Curculio Curculis lupus: biology, behavior and morphology of immatures of the cannibal weevil Anchylorhynchus eriospathae G. G. Bondar, 1943
Weevils are one of the largest groups of living organisms, with more than 60,000 species feeding mostly on plants. With only one exception, their described larvae are typical plant-feeders, with mouthparts adapted to chewing plant material. Here we describe the second case of a weevil with early-instar larvae adapted to killing conspecifics. We have studied the life history of Anchylorhynchus eriospathae G. G. Bondar, 1943 (Curculioninae: Derelomini sensu Caldara, Franz & Oberprieler (2014)), a species whose immatures feed internally on palm flowers and fruits. We provide detailed descriptions of all immature stages, including the extremely modified first-instar larva. Unlike other weevils and later instars, this stage exhibits a flat body with very long ventropedal lobe setae, a large and prognathous head with a gula, and falciform mandibles, each with a serrate retinaculum, that are used to fight with and eventually kill other first-instar larvae. We also provide biological notes on all stages and the results of behavioral tests that showed that larval aggression occurs only among early life stages. Finally we show that adult size is highly dependent on timing of oviposition. This specialized killer first instar probably evolved independently from the one other case known in weevils, in Revena rubiginosa (Conoderinae: Bariditae sensu Prena, Colonnelli & Hespenheide (2014)). Interestingly, both lineages inhabit the same hosts, raising the possibility that both intra- and inter-specific competition shaped those phenotypes. Given the scarcity of knowledge on early larval stages of concealed insect herbivores, it is possible that our findings represent an instance of a much broader phenomenon. Our observations also allowed us to conclude that Anchylorhynchus eriospathae and A. hatschbachi G. G. Bondar, 1943 are actually the same species, which we synonymize here by considering the latter as a junior synonym (new synonymy).
de Medeiros et al. (2014) Curculio Curculis lupus: biology, behavior and morphology of immatures of the cannibal weevil Anchylorhynchus eriospathae G. G. Bondar, 1943. PeerJ 2:e502 https://doi.org/10.7717/peerj.502
Mechanical properties of the cuticles of three cockroach species that differ in their wind-evoked escape behavior
The structural and material properties of insect cuticle remain largely unexplored, even though they comprise the majority (approximately 80%) of animals. Insect cuticle serves many functions, including protection against predatory attacks, which is especially beneficial to species failing to employ effective running escape responses. Despite recent advances in our understanding of insect escape behaviors and the biomechanics of insect cuticle, there are limited studies on the protective qualities of cuticle to extreme mechanical stresses and strains imposed by predatory attacks, and how these qualities vary between species employing different escape responses. Blattarians (cockroaches) provide an appropriate model system for such studies. Wind-evoked running escape responses are strong in Periplaneta americana, weak in Blaberus craniifer and absent in Gromphodorhina portentosa, putting the latter two species at greater risk of being struck by a predator. We hypothesized that the exoskeletons in these two larger species could provide more protection from predatory strikes relative to the exoskeleton of P. americana. We quantified the protective qualities of the exoskeletons by measuring the puncture resistance, tensile strength, strain energy storage, and peak strain in fresh samples of thoracic and abdominal cuticles from these three species. We found a continuum in puncture resistance, tensile strength, and strain energy storage between the three species, which were greatest in G. portentosa, moderate in B. craniifer, and smallest in P. americana. Histological measurements of total cuticle thickness followed this same pattern. However, peak strain followed a different trend between species. The comparisons in the material properties drawn between the cuticles of G. portentosa, B. craniifer, and P. americana demonstrate parallels between cuticular biomechanics and predator running escape responses.
Clark et al. (2014) Mechanical properties of the cuticles of three cockroach species that differ in their wind-evoked escape behavior. PeerJ 2:e501 https://doi.org/10.7717/peerj.501
Background. Biobanks are an important research resource that provides researchers with biological samples, tools and data, but have also been associated with a range of ethical, legal and policy issues and concerns. Although there have been studies examining the views of different stakeholders, such as donors, researchers and the general public, the media portrayal of biobanks has been absent from this body of research. This study therefore examines how biobanking has been represented in major print newspapers from Australia, Canada, the United Kingdom and the United States to identify the issues and concerns surrounding biobanks that have featured most prominently in the print media discourse. Methods. Using Factiva, articles published in major broadsheet newspapers in Canada, the US, the UK, and Australia were identified using specified search terms. The final sample size consisted of 163 articles. Results. Majority of articles mentioned or discussed the benefits of biobanking, with medical research being the most prevalent benefit mentioned. Fewer articles discussed risks associated with biobanking. Researchers were the group of people most quoted in the articles, followed by biobank employees. Biobanking was portrayed as mostly neutral or positive, with few articles portraying biobanking in a negative manner. Conclusion. Reporting on biobanks in the print media heavily favours discussions of related benefits over risks. Members of the scientific research community appear to be a primary source of this positive tone. Under-reporting of risks and a downtrend in reporting on legal and regulatory issues suggests that the print media views such matters as less newsworthy than perceived benefits of biobanking.
Ogbogu et al. (2014) Newspaper coverage of biobanks. PeerJ 2:e500 https://doi.org/10.7717/peerj.500
In vitro transcription accurately predicts lac repressor phenotype in vivo in Escherichia coli
A multitude of studies have looked at the in vivo and in vitro behavior of the lac repressor binding to DNA and effector molecules in order to study transcriptional repression, however these studies are not always reconcilable. Here we use in vitro transcription to directly mimic the in vivo system in order to build a self consistent set of experiments to directly compare in vivo and in vitro genetic repression. A thermodynamic model of the lac repressor binding to operator DNA and effector is used to link DNA occupancy to either normalized in vitro mRNA product or normalized in vivo fluorescence of a regulated gene, YFP. An accurate measurement of repressor, DNA and effector concentrations were made both in vivo and in vitro allowing for direct modeling of the entire thermodynamic equilibrium. In vivo repression profiles are accurately predicted from the given in vitro parameters when molecular crowding is considered. Interestingly, our measured repressor–operator DNA affinity differs significantly from previous in vitro measurements. The literature values are unable to replicate in vivo binding data. We therefore conclude that the repressor-DNA affinity is much weaker than previously thought. This finding would suggest that in vitro techniques that are specifically designed to mimic the in vivo process may be necessary to replicate the native system.
Sochor (2014) In vitro transcription accurately predicts lac repressor phenotype in vivo in Escherichia coli. PeerJ 2:e498 https://doi.org/10.7717/peerj.498
Adherence to an overweight and obesity treatment: how to motivate a patient?
Objective. To explore anthropometric changes in normal-weight, overweight and obese subjects who did not dropout or fail a weight loss program over the 16 treatment weeks to improve patient motivation and treatment adherence. Methods. A clinical intervention study was conducted among 271 (including 100 dropouts and/or failures) obese and overweight patients who consulted a nutrition clinic in Barranquilla (Colombia) for the purpose of nutritional assessment. They were subject to a personalized weekly follow-up consultation over the course of 16 weeks in which initial and the final Body Mass Index (BMI, kg/m2), photographs, food consumption patterns, percentage weight loss, waist and hip circumference were registered and grouped according to BMI, measuring treatment response. Data’s nonparametric statistical comparison was made. Results. In 62 patients from the BMI < 25 group, there is weight loss of 2.6% (3.1 SD), 5.5% (3.3 SD) in waist circumference and 3.0% (2.5 SD) in hip circumference. In 67 patients from the 25 ≥ BMI < 30 group, there is weight loss of 3.8% (4.1 SD), 5.7% (4.5 SD) in waist circumference loss and 3.7% (3.0 SD) in hip circumference loss. In 42 patients from the BMI > 30 group, there is weight loss of 4.8% (3.7 SD), 7.0% (3.6 SD) in waist circumference loss and 3.9% (2.4 SD) in hip circumference loss. Monitoring is done every 4 weeks by the Friedman test, with significant differences between the three groups (p < 0.001). Patients do not drop out of treatment because they start to see physical results in waist decrease. When comparing final values of initial waist/hip circumference ratios and waist/height ratios, a clear decrease in the three BMI groups was observed (p < 0.001). Conclusion. After three weeks of continuous treatment patients improved in all overweight and obesity parameter indicators; there were not statistically significant differences in hip circumference (HC) and waist loss (WC) (%) among the three BMI groups (normal-weight, overweight, and obesity). In contrast, there were statistically significant differences in weight loss (%) and waist-to-hip ratios. Based on anthropometric outcomes and patient perception of their body image it can be concluded that the waist circumference loss is the parameter that retains obese patients in the weight loss program.
Kuzmar et al. (2014) Adherence to an overweight and obesity treatment: how to motivate a patient?. PeerJ 2:e495 https://doi.org/10.7717/peerj.495
Prevalence of Entamoeba species in captive primates in zoological gardens in the UK
The aim of this study was to determine the prevalence of amoebic infection in non-human primates (NHPs) from six Zoological gardens in the United Kingdom. Initially, 126 faecal samples were collected from 37 individually identified NHPs at Twycross Zoo, UK, and were subjected to microscopic examination. A subsequent, nationwide experiment included 350 faecal samples from 89 individually identified NHPs and 73 unidentified NHPs from a number of UK captive wildlife facilities: Twycross Zoo (n = 60), Colchester Zoo (n = 3), Edinburgh Zoo (n = 6), Port Lympne Wild Animal Park (n = 58), Howletts Wild Animal Park (n = 31), and Cotswold Wildlife Park (n = 4). Samples were examined by PCR and sequencing using four specific primer sets designed to differentiate between the pathogenic E. histolytica, the non-pathogenic E. dispar, and non-pathogenic uninucleate cyst-producing Entamoeba species. In the first experiment, Entamoeba was detected in 30 primates (81.1%). Six (16.2%) primates were infected with E. histolytica species complex. The highest carriage of Entamoeba species was found in Old World Colobinae primates. In the nationwide experiment, molecular analysis of faecal samples revealed notable rates of Entamoeba infection (101 samples, 28.9%), including one sample infected with E. histolytica, 14 samples with E. dispar, and 86 samples with uninucleated-cyst producing Entamoeba species. Sequences of positive uninucleated-cyst producing Entamoeba samples from Twycross Zoo clustered with the E. polecki reference sequences ST4 reported in Homo sapiens, and are widely separated from other Entamoeba species. These findings suggest a low prevalence of the pathogenic Entamoeba infection, but notable prevalence of non-pathogenic E. polecki infection in NHPs in the UK.
Regan et al. (2014) Prevalence of Entamoeba species in captive primates in zoological gardens in the UK. PeerJ 2:e492 https://doi.org/10.7717/peerj.492
Eleutherodactylus frogs show frequency but no temporal partitioning: implications for the acoustic niche hypothesis
Individuals in acoustic communities compete for the use of the sound resource for communication, a problem that can be studied as niche competition. The acoustic niche hypothesis presents a way to study the partitioning of the resource, but the studies have to take into account the three dimensions of this niche: time, acoustic frequency, and space. I used an Automated Digital Recording System to determine the partitioning of time and acoustic frequency of eight frogs of the genus Eleutherodactylus from Puerto Rico. The calling activity was measured using a calling index. The community exhibited no temporal partitioning since most species called at the same time, between sunset and midnight. The species partitioned the acoustic frequency of their signals, which, in addition to the microhabitat partitioning, can provide some insight into how these species deal with the problem. This data also suggest that monitoring projects with this group should take place only before midnight to avoid false negatives.
Villanueva-Rivera (2014) Eleutherodactylus frogs show frequency but no temporal partitioning: implications for the acoustic niche hypothesis. PeerJ 2:e496 https://doi.org/10.7717/peerj.496
Subtle neuropsychiatric and neurocognitive changes in hereditary gelsolin amyloidosis (AGel amyloidosis)
Hereditary gelsolin amyloidosis (AGel amyloidosis) is an autosomal dominant form of systemic amyloidosis caused by a c.640G>A or c.640G>T mutation in the gene coding for gelsolin. Principal clinical manifestations include corneal lattice dystrophy, cranial neuropathy and cutis laxa with vascular fragility. Signs of minor CNS involvement have also been observed, possibly related to cerebral amyloid angiopathy (CAA). To investigate further if AGel amyloidosis carries a risk for a specific neuropsychological or psychiatric symptomatology we studied 35 AGel patients and 29 control subjects. Neuropsychological tests showed abnormalities in visuocontructional and -spatial performance in AGel patients, also some indication of problems in processing efficacy was found. At psychiatric evaluation the patient group showed more psychiatric symptomatology, mainly depression. In brain MRI, available in 16 patients and 14 controls, we found microhemorrhages or microcalcifications only in the patient group, although the number of findings was small. Our study shows that AGel amyloidosis can be associated with visuoconstructional problems and depression, but severe neuropsychiatric involvement is not characteristic. The gelsolin mutation may even induce cerebrovascular fragility, but further epidemiological and histopathological as well as longitudinal follow-up studies are needed to clarify gelsolin-related vascular pathology and its clinical consequences.
Kantanen et al. (2014) Subtle neuropsychiatric and neurocognitive changes in hereditary gelsolin amyloidosis (AGel amyloidosis). PeerJ 2:e493 https://doi.org/10.7717/peerj.493
SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading
Background. Unlike full reading, ‘skim-reading’ involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles that are being published ongoingly in life sciences. Methods. To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used to construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed. Last but not least, we describe a methodology for automated experimental evaluation of the presented approach. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. Results. We provide a web-based prototype (called ‘SKIMMR’) that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are the most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson’s Disease. Finally, we report on the results of experimental evaluation using the two domains and one additional dataset based on the TREC challenge. The results show how the presented method for machine-aided skim reading outperforms tools like PubMed regarding focused browsing and informativeness of the browsing context.
Nováček et al. (2014) SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading. PeerJ 2:e483 https://doi.org/10.7717/peerj.483
Involvement of cortical midline structures in the processing of autobiographical information
The term autobiographical self has been used to refer to a mental state that permits reflection on self-identity and personality and the answer to related questions (Damasio, 1998). It requires the retrieval and integrated assembly of memories of facts and events that define an individual’s biography. The neural mechanisms behind this state have not been fully elucidated, but it has been suggested that cortical midline structures (CMSs) are critically involved in processing self-related information. To date, the investigation of the involvement of CMSs in autobiographical-self processes has largely focused on the comparison between self and other in relation to one domain of information, personality traits, and has yielded conflicting results. Here, we investigated how activity in CMSs varies with (1) the target of the information (self versus an acquaintance), (2) the domain of information (personality traits versus facts), and (3) differences across individuals regarding how descriptive and how important/relevant the information targeted by the questions was, and regarding the amount of memory retrieved in order to answer the questions. We used an fMRI block-design in which 19 participants answered questions about traits and biographic facts, in relation to themselves and a distant acquaintance. In addition, the participants rated the descriptiveness and importance of the information targeted by the questions, and estimated the amount of memory retrieved to answer the questions. Our results showed that CMSs were active for both facts and traits and for both self and other, and that the level of activity in the posteromedial cortices was generally higher for other than for self. Moreover, the activity in CMSs also varied with the amount of memory retrieved to answer the questions and with descriptiveness and importance of the information. These findings suggest that involvement of CMSs during the evaluation of information is not specific for self, and depends on varied factors related to memory retrieval prompted by the questions and to processes required to answer them.
Araujo et al. (2014) Involvement of cortical midline structures in the processing of autobiographical information. PeerJ 2:e481 https://doi.org/10.7717/peerj.481
The bacterial communities of Drosophila suzukii collected from undamaged cherries
Drosophila suzukii is an introduced pest insect that feeds on undamaged, attached fruit. This diet is distinct from the fallen, discomposing fruits utilized by most other species of Drosophila. Since the bacterial microbiota of Drosophila, and of many other animals, is affected by diet, we hypothesized that the bacteria associated with D. suzukii are distinct from that of other Drosophila. Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. We find that the bacterial communities associated with these samples of D. suzukii contain a high frequency of Tatumella. Gluconobacter and Acetobacter, two taxa with known associations with Drosophila, were also found, although at lower frequency than Tatumella in four of the five samples examined. Sampling D. suzukii from different locations and/or while feeding on different fruits is needed to determine the generality of the results determined by these samples. Nevertheless this is, to our knowledge, the first study characterizing the bacterial communities of this ecologically unique and economically important species of Drosophila.
Chandler et al. (2014) The bacterial communities of Drosophila suzukii collected from undamaged cherries. PeerJ 2:e474 https://doi.org/10.7717/peerj.474
Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning
Automatic species classification of birds from their sound is a computational tool of increasing importance in ecology, conservation monitoring and vocal communication studies. To make classification useful in practice, it is crucial to improve its accuracy while ensuring that it can run at big data scales. Many approaches use acoustic measures based on spectrogram-type data, such as the Mel-frequency cepstral coefficient (MFCC) features which represent a manually-designed summary of spectral information. However, recent work in machine learning has demonstrated that features learnt automatically from data can often outperform manually-designed feature transforms. Feature learning can be performed at large scale and “unsupervised”, meaning it requires no manual data labelling, yet it can improve performance on “supervised” tasks such as classification. In this work we introduce a technique for feature learning from large volumes of bird sound recordings, inspired by techniques that have proven useful in other domains. We experimentally compare twelve different feature representations derived from the Mel spectrum (of which six use this technique), using four large and diverse databases of bird vocalisations, classified using a random forest classifier. We demonstrate that in our classification tasks, MFCCs can often lead to worse performance than the raw Mel spectral data from which they are derived. Conversely, we demonstrate that unsupervised feature learning provides a substantial boost over MFCCs and Mel spectra without adding computational complexity after the model has been trained. The boost is particularly notable for single-label classification tasks at large scale. The spectro-temporal activations learned through our procedure resemble spectro-temporal receptive fields calculated from avian primary auditory forebrain. However, for one of our datasets, which contains substantial audio data but few annotations, increased performance is not discernible. We study the interaction between dataset characteristics and choice of feature representation through further empirical analysis.
Stowell et al. (2014) Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning. PeerJ 2:e488 https://doi.org/10.7717/peerj.488
Data-mining of potential antitubercular activities from molecular ingredients of traditional Chinese medicines
Background. Traditional Chinese medicine encompasses a well established alternate system of medicine based on a broad range of herbal formulations and is practiced extensively in the region for the treatment of a wide variety of diseases. In recent years, several reports describe in depth studies of the molecular ingredients of traditional Chinese medicines on the biological activities including anti-bacterial activities. The availability of a well-curated dataset of molecular ingredients of traditional Chinese medicines and accurate in-silico cheminformatics models for data mining for antitubercular agents and computational filters to prioritize molecules has prompted us to search for potential hits from these datasets. Results. We used a consensus approach to predict molecules with potential antitubercular activities from a large dataset of molecular ingredients of traditional Chinese medicines available in the public domain. We further prioritized 160 molecules based on five computational filters (SMARTSfilter) so as to avoid potentially undesirable molecules. We further examined the molecules for permeability across Mycobacterial cell wall and for potential activities against non-replicating and drug tolerant Mycobacteria. Additional in-depth literature surveys for the reported antitubercular activities of the molecular ingredients and their sources were considered for drawing support to prioritization. Conclusions. Our analysis suggests that datasets of molecular ingredients of traditional Chinese medicines offer a new opportunity to mine for potential biological activities. In this report, we suggest a proof-of-concept methodology to prioritize molecules for further experimental assays using a variety of computational tools. We also additionally suggest that a subset of prioritized molecules could be used for evaluation for tuberculosis due to their additional effect against non-replicating tuberculosis as well as the additional hepato-protection offered by the source of these ingredients.
Jamal et al. (2014) Data-mining of potential antitubercular activities from molecular ingredients of traditional Chinese medicines. PeerJ 2:e476 https://doi.org/10.7717/peerj.476
Take a stand on your decisions, or take a sit: posture does not affect risk preferences in an economic task
Physiological and emotional states can affect our decision-making processes, even when these states are seemingly insignificant to the decision at hand. We examined whether posture and postural threat affect decisions in a non-related economic domain. Healthy young adults made a series of choices between economic lotteries in various conditions, including changes in body posture (sitting vs. standing) and changes in elevation (ground level vs. atop a 0.8-meter-high platform). We compared three metrics between conditions to assess changes in risk-sensitivity: frequency of risky choices, and parameter fits of both utility and probability weighting parameters using cumulative prospect theory. We also measured skin conductance level to evaluate physiological response to the postural threat. Our results demonstrate that body posture does not significantly affect decision making. Secondly, despite increased skin conductance level, economic risk-sensitivity was unaffected by increased threat. Our findings indicate that economic choices are fairly robust to the physiological and emotional changes that result from posture or postural threat.
O’Brien et al. (2014) Take a stand on your decisions, or take a sit: posture does not affect risk preferences in an economic task. PeerJ 2:e475 https://doi.org/10.7717/peerj.475
Resource availability and repeated defoliation mediate compensatory growth in trembling aspen (Populus tremuloides) seedlings
Plant ecologists have debated the mechanisms used by plants to cope with the impact of herbivore damage. While plant resistance mechanisms have received much attention, plant compensatory growth as a type of plant tolerance mechanisms has been less studied. We conducted a greenhouse experiment to evaluate compensatory growth for trembling aspen (Populus tremuloides) seedlings under varying intensities and frequencies of simulated defoliation, with or without nutrient enriched media. For the purpose of this study, changes in biomass production and non-structural carbohydrate concentrations (NSC) of roots and leaves were considered compensatory responses. All defoliated seedlings showed biomass accumulation under low defoliation intensity and frequency, regardless of resource availability; however, as defoliation intensity and frequency increased, compensatory growth of seedlings was altered depending on resource availability. Seedlings in a resource-rich environment showed complete compensation, in contrast responses ranged from undercompensation to complete compensation in a resource-limited environment. Furthermore, at the highest defoliation intensity and frequency, NSC concentrations in leaves and roots were similar between defoliated and non-defoliated seedlings in a resource-rich environment; in contrast, defoliated seedlings with limited resources sustained the most biomass loss, had lower amounts of stored NSC. Using these results, we developed a new predictive framework incorporating the interactions between frequency and intensity of defoliation and resource availability as modulators of plant compensatory responses.
Erbilgin et al. (2014) Resource availability and repeated defoliation mediate compensatory growth in trembling aspen (Populus tremuloides) seedlings. PeerJ 2:e491 https://doi.org/10.7717/peerj.491
Microhabitat use, population densities, and size distributions of sulfur cave-dwelling Poecilia mexicana
The Cueva del Azufre in Tabasco, Mexico, is a nutrient-rich cave and its inhabitants need to cope with high levels of dissolved hydrogen sulfide and extreme hypoxia. One of the successful colonizers of this cave is the poeciliid fish Poecilia mexicana, which has received considerable attention as a model organism to examine evolutionary adaptations to extreme environmental conditions. Nonetheless, basic ecological data on the endemic cave molly population are still missing; here we aim to provide data on population densities, size class compositions and use of different microhabitats. We found high overall densities in the cave and highest densities at the middle part of the cave with more than 200 individuals per square meter. These sites have lower H2S concentrations compared to the inner parts where most large sulfide sources are located, but they are annually exposed to a religious harvesting ceremony of local Zoque people called La Pesca. We found a marked shift in size/age compositions towards an overabundance of smaller, juvenile fish at those sites. We discuss these findings in relation to several environmental gradients within the cave (i.e., differences in toxicity and lighting conditions), but we also tentatively argue that the annual fish harvest during a religious ceremony (La Pesca) locally diminishes competition (and possibly, cannibalism by large adults), which is followed by a phase of overcompensation of fish densities.
Jourdan et al. (2014) Microhabitat use, population densities, and size distributions of sulfur cave-dwelling Poecilia mexicana. PeerJ 2:e490 https://doi.org/10.7717/peerj.490
Prosocial skills may be necessary for better peer functioning in children with symptoms of disruptive behavior disorders
Children with disruptive behavior disorders experience substantial social challenges; however, the factors that account for (i.e., mediate), or influence (i.e., moderate), peer problems are not well understood. This study tested whether symptoms of Oppositional Defiant Disorder and Conduct Disorder were associated with peer impairment and whether prosocial skills mediated or moderated these associations. Teacher ratings were gathered for 149 children (Mage = 9.09, SD = 1.71, 26% female) referred for behavioral concerns to an urban child psychiatry clinic. Path-analytic linear regressions testing mediation and moderation effects showed that prosocial skills significantly moderated the negative effects of symptoms of Conduct Disorder on peer impairment. Children showed less peer impairment only when they had relatively few conduct symptoms and high prosocial skills. Measurement of prosocial skills, in addition to conduct problems, may best capture factors which contribute to peer problems of children with disruptive behaviors.
Andrade et al. (2014) Prosocial skills may be necessary for better peer functioning in children with symptoms of disruptive behavior disorders. PeerJ 2:e487 https://doi.org/10.7717/peerj.487
Surfactant protein C peptides with salt-bridges (“ion-locks”) promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein
Background. Surfactant protein C (SP-C; 35 residues) in lungs has a cationic N-terminal domain with two cysteines covalently linked to palmitoyls and a C-terminal region enriched in Val, Leu and Ile. Native SP-C shows high surface activity, due to SP-C inserting in the bilayer with its cationic N-terminus binding to the polar headgroup and its hydrophobic C-terminus embedded as a tilted, transmembrane α-helix. The palmitoylcysteines in SP-C act as ‘helical adjuvants’ to maintain activity by overriding the β-sheet propensities of the native sequences. Objective. We studied SP-C peptides lacking palmitoyls, but containing glutamate and lysine at 4-residue intervals, to assess whether SP-C peptides with salt-bridges (“ion-locks”) promote surface activity by mimicking the α-helix and membrane topography of native SP-C. Methods. SP-C mimics were synthesized that reproduce native sequences, but without palmitoyls (i.e., SP-Css or SP-Cff, with serines or phenylalanines replacing the two cysteines). Ion-lock SP-C molecules were prepared by incorporating single or double Glu−–Lys+ into the parent SP-C’s. The secondary structures of SP-C mimics were studied with Fourier transform infrared (FTIR) spectroscopy and PASTA, an algorithm that predicts β-sheet propensities based on the energies of the various β-sheet pairings. The membrane topography of SP-C mimics was investigated with orientated and hydrogen/deuterium (H/D) exchange FTIR, and also Membrane Protein Explorer (MPEx) hydropathy analysis. In vitro surface activity was determined using adsorption surface pressure isotherms and captive bubble surfactometry, and in vivo surface activity from lung function measures in a rabbit model of surfactant deficiency. Results. PASTA calculations predicted that the SP-Css and SP-Cff peptides should each form parallel β-sheet aggregates, with FTIR spectroscopy confirming high parallel β-sheet with ‘amyloid-like’ properties. The enhanced β-sheet properties for SP-Css and SP-Cff are likely responsible for their low surfactant activities in the in vitro and in vivo assays. Although standard 12C-FTIR study showed that the α-helicity of these SP-C sequences in lipids was uniformly increased with Glu−–Lys+ insertions, elevated surfactant activity was only selectively observed. Additional results from oriented and H/D exchange FTIR experiments indicated that the high surfactant activities depend on the SP-C ion-locks recapitulating both the α-helicity and the membrane topography of native SP-C. SP-Css ion-lock 1, an SP-Css with a salt-bridge for a Glu−–Lys+ ion-pair predicted from MPEx hydropathy calculations, demonstrated enhanced surfactant activity and a transmembrane helix simulating those of native SP-C. Conclusion. Highly active SP-C mimics were developed that replace the palmitoyls of SP-C with intrapeptide salt-bridges and represent a new class of synthetic surfactants with therapeutic interest.
Walther et al. (2014) Surfactant protein C peptides with salt-bridges (“ion-locks”) promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein. PeerJ 2:e485 https://doi.org/10.7717/peerj.485
Applying the cost of generating force hypothesis to uphill running
Historically, several different approaches have been applied to explain the metabolic cost of uphill human running. Most of these approaches result in unrealistically high values for the efficiency of performing vertical work during running uphill, or are only valid for running up steep inclines. The purpose of this study was to reexamine the metabolic cost of uphill running, based upon our understanding of level running energetics and ground reaction forces during uphill running. In contrast to the vertical efficiency approach, we propose that during incline running at a certain velocity, the forces (and hence metabolic energy) required for braking and propelling the body mass parallel to the running surface are less than during level running. Based on this idea, we propose that the metabolic rate during uphill running can be predicted by a model, which posits that (1) the metabolic cost of perpendicular bouncing remains the same as during level running, (2) the metabolic cost of running parallel to the running surface decreases with incline, (3) the delta efficiency of producing mechanical power to lift the COM vertically is constant, independent of incline and running velocity, and (4) the costs of leg and arm swing do not change with incline. To test this approach, we collected ground reaction force (GRF) data for eight runners who ran thirty 30-second trials (velocity: 2.0–3.0 m/s; incline: 0–9°). We also measured the metabolic rates of eight different runners for 17, 7-minute trials (velocity: 2.0–3.0 m/s; incline: 0–8°). During uphill running, parallel braking GRF approached zero for the 9° incline trials. Thus, we modeled the metabolic cost of parallel running as exponentially decreasing with incline. With that assumption, best-fit parameters for the metabolic rate data indicate that the efficiency of producing mechanical power to lift the center of mass vertically was independent of incline and running velocity, with a value of ∼29%. The metabolic cost of uphill running is not simply equal to the sum of the cost of level running and the cost of performing work to lift the body mass against gravity. Rather, it reflects a constant cost of perpendicular bouncing, decreased costs of parallel braking and propulsion and of course the cost of lifting body mass against gravity.
Hoogkamer et al. (2014) Applying the cost of generating force hypothesis to uphill running. PeerJ 2:e482 https://doi.org/10.7717/peerj.482
Plant dieback under exceptional drought driven by elevation, not by plant traits, in Big Bend National Park, Texas, USA
In 2011, Big Bend National Park, Texas, USA, experienced the most severe single year drought in its recorded history, resulting in significant plant mortality. We used this event to test how perennial plant response to drought varied across elevation, plant growth form and leaf traits. In October 2010 and October 2011, we measured plant cover by species at six evenly-spaced elevations ranging from Chihuahuan desert (666 m) to oak forest in the Chisos mountains (1,920 m). We asked the following questions: what was the relationship between elevation and stem dieback and did susceptibility to drought differ among functional groups or by leaf traits? In 2010, pre-drought, we measured leaf mass per area (LMA) on each species. In 2011, the percent of canopy dieback for each individual was visually estimated. Living canopy cover decreased significantly after the drought of 2011 and dieback decreased with elevation. There was no relationship between LMA and dieback within elevations. The negative relationship between proportional dieback and elevation was consistent in shrub and succulent species, which were the most common growth forms across elevations, indicating that dieback was largely driven by elevation and not by species traits. Growth form turnover did not influence canopy dieback; differences in canopy cover and proportional dieback among elevations were driven primarily by differences in drought severity. These results indicate that the 2011 drought in Big Bend National Park had a large effect on communities at all elevations with average dieback for all woody plants ranging from 8% dieback at the highest elevation to 83% dieback at lowest elevations.
Waring et al. (2014) Plant dieback under exceptional drought driven by elevation, not by plant traits, in Big Bend National Park, Texas, USA. PeerJ 2:e477 https://doi.org/10.7717/peerj.477
Physical activity habits and preferences in the month prior to a first-ever stroke
Background. Physical inactivity is a powerful risk factor for stroke and other chronic diseases. The aim of this study was to explore physical activity habits and preferences in the month leading up to a first-ever stroke, and to determine whether participants were aware of the link between stroke and physical activity. Methods. We undertook an observational study with 81 participants recently admitted to a stroke unit. Participants reported their pre-morbid physical activity preferences and habits and completed the Barriers to Physical Activity and Disability Survey. Data were analysed with summative content analysis and descriptive statistics. Results. Only 31% of participants were aware that physical inactivity was associated with stroke. Most participants defined physical activity with examples of instrumental activities of daily living (IADL) and walking (48% of responses), and IADLs constituted their most frequent regular physical activity (38% of responses). The barriers to physical activity reported by participants most frequently were lack of motivation (52%), lack of interest (50%) and lack of energy (42%). Conclusions. Regular physical activity is important to prevent stroke and other chronic diseases but adults at risk of stroke have little awareness of the risks of physical inactivity and little motivation to undertake regular exercise.
McDonnell et al. (2014) Physical activity habits and preferences in the month prior to a first-ever stroke. PeerJ 2:e489 https://doi.org/10.7717/peerj.489
HIV-positive parents, HIV-positive children, and HIV-negative children’s perspectives on disclosure of a parent’s and child’s illness in Kenya
HIV disclosure from parent to child is complex and challenging to HIV-positive parents and healthcare professionals. The purpose of the study was to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. Sixteen HIV-positive parents, seven HIV-positive children, and five HIV-negative children completed semistructured, in-depth interviews. Data were analyzed using the Van Kaam method; NVivo 8 software was used to assist data analysis. We present data on the process of disclosure based on how participants recommended full disclosure be approached to HIV-positive and negative children. Participants recommended disclosure as a process starting at five years with full disclosure delivered at 10 years when the child was capable of understanding the illness, or by 14 years when the child was mature enough to receive the news if full disclosure had not been conducted earlier. Important considerations at the time of full disclosure included the parent’s and/or child’s health statuses, number of infected family members’ illnesses to be disclosed to the child, child’s maturity and understanding level, and the person best suited to deliver full disclosure to the child. The results also revealed it was important to address important life events such as taking a national school examination during disclosure planning and delivery. Recommendations are made for inclusion into HIV disclosure guidelines, manuals, and programs in resource-poor nations with high HIV prevalence.
Gachanja et al. (2014) HIV-positive parents, HIV-positive children, and HIV-negative children’s perspectives on disclosure of a parent’s and child’s illness in Kenya. PeerJ 2:e486 https://doi.org/10.7717/peerj.486
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition
The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.
Bernardo et al. (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ 2:e470 https://doi.org/10.7717/peerj.470
Augmented reality in healthcare education: an integrative review
Background. The effective development of healthcare competencies poses great educational challenges. A possible approach to provide learning opportunities is the use of augmented reality (AR) where virtual learning experiences can be embedded in a real physical context. The aim of this study was to provide a comprehensive overview of the current state of the art in terms of user acceptance, the AR applications developed and the effect of AR on the development of competencies in healthcare. Methods. We conducted an integrative review. Integrative reviews are the broadest type of research review methods allowing for the inclusion of various research designs to more fully understand a phenomenon of concern. Our review included multi-disciplinary research publications in English reported until 2012. Results. 2529 research papers were found from ERIC, CINAHL, Medline, PubMed, Web of Science and Springer-link. Three qualitative, 20 quantitative and 2 mixed studies were included. Using a thematic analysis, we’ve described three aspects related to the research, technology and education. This study showed that AR was applied in a wide range of topics in healthcare education. Furthermore acceptance for AR as a learning technology was reported among the learners and its potential for improving different types of competencies. Discussion. AR is still considered as a novelty in the literature. Most of the studies reported early prototypes. Also the designed AR applications lacked an explicit pedagogical theoretical framework. Finally the learning strategies adopted were of the traditional style ‘see one, do one and teach one’ and do not integrate clinical competencies to ensure patients’ safety.
Zhu et al. (2014) Augmented reality in healthcare education: an integrative review. PeerJ 2:e469 https://doi.org/10.7717/peerj.469
Attrition in a 30-year follow-up of a perinatal birth risk cohort: factors change with age
Background. Attrition is a major cause of potential bias in longitudinal studies and clinical trials. Attrition rate above 20% raises concern of the reliability of the results. Few studies have looked at the factors behind attrition in follow-ups spanning decades. Methods. We analyzed attrition and associated factors of a 30-year follow-up cohort of subjects who were born with perinatal risks for neurodevelopmental disorders. Attrition rates were calculated at different stages of follow-up and differences between responders and non-responders were tested. To find combinations of variables influencing attrition and investigate their relative importance at birth, 5, 9, 16 and 30 years of follow-up we used the random forest classification. Results. Initial loss of potential participants was 13%. Attrition was 16% at five, 24% at nine, 35% at 16 and 46% at 30 years. The only group difference that emerged between responders and non-responders was in socioeconomic status (SES). The variables identified by random forest classification analysis were classified into Birth related, Development related and SES related. Variables from all these categories contributed to attrition, but SES related variables were less important than birth and development associated variables. Classification accuracy ranged between 0.74 and 0.96 depending on age. Discussion. Lower SES is linked to attrition in many studies. Our results point to the importance of the growth and development related factors in a longitudinal study. Parents’ decisions to participate depend on the characteristics of the child. The same association was also seen when the child, now grown up, decided to participate at 30 years. In addition, birth related medical variables are associated with the attrition still at the age of 30. Our results using a data mining approach suggest that attrition in longitudinal studies is influenced by complex interactions of a multitude of variables, which are not necessarily evident using other multivariate techniques.
Launes et al. (2014) Attrition in a 30-year follow-up of a perinatal birth risk cohort: factors change with age. PeerJ 2:e480 https://doi.org/10.7717/peerj.480
Local domestication of lactic acid bacteria via cassava beer fermentation
Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) is thought to improve nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples. Significantly greater phylogenetic similarity was observed among chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human-mediated factors, may be responsible for creating locally distinct ferments. Our results add to evidence from other fermentation systems suggesting that traditional fermentation may be a form of domestication, providing endemic beneficial inocula for consumers, but additional research is needed to identify the mechanisms and extent of microbial dispersal.
Colehour et al. (2014) Local domestication of lactic acid bacteria via cassava beer fermentation. PeerJ 2:e479 https://doi.org/10.7717/peerj.479
Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR
Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation analysis has been implemented for Cystic Fibrosis (CF) carrier screening, and molecular diagnosis of CF and congenital bilateral absence of the vas deferens (CBAVD). Although poly-T allele analysis in intron 8 of CFTR is required when a patient is positive for R117H, it is not recommended for routine carrier screening. Therefore, commercial kits for CFTR mutation analysis were designed either to mask the poly-T allele results, unless a patient is R117H positive, or to have the poly-T analysis as a standalone reflex test using the same commercial platform. There are other standalone assays developed to detect poly-T alleles, such as heteroduplex analysis, High Resolution Melting (HRM) curve analysis, allele-specific PCR (AS-PCR) and Sanger sequencing. In this report, we developed a simple and easy-to-implement multiplex AS-PCR assay using unlabeled standard length primers, which can be used as a reflex or standalone test for CFTR poly-T track analysis. Out of 115 human gDNA samples tested, results from our new AS-PCR matched to the previous known poly-T results or results from Sanger sequencing.
Chen et al. (2014) Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR. PeerJ 2:e468 https://doi.org/10.7717/peerj.468
Hemigrapsus sanguineus in Long Island salt marshes: experimental evaluation of the interactions between an invasive crab and resident ecosystem engineers
The invasive Asian shore crab, Hemigrapsus sanguineus, has recently been observed occupying salt marshes, a novel environment for this crab species. As it invades this new habitat, it is likely to interact with a number of important salt marsh species. To understand the potential effects of H. sanguineus on this ecosystem, interactions between this invasive crab and important salt marsh ecosystem engineers were examined. Laboratory experiments demonstrated competition for burrows between H. sanguineus and the native fiddler crab, Uca pugilator. Results indicate that H. sanguineus is able to displace an established fiddler crab from its burrow. Feeding experiments revealed that the presence of H. sanguineus has a significantly negative impact on the number as well as the biomass of ribbed mussels (Geukensia demissa) consumed by the green crab, Carcinus maenas, although this only occurred at high predator densities. In addition, when both crabs foraged together, there was a significant shift in the size of mussels consumed. These interactions suggests that H. sanguineus may have long-term impacts and wide-ranging negative effects on the saltmarsh ecosystem.
Peterson et al. (2014) Hemigrapsus sanguineus in Long Island salt marshes: experimental evaluation of the interactions between an invasive crab and resident ecosystem engineers. PeerJ 2:e472 https://doi.org/10.7717/peerj.472
The first juvenile specimens of Plateosaurus engelhardti from Frick, Switzerland: isolated neural arches and their implications for developmental plasticity in a basal sauropodomorph
The dinosaur Plateosaurus engelhardti is the most abundant dinosaur in the Late Triassic of Europe and the best known basal sauropodomorph. Plateosaurus engelhardti was one of the first sauropodomorph dinosaurs to display a large body size. Remains can be found in the Norian stage of the Late Triassic in over 40 localities in Central Europe (France, Germany, and Switzerland) and in Greenland. Since the first discovery of P. engelhardti no juvenile specimens of this species had been described in detail. Here we describe the first remains of juvenile individuals, isolated cervical and dorsal neural arches from Switzerland. These were separated postmortem from their respective centra because of unfused neurocentral sutures. However the specimens share the same neural arch morphology found in adults. Morphometric analysis suggests body lengths of the juvenile individuals that is greater than those of most adult specimens. This supports the hypothesis of developmental plasticity in Plateosaurus engelhardti that previously had been based on histological data only. Alternative hypotheses for explaining the poor correlation between ontogenetic stage and size in this taxon are multiple species or sexual morphs with little morphological variance or time-averaging of individuals from populations differing in body size.
Hofmann et al. (2014) The first juvenile specimens of Plateosaurus engelhardti from Frick, Switzerland: isolated neural arches and their implications for developmental plasticity in a basal sauropodomorph. PeerJ 2:e458 https://doi.org/10.7717/peerj.458
Anatomical and biomechanical traits of broiler chickens across ontogeny. Part II. Body segment inertial properties and muscle architecture of the pelvic limb
In broiler chickens, genetic success for desired production traits is often shadowed by welfare concerns related to musculoskeletal health. Whilst these concerns are clear, a viable solution is still elusive. Part of the solution lies in knowing how anatomical changes in afflicted body systems that occur across ontogeny influence standing and moving. Here, to demonstrate these changes we quantify the segment inertial properties of the whole body, trunk (legs removed) and the right pelvic limb segments of five broilers at three different age groups across development. We also consider how muscle architecture (mass, fascicle length and other properties related to mechanics) changes for selected muscles of the pelvic limb. All broilers used had no observed lameness, but we document the limb pathologies identified post mortem, since these two factors do not always correlate, as shown here. The most common leg disorders, including bacterial chondronecrosis with osteomyelitis and rotational and angular deformities of the lower limb, were observed in chickens at all developmental stages. Whole limb morphology is not uniform relative to body size, with broilers obtaining large thighs and feet between four and six weeks of age. This implies that the energetic cost of swinging the limbs is markedly increased across this growth period, perhaps contributing to reduced activity levels. Hindlimb bone length does not change during this period, which may be advantageous for increased stability despite the increased energetic costs. Increased pectoral muscle growth appears to move the centre of mass cranio-dorsally in the last two weeks of growth. This has direct consequences for locomotion (potentially greater limb muscle stresses during standing and moving). Our study is the first to measure these changes in the musculoskeletal system across growth in chickens, and reveals how artificially selected changes of the morphology of the pectoral apparatus may cause deficits in locomotion.
Paxton et al. (2014) Anatomical and biomechanical traits of broiler chickens across ontogeny. Part II. Body segment inertial properties and muscle architecture of the pelvic limb. PeerJ 2:e473 https://doi.org/10.7717/peerj.473
Anatomical and biomechanical traits of broiler chickens across ontogeny. Part I. Anatomy of the musculoskeletal respiratory apparatus and changes in organ size
Genetic selection for improved meat yields, digestive efficiency and growth rates have transformed the biology of broiler chickens. Modern birds undergo a 50-fold multiplication in body mass in just six weeks, from hatching to slaughter weight. However, this selection for rapid growth and improvements in broiler productivity is also widely thought to be associated with increased welfare problems as many birds suffer from leg, circulatory and respiratory diseases. To understand growth-related changes in musculoskeletal and organ morphology and respiratory skeletal development over the standard six-week rearing period, we present data from post-hatch cadaveric commercial broiler chickens aged 0, 2, 4 and 6 weeks. The heart, lungs and intestines decreased in size for hatch to slaughter weight when considered as a proportion of body mass. Proportional liver size increased in the two weeks after hatch but decreased between 2 and 6 weeks. Breast muscle mass on the other hand displayed strong positive allometry, increasing in mass faster than the increase in body mass. Contrastingly, less rapid isometric growth was found in the external oblique muscle, a major respiratory muscle that moves the sternum dorsally during expiration. Considered together with the relatively slow ossification of elements of the respiratory skeleton, it seems that rapid growth of the breast muscles might compromise the efficacy of the respiratory apparatus. Furthermore, the relative reduction in size of the major organs indicates that selective breeding in meat-producing birds has unintended consequences that may bias these birds toward compromised welfare and could limit further improvements in meat-production and feed efficiency.
Tickle et al. (2014) Anatomical and biomechanical traits of broiler chickens across ontogeny. Part I. Anatomy of the musculoskeletal respiratory apparatus and changes in organ size. PeerJ 2:e432 https://doi.org/10.7717/peerj.432
Is painting by elephants in zoos as enriching as we are led to believe?
The relationship between the activity of painting and performance of stereotyped and other stress-related behaviour was investigated in four captive Asian elephants at Melbourne Zoo, Australia. The activity involved the elephant being instructed to paint on a canvas by its keeper in front of an audience. Painting by elephants in zoos is commonly believed to be a form of enrichment, but this assumption had not been based on any systematic research. If an activity is enriching we would expect stress-related behaviour to be reduced but we found no evidence of the elephants anticipating the painting activity and no effect on the performance of stereotyped or other stress-related behaviour either before or after the painting session. This indicates that the activity does not fulfil one of the main aims of enrichment. However, if an elephant was not selected to paint on a given day this was associated with higher levels of non-interactive behaviour, a possible indicator of stress. Behavioural observations associated with ear, eye and trunk positions during the painting session showed that the elephant’s attentiveness to the painting activity or to the keeper giving instruction varied between individuals. Apart from positive reinforcement from the keeper, the results indicated that elephants gain little enrichment from the activity of painting. Hence, the benefits of this activity appear to be limited to the aesthetic appeal of these paintings to the people viewing them.
English et al. (2014) Is painting by elephants in zoos as enriching as we are led to believe?. PeerJ 2:e471 https://doi.org/10.7717/peerj.471
Modified generalized method of moments for a robust estimation of polytomous logistic model
The maximum likelihood estimation (MLE) method, typically used for polytomous logistic regression, is prone to bias due to both misclassification in outcome and contamination in the design matrix. Hence, robust estimators are needed. In this study, we propose such a method for nominal response data with continuous covariates. A generalized method of weighted moments (GMWM) approach is developed for dealing with contaminated polytomous response data. In this approach, distances are calculated based on individual sample moments. And Huber weights are applied to those observations with large distances. Mellow-type weights are also used to downplay leverage points. We describe theoretical properties of the proposed approach. Simulations suggest that the GMWM performs very well in correcting contamination-caused biases. An empirical application of the GMWM estimator on data from a survey demonstrates its usefulness.
Wang (2014) Modified generalized method of moments for a robust estimation of polytomous logistic model. PeerJ 2:e467 https://doi.org/10.7717/peerj.467
The role of fragmentation and landscape changes in the ecological release of common nest predators in the Neotropics
Loss of large mammalian carnivores may allow smaller mesopredators to become abundant and threaten other community members. There is considerable debate about mesopredator release and the role that other potential factors such as landscape variables and human alterations to land cover lead to increased mesopredator abundance. We used camera traps to detect four mesopredators (tayra, Eira barbara; white-nosed coati, Nasua narica; northern raccoon, Procyon lotor; and common opossum, Didelphis opossum) in a biological corridor in Costa Rica to estimate habitat covariates that influenced the species’ detection and occurrence. We selected these mesopredators because as semi-arboreal species they might be common nest predators, posing a serious threat to resident and migratory songbirds. Pineapple production had a pronounced positive effect on the detectability of tayras, while forest cover had a negative effect on the detection of coatis. This suggests that abundance might be elevated due to the availability of agricultural food resources and foraging activities are concentrated in forest fragments and pineapple edge habitats. Raccoon and opossum models exhibited little influence on detection from habitat covariates. Occurrence models did not suggest any significant factors influencing site use by nest predators, revealing that all four species are habitat generalists adapted to co-existing in human altered landscapes. Furthermore, fragmentation and land cover changes may predispose nesting birds, herpetofauna, and small mammals to heightened predation risk by mesopredators in the Neotropics.
Cove et al. (2014) The role of fragmentation and landscape changes in the ecological release of common nest predators in the Neotropics. PeerJ 2:e464 https://doi.org/10.7717/peerj.464
Automated analysis of invadopodia dynamics in live cells
Multiple cell types form specialized protein complexes that are used by the cell to actively degrade the surrounding extracellular matrix. These structures are called podosomes or invadopodia and collectively referred to as invadosomes. Due to their potential importance in both healthy physiology as well as in pathological conditions such as cancer, the characterization of these structures has been of increasing interest. Following early descriptions of invadopodia, assays were developed which labelled the matrix underneath metastatic cancer cells allowing for the assessment of invadopodia activity in motile cells. However, characterization of invadopodia using these methods has traditionally been done manually with time-consuming and potentially biased quantification methods, limiting the number of experiments and the quantity of data that can be analysed. We have developed a system to automate the segmentation, tracking and quantification of invadopodia in time-lapse fluorescence image sets at both the single invadopodia level and whole cell level. We rigorously tested the ability of the method to detect changes in invadopodia formation and dynamics through the use of well-characterized small molecule inhibitors, with known effects on invadopodia. Our results demonstrate the ability of this analysis method to quantify changes in invadopodia formation from live cell imaging data in a high throughput, automated manner.
Berginski et al. (2014) Automated analysis of invadopodia dynamics in live cells. PeerJ 2:e462 https://doi.org/10.7717/peerj.462
A complete, multi-level conformational clustering of antibody complementarity-determining regions
Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
Nikoloudis et al. (2014) A complete, multi-level conformational clustering of antibody complementarity-determining regions. PeerJ 2:e456 https://doi.org/10.7717/peerj.456
Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence
The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
Nikoloudis et al. (2014) Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence. PeerJ 2:e455 https://doi.org/10.7717/peerj.455
Measurement uncertainties in quantifying aeolian mass flux: evidence from wind tunnel and field site data
Aeolian sediment traps are widely used to estimate the total volume of wind-driven sediment transport, but also to study the vertical mass distribution of a saltating sand cloud. The reliability of sediment flux estimations from such measurements are dependent upon the specific configuration of the measurement compartments and the analysis approach used. In this study, we analyse the uncertainty of these measurements by investigating the vertical cumulative distribution and relative sediment flux derived from both wind tunnel and field studies. Vertical flux data was examined using existing data in combination with a newly acquired dataset; comprising meteorological data and sediment fluxes from six different events, using three customized catchers at Ameland beaches in northern Netherlands. Fast-temporal data collected in a wind tunnel shows that the median transport height has a scattered pattern between impact and fluid threshold, that increases linearly with shear velocities above the fluid threshold. For finer sediment, a larger proportion was transported closer to the surface compared to coarser sediment fractions. It was also shown that errors originating from the distribution of sampling compartments, specifically the location of the lowest sediment trap relative to the surface, can be identified using the relative sediment flux. In the field, surface conditions such as surface moisture, surface crusts or frozen surfaces have a more pronounced but localized effect than shear velocity. Uncertainty in aeolian mass flux estimates can be reduced by placing multiple compartments in closer proximity to the surface.
Poortinga et al. (2014) Measurement uncertainties in quantifying aeolian mass flux: evidence from wind tunnel and field site data. PeerJ 2:e454 https://doi.org/10.7717/peerj.454
Local norms of cheating and the cultural evolution of crime and punishment: a study of two urban neighborhoods
The prevalence of antisocial behavior varies across time and place. The likelihood of committing such behavior is affected by, and also affects, the local social environment. To further our understanding of this dynamic process, we conducted two studies of antisocial behavior, punishment, and social norms. These studies took place in two neighborhoods in Newcastle Upon Tyne, England. According to a previous study, Neighborhood A enjoys relatively low frequencies of antisocial behavior and crime and high levels of social capital. In contrast, Neighborhood B is characterized by relatively high frequencies of antisocial behavior and crime and low levels of social capital. In Study 1, we used an economic game to assess neighborhood differences in theft, third-party punishment (3PP) of theft, and expectation of 3PP. Participants also reported their perceived neighborhood frequency of cooperative norm violation (“cheating”). Participants in Neighborhood B thought that their neighbors commonly cheat but did not condone cheating. They stole more money from their neighbors in the game, and were less punitive of those who did, than the residents of Neighborhood A. Perceived cheating was positively associated with theft, negatively associated with the expectation of 3PP, and central to the neighborhood difference. Lower trust in one’s neighbors and a greater subjective value of the monetary cost of punishment contributed to the reduced punishment observed in Neighborhood B. In Study 2, we examined the causality of cooperative norm violation on expectation of 3PP with a norms manipulation. Residents in Neighborhood B who were informed that cheating is locally uncommon were more expectant of 3PP. In sum, our results provide support for three potentially simultaneous positive feedback mechanisms by which the perception that others are behaving antisocially can lead to further antisocial behavior: (1) motivation to avoid being suckered, (2) decreased punishment of antisocial behavior, and (3) decreased expectation of punishment of antisocial behavior. Consideration of these mechanisms and of norm psychology will help us to understand how neighborhoods can descend into an antisocial culture and get stuck there.
Schroeder et al. (2014) Local norms of cheating and the cultural evolution of crime and punishment: a study of two urban neighborhoods. PeerJ 2:e450 https://doi.org/10.7717/peerj.450
Neighbourhood walkability, leisure-time and transport-related physical activity in a mixed urban–rural area
Objectives. To develop a walkability index specific to mixed rural/suburban areas, and to explore the relationship between walkability scores and leisure time physical activity. Methods. Respondents were geocoded with 500 m and 1,000 m buffer zones around each address. A walkability index was derived from intersections, residential density, and land-use mix according to built environment measures. Multivariable logistic regression models were used to quantify the association between the index and physical activity levels. Analyses used cross-sectional data from the 2007–2008 Canadian Community Health Survey (n = 1158; ≥18 y). Results. Respondents living in highly walkable 500 m buffer zones (upper quartiles of the walkability index) were more likely to walk or cycle for leisure than those living in low-walkable buffer zones (quartile 1). When a 1,000 m buffer zone was applied, respondents in more walkable neighbourhoods were more likely to walk or cycle for both leisure-time and transport-related purposes. Conclusion. Developing a walkability index can assist in exploring the associations between measures of the built environment and physical activity to prioritize neighborhood change.
de Sa et al. (2014) Neighbourhood walkability, leisure-time and transport-related physical activity in a mixed urban–rural area. PeerJ 2:e440 https://doi.org/10.7717/peerj.440