina Kiguradze creator: William H. Temps creator: Paul R. Yarnold creator: John Cashy creator: Robert E. Brannigan creator: Beatrice Nardone creator: Giuseppe Micali creator: Dennis Paul West creator: Steven M. Belknap uri: https://doi.org/10.7717/peerj.3020 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Kiguradze et al. title: Differential bicodon usage in lowly and highly abundant proteins link: https://peerj.com/articles/3081 last-modified: 2017-03-09 description: Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins. These usage preferences cannot be explained by the frequency usage of the single codons. The statistical analysis of coding sequences of nine organisms reveals that in many cases bicodon preferences are shared between related organisms. Furthermore, it is observed that misfolding in the drug-transport protein, encoded by MDR1 gene, is better explained by a big change in the pause propensity due to the synonymous bicodon variant, rather than by a relatively small change in codon usage. These findings suggest that codon pair usage can be a more powerful framework to understand translation elongation rate, protein folding efficiency, and to improve protocols to optimize heterologous gene expression. creator: Luis A. Diambra uri: https://doi.org/10.7717/peerj.3081 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Diambra title: Frequent discordance between morphology and mitochondrial DNA in a species group of European water beetles (Coleoptera: Dytiscidae) link: https://peerj.com/articles/3076 last-modified: 2017-03-09 description: The Hydroporus memnonius species group includes both widespread and range restricted diving beetle taxa in the western Palaearctic, some of which have been divided into a number of geographical subspecies. Of these, Hydroporus necopinatus is distributed in the far west of Europe, from central Spain to southern Britain, and has been split into three subspecies, occurring in Iberia (necopinatus sst.), France (robertorum) and England (roni) respectively—the last of these being a rare example of an insect taxon apparently endemic to northern Europe. Here we explore inter-relationships between populations and subspecies of H. necopinatus and related members of the Hydroporus melanarius subgroup, using mitochondrial COI sequence data. We reveal widespread discordance between mitochondrial DNA sequence variation and morphology in areas where H. necopinatus and H. melanarius come into contact, consistent with historical introgressive hybridization between these taxa. In light of this discordance, the lack of clear genetic divergence between H. necopinatus subspecies, and the fact that both robertorum and roni are morphologically intermediate between H. necopinatus sstr. and H. melanarius, we suggest that these taxa may be of hybridogenic origin, rather than representing discrete evolutionary lineages. creator: David T. Bilton creator: Lucy Turner creator: Garth N. Foster uri: https://doi.org/10.7717/peerj.3076 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bilton et al. title: Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time link: https://peerj.com/articles/3075 last-modified: 2017-03-09 description: It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation. creator: Sheila Torres creator: Jonathan B. Clayton creator: Jessica L. Danzeisen creator: Tonya Ward creator: Hu Huang creator: Dan Knights creator: Timothy J. Johnson uri: https://doi.org/10.7717/peerj.3075 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Torres et al. title: Human head orientation and eye visibility as indicators of attention for goats (Capra hircus) link: https://peerj.com/articles/3073 last-modified: 2017-03-09 description: Animals domesticated for working closely with humans (e.g. dogs) have been shown to be remarkable in adjusting their behaviour to human attentional stance. However, there is little evidence for this form of information perception in species domesticated for production rather than companionship. We tested domestic ungulates (goats) for their ability to differentiate attentional states of humans. In the first experiment, we investigated the effect of body and head orientation of one human experimenter on approach behaviour by goats. Test subjects (N = 24) significantly changed their behaviour when the experimenter turned its back to the subjects, but did not take into account head orientation alone. In the second experiment, goats (N = 24) could choose to approach one of two experimenters, while only one was paying attention to them. Goats preferred to approach humans that oriented their body and head towards the subject, whereas head orientation alone had no effect on choice behaviour. In the third experiment, goats (N = 32) were transferred to a separate test arena and were rewarded for approaching two experimenters providing a food reward during training trials. In subsequent probe test trials, goats had to choose between the two experimenters differing in their attentional states. Like in Experiments 1 and 2, goats did not show a preference for the attentive person when the inattentive person turned her head away from the subject. In this last experiment, goats preferred to approach the attentive person compared to a person who closed their eyes or covered the whole face with a blind. However, goats showed no preference when one person covered only the eyes. Our results show that animals bred for production rather than companionship show differences in their approach and choice behaviour depending on human attentive state. However, our results contrast with previous findings regarding the use of the head orientation to attribute attention and show the importance of cross-validating results. creator: Christian Nawroth creator: Alan G. McElligott uri: https://doi.org/10.7717/peerj.3073 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Nawroth and McElligott title: Differential attraction of drosophilids to banana baits inoculated with Saccharomyces cerevisiae and Hanseniaspora uvarum within a Neotropical forest remnant link: https://peerj.com/articles/3063 last-modified: 2017-03-09 description: BackgroundYeasts are a necessary requisite in the diet of most Drosophila species that, in turn, may vector their dispersal in natural environments. Differential attractiveness experiments and the isolation of yeasts consumed by Drosophila may be informative for characterizing this association. Hanseniaspora uvarum is among the most common yeast species isolated from Drosophila crops, with high attractiveness to drosophilids. Saccharomyces cerevisiae has been widely used to collect flies, and it allows broad sampling of almost all local Drosophila species. Pronounced differences in the field concerning Drosophila attractivity to baits seeded with these yeast species have been previously reported. However, few explicit generalizations have been set. Since late fifties, no field experiments of Drosophila attractivity were carried out in the Neotropical region, which is facing shifts in abiotic and biotic factors. Our objective is to characterize preference behavior that mediates the interaction in the wild among Neotropical Drosophila species and yeasts associated with them. We want to set a broad generalization about drosophilids attracted to these yeasts. Here we present the results of a differential attractiveness experiment we carried out in a natural Atlantic Rainforest fragment to assess the preferences of Drosophila species groups to baits inoculated with H. uvarum and S. cerevisiae.MethodsBoth yeast species were cultured in GYMP broth and separately poured in autoclaved mashed banana that was left fermenting. In the field, we collected drosophilids over five arrays of three different baits: non-inoculated autoclaved banana and banana inoculated with each yeast. In the laboratory the drosophilids were sorted to five sets according to their external morphology and/or genitalia: tripunctata; guarani; willistoni; exotic; and the remaining flies pooled in others.Results and ConclusionsUninoculated banana baits attracted virtually no flies. We found significant departures from random distribution over the other two baits (1:1 proportion) for all sets, except the pooled others. Flies of the sets willistoni and exotic preferred H. uvarum over S. cerevisiae, while the remaining sets were more attracted to S. cerevisiae. Previously, various authors reported similar patterns in attraction experiments with S. cerevisiae and H. uvarum. It is also noteworthy that both yeast species have been isolated from natural substrates and crops of Drosophila species. Taken together, these results suggest that the preferences among Drosophila species groups may be reflecting deep and stable relations with yeast species in natural environments. They can be summarized as: forest dwelling species from subgenus Drosophila (such as tripunctata and guarani groups) are attracted to banana baits seeded with S. cerevisiae; while exotic (as D. melanogaster) and subgenus Sophophora species are preferentially attracted to baits seeded with H. uvarum. creator: Marcos R.D. Batista creator: Fabiana Uno creator: Rafael D. Chaves creator: Rosana Tidon creator: Carlos A. Rosa creator: Louis B. Klaczko uri: https://doi.org/10.7717/peerj.3063 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Batista et al. title: A novel application of mark-recapture to examine behaviour associated with the online trade in elephant ivory link: https://peerj.com/articles/3048 last-modified: 2017-03-09 description: The illegal trade in elephant ivory is driving the unlawful killing of elephants such that populations are now suffering unsustainable reductions. The internet is increasingly being used as a platform to conduct illegal wildlife trade, including elephant ivory. As a globally accessible medium the internet is as highly attractive to those involved in the illegal trade as it is challenging to regulate. Characterising the online illegal wildlife (ivory) trade is complex, yet key to informing enforcement activities. We applied mark-recapture to investigate behaviour associated with the online trade in elephant ivory on eBay UK as a generalist online marketplace. Our results indicate that trade takes place via eBay UK, despite its policy prohibiting this, and that two distinct trading populations exist, characterised by the pattern of their ivory sales. We suggest these may represent a large number of occasional (or non-commercial) sellers and a smaller number of dedicated (or commercial) sellers. Directing resource towards reducing the volume of occasional sales, such as through education, would enable greater focus to be placed upon characterising the extent and value of the illegal, “commercial” online ivory trade. MRC has the potential to characterise the illegal trade in ivory and diverse wildlife commodities traded using various online platforms. creator: Lydia M. Yeo creator: Rachel S. McCrea creator: David L. Roberts uri: https://doi.org/10.7717/peerj.3048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yeo et al. title: Aerodynamic forces and flows of the full and partial clap-fling motions in insects link: https://peerj.com/articles/3002 last-modified: 2017-03-09 description: Most of the previous studies on Weis-Fogh clap-fling mechanism have focused on the vortex structures and velocity fields. Detailed pressure distribution results are provided for the first time in this study to reveal the differences between the full and the partial clap-fling motions. The two motions are studied by numerically solving the Navier–Stokes equations in moving overset grids. The Reynolds number is set to 20, relevant to the tiny flying insects. The following has been shown: (1) During the clap phase, the wings clap together and create a high pressure region in the closing gap between wings, greatly increasing the positive pressure on the lower surface of wing, while pressure on the upper surface is almost unchanged by the interaction; during the fling phase, the wings fling apart and create a low pressure region in the opening gap between wings, greatly increasing the suction pressure on the upper surface of wing, while pressure on the lower surface is almost unchanged by the interaction; (2) The interference effect between wings is most severe at the end of clap phase and the start of the fling phase: two sharp force peaks (8–9 times larger than that of the one-winged case) are generated. But the total force peaks are manifested mostly as drag and barely as lift of the wing, owing to the vertical orientation of the wing section; (3) The wing–wing interaction effect in the partial clap-fling case is much weaker than that in the full clap-fling case, avoiding the generation of huge drag. Compared with a single wing flapping with the same motion, mean lift in the partial case is enhanced by 12% without suffering any efficiency degradation, indicating that partial clap-fling is a more practical choice for tiny insects to employ. creator: Xin Cheng creator: Mao Sun uri: https://doi.org/10.7717/peerj.3002 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cheng and Sun title: Description of Arundel Clay ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: biogeographic implications link: https://peerj.com/articles/3110 last-modified: 2017-03-08 description: The fossil record of dinosaurs from the Early Cretaceous of Eastern North America is scant, especially since a few stratigraphic units from the east are fossiliferous. Among these stratigraphic units, the Arundel Clay of the eastern seaboard has produced the best-characterized dinosaur faunas known from the Early Cretaceous of Eastern North America. The diverse dinosaur fauna of the Arundel Clay has been thoroughly discussed previously, but a few of the dinosaur species originally described from the Arundel Clay are still regarded as valid genera. Much of the Arundel material is in need of review and redescription. Among the fossils of dinosaurs from this stratigraphic unit are those referred to ornithomimosaurs. Here, the researcher describes ornithomimosaur remains from the Arundel Clay of Prince George’s County, Maryland which may be from two distinct ornithomimosaur taxa. These remains provide key information on the theropods of the Early Cretaceous of Eastern North America. Recent discoveries of small theropod material from the Arundel Clay possibly belonging to ornithomimosaurs are also reviewed and described for the first time. The description of the Arundel material herein along with recent discoveries of basal ornithomimosaurs in the past 15 years has allowed for comparisons with the coelurosaur Nedcolbertia justinhofmanni, suggesting the latter animal was a basal ornithomimosaur rather than a “generalized” coelurosaur as it was originally described. Comparisons between the Arundel ornithomimosaur material and similar Asian and European specimens suggest that both extremely basal ornithomimosaurs and more intermediate or derived forms may have coexisted throughout the northern hemisphere during the Early Cretaceous. creator: Chase Doran Brownstein uri: https://doi.org/10.7717/peerj.3110 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Brownstein