[Experimental] List of manuscripts available for review volunteers
23 manuscripts available for review volunteers
January 14, 2017
Background. Software maintenance is an important activity in the process of software engineering where over time maintenance team members leave and new members join. The identification of files being changes together frequently has been proposed several times. Yet, existing studies about these file changes ignore the feedback from developers as well as the impact on the performance of maintenance and rely on the analysis findings and expert evaluation.
Methods. We conducted an experiment with the goal to investigate the usefulness of coupled file changes during maintenance tasks when developers are inexperienced in programming or when they are new on the project. Using data mining on software repositories we can identify files that changed most frequently together in the past. We extract coupled file changes from the Git repository of a Java software system and join them with corresponding attributes from the versioning and issue tracking system and the project documentation. We present a controlled experiment involving 36 student participants where we investigate if coupled file change suggestions influence the correctness of the task solutions and the time to complete them.
Results. The results show that coupled file change suggestions significantly increase the correctness of the solutions. However, there is only a small effect on the time to complete the tasks. We also derived a set of the most useful attributes based on the developers feedback.
Discussion. Coupled file changes and a limited number of the proposed attributes are useful for inexperienced developers working on maintenance tasks whereby although the developers using these suggestions solved more tasks, they still need time to organize and understand and implement this information.
January 11, 2017
Background. Theory predicts strong bottom-up control in detritus-based food webs, yet field experiments with detritus-based terrestrial systems have uncovered contradictory evidence regarding the strength and pervasiveness of bottom-up control processes. Two factors likely leading to contradictory results are experiment duration, which influences exposure to temporal variation in abiotic factors such as rainfall and affects the likelihood of detecting approach to a new equilibrium; and openness of the experimental units to immigration and migration. To investigate the contribution of these two factors, we conducted a long-term experiment with open and fenced plots in the forest that was the site of an earlier, short-term experiment (3.5 months) with open plots (Chen & Wise 1999) that produced evidence of strong bottom-up control for 14 taxonomic groupings of primary consumers of litter and fungi (microbi-detritivores) and their predators. Methods. We added artificial high-quality detritus to ten 2 x 2-m forest-floor plots at bi-weekly intervals from April through September in three consecutive years (Supplemented treatment). Ten comparable Ambient plots were controls. Half of the Supplemented and Ambient plots were enclosed by metal fencing. Results. Arthropod community structure (based upon 18 response variables) diverged over time between Supplemented and Ambient treatments, with no effect of Fencing on the multivariate response pattern. Fencing possibly influenced only ca. 20% of the subsequent univariate analyses. Multi- and univariate analyses revealed bottom-up control by fall of Year 1 of some, but not all, microbi-detritivores and predators. During the following two years the pattern of responses became more complex than that observed by Chen & Wise (1999). Some taxa showed consistent bottom-up control whereas many did not. Variation across years could not be explained completely by differences in rainfall because some taxa exhibited negative, not positive, responses to detrital supplementation. Discussion. Our 3-yr experiment did not confirm the conclusion of strong, pervasive bottom-up control of microbi-detritivores and predators reported by Chen and Wise (1999). Our longer-term experiment revealed a more complex pattern of responses, a pattern much closer to the range of outcomes reported in the literature for many short-term experiments. Much of the variation in responses across studies likely reflects variation in factors such as rainfall and the quality of added detritus. Nevertheless, it is also possible that long-term resource enhancement can drive a community towards a new equilibrium state that differs from what would have been predicted from the initial short-term responses exhibited by primary and secondary consumers.
January 11, 2017
Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Various methods that model the absorbance of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Here, I employ Akaike’s Information Criterion (AIC) to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data and histological parameters. This technique correctly selects among alternative models, and identifies between one and four spectral classes for the dark-acclimated visual systems of the velvet worm, Principapillatus hitoyensis, the branchiopod water flea, Daphnia magna, normal humans, and humans with enhanced S-cone syndrome: a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. I also include data from the Asian swallowtail, Papilio xuthus, which has at least five main spectral photoreceptor classes in its compound eyes, to illustrate potential effects of model oversimplification on multi-model inference. This technique will be informative for future opsin expression studies and to support extracellular or intracellular electroretinography.
January 11, 2017
The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.
January 6, 2017
In order to understand the distribution and prevalence of Ommatissus lybicus (Homoptera: Tropiduchidae) as well as analyse their current biographical patterns and predict their future spread, comprehensive and highly sophisticated information on the environmental, climatic, and agricultural practices are essential. The analytical techniques available in modern spatial analysis packages, such as Remote Sensing and Geographical Information Systems, can help detect and model spatial links and correlations between the presence, absence and density of O. lybicus in response to climatic, environmental and human factors. The main objective of this paper is to review remote sensing and geographical information analytical techniques that can be applied in mapping and modelling the habitat and population density of O. lybicus in Oman. An exhaustive search of related literature revealed that there are few studies linking location-based infestation levels of pests like the O. lybicus with climatic, environmental and human practice related variables in the Middle East. Our review also highlights the accumulated knowledge and addresses the gaps in this area of research. Furthermore, it makes recommendations for future studies, and gives suggestions on monitoring and surveillance sites that are necessary in designing both local and regional level integrated pest management (IPM) policing of palm tree and other affected cultivated crops.
January 4, 2017
Background. Osteoarthritis is the leading cause of chronic joint pain, causing important productivity and economic losses. It is believed that peripheral and centralized sensitization play a role in the creation and maintenance of a chronic painful state. Different animal models have been employed for the investigation of pain mechanisms and evaluation of potential treatments, but none of them are ideal in terms of reproducibly, reliability and translational value. Methods. In the search for better animal model, this pilot study was performed with the goal of evaluating pain functional outcomes and spinal biomarkers between three surgical rat models of osteoarthritic pain, i.e. destabilization of the medial meniscus, cranial cruciate ligament transection and the combination of both, and comparing those results to the intra-articular injection of monosodium iodoacetate. Six rats were assigned to each model group and a Sham group. Static weight bearing, punctate tactile paw withdrawal threshold, and spinal neuropeptides (substance P, calcitonin gene-related peptide, bradykinin, and somatostatin) were evaluated for each group. Results. Both the monosodium iodoacetate and combination models induced functional alterations in static weight bearing and punctate tactile paw withdrawal threshold, the changes being more persistent in the combination group. Both also produced an increased release of pro-nociceptive and anti-nociceptive neuropeptides at different time-points. When surgical models were compared, the cranial cruciate ligament transection and destabilization of the medial meniscus models were less interesting, with temporary functional alterations, and no significant change in neuropeptides. Discussion. The surgical induction of osteoarthritis was accompanied by quantifiable neurophysiologic changes relating to non-physiologic pain. Comparison with the monosodium iodoacetate model showed that the interest of a surgical model, especially the combination of destabilization of the medial meniscus and cranial cruciate ligament transection, might reside in more persistent and progressive changes, a model that may represent better the human post-traumatic osteoarthritis.
December 31, 2016
Plastic pollution has been recognized as a major pollutant of the open ocean, but the extent and impact of plastic pollution on the coral reef environment has yet to be fully understood. In this study, the distribution of both macro- (>5mm) and micro- plastic (<5mm) of a typical coral reef ecosystem— the fringing reef of an isolated South Pacific island, Mo’orea, French Polynesia—was quantified. During the course of the study, macroplastic was found on every beach on the island, and distribution of plastic was categorized by site type and the presence of Turbinaria oranata, a common macroalgae of Mo’orea. Microplastic (plastic pieces <5mm) was found in the water column of the fringing reef of the island, at a concentration of 0.74 plastic pieces per square meter. To test the impact on coral reef organisms of the plastic pollution found in the fringing reef, microplastic was exposed to a species of soft coral, Discosoma spp.in a laboratory setting. The resilience of Discosoma spp.in fluctuating temperatures and rising CO2 levels is well understood, but the effect of plastic pollution on Discosoma spp. and other corallimorphs has never before been analyzed. This study reports for the first time the ingestion of microplastic by the soft coral Discosoma spp. Positively buoyant and negatively buoyant microplastic were both ingested over different time frames. In addition, wild (not experimentally introduced) microplastic was found in the stomach cavity of the organism. These findings indicate that plastic debris are being ingested by Discosoma spp. and may impair the health of this prevalent coral reef organism.
December 21, 2016

Background. The ‘whirling’ defensive behavior of Pholcus ancoralis (L. Koch, 1865) was studied in a forest and laboratory in Mo’orea, French Polynesia. This behavior involves fast web-borne gyration to dissuade predators and is widespread in the Pholcidae family.

Methods. Different local predators (Anterhyncium rufipes, Lipinia noctua, and Thorelliola ensifera) were placed in two-chambered systems with P. ancoralis individuals and qualitative data on whirling frequency and duration were obtained.

Results. Potter wasps (Anterhyncium rufipes) triggered whirling in 50% of trials and moth skinks (Lipinia noctua) triggered whirling in 20% of trials. The average durations of the behavior triggered by each were 853 and 455 seconds, respectively. Pacific horned jumping spiders (Thorelliola ensifera) triggered whirling in 10% of trials with an average duration of only 20 seconds.

Discussion. Wasps triggered whirling the most frequently and of a long average duration. This has not been seen in other studied pholcids. This difference in predator specificity of whirling may be due to differences in habitat between pholcid species.

December 19, 2016
Acinetobacter baumannii has emerged as an important pathogen related to serious infections and nosocomial outbreaks around the world. The aim of this study was to detect the distribution of carbapenemases and efflux pump in carbopenems-resistance Acinetobacter baumannii(CRAB). In this study, 100 isolates of CRAB were collected from clinical specimens. Agar dilution was conducted to determine the minimum inhibitory concentrations (MICs) to 15 kinds of antibiotic. Genes of carbapenemases and efflux pumps were amplified by PCR. The expression difference of pump genes was also analyzed by real-time PCR between CRAB and carbopenems- sensitive Acinetobacter baumannii (CSAB). We found that most antibiotics, including aminoglycosides, fluoroquinolones and cephalosporins showed high MIC values in CRAB. While, all isolates were sensitive to polymyxin B. Among CRAB, 54, 32 and 16 isolates were positive for SHV-12,PER-1 and TEM-1, respectively. 86 isolates were positive for OXA-23. 55, 33 and 5 isolates carried adeB, adeJ and adeE genes. The expression level of adeB in CRAB was ten times higher than that in CSAB. Moreover, isolates with single adeE gene were detected for the first time in Acinetobacter baumannii.
December 19, 2016
The Cleveland-Lloyd Dinosaur Quarry (CLDQ) is the densest deposit of Jurassic theropod dinosaurs discovered to date. Unlike typical Jurassic bone deposits, it is dominated by the presence of Allosaurus fragilis. Since excavation began in the 1920’s numerous hypotheses have been put forward to explain the taphonomy of CLDQ, including a predator trap, a drought assemblage, and a poisoned spring. In an effort to reconcile the various interpretations of the quarry and reach a consensus on the depositional history of CLDQ, new data is required to develop a robust taphonomic framework congruent with all available data. Here we present two new data sets which aid in the development of such a robust taphonomic framework for CLDQ. First, x-ray fluorescence analysis of CLDQ sediments indicate elevated barite and sulfide minerals relative to other sediments from the Morrison Formation, suggesting an ephemeral environment dominated by periods of hypereutrophic conditions during bone accumulation. Second, the degree of weathering and hydraulic equivalency of small bone fragments dispersed throughout the matrix were analyzed from CLDQ. Results of these analyses suggest that bone fragments are autochthonous or parautochthonous and are derived from bones deposited in the assemblage. The variability in abrasion exhibited by the fragments is most parsimoniously explained by periodic reworking and redeposition during seasonal fluctuations throughout the duration of the quarry assemblage. Collectively, these data support some previous interpretations that the CLDQ represents an attritional assemblage in a poorly-drained overbank deposit where vertebrate remains were introduced post-mortem to an ephemeral pond during flood conditions. Furthermore, elevated heavy metals and rare earth elements detected at the quarry are likely a diagenetic signal, potentially produced in part from an abundance of vertebrate remains, and not the primary driver for the accumulation of carcasses. These new data help to explain the specific depositional environment of the quarry and represent a significant step in understanding the taphonomy of the bone bed and Late Jurassic paleoecology.
December 16, 2016
The role of serotonin (5-hydroxytryptamine, 5-HT) in social behavior regulation is not fully understood. While 5-HT has generally been associated with inhibition of aggressive behavior across multiple classes of vertebrates, less is known about its effects on sexual, especially non-copulatory courtship display behaviors. Furthermore, most research has examined effects at 5-HT release sites, while studies examining the behavioral relevance of source cell populations have generated contradictory findings. This study utilized immunohistochemistry to examine the colocalization of 5-HT with Fos, an immediate early gene product and marker of neural activity, in source cell populations of the brains of brown anoles (Anolissagrei) exposed to either aggression, courtship, or control social interactions. Supporting previous research, copulation was associated with a decrease in 5-HT activity, while a novel link between 5-HT activity and latency to non-copulatory courtship was also found. Within the aggression group, intensity and frequency of behavior were both associated with decreased 5-HT activity. An effect of social context was also seen, with anoles exposed to either courtship or aggression encounters showing decreased 5-HT activity in certain cell populations compared to controls. Interestingly, context effects and behavioral effects were seen at separate brain nuclei, suggesting the presence of separate systems with distinct functional roles.
December 16, 2016
Dam removal is an increasingly popular river-restoration tool, but our understanding of ecological responses to dam removal over time is still in the early stages. We quantified seasonal benthic macroinvertebrate density, taxonomic composition, and functional traits after lowhead dam removal in three reaches (two upstream of former dam [one restored, one unrestored], and one downstream of former dam) of the Olentangy River, Ohio, USA for three years. Breakpoint analysis indicated that macroinvertebrate community density, generic richness, and Shannon-Weiner diversity decreased between ~9 and ~15 months after dam removal; all three variables consistently increased thereafter. These threshold responses were dependent on reach location: density and richness increased ~15 months after removal in upstream reaches versus ~19 months downstream of the former dam. Initial macroinvertebrate density declines were likely related to seasonality or life-history characteristics, but density increased up to 2.27× from year to year in three out of four seasons (late autumn, early spring, summer) across all reaches. Non-metric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) revealed that macroinvertebrate community composition was similar among the three reaches, but differed seasonally. Seasonal differences among communities tended to decrease after dam removal. We detected community-wide shifts in functional traits such as multivoltinism, depositional habitat use, burrowing, and collector-gatherer feeding mode. We observed that these traits were expressed most strongly with Chironomidae, which was the most abundant family. Our results suggest that seasonal environmental conditions can play a role in the response and recovery of macroinvertebrate communities – often used to monitor ecosystem condition – following dam removal. In particular, macroinvertebrate density and diversity can show recovery after dam removal, especially in seasons when macroinvertebrate density is typically lowest, with concomitant changes to functional trait abundance. Thus, we recommend scientists and managers consider responses to dam removal throughout the year. Further, similar density, generic richness, and functional traits among reaches suggest that channel restoration after dam removal may initially have equivocal effects on invertebrate communities.
December 14, 2016

Background. The experience of ‘sensed presence’ – a feeling or sense that another entity, individual or being is present despite no clear sensory or perceptual evidence – is known to occur in the general population, appears more frequently in religious or spiritual contexts, and seems to be prominent in certain psychiatric or neurological conditions and may reflect specific functions of social cognition or body-image representation systems in the brain. Previous research has relied on ad-hoc measures of the experience and no specific psychometric scale to measure the experiences exists to date.

Methods. Based on the phenomenological description in the literature, we created the 16-item Sensed Presence Questionnaire (SenPQ). We recruited participants from i) a general population sample, and; ii) a sample including specific selection for religious affiliation, to complete the SenPQ and additional measures of well-being, schizotypy, social anxiety, social imagery and spiritual experience. We completed an analysis to test internal reliability, the ability of the SenPQ to distinguish between religious and non-religious participants, and whether the SenPQ was specifically related to positive schizotypical experiences and social imagery. A factor analysis was also conducted to examine underlying latent variables.

Results. The SenPQ was found to be reliable and valid, with religious participants significantly endorsing more items than non-religious participants and the scale showing a selective relationship with construct relevant measures. Principal components analysis indicates two underlying factors interpreted as reflecting ‘benign’ and a ‘malign’ sensed presence experiences.

Discussion. The SenPQ appears to be a reliable and valid measure of sensed presence experience although further validation in neurological and psychiatric conditions in warranted.

December 13, 2016
The evaluation of multisegment coordination is important for gaining a better understanding of gait and physical activities in humans. Therefore, the aim of this study was to verify whether the use of knee sleeves affected the coordination of lower-limb segments during level walking and one-leg hopping. Eleven healthy male adults participated in this study. They were asked to walk 10 m on a level ground and perform one-leg hops without wearing a knee sleeve and while wearing a knee sleeve. The segment angles and the response velocities of the thigh, shank, and foot were measured and calculated by using a motion analysis system. Then, the phases between the segment angle and the velocity were calculated; the continuous relative phase (CRP) was calculated as the phase of the distal segment subtracted from the phase of the proximal segment and was denoted as CRPTS (thigh–shank), CRPSF (shank–foot), and CRPTF (thigh–foot). Root mean square (RMS) values were used for the evaluation of in-phase or out-of-phase states, and standard deviation (SD) values were used for the evaluation of variability in the stance and swing phases during level walking and in the preflight, flight, and landing phases during one-leg hopping. The walking velocity and flight time improved when the knee sleeve was worn (p < 0.05). The segment angles of the thigh and shank changed when the knee sleeve was worn during level walking and one-leg hopping. The RMS values of CRPTS and CRPSF in the stance phase and the RMS values of CRPSF in the preflight and landing phases changed (p < 0.05 in all cases). The SD values of CRPTS in the landing phase and the SD values of CRPSF in the preflight and landing phases increased (p < 0.05 in all cases). These results indicated that wearing a knee sleeve caused changes in not only segment kinematics but also segment coordination. In conclusion, wearing a knee sleeve might be an effective technique to prevent injuries without any inhibitory effects.
December 12, 2016
Background. Stroke survivors often have multiple cardiovascular risk factors that necessitate promoting engagement in multiple healthy behaviors. However, observational studies of stroke survivors have typically focused on promoting a single health behavior. Thus, there is a poor understanding of linkages between healthy behaviors and the circumstances in which factors, such as stroke impairments, may influence a single or multiple health behaviors. Methods. We conducted a mixed methods convergent parallel study of 25 stroke survivors to examine the relationships between stroke impairments and physical activity, sleep, and nutrition. Our goal was to gain further insight into possible strategies to promote multiple health behaviors among stroke survivors. This study focused on physical activity, sleep, and nutrition because of their importance in achieving energy balance, maintaining a healthy weight, and reducing cardiovascular risks. Qualitative and quantitative data were collected concurrently, with the former being prioritized over the latter in order to develop a conceptual model of multiple health behaviors. Qualitative and quantitative data were analyzed independently and then were integrated during the inference stage to identify meta-inferences. The 25 stroke survivors completed closed-ended questionnaires on healthy behaviors and physical function. They also participated in face-to-face focus groups and one-to-one phone interviews. Results. We found statistically significant and moderate correlations between hand function and healthy eating habits (r = 0.45), sleep disturbances and limitations in activities of daily living (r = -0.55), BMI and limitations in activities of daily living (r = -0.49), physical activity and limitations in activities of daily living (r = 0.41), mobility impairments and BMI (r = -0.41), sleep disturbances and physical activity (r = -0.48), sleep disturbances and BMI (r = 0.48), and physical activity and BMI (r = -0.45). We identified five qualitative themes: (1) Impairments: reduced autonomy, (2) Environmental forces: caregivers and information, (3) Re-evaluation: priorities and attributions, (4) Resiliency: finding motivation and solutions, and (5) Negative affectivity: stress and self-consciousness.Three meta-inferences and a conceptual model described circumstances in which factors could influence single or multiple health behaviors. Discussion. This is the first mixed methods study of stroke survivors to elaborate on relationships between multiple health behaviors, BMI, and physical function. A conceptual model illustrates addressing sleep disturbances, activity limitations, self-image, and emotions to promote multiple health behaviors. We discuss the relevance of the meta-inferences in designing multiple behavior change interventions for stroke survivors.
December 12, 2016

Background. Natural hybridization plays a fundamental role in the evolution of various plant taxa, occasionally results in the formation of an entirely novel species. Since hybrids combine parental genotypes, they generate phenotypic traits that are often intermediate between their parental taxa, and these traits frequently serve as evidence for hybridization in morphological analyses. Ligularia × maoniushanensis was named as a natural hybrid species between L.duciformis and L. paradoxa mainly based on the morphological, reproductive traits and ISSR markers.

Methods. We investigated the taxonomic status and genetic structure of L. × maoniushanensis based on three cpDNA (psbA-trnH, trnL-rpl32 and trnQ-5’rps16), nuclear internal transcribed spacer (nrITS), SSR and ISSR markers.

Results. NrITS data analysis clearly distinguished two putative parental species and sympatric species, also supported the hypothesis that L. × maoniushanensis is a hybrid offspring between L. duciformis and L. paradoxa. Moreover, several morphologically identified individuals of L. duciformis and L. paradoxa could be introgressive. For cpDNA data, the hybridization was unidirectional in Mt. Maoniu where L. paradoxa was the mother of hybrids, while the hybridization was bidirectional and asymmetrical in Heihai Hu. STRUCTURE analysis of SSR data detected two distinct clusters of three taxa. NewHybrids analysis showed most individualsof L. × maoniushanensis had relatively high posterior probability as F2 hybrids that are not sufficient for hybrid generation determination. NewHybrids results of ISSR data were consistent with the SSR results.

Conclusions. Our data provided convincing evidence for hybridization and introgression between L. duciformis and L. paradoxa. The results of genetic structure demonstrated that L. × maoniushanensis is currently a mixture of hybrid offspring. Under frequent hybridization, these hybrid offspring would remain hybrid swarms with no reproductive isolation from their parents, which might impede the normal formation of a new species.

December 10, 2016
Mixed-species shoals of fish are frequently found in the field; however, little is known about individual-level interactions within these groups. We analyzed the collective motion of two cyprinids (Chinese bream, Parabramis pekinensis, and qingbo, Spinibarbus sinensis) that occupy partially overlapping habitats but differ in social behavior (high vs low aggressiveness) and preferred flow regime (fast vs slow water velocity). The spontaneous swimming activity, group cohesion (suggested by group member distance), synchronization of speed, coordination of orientation among members (suggested by separation swimming angle), occupied position (suggested by percentage of time a given individual swam at the front of a shoal), and responses to an artificial fright stimulus were measured with eight repetitions in four individuals of either Chinese bream or qingbo (conspecific group) and two Chinese bream plus two qingbo (heterospecific group). Chinese bream showed lower swimming activity and coordination than qingbo in conspecific groups, possibly due to the difference between their preferred habitats. However, this difference vanished as Chinese bream elevated their swimming activity to coordinate with heterospecific groups. This finding plus the similar separation swimming angle (SSA) values among the three experimental groups suggested that both species may share similar ineraction rules regarding shoaling behavior. However, qingbo showed greater separation distances than Chinese bream even in heterospecific groups, suggesting that there is an underlying difference between the two species’ shoaling mechanisms. Chinese bream showed higher variation in spatial distribution than qingbo, possibly due to the difference in behavior and/or habitat, whereas there was an unexpected lack of difference between the two species in the percentage of time spent at the front of a heterospecific group. Both species’ decreased response ratio to fright stimuli in a heterospecific group and the decreased consistency of responses between species compared with those within species suggest that information is transferred less efficiently in heterospecific groups. In conclusion, Chinese bream adjusted their swimming activity to that of qingbo in heterospecific groups to coordinate group movement; however, the ecological benefits of shoaling, such as defense against predators, might decrease due to the decreased information transfer.
December 8, 2016
Cascaded performance and compartments of constructed wetlands may harbor the internal eco-environmental gradients and further differentiate the niche and community structure of ammonia-oxidizing archaea (AOA). Here, we used quantitative PCR and 454 pyrosequencing of AOA amoA gene to investigate the abundance, diversity, composition, and driving factors of sedimentary AOA community in a created riparian wetland---Shijiuyang constructed wetland (SJY-CW) in China. Results showed that the heterogeneous wetland with serial-connected combinations of pretreatment pond, plant-bed/ditch system, and post-treatment pond as well as the third through fifth year succession (2011--2013, corresponding to the third through fifth year of actual operation after the initial two-year trial operation) had exerted significant spatiotemporal niche selection effects on AOA abundance and composition. AOA abundance in the pre- and post-treatment ponds was almost invariant in 2011--2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with the succession of SJY-CW. The AOA abundance ended up with one order of magnitude lower and tended to be consistent in the whole wetland. In contrast to abundance, the temporal niche differentiation of AOA diversity was insignificant. Nonetheless, a rough decrease trend was detected for the average community richness index Chao1 and diversity index Shannon H' in 2011--2013. Community structure analysis showed that Nitrososphaera was dominant genus, while Nitrosopumilus cluster and Nitrososphaera sister cluster increased with the succession of SJY-CW. Hierarchical clustering analysis and redundancy analysis both verified the horizontal shifts of AOA communities and these shifts inclined to occur in the most heterogeneous plant-bed/ditch system. Operational duration of the wetland which comprehensively reflected the wetland hydrology, water quality, and associated functions became the key factor driving the AOA abundance and community shift in SJY-CW sediments. In a nutshell, with the third through fifth year succession of wetland, the sedimentary ammonia-oxidizing archaea tended to be characterized by temporally decreased and spatially consistent abundance, while spatially variable and temporally decreased richness and diversity; regarding the AOA community structure, temporally from local species and relatively uniform distribution to mixing with allochthonous species and highly diversified distribution, while spatially occurring significant horizontal shifts of AOA amoA genes. These results showed the considerable if not significant niche selection effect of AOA abundance, diversity, and community structure with the operation of SJY-CW, and this will have some implications on the microbial ecology of archaeal ammonia-oxidization in a man-made wetland ecosystem.
December 5, 2016
Background: The kidney is always subjected to high metabolic demand. The aim of this study was to characterize metabolic profiles of a rat model of chronic kidney disease (CKD) with cardiorenal syndrome (CRS) induced by prolonged hypertension.
Methods: We used inbred male Dahl salt-sensitive (DS) rats fed an 8% NaCl diet from 6 weeks of age (high salt: HS) or a 0.3% NaCl diet as controls (low salt: LS). We analyzed function, pathology, metabolome, and the gene expression related to energy metabolism of kidney.
Results: DS rats with an HS diet showed hypertension at 11 weeks of age and elevated serum levels of creatinine and blood urea nitrogen with heart failure at 21 weeks of age. The fibrotic area in the kidneys increased at 21 weeks of age. In addition, gene expression related to mitochondrial function was largely decreased. The levels of citrate and isocitrate increased and the gene expression of alpha-ketoglutarate dehydrogenase and succinyl-CoA synthetase decreased, enzymes that metabolize citrate and isocitrate, respectively. In addition, the levels of succinate and acetyl Co-A decreased, both of which are metabolites of the TCA cycle.
Conclusions: DS rats fed an HS diet were deemed a suitable model of CKD with CRS. Gene expression and metabolites related to energy metabolism and mitochondria in the kidney significantly changed in DS rats with hypertension in accordance with the progression of renal injury.
November 25, 2016
Background. The enzymatic degradation of quorum sensing (QS) molecules (called quorum quenching, QQ) has been considered as a promising anti-virulence therapy to treat biofilm-related infections and combat antibiotic resistance. The recently-discovered QQ enzyme MomL has been reported to efficiently degrade different N-acyl homoserine lactones (AHLs) of various Gram-negative pathogens. Here we investigated the effect of MomL on biofilms formed by two important nosocomial pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii. Methods. MomL was expressed in E.coli BL21 and purified. The activity of MomL on AHLs with hydroxyl substituent was tested. Biofilms of P. aeruginosa PAO1 and Acinetobacter strains were formed in 96-well microtiter plates. Biofilm formation was evaluated by crystal violet staining, plating and fluorescence microscopy. The effect of MomL on biofilm susceptibility to antibiotics was also tested. We further evaluate MomL in dual-species biofilms formed by P. aeruginosa and A. baumanii, and in biofilms formed in a wound model. The effect of MomL on virulence of A. baumanii was also tested in the Caenorhabditis elegans model. Results. MomL reduced biofilm formation and biofilm susceptibility to different antibiotics in biofilms of P. aeruginosa PAO1 and A. baumannii LMG 10531 formed in microtiter plates in vitro. However, no significant differences were detected in the dual-species biofilm and in wound model biofilms. In addition, MomL did not affect virulence of A. baumannii in the C. elegans model. Finally, the effect of MomL on biofilm of Acinetobacter strains seems to be strain-dependent. Discussion. Our results indicate that although MomL showed a promising anti-biofilm effect against P. aeruginosa and A. baumanii biofilms formed in microtiter plates, the effect on biofilm formation under conditions more likely to mimic the real-life situation was much less pronounced or even absent. Our data indicate that in order to obtain a better picture of potential applicability of QQ enzymes for the treatment of biofilm-related infections, more elaborate model systems need to be used.
November 21, 2016
Breast cancer spheroid has been widely used as in vitro model of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance. From the miRNA profile, miR-15b, miR-34a, miR-148a, miR-628 and miR-196b were shown to be involved in CSCs-associated signalling pathways in both models of spheroids which highlights the involvement of these miRNAs in maintaining the CSCs features. In addition, unique clusters of miRNAs namely miR-205, miR-181a and miR-204 were found in basal-like spheroid whereas miR-125, miR-760, miR-30c and miR-136 were identified in luminal-like spheroid. Our results highlight the roles of miRNAs as well as providing novel perspectives of the relevant pathways underlying spheroid-enriched CSCs in breast cancer.
November 18, 2016
The macroalgal species Avrainvillea sp. and Halimeda kanaloana form expansive meadows which extend to depths of 80 m or more in the waters off of east O‘ahu and west Maui, respectively. We examined the fish fauna associated with these meadows using visual surveys and collections made with clove oil anesthetic. A total of 49 species from 25 families were recorded from H. kanaloana meadows and surrounding sandy areas, whereas 28 species from 19 families were recorded for Avrainvillea habitats. Percent endemism was 28.6% and 10.7%, respectively. Wrasses (Family Labridae) were the most speciose taxon in both habitats (11 and six species, respectively), followed by gobies for H. kanaloana (six species). The wrasse Oxycheilinus bimaculatus and cardinalfish Apogonichthys perdix were the most frequently-occurring species within the H. kanaloana and Avrainvillea canopies, respectively. Obligate herbivores and food-fish species were rare in both habitats. For both macroalgal species, the density and abundance of small epibenthic fishes were greater in open sand relative to the meadow canopy. We hypothesize that the holdfasts present within the canopy may impede benthic-dwelling or bioturbator species, which accounted for 86% and 57% of individuals collected in sand adjacent to H. kanaloana and Avrainvillea habitats, respectively. Of the 65 unique species recorded in this study, 16 (25%) were detected in clove oil stations alone, illustrating the utility of clove-oil anesthetic in assessing the diversity and abundance of small-bodied epibenthic fishes.
October 26, 2016
Candida albicans is one of the most frequent opportunistic pathogens in fungal infection. Secreted aspartic protease 2 (Sap2) and heat shock protein 90 (Hsp90) are two virulent factors of C. albicans , which play important roles in diagnosis of C. albicans infection. In this study, we used indirect competitive ELISA and indirect ELISA methods to detect the change of antigens/antibodies in the course of infection. Both Sap2 and Hsp90 had a changeable tendency during development of infection, and Sap2 existed longer than Hsp90. It can be deduced that Sap2 was useful for early diagnosis of infection. Sap2 and Hsp90 antibodies first increased and then reduced, but the level of Hsp90 antibodies on day 32 was higher than the first day, which indicated that Hsp90 antibodies could be used as a useful prognostic indicator. In conclusion, this research is the first study of two antigen/antibody changes by a figure model. By analyzing the product of the two antigens and antibodies, disease progression and severity could be predicted. Thus, the data has important implication in early diagnosis of candidiasis.

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