Vocal correlates of individual sooty mangabey travel speed and direction
Many group-living animals coordinate movements with acoustic signals, but so far most studies have focused on how group movements are initiated. In this study, we investigated movement patterns of wild sooty mangabeys (Cercocebus atys), a mostly terrestrial, forest-dwelling primate. We provide quantitative results showing that vocalization rates of mangabey subgroups, but not of focal individuals, correlated with focal individuals’ current movement patterns. More interestingly, vocal behaviour predicted whether individuals changed future speed, and possibly future travel direction. The role of vocalizations as a potential mechanism for the regulation of group movement was further highlighted by interaction effects that include subgroup size and the quality of poly-specific associations. Collectively, our results suggest that primate vocal behaviour can function beyond travel initiation in coordination and regulation of group movements.
Neumann et al. (2016) Vocal correlates of individual sooty mangabey travel speed and direction. PeerJ 4:e2298 https://doi.org/10.7717/peerj.2298
Larval settlement and metamorphosis in a marine gastropod in response to multiple conspecific cues
Larvae of the marine gastropod Crepidula fornicata must complete a transition from the plankton, where they are highly dispersed, to an aggregated group of benthic adults. Previous research has shown that selective settlement of larvae on conspecific adults is mediated by a water-borne chemical cue. However, variable experimental conditions have been used to study this cue, and standardization is needed in order to investigate factors that may have weak effects on settlement. In this study, we developed a time-course bioassay based on a full-factorial design with temporal blocking and statistical analysis of larval settlement rates in the lab. We tested this bioassay by examining settlement in the presence of an abiotic cue (KCl), and biotic cues (water conditioned with adult conspecifics and conspecific pedal mucus). Results confirmed settlement in the presence of both KCl and adult-conditioned water, and discovered the induction of settlement by pedal mucus. This optimized, standardized bioassay will be used in future experiments to characterize the complex process of larval settlement in C. fornicata, particularly to measure components of potentially small effect.
Cahill et al. (2016) Larval settlement and metamorphosis in a marine gastropod in response to multiple conspecific cues. PeerJ 4:e2295 https://doi.org/10.7717/peerj.2295
Engineering a light-controlled F1 ATPase using structure-based protein design
The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light.
Hoersch (2016) Engineering a light-controlled F1 ATPase using structure-based protein design. PeerJ 4:e2286 https://doi.org/10.7717/peerj.2286
Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia
The intertidal zone is a transitional environment that undergoes daily environmental fluctuations as tides rise and fall. Relatively few fish species are adapted to endure the physiological pressures of this environment. This study focused on Bathygobius cocosensis (Gobiidae), a common intertidal fish in New South Wales, Australia. We investigated whether shore height impacted site fidelity, survival probability, fish size, and morphological traits with respect to tidal height. Mark-recapture methods were used over a five month period to determine if individuals in high shore pools had greater site fidelity; fish in high tide pools were more than twice as likely to be recaptured in their original pool than fish from low tide pools. High pool individuals were, on average, smaller with larger eyes and longer snouts relative to their size as compared to low pool individuals. We discuss several mechanisms that could cause the observed pattern in morphological variation. Ultimately, this study suggests that within species behaviour and morphology differ by tidal position for an intertidal fish.
Malard et al. (2016) Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia. PeerJ 4:e2263 https://doi.org/10.7717/peerj.2263
Three-dimensional geometrical changes of the human tibialis anterior muscle and its central aponeurosis measured with three-dimensional ultrasound during isometric contractions
Background. Muscles not only shorten during contraction to perform mechanical work, but they also bulge radially because of the isovolumetric constraint on muscle fibres. Muscle bulging may have important implications for muscle performance, however quantifying three-dimensional (3D) muscle shape changes in human muscle is problematic because of difficulties with sustaining contractions for the duration of an in vivo scan. Although two-dimensional ultrasound imaging is useful for measuring local muscle deformations, assumptions must be made about global muscle shape changes, which could lead to errors in fully understanding the mechanical behaviour of muscle and its surrounding connective tissues, such as aponeurosis. Therefore, the aims of this investigation were (a) to determine the intra-session reliability of a novel 3D ultrasound (3DUS) imaging method for measuring in vivo human muscle and aponeurosis deformations and (b) to examine how contraction intensity influences in vivo human muscle and aponeurosis strains during isometric contractions. Methods. Participants (n = 12) were seated in a reclined position with their left knee extended and ankle at 90° and performed isometric dorsiflexion contractions up to 50% of maximal voluntary contraction. 3DUS scans of the tibialis anterior (TA) muscle belly were performed during the contractions and at rest to assess muscle volume, muscle length, muscle cross-sectional area, muscle thickness and width, fascicle length and pennation angle, and central aponeurosis width and length. The 3DUS scan involved synchronous B-mode ultrasound imaging and 3D motion capture of the position and orientation of the ultrasound transducer, while successive cross-sectional slices were captured by sweeping the transducer along the muscle. Results. 3DUS was shown to be highly reliable across measures of muscle volume, muscle length, fascicle length and central aponeurosis length (ICC ≥ 0.98, CV < 1%). The TA remained isovolumetric across contraction conditions and progressively shortened along its line of action as contraction intensity increased. This caused the muscle to bulge centrally, predominantly in thickness, while muscle fascicles shortened and pennation angle increased as a function of contraction intensity. This resulted in central aponeurosis strains in both the transverse and longitudinal directions increasing with contraction intensity. Discussion. 3DUS is a reliable and viable method for quantifying multidirectional muscle and aponeurosis strains during isometric contractions within the same session. Contracting muscle fibres do work in directions along and orthogonal to the muscle’s line of action and central aponeurosis length and width appear to be a function of muscle fascicle shortening and transverse expansion of the muscle fibres, which is dependent on contraction intensity. How factors other than muscle force change the elastic mechanical behaviour of the aponeurosis requires further investigation.
Raiteri et al. (2016) Three-dimensional geometrical changes of the human tibialis anterior muscle and its central aponeurosis measured with three-dimensional ultrasound during isometric contractions. PeerJ 4:e2260 https://doi.org/10.7717/peerj.2260
Perception of the risk of adverse reactions to analgesics: differences between medical students and residents
Background. Medications are not exempt from adverse drug reactions (ADR) and how the physician perceives the risk of prescription drugs could influence their availability to report ADR and their prescription behavior. Methods. We assess the perception of risk and the perception of ADR associated with COX2-Inbitors, paracetamol, NSAIDs, and morphine in medical students and residents of northeast of Mexico. Results. The analgesic with the highest risk perception in both group of students was morphine, while the drug with the least risk perceived was paracetamol. Addiction and gastrointestinal bleeding were the ADR with the highest score for morphine and NSAIDs respectively. Discussion. Our findings show that medical students give higher risk scores than residents toward risk due to analgesics. Continuing training and informing physicians about ADRs is necessary since the lack of training is known to induce inadequate use of drugs.
Castillo-Guzman et al. (2016) Perception of the risk of adverse reactions to analgesics: differences between medical students and residents. PeerJ 4:e2255 https://doi.org/10.7717/peerj.2255
A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model
Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software.
Pinthong et al. (2016) A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model. PeerJ 4:e2248 https://doi.org/10.7717/peerj.2248
The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded.
Duan et al. (2016) The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China. PeerJ 4:e2185 https://doi.org/10.7717/peerj.2185
What are the probable predictors of urinary incontinence during pregnancy?
Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated. Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant. Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the occurence of UI: Age (OR = 0.845, 95% CI [0.268–2.669]), being a housewife (OR = 1.800, 95% CI [0.850–3.810]), anemia (OR = 0.939, 95% CI [0.464–1.901]), parity (OR = 0.519, 95% CI [0.325–0.829]), miscarriage (OR = 1.219, 95% CI [0.588–2.825]) and living in rural areas (OR = 1.800, 95% CI [0.887–3.653]). Height (p = 0, 037), educational status (0.016), miscarriage (0.002), parity (0.006) and place of living (0.020) were significant factors. Conclusions.Many pregnant women are suffering from UI, which warrants a significant public health consideration in the region. Age, height, being a housewife or graduation level higher than primary school, living in rural, parity, miscarriage, and anemia were the factors in favor of the onset of UI. The authors plan a health promotion program in the region according to the results in order to provide information to health caregivers, especially family physicians, and to educate women about the predictors of UI and pelvic floor exercises for primary prevention and secondary relief of UI during and after pregnancy and provide some hygienic supplies to the poor in this aspect.
Demircan et al. (2016) What are the probable predictors of urinary incontinence during pregnancy?. PeerJ 4:e2283 https://doi.org/10.7717/peerj.2283
Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles
The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
Alfaro-Núñez et al. (2016) Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles. PeerJ 4:e2274 https://doi.org/10.7717/peerj.2274