A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis
Inferring growth for aquatic species is dependent upon accurate descriptions of age-length relationships, which may be degraded by measurement error in observed ages. Ageing error arises from biased and/or imprecise age determinations as a consequence of misinterpretation by readers or inability of ageing structures to accurately reflect true age. A Bayesian errors-in-variables (EIV) approach (i.e., measurement-error modeling) can account for ageing uncertainty during nonlinear growth curve estimation by allowing observed ages to be parametrically modeled as random deviates. Information on the latent age composition then comes from the specified prior distribution, which represents the true age structure of the sampled fish population. In this study, weakfish growth was modeled by means of traditional and measurement-error von Bertalanffy growth curves using otolith- or scale-estimated ages. Age determinations were assumed to be log-normally distributed, thereby incorporating multiplicative error with respect to ageing uncertainty. The prior distribution for true age was assumed to be uniformly distributed between ±4 of the observed age (yr) for each individual. Measurement-error growth models described weakfish that reached larger sizes but at slower rates, with median length-at-age being overestimated by traditional growth curves for the observed age range. In addition, measurement-error models produced slightly narrower credible intervals for parameters of the von Bertalanffy growth function, which may be an artifact of the specified prior distributions. Subjectivity is always apparent in the ageing of fishes and it is recommended that measurement-error growth models be used in conjunction with otolith-estimated ages to accurately capture the age-length relationship that is subsequently used in fisheries stock assessment and management.
Hatch et al. (2016) A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis. PeerJ 4:e2431 https://doi.org/10.7717/peerj.2431
New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti)
The Ziphiidae (beaked whales) represent a large group of open-ocean odontocetes (toothed cetaceans), whose elusive and deep diving behavior prevents direct observation in their natural habitat. Despite their generally large body size, broad geographical distribution, and high species number, ziphiids thus remain poorly known. Furthermore, the evolutionary processes that have led to their extreme adaptations and impressive extant diversity are still poorly understood. Here we report new fossil beaked whales from the late Miocene of the Pisco Formation (southern Peru). The best preserved remains here described are referred to two new genera and species, the Messinian Chavinziphius maxillocristatus and the Tortonian Chimuziphius coloradensis, based on skull remains from two marine vertebrate-rich localities: Cerro Los Quesos and Cerro Colorado, respectively. C. maxillocristatus is medium sized retains a complete set of functional lower teeth, and bears robust rostral maxillary crests similar to those of the extant Berardius. By contrast, C. coloradensis is small and characterized by large triangular nasals and moderately thickened premaxillae that dorsally close the mesorostral groove. Both species confirm the high past diversity of Ziphiidae, the richest cetacean family in terms of the number of genera and species. Our new phylogenetic and biogeographical analyses depart markedly from earlier studies in dividing beaked whales into two major clades: the Messapicetus clade, which, along with other stem ziphiids, once dominated the southeastern Pacific and North Atlantic; and crown Ziphiidae, the majority of which are found in deep-water regions of the Southern Ocean, with possible subsequent dispersal both globally (Mesoplodon and Ziphius) and to the cooler waters of the northern oceans (Berardius and Hyperoodon). Despite this relatively clear separation, both lineages seem to follow similar evolutionary trends, including (1) a progressive reduction of dentition; (2) an increase in the compactness and thickness of the rostral bones; (3) similar changes in facial morphology (e.g., elevation of the vertex); and (4) an increase of body size. We suggest that these trends may be linked to a convergent ecological shift to deep diving and suction feeding.
Bianucci et al. (2016) New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti). PeerJ 4:e2479 https://doi.org/10.7717/peerj.2479
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. Conclusions This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.
Burke et al. (2016) A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq. PeerJ 4:e2492 https://doi.org/10.7717/peerj.2492
Spermatozoon ultrastructure in two monorchiid digeneans
Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris share several characters such as the presence of two axonemes of different lengths showing the 9+“1” pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, granules of glycogen and similar morphologies of the anterior and posterior extremities. The slight differences between the male gamete of O. dinema and P. selaris are the length of the first axoneme and the position of the second mitochondrion. This study also elucidates the general morphology of the spermatozoon in all monorchiid species described so far, which corresponds to a unique spermatozoon type. Other interesting finds concern the spermatological similarities between monorchiid spermatozoa and the mature spermatozoon reported in the apocreadiid Neoapocreadium chabaudi. These similarities allow us to suggest a close phylogenetical relationship between the Monorchiidae and the Apocreadiidae, although more studies are needed, especially in the unexplored taxa.
Quilichini et al. (2016) Spermatozoon ultrastructure in two monorchiid digeneans. PeerJ 4:e2488 https://doi.org/10.7717/peerj.2488
CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients
Introduction Rituximab (RTX) is a B cell-depleting agent approved for the treatment of granulomatosis with polyangiitis (GPA). RTX reduces antibody producing precursor plasma cells and inhibits B and T cells interaction. Infections related to T cell immunodeficiency are not infrequent during RTX treatment. Our study investigated CD4 cell count and CD4/CD8 ratio in GPA patients during the first two years of long-term RTX treatment. Methods A single centre cohort study of 35 patients who received median total cumulative dose of cyclophosphamide (CYC) of 15 g and were treated with RTX 2 g followed by retreatment with either 2 g once annually or 1 g biannually. Serum levels of total immunoglobulin (Ig) and lymphocytes subsets were recorded at RTX initiation and at 3, 6, 12, 18 and 24 months. Low CD4 count and inverted CD4/CD8 ratio were defined as CD4 < 0.3 × 109/l and ratio < 1. Results The CD4 cell count and CD4/CD8 ratio decreased slightly following the initial RTX treatment and then increased gradually during maintenance treatment. While the proportion of patients with low CD4 cell count decreased from 43% at baseline to 18% at 24 months, the ratio remained inverted in 40%. Oral daily prednisolone dose at baseline, CYC exposure and the maintenance regimen did not influence the CD4 cell count and ratio. Being older (p = 0.012) and having a higher CRP (p = 0.044) and ESR (p = 0.024) at baseline significantly increased the risk of inverted CD4/CD8 ratio at 24 months. Inverted ratio at baseline associated with lower total Ig levels during the study. Conclusions Overall, the CD4 and CD4/CD8 ratio increased during maintenance RTX therapy in GPA with no discernible impact of other immunosuppressive therapy. However the increase in CD4 was not followed by an increase in the CD4/CD8 ratio, especially in older patients. Inverted CD4/CD8 ratio associated with lower Ig levels, suggesting a more profound B cell depleting effect of RTX with a relative increase in CD8+ lymphocytes.
Besada et al. (2016) CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients. PeerJ 4:e2487 https://doi.org/10.7717/peerj.2487
Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth
Background Parenteral nutrition associated cholestasis (PNAC) is a frequently observed pathology in extremely low birth weight (ELBW) infants. Its pathogenesis is determined by the composition and duration of parenteral nutrition (PN) as well as the tolerance of enteral feeds (EF). “Aggressive” nutrition is increasingly used in ELBW infants to improve postnatal growth. Little is known about the effect of “aggressive” nutrition on the incidence of PNAC. We analyzed the influence of implementing an “aggressive” nutritional regimen on the incidence of PNAC and growth in a cohort of ELBW infants. Methods ELBW infants were nourished using a “conservative” (2005–6; n = 77) or “aggressive” (2007–9; n = 85) nutritional regimen that differed in the composition of PN after birth as well as the composition and timing of advancement of EFs. We analyzed the incidence of PNAC (conjugated bilirubin > 1.5 mg/dl (25 µmol/l)) corrected for confounders of cholestasis (i.e., NEC and/or gastrointestinal surgery, sepsis, birth weight, Z-score of birth weight, time on PN and male sex), growth until discharge (as the most important secondary outcome) and neonatal morbidities. Results The incidence of PNAC was significantly lower during the period of “aggressive” vs. “conservative “nutrition (27% vs. 46%, P < 0.05; adjusted OR 0.275 [0.116–0.651], P < 0.01). Body weight (+411g), head circumference (+1 cm) and length (+1 cm) at discharge were significantly higher. Extra-uterine growth failure (defined as a Z-score difference from birth to discharge lower than −1) was significantly reduced for body weight (85% vs. 35%), head circumference (77% vs. 45%) and length (85% vs. 65%) (P < 0.05). The body mass index (BMI) at discharge was significantly higher (11.1 vs. 12.4) using “aggressive” nutrition and growth became more proportionate with significantly less infants being discharged below the 10th BMI percentile (44% vs. 9%), while the percentage of infants discharged over the 90th BMI percentile (3% vs. 5%) did not significantly increase. Discussion “Aggressive” nutrition of ELBW infants was associated with a significant decrease of PNAC and marked improvement of postnatal growth.
Repa et al. (2016) Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth. PeerJ 4:e2483 https://doi.org/10.7717/peerj.2483
Overland movement in African clawed frogs (Xenopus laevis): a systematic review
African clawed frogs (Xenopus laevis) are often referred to as ‘purely aquatic’ but there are many publications which suggest extensive overland movements. Previous reviews which considered the topic have not answered the following questions: (1) is there evidence for overland dispersal in native and invasive ranges; (2) what is the range of distances moved overland; (3) when does overland movement occur; and (4) is there evidence of breeding migratory behaviour? A systematic review was chosen to synthesise and critically analyse all literature on the overland movement in Xenopus laevis. Database searches resulted in 57 documents which revealed a paucity of empirical studies, with 28 containing no data, and 19 having anecdotal content. Overwhelming evidence shows that both native and invasive populations of X. laevis move overland, with well documented examples for several other members of the genus (X. borealis, X. gilli, X. muelleri, X. fraseriand X. tropicalis). Reports of distances moved overland were from 40 m to 2 km, with no apparent difference between native and invasive ranges. Overland movements are not confined to wet seasons or conditions, but the literature suggests that moving overland does not occur in the middle of the day. Migrations to temporary water-bodies for breeding have been suggested, but without any corroborating data.
Measey (2016) Overland movement in African clawed frogs (Xenopus laevis): a systematic review. PeerJ 4:e2474 https://doi.org/10.7717/peerj.2474
Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information
Background Highlighted text in the Internet (i.e., hypertext) is predominantly blue and underlined. The perceptibility of these hypertext characteristics was heavily questioned by applied research and empirical tests resulted in inconclusive results. The ability to recognize blue text in foveal and parafoveal vision was identified as potentially constrained by the low number of foveally centered blue light sensitive retinal cells. The present study investigates if foveal and parafoveal perceptibility of blue hypertext is reduced in comparison to normal black text during reading. Methods A silent-sentence reading study with simultaneous eye movement recordings and the invisible boundary paradigm, which allows the investigation of foveal and parafoveal perceptibility, separately, was realized (comparing fixation times after degraded vs. un-degraded parafoveal previews). Target words in sentences were presented in either black or blue and either underlined or normal. Results No effect of color and underlining, but a preview benefit could be detected for first pass reading measures. Fixation time measures that included re-reading, e.g., total viewing times, showed, in addition to a preview effect, a reduced fixation time for not highlighted (black not underlined) in contrast to highlighted target words (either blue or underlined or both). Discussion The present pattern reflects no detectable perceptual disadvantage of hyperlink stimuli but increased attraction of attention resources, after first pass reading, through highlighting. Blue or underlined text allows readers to easily perceive hypertext and at the same time readers re-visited highlighted words longer. On the basis of the present evidence, blue hypertext can be safely recommended to web designers for future use.
Gagl (2016) Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information. PeerJ 4:e2467 https://doi.org/10.7717/peerj.2467
Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplification to related species
Rapid anthropogenic land use change threatens the primary habitat of the Chestnut short-tailed bat (Carollia castanea) throughout much of its range. Information on population genetic structure can inform management strategies for this widespread frugivorous bat, and effective protection of C. castanea will also benefit the more than 20 mutualistic plant species of which this bat is the primary seed disperser. To facilitate understanding of population genetic structure in this species, fourteen novel microsatellite markers were developed using restriction-site-associated DNA libraries and Illumina sequencing and tested on 28 individuals from 13 locations in Costa Rica. These are the first microsatellite markers developed for C. castanea. All loci were polymorphic, with number of alleles ranging from 2–11 and average observed heterozygosity of 0.631. Markers were also cross-amplified in three additional frugivorous bat species threatened by habitat loss and fragmentation: Sowell’s short-tailed bat (Carollia sowelli), Seba’s short-tailed bat (Carollia perspicillata), and the Jamaican fruit bat (Artibeus jamaicensis), and 10, 11, and 8 were polymorphic, respectively.
Cleary et al. (2016) Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplification to related species. PeerJ 4:e2465 https://doi.org/10.7717/peerj.2465
Hyperbrain features of team mental models within a juggling paradigm: a proof of concept
Background Research on cooperative behavior and the social brain exists, but little research has focused on real-time motor cooperative behavior and its neural correlates. In this proof of concept study, we explored the conceptual notion of shared and complementary mental models through EEG mapping of two brains performing a real-world interactive motor task of increasing difficulty. We used the recently introduced participative “juggling paradigm,” and collected neuro-physiological and psycho-social data. We were interested in analyzing the between-brains coupling during a dyadic juggling task, and in exploring the relationship between the motor task execution, the jugglers’skill level and the task difficulty. We also investigated how this relationship could be mirrored in the coupled functional organization of the interacting brains. Methods To capture the neural schemas underlying the notion of shared and complementary mental models, we examined the functional connectivity patterns and hyperbrain features of a juggling dyad involved in cooperative motor tasks of increasing difficulty. Jugglers’ cortical activity was measured using two synchronized 32-channel EEG systems during dyadic juggling performed with 3, 4, 5 and 6 balls. Individual and hyperbrain functional connections were quantified through coherence maps calculated across all electrode pairs in the theta and alpha bands (4–8 and 8–12 Hz). Graph metrics were used to typify the global topology and efficiency of the functional networks for the four difficulty levels in the theta and alpha bands. Results Results indicated that, as task difficulty increased, the cortical functional organization of the more skilled juggler became progressively more segregated in both frequency bands, with a small-world organization in the theta band during easier tasks, indicative of a flow-like state in line with the neural efficiency hypothesis. Conversely, more integrated functional patterns were observed for the less skilled juggler in both frequency bands, possibly related to cognitive overload due to the difficulty of the task at hand (reinvestment hypothesis). At the hyperbrain level, a segregated functional organization involving areas of the visuo-attentional networks of both jugglers was observed in both frequency bands and for the easier task only. Discussion These results suggest that cooperative juggling is supported by integrated activity of specialized cortical areas from both brains only during easier tasks, whereas it relies on individual skills, mirrored in uncorrelated individual brain activations, during more difficult tasks. These findings suggest that task difficulty and jugglers’ personal skills may influence the features of the hyperbrain network in its shared/integrative and complementary/segregative tendencies.
Filho et al. (2016) Hyperbrain features of team mental models within a juggling paradigm: a proof of concept. PeerJ 4:e2457 https://doi.org/10.7717/peerj.2457