bluuebunny/crossref_metadata_2025 huggingface dataset:
Eco-conscious resort construction reduces living coral coverage, species richness, species abundance, and increases algae coverage
Authors: Mullen Ryan DN
Published: January 2018

Tourism today is moving towards sustainable approaches because the industry poses significant threats to the environment. This includes a shift in construction type: to building structures that aim to coexist with their surroundings. One example of this is the overwater resort bungalow. Although there is a substantial amount of research on the effects of coastal development on the environment, there is little research on the effects of sustainable approaches. This study aimed to quantify the effects of oceanic overwater resort bungalows on coral reef ecosystems. Two overwater bungalow resort sites were investigated on the island of Mo’orea in French Polynesia to see whether or not they impacted their environment. The percentage of living coral coverage, percentage of algae coverage, species abundance, and richness, were examined by surveying different areas of the lagoon that all varied in distance away from the bungalow chain. The resort sites were ultimately compared to two control sites, both without bungalows and slightly removed from the resort sites, in order to account for other factors influencing the response variables. Living coral coverage, species abundance, and species richness, were all positively correlated with distance away from the bungalow chain. Algae coverage was negatively correlated with an increase in distance. The data collected provides evidence that bungalows are impacting the environment they are situated in. Increased algae presence near the bungalow chain may be due to shade coverage produced by the bungalows. Decreased living coral coverage, species richness, and species abundance, in close proximity to the chain, may be due to the impacts of initial construction, tourists, and competition. Regulations need to be imposed on future construction of bungalows in order to avoid prolonged and greater effects on reef ecosystems. It also needs to be considered that all ecofriendly structures may be inherently affecting the environments they surround.
A new reconstruction of Struthiosaurus austriacus Bunzel 1871
Authors: Frotzler Norbert
Published: January 2018

A novel reconstruction of the nodosaurid dinosaur Struthiosaurus austriacus Bunzel 1871 is presented. Because bones and dermal armor are preserved as disarticulated elements only and because of the lack of field notes from the original excavation(s), any attempt to reconstruct the animal is complicated. To date, no reconstruction is available for Struthiosaurus austriacus. This study primarily focuses on aspects of function and arrangement of dermal armor. The re-investigation of the original material of S. austriacus revealed that - in all likelihood - many plates from the left side of the body may well belong to a single individual. This observation is an important step towards the successful reconstruction of S. austriacus.
IoT and Robotics: a synergy
Authors: Roy Chowdhury Ankur
Published: January 2018

The Internet of Robotic Things (IoRT) is a concept first introduced by Dan Kara at ABI Research, which talks about augmenting the existing IoT with active sensorization; thereby, opening the doors to novel business ideas, at the intersection of both IoT and Robotics. This position paper considers the synergy between IoT and robotics: it talks about the technologies in IoT that would benefit the robotics domain. The advent of Cloud Robotics and its role in aiding robot functions like sensing, manipulation, and mobility. The paper then discusses the ways in which robots can extend the capabilities of existing IoT infrastructure by acting as a special class of edge device. IoT-aided robotic applications are discussed in various domains like health-care, military, industrial plants and rescue operations. The paper concludes by considering the use case of an Intelligent Transportation System endowed by an IoRT-inspired architecture.
A comprehensive simulation study on classification of RNA-Seq data
Authors: Zararsiz Gokmen , Göksülük Dinçer , Korkmaz Selçuk , Eldem Vahap , Ertürk Zararsız Gözde , Duru İzzet Parug , Ozturk Ahmet , Öztürk Ahmet
Published: January 2018

RNA sequencing (RNA-Seq) is a powerful technique for thegene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies.Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of geneexpression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption. Hence, these methods cannot be directly applied to RNA-Seq data since they violate both data structure and distributional assumptions. However, it is possible to apply these algorithms with appropriate modifications to RNA-Seq data. One way is to develop count-based classifiers, such as Poisson linear discriminant analysis and negative binomial linear discriminant analysis. Another way is to bring the data hierarchically closer to microarrays and apply microarray-based classifiers.In this study, we compared several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF). We also examined the effect of several parameters such asoverdispersion, sample size, number of genes, number of classes, differential-expression rate, andthe transformation method on model performances.A comprehensive simulation study is conducted and the results are compared with the results of two miRNA and two mRNA experimental datasets. The results revealed that increasing the sample size, differential-expression rate, and number of genes and decreasing the dispersion parameter and number of groups lead to an increase in classification accuracy. Similar with differential-expression studies, the classification of RNA-Seq data requires careful attention when handling data overdispersion. We conclude that, as a count-based classifier, the power transformed PLDA and, as a microarray-based classifier, vst or rlog transformed RF and SVM clas sifiers may be a good choice for classification. An R/BIOCONDUCTOR package, MLSeq, is freely available at https://www.bioconductor.org/packages/release/bioc/html/MLSeq.html .
Text parsing with Markov logic network
Authors: Wang Nan
Published: January 2018

This document describes a novel way to extract structure information from plain text using Markov Decision Process. In the age of big data, unstructured information such as text, photos and videos be- comes abundant. However, data warehouse requires structured data with well-defined schema. It has been a challenge for the computer science community to extract useful data under strict schema from unstructured data schema. Here we proposed an automated system that is able to understand and infer the most likely counterpart in text stream that corresponds to a led under the requested schema. The designed algorithm formulated the plain text using context dependent grammar with various weights, which would be sued to decide which eld of the structured schema a particular piece of unstructured data belongs to. A machine-learning algorithm is used to learn the weights from training data. We implemented this automated system and applied it to extract schema data from plain US bankruptcy petition forms.
Hummingbird foraging preferences under natural and experimental conditions
Authors: López-Segoviano Gabriel , Arizmendi Maria del Coro
Published: January 2018

Background. Different studies have assessed hummingbirds’ preferences for feeding resources, mainly according to floral characteristics such as shape, color, and morphology, in addition to the nectar concentration, quantity, and sugar composition of flowers visited. Flower preferences can also depend on hummingbirds’ life history with respect to flower use. Hence, latitudinal migrant hummingbirds likely differ from resident species as they are accustomed to using a wider range of resources. In this study, we assessed the flower preferences of a migrant and a resident species that are common during winter in northern Mexico using both observational and experimental methods. Methods. We assessed hummingbird preferences for the most common plant species in the study region. In particular, we compared the preferences of two common hummingbird species, one resident (Amazilia beryllina) and one latitudinal migrant (Selasphorus rufus), for the most regionally common plant species, Cestrum thyrsoideum and Salvia iodantha, which have different color flowers yet produce similar energetic rewards. We calculated the Jacob selectivity index from preference data obtained under natural field conditions and with a flight cage in order to evaluate specific interactions. Results: Both hummingbird species showed different visitation rates to the studied plants under natural conditions in the study site. A. beryllina visited the yellow flowers of C. thyrsoideum more frequently, while S. rufus visited the fuchsia flowers of S. iodantha with greater frequency. In the flight cages, both species preferred the fuchsia flowers of S. iodantha when presented in similar or lesser abundance than the yellow flowers. Discussion. Under natural conditions, A. beryllina visited C. thyrsoideum to a greater extent in comparison with S. iodantha yet preferred S. iodantha in the flight cage when other hummingbirds were absent and even when S. iodantha was not the most abundant species. This could confirm that competition is an important process that drives the niche displacement of A. beryllina. On the other hand, the latitudinal migratory species S. rufus maintained its preferences for flowers of a familiar color under both natural and experimental conditions. Conclusions. Our results showed that the feeding preferences of the studied hummingbird species depend on the life history of each species. Therefore, the response of these migratory hummingbird species to feeding resources and possible exclusion from their preferred resources depends on their type of migration, territoriality, and possible associations with local plants.
Isolation and characterization of a new cell line of retinoblastoma
Authors: Ghasemi Fariba , Heidari Keshel Saeed , Mirakhorli Mojgan , Roozafzoon Reza , Rajabi Mohammad Taher , Tabatabaie Seid Zia , Farzanfar Farideh , Khoshzaban Ahad , Asadi-Amoli Fahimeh
Published: January 2018

BACKGROUNDː This article describes the characterization of a new cell line (IRB-1), which was established from an Iranian child with retinoblastoma.

METHODSː Using cell culture techniques, we isolated a clonal population from primary Cultures of retinoblastoma tumor samples and after several passages an established cell line, IRB-1, was obtained. The following techniques were performed: cell proliferation studies by MTT assays, scanning electron microscopy, cell surface analyses by flowcytometry, creation of neurospheres in soft agar and the expression of ABCG2, RAR-α, GFAP, and ACTB genes by real time PCR.

RESULTSː Of total 6 received samples, only a single cell line was successfully isolatedfrom a group E sporadic unilateral retinoblastoma. The primarily enucleated left eye had a differentiated retinoblastoma, with a slight degree of necrosis in pathology report. The adherent cultured cells were in spindle-shaped morphology with similar appendages and pulled neurons. Doubling time is 36 ± 5 hours. After 30 days, the effect of retinoic acid on isolated cells and expression of RAR-α receptor was appeared. Chromosomal abnormalities in chromosomes 3, 9, 10, 11, 14, 16, 17, and 22 were observed. Specific gene expression of ABCG2, RAR-α, and ACTB gene expression of GFAP positive expression of these genes in the control cells were observed. This cell line passaged 132 consecutive times.

Discussionː IRB-1 is a novel human adherent RB cell line, which with interesting characteristics of adherent and flocculent growth and more chromosomal imbalances different from other RB cell lines. A novel human RB cell line, IRB-1, was established from a 1-year old patient with a unilateral sporadic RB at Farabi Hospital- Tehran University Medical Sciences. The cultural characteristics of IRB-1 cell line were comparable to those of Y79 in characteristic.
Habitat of the deep-sea anemone, Cribrinopsis japonica, with shrimp: Does Cribrinopsis japonica establish a symbiotic relationship with shrimp?
Authors: Shimada Eriko , Tsuruwaka Yusuke
Published: January 2018

We recently found Cribrinopsis japonica Tsutsui & Tsuruwaka, 2014 (Shinkai-hakutou-ginchaku in Japanese name) at the depth between 384 and 800 m in Toyama Bay, Sea of Japan. Since then, C. japonica has been reared under atmospheric pressure in the laboratory for seven years. C. japonica may use a fluorescent protein carried in its tentacles to lure shrimp (Tsutsui et al., 2016*1). However, the ecology of C. japonica in the deep-sea is hardly known. To elucidate the unknown ecology, we coupled one of the first long-term in situ studies of deep-sea organisms with complementary laboratory experiments. Our exploration of deep-sea benthos revealed that C. japonica inhabits the deepest areas of the sea floor at 1,960 m. Moreover, 80% of C. japonica in the deep-sea stayed together with the deep-sea shrimp. In the laboratory environment, when we added the same shrimp species which was observed in situ to the rearing tank with C. japonica, C. japonica stayed closer with the shrimp without attacking using the tentacles. It is rare to observe different animals together at one place or space since there are very few animals in the ocean floor at > 1,000 m depth in the Sea of Japan (Motokawa & Kajihara, 2017*2). In such depopulated environment, it is conceivable that C. japonica and the shrimp may receive benefit mutually or one side by establishing a ‘symbiotic relationship.’ We will elucidate their relationship in more details by studying the possible ‘symbiosis’ in the laboratory.
Experts correctly describe demography associated with historical decline of the endangered Indiana bat, but not recent period of stationarity
Authors: Thogmartin Wayne , Sanders-Reed Carol , Szymanski Jennifer , Pruitt Lori , Runge Michael
Published: January 2018

Demographic characteristics of bats are often insufficiently described for modeling populations. In data poor situations, experts are often relied upon for characterizing ecological systems. In concert with the development of a matrix model describing Indiana bat (Myotis sodalis) demography, we elicited estimates for parameterizing this model from 12 experts. We conducted this elicitation in two stages, requesting expert values for 12 demographic rates. These rates were adult and juvenile seasonal (winter, summer, fall) survival rates, pup survival in fall, and propensity and success at breeding. Experts were most in agreement about adult fall survival (3% Coefficient of Variation) and least in agreement about propensity of juveniles to breed (37% CV). The experts showed greater concordance for adult ( mean CV, adult = 6.2%) than for juvenile parameters ( mean CV, juvenile = 16.4%), and slightly more agreement for survival (mean CV, survival = 9.8%) compared to reproductive rates ( mean CV, reproduction = 15.1%). However, survival and reproduction were negatively and positively biased, respectively, relative to a stationary dynamic. Despite the species exhibiting near stationary dynamics for two decades prior to the onset of a potential extinction-causing agent, white-nose syndrome, expert estimates indicated a population decline of -11% per year (95% CI = -2%, -20%); quasi-extinction was predicted within a century ( mean = 61 years to QE, range = 32, 97) by 10 of the 12 experts. Were we to use these expert estimates in our modeling efforts, we would have errantly trained our models to a rapidly declining demography asymptomatic of recent demographic behavior. While experts are sometimes the only source of information, a clear understanding of the temporal and spatial context of the information being elicited is necessary to guard against wayward predictions.
Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds
Authors: Di Tommaso Paolo , Floden Evan , Chatzou Maria , Notredame Cedric
Published: January 2018

Reproducibility has become one of biology’s most pressing issues. This impasse has been fuelled by the combined reliance on increasingly complex data analysis methods and the exponential growth of biological datasets. Nextflow is a pipeline orchestration tool that has been designed to ease deployment and guarantee reproducibility across platforms. It allows the seamless parallelization and deployment of any existing application with minimal development and maintenance overhead, irrespective of the original programming language. These capabilities guarantee consistent results over time and across different computing platforms.
Movements and use of space by Mangrove Cuckoos (Coccyzus minor) in Florida, USA
Authors: Lloyd John D
Published: January 2018

I used radio-telemetry to track the movements of Mangrove Cuckoos (Coccyzus minor) captured in southwest Florida. Relatively little is known about the natural history of Mangrove Cuckoos, and my goal was to provide an initial description of how individuals use space, with a focus on the size and placement of home ranges. I captured and affixed VHF radio-transmitters to 32 individuals between 2012 and 2015, and obtained a sufficient number of relocations from 16 of them to estimate home-range boundaries and describe patterns of movement. Home-range area varied widely among individuals, but in general, was roughly four times larger than expected based on the body size of Mangrove Cuckoos. The median core area (50% isopleth) of a home range was 42 ha (range: 9 – 91 ha), and the median overall home range (90% isopleth) was 128 ha (range: 28 – 319 ha). The median distance between estimated locations recorded on subsequent days was 298 m (95% CI = 187 m – 409 m), but variation within and among individuals was substantial, and it was not uncommon to relocate individuals >1 km from their location on the previous day. Site fidelity by individual birds was low; although Mangrove Cuckoos were present year-round within the study area, I did not observe any individuals that remained on a single home range throughout the year. Although individual birds showed no evidence of avoiding anthropogenic edges, they did not incorporate developed areas into their daily movements and home ranges consisted almost entirely of mangrove forest. The persistence of the species in the study area depended on a network of conserved lands – mostly public, but some privately conserved land as well – because large patches of mangrove forest did not occur on tracts left unprotected from development.
Understanding Web 2.0 service models, applications, reflections, perspectives, and beyond
Authors: Liu Yi , Kim Kwangjo
Published: January 2018

Since 2004 the term “Web 2.0” has generated a revolution on the World Wide Web and it has developed new ideas, services, application to improve and facilitate communications through the web. Technologies associated with the second-generation of the World Wide Web enable virtually anyone to share their data, documents, observations, and opinions on the Internet. The serious applications of Web 2.0 are sparse and this paper assesses its use in the context of applications, reflections, and collaborative spatial decision-making based on Web generations and in a particular Web 2.0.
Assessing the histidine tautomer fractions in proteins. Test on diisopropylfluorophosphatase, a large all-β protein, from Loligo vulgaris
Authors: Vorobjev Yury N , Scheraga Harold A , Vila Jorge A
Published: January 2018

The importance of histidine tautomerism for an accurate drug/protein structure determination and their relevance for the interaction between biological systems is recognized. Consequently, here we used a recently introduced method to determine the pKa values of ionizable residues and fractions of ionized and tautomeric forms of histidine and acid residues in protein, as a function of pH, to analyze a histidine-rich protein, specifically, to study the accuracy of the prediction of the tautomeric fractions of the imidazole ring of each of the 6 histidine residues of diisopropylfluorophosphatase (pdb id 1E1A), a 314-residue all beta-protein, from Loligo vulgaris. The average tautomeric fractions of the His was compute by using an approach that includes, but is not limited to, molecular dynamics simulations coupled with calculations of the ionization states for all 94 ionizable residues of the protein 1E1A in water at pH 6.5 and 300 K. The results of the analysis on protein 1E1A indicate that: (i) the averaged calculated fractions of histidine tautomers, namely for the Nd1-H and Ne2-H forms, respectively, are in good agreement, within ~11%, with the prediction of an NMR-based methodology; and (ii) the tautomer fractions among the six His residues are very different, mainly because the tautomer preferences are determined by the protein environment. This work provides critical insight about the limitations of continuum dielectric models to reproduce NMR-based tautomeric fractions, and may spur significant progress in our effort to develop fast and accurate methods to determine the forms of the imidazole ring of His in proteins as a function of pH.
Linearization improves the repeatability of quantitative Dynamic Contrast-Enhanced MRI
Authors: Jones Kyle M. , Borders Marisa H. , Fitzpatrick Kimberly A. , Pagel Mark D. , Cárdenas-Rodríguez Julio
Published: January 2018

We studied the effect of linearization on the repeatability of the Tofts and reference region models (RRM) for Dynamic Contrast-Enhanced MRI (DCE MRI). We compared the repeatabilities of these two linearized models, the standard non-linear version, and semi-quantitative methods of analysis. Simulated and experimental DCE MRI data from 12 rats with a flank tumor of C6 glioma acquired over three consecutive days were analyzed using four quantitative and semi-quantitative DCE MRI metrics. The quantitative methods used were: 1) Linear Tofts model (LTM), 2) Non-linear Tofts model (NTM), 3) Linear RRM (LRRM), and 4) Non-linear RRM (NRRM). The following semi-quantitative metrics were used: 1) Maximum enhancement ratio (MER), 2) time to peak (TTP), 3) initial area under the curve (iauc64), and 4) slope. LTM and NTM were used to estimate Ktrans, while LRRM and NRRM were used to estimate Ktrans relative to muscle (RKtrans). Repeatability was assessed by calculating the within-subject coefficient of variation (wSCV) and the percent intra-subject variation (iSV) determined with the Gage repeatability and reproducibility (R&R) analysis. The iSV for RKtrans using LRRM was two-fold lower compared to NRRM at all simulated and experimental conditions. A similar trend was observed for the Tofts model, where LTM was at least 50% more repeatable than the NTM under all experimental and simulated conditions. The semi-quantitative metrics iauc64 and MER were as equally reproducible as Ktrans and RKtrans estimated by LTM and LRRM respectively. The iSV for iauc64 and MER were significantly lower than the iSV for slope and TTP. In simulations and experimental results, linearization improves the repeatability of quantitative DCE MRI by at least 30%, making it as repeatable as semi-quantitative metrics.
An interview-based approach to assess sea turtle bycatch in Italian waters
Authors: Lucchetti Alessandro , Vasapollo Claudio , Virgili Massimo
Published: January 2018

The loggerhead sea turtle (Caretta caretta, Linnaeus, 1758) is the most abundant sea turtle species in the Mediterranean Sea, where commercial fishing appears to be the main driver of mortality. So far, information on sea turtle bycatch in Italy is limited both in space and time due to logistical problems in data collected through onboard observations and on a limited number of vessels involved. In the present study, sea turtle bycatch in Italian waters was examined by collecting fishermen's information on turtle bycatch through an interview-based approach. Their replies enabled the identification of bycatch hotspots in relation to area, season and to the main gear types. The most harmful fishing gears resulted to be trawl nets, showing the highest probabilities of turtle bycatch with a hotspot in the Adriatic Sea, followed by longlines in the Ionian Sea and in the Sicily Channel. Estimates obtained by the present results showed that more than 52,000 capture events and 10,000 deaths occurred in Italian waters in 2014, highlighting a more alarming scenario than earlier studies. The work shows that in case of poor data from other sources, direct questioning of fishermen and stakeholders could represent a useful and cost-effective approach capable of providing sufficient data to estimate annual bycatch rates and identify high-risk gear/location/season combinations.
A Science gateway for biodiversity and climate change research
Authors: Elia Donatello , Nuzzo Alessandra , Nassisi Paola , Fiore Sandro , Blanquer Ignacio , Brasileiro Francisco V. , Rufino Iana A. A. , Seijmonsbergen Arie C. , Anders Niels S. , Galvao Carlos de O. , Cunha John E. de B. L. , de Sousa-Baena Mariane , Canhos Vanderlei P. , Aloisio Giovanni
Published: January 2018

Climate and biodiversity systems are closely interlaced across a wide range of scales. To better understand the mutual interaction between climate change and biodiversity there is a strong need for multidisciplinary skills, tools and a large variety of heterogeneous, distributed data sources. In this regard, the EUBrazilCloudConnect project provides a user-centric research environment built on top of a federated cloud infrastructure across Europe and Brazil to serve scientific needs. One of the test cases implemented in this project focuses on climate change and biodiversity research. The BioClimate is the Science Gateway of the use case. It aims at providing end-users with a highly integrated environment, addressing mainly data analytics requirements. This paper presents a complete overview about BioClimate and the scientific environment delivered to the user community at the end of the project.
Toward a collective understanding of medical education research: The DIMER dialogue instrument
Authors: Zary Nabil , Chue Shien
Published: January 2018

Medical education research embraces theoretical and methodological diversities. Researchers are motivated by the quest for deepening knowledge as well as attracting funding for new educational initiatives and technologies. However, it remains a daunting endeavour to locate and aggregate findings into consistent themes. Reasons are at least twofold. The discourse of a discipline provides the language for representing its work and crossing between disciplines is challenging. Secondly, medical education is understood as an idiosyncratic collection of concepts appropriated from other educational field and the medical education community is unsure about whether to construe medical education as a medical or a social science. To overcome these challenges, we propose a dialogue instrument that draws together cross cutting research perspectives, stakeholders & learning domains to build bridges within medical curriculum, methods, assessment and experiences research. Consequently, this dialogue instrument advocates a nuance understanding of medical education research as a means for building collective knowledge for impacting education and health outcomes.
Short-term starvation at low temperature prior to harvest does not impact the health and acute stress response of adult Atlantic salmon
Authors: Waagbø Rune , Jørgensen Sven Martin , Timmerhaus Gerrit , Breck Olav , Olsvik Pål A
Published: January 2018

Period of starvation is regarded as a sound practice in aquaculture prior to handling, transportation and harvest, to minimise impacts on welfare and ensure proper hygiene after harvest. However, documentation of welfare issues such as stress following starvation and handling in adult Atlantic salmon are lacking. This study aimed to examine gut emptying and potential stress during a two weeks starvation period, and whether this starvation period changes the tolerance for physical stress. The study confirmed slower emptying of the gut segments at low temperature. Plasma and bile cortisol, and selected clinical analyses were used to characterize potential stress, as well as the response to acute physical crowding stress during the starvation period. Neither the general stress level nor the ability to cope with handling stress was affected by a 14 days starvation period. Down-regulation of selected nutritional related gene markers in liver indicated classical starvation responses, with reduced metabolism and oxidative pressure, and sparing of nutrients. The response to acute handling stress was not affected by two weeks of starvation. There were minor effects of starvation on stress and health markers, as evaluated by plasma lysozyme activity and gene expression of selected inflammation marker proteins in heart and skin tissues.
Redefining the landscape of fear conceptual framework; a review of current applications and misuses
Authors: Bleicher Sonny S
Published: January 2018

Landscapes of Fear (LOF), the spatially explicit distribution of perceived predation risk as seen by a population, is increasingly cited in ecological literature and has become a frequently used “buzz-word”. With the increase in popularity, it became necessary to clarify the definition for the term, suggest boundaries and propose a common framework for its use. The LOF, as a progeny of the “ecology of fear” conceptual framework, defines fear as the strategic manifest of the cost-benefit analysis of food and safety tradeoffs. In addition to direct predation risk, the LOF is affected by individuals’ energetic-state, inter- and intra-specific competition and is constrained by the evolutionary history of each species. Herein, based on current applications of the LOF conceptual framework, I suggest the future research in this framework will be directed towards: (1) finding applied management uses as a trait defining a population’s habitat-use and habitat-suitability; (2) studying multi-dimensional distribution of risk-assessment through time and space; (3) studying variability between individuals within a population; and (4) measuring eco-neurological implications of risk as a feature of environmental heterogeneity.
The landscape of fear conceptual framework: definition and review of current applications and misuses
Authors: Bleicher Sonny S
Published: January 2018

Landscapes of Fear (LOF), the spatially explicit distribution of perceived predation risk as seen by a population, is increasingly cited in ecological literature and has become a frequently used “buzz-word”. With the increase in popularity, it became necessary to clarify the definition for the term, suggest boundaries and propose a common framework for its use. The LOF, as a progeny of the “ecology of fear” conceptual framework, defines fear as the strategic manifest of the cost-benefit analysis of food and safety tradeoffs. In addition to direct predation risk, the LOF is affected by individuals’ energetic-state, inter- and intra-specific competition and is constrained by the evolutionary history of each species. Herein, based on current applications of the LOF conceptual framework, I suggest the future research in this framework will be directed towards: (1) finding applied management uses as a trait defining a population’s habitat-use and habitat-suitability; (2) studying multi-dimensional distribution of risk-assessment through time and space; (3) studying variability between individuals within a population; and (4) measuring eco-neurological implications of risk as a feature of environmental heterogeneity.
Who are the important sea turtle nest predators at Wreck Rock beach?
Authors: Lei Juan , Booth David T
Published: January 2018

Excessive sea turtle nest predation is a problem for conservation management of sea turtle populations. This study assessed the predation of the endangered loggerhead sea turtle (Caretta caretta ) nests at the Wreck Rock beach adjacent to Deepwater National Park in Southeast Queensland, Australia after a control program for feral foxes was instigated. The presence of predators on the nesting dune was evaluated by passive soil plots (2 x 1 m) every 100m along the dune front. There were 21 (2014-2015) and 41 (2015-2016) plots established along the dune and these were monitored for predator tracks daily over three consecutive months in both nesting seasons. Camera traps were also set to record the predator’s activity around selected nests. The tracks of the fox (Vulpes vulpes ) and goanna (lace monitor Varanus varius and/or yellow-spotted goanna V. panoptes; we could not distinguish these two species tracks from each other) were found on sand plots. Goannas were widely distributed along the beach and had an eight times higher Passive Activity Index (PAI) (0.31 in 2014-2015 and 0.16 in 2015-2016) compared to foxes (PAI 0.04 in 2014-2015 and 0.02 in 2015-2016). Camera trap data indicated that the appearance of yellow-spotted goannas at loggerhead turtle nests was more frequent than lace monitors and further that lace monitors only predated these nests after they had been previously opened by yellow-spotted goannas. No foxes were recorded at nests with camera traps. This study suggests that large male yellow-spotted goannas are the major predator of sea turtle nests at the Wreck Rock beach nesting aggregation.
Ungulates rely less on visual cues, but more on adapting movement behaviour, when searching for forage
Authors: Venter Jan A , Prins Herbert H. T. , Mashanova Alla , Slotow Rob
Published: January 2018

Finding suitable forage patches in a heterogeneous landscape, where patches change dynamically both spatially and temporally could be challenging to large herbivores, especially if they have no a priori knowledge of the location of the patches. We tested whether three large grazing herbivores with a variety of different traits, improve their efficiency when foraging at a heterogeneous habitat patch scale, by using visual cues to gain a priori knowledge about potential higher value foraging patches. For each species (zebra (Equus burchelli ), red hartebeest (Alcelaphus buselaphus subspecies camaa ) and eland ( Tragelaphus oryx )), we used step lengths and directionality of movement to infer whether they were using visual cues to find suitable forage patches at a habitat patch scale. Step lengths were significantly longer for all species when moving to non-visible patches than to visible patches, but all movements showed little directionality. Of the three species, zebra movements were the most directional. Red hartebeest had the shortest step lengths and zebra the longest. We conclude that these large grazing herbivores may not exclusively use visual cues when foraging at a habitat patch scale, but would rather adapt their movement behaviour, mainly step length, to the heterogeneity of the specific landscape.
A data set with kinematic and ground reaction forces of human balance
Authors: dos Santos Damiana A , Fukuchi Claudiane A , Fukuchi Reginaldo K , Duarte Marcos
Published: January 2018

This article describes a public data set with the three-dimensional kinematics of the whole body and the ground reaction forces (with a dual force platform setup) of subjects standing still for 60 s in different conditions, in which the vision and the standing surface were manipulated. Twenty-seven young subjects and 22 old subjects were evaluated. The data set comprises a file with metadata plus 1,813 files with the ground reaction force (GRF) and kinematics data for the 49 subjects (three files for each of the 12 trials plus one file for each subject). The file with metadata has information about each subject’s sociocultural, demographic, and health characteristics. The files with the GRF have the data from each force platform and from the resultant GRF (including the center of pressure data). The files with the kinematics have the three-dimensional position of the 42 markers used for the kinematic model of the whole body and the 73 calculated angles. In this text, we illustrate how to access, analyze, and visualize the data set. All the data is available at Figshare (DOI: 10.6084/m9.figshare.4525082 ), and a companion Jupyter Notebook (available at https://github.com/demotu/datasets ) presents the programming code to generate analyses and other examples.
Optimizing pedigrees: a numerical approach
Authors: Ang Justin
Published: January 2018

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. For example, it is hard to distinguish carriers from unaﬀected individuals in pedigrees. In order to ﬁnd such information, we must trace back and manually evaluate the tree, which is both cumbersome and ineﬃcient. I have discovered a way to represent individuals in the pedigree using numbers, such that the probability of an individual inheriting a certain trait can be easily calculated from their parents.
Optimizing pedigrees: Using a biasing system to determine likely inheritance systems
Authors: Ang Justin
Published: January 2018

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there has yet to be a system that tells us the probabilities of a tree following certain inheritance systems. My system intends to do that by creating a flexible numerical system, which can then be tested for variance. My system attempts to adapt inheritance system to known pedigree data. Then, it calculates where the calculated values differ from the known pedigree data. It aggregates these values, then uses them in a chi-squared analysis in order to determine how likely the inheritance system is to match the pedigree. This is done for many different systems, until we have a good idea of what system the pedigree matches or doesn't match.
A comparison of anesthesia techniques for entomological experimentation: Longevity of the leaf-mining fly pest Scaptomyza flava Fallén (Drosophilidae)
Authors: Rayl Ryan , Wratten Stephen
Published: January 2018

Historically, handling insects has usually involved their being killed, but non-lethal approaches are necessary when evaluating the biology of such organisms. Anesthesia has been used as one of these non-lethal approaches. Two common anesthetics used in this way have been carbon dioxide and chilling. These have been used frequently in the literature but have sub-lethal effects on insects that may affect further experimentation. An alternative anesthetic that has potential for experimental use is triethylamine (TEA). This shows promise because of its ease of use and potency as an insect anesthetic, but evidence, if any, of the sub-lethal effects is almost non-existent in the literature. Here, longevity was use as a proxy for fitness as this is a common approach to laboratory work of this type for pests and their natural enemies. A series of experiments were carried out to find the optimal rates for these three selected anesthetics. The organism selected for this work was the fly Scaptomyza flava (Fallén), the larvae of which mine the leaves of commercial brassica crops worldwide. It is a ‘cosmetic’ pest in that damage thresholds for crop rejection are very low and prophylactic use of insecticides is the norm. One way of mitigating the negative environmental aspects of this approach is to enhance biological control. One such way of enhancing biological control is the use of flowering plants, as they can provide alternative resources to natural enemies, which can enhance their ability to control pests. To evaluate these flowering plants, handling of the insects is necessary and anesthesia is used for this purpose. For each anesthetic an optimal rate was found, then these rates were compared to each other in a subsequent experiment. These anesthetics differed markedly in their value in terms of the duration of the anesthesia and other practical considerations. TEA had the longest effect, CO2 and chilling had the shortest. All three were similar in their effects on longevity (i.e. recovery time and mortality rates).
Computational screening of microalgae and cyanobacteria RuBisCO as potential precursor for bioactive peptides
Authors: Selvaraj Gurudeeban , Kaliamurthi Satyavani , Cakmak Zeynep Elibol , Cakmak Turgay
Published: January 2018

Ribulose-1,5-bisphosphate carboxylase/oxygense (RuBisCO) is present in plants and autotrophic organisms like microalgae. The aim of this study was to perform an in silico evaluation of RuBisCo protein in microalgae and cyanobacteria as potential precursors of bioactive peptides, as well as to determine whether such peptides can be released by selected proteolytic enzymes. Fourteen RuBioCo sequences of microalgae and cyanobacteria were analysed by using the BIOPEP server amd database. The biological activity, enzyme action and calculation of active peptide tools were used to determine the frequency of occurrence of fragments, proteolysis, and the frequency of release of fragments with given activity by selected enzymes. The physio-chemical parameters of the selected sequences were performed with Protpram tool. Amongst the RuBisCo proteins of selected algae, Chaetoceros. calcitrans exhibits the best prospect as a source of DPP-IV inhibiting peptides, Chlorella pyrenoidosa for ACE inhibitor and Aphanizomenon flos-aquae for antioxidative, activating ubiquitin, and antiamnestic activities. High number of bioactive fragments in Aphanizomenon flos-aquae, Dunaliella salina, Chlorella pyrenoidosa, and Chlorella vulgaris are associated with a high content of glycine and proline amino acids that are most rich in biologically active fragments. Papain and Proteinase K, an enzyme with wide specificity, can release considerably more biologically active fragments than bromealin and chymotrpsin. These findings will contribute towards consumption of microalgal and cyanobacterial RuBisCO as alternative sources of bioactive peptide fragments based nutraceuticals for human.
Jumping performance of Locusta migratoria and relationship between jumping performance and ground roughness
Authors: Mo Xiaojuan , Ge Wenjie , Romano Donato , Donati Elisa , Stefanini Cesare , Dario Paolo
Published: January 2018

Locusts are famous for its excellent jumping performance. Jumping helps locusts avoid predators and initiate flight. In this paper, high-speed videos are recorded to analyze the jumping performance of Locusta migratoria Linnaeus from ground with different roughness. By the established simplified theoretical model, we calculated L.migratoria normally can get 1.8318 m/s takeoff velocity and maximum acceleration about 66.72 m/s2 with takeoff angle at about 36°. Locusts are prone to slip when jumping from smooth surface especially for locusts with only one leg. The analyzed results show that locusts can increase their takeoff acceleration to get bigger takeoff velocity to adapt to different terrains, and takeoff velocity has no connection with takeoff angle while bigger takeoff angle have the possibility to help locusts to jump successfully with only one leg left or from smooth surface.
Arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication
Authors: Castagnola Anais , Jackson Jerreme , Perera Omaththage P , Oppert Cris , Eda Shigetoshi , Jurat-Fuentes Juan Luis
Published: January 2018

Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we report the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. Biological activity of the Cry1Ac-induced secretome was monitored as higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified 4 proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin protein not detected in the control secretome. Feeding of purified arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify arylphorin as a protein with a putative relevant role in the midgut regeneration process in response to Cry1Ac intoxication.
Short-term deleterious effects of standard isolation and cultivation methods on new tropical freshwater microalgae strains
Authors: Aray-Andrade M. Magdalena , Uyaguari-Diaz Miguel I , Bermúdez Monsalve J. Rafael
Published: January 2018

Algae with potential biotechnological applications in different industries are commonly isolate 5 from the environment in order to obtain pure (axenic) stocks that can be safely stored for long 6 periods of time. To obtain axenic cultures, antibiotics are frequently used, and cryopreservation 7 is applied to keep standing stocks. However, many of these now standard methods were 8 developed using strains coming from pristine-to-low intervened environments and cold-to- 9 temperate regions. Thus, it is still not well understand the potential effect of said methods on the 10 life cycle and biochemical profile of algae isolates from hiper-eutrophic and constant high- 11 temperature tropical regions, which could potentially render them unsuitable for their intended 12 biotechnological application. In this study, we did a genetic characterization (18s mDNA) and 13 evaluated the effect of purification (use of the antibiotic chloramphenicol, CPA) and 14 cryopreservation (dimethyl sulfoxide (DMSO)-sucrose mix and Glycerol) on the growth rate and 15 lipid content of four new tropical freshwater algal isolates: Chorella sp. M2, Chlorella sp. M6, 16 Scenedesmus sp. R3, and Coelastrella sp. A2, from the Ecuadorian coast. The genetic 17 characterization showed a clear discrimination between strains. All strains cultured with CPA 18 had a lower growth rate. After cryopreservation Coelastrella sp. A2 did not grow with both 19 methods; Chorella sp. M2, Chlorella sp. M6 and Scenedesmus sp. R3 presented no significant 20 difference in growth rate between the cryopreservants. A significantly higher lipid content was 21 observed in biomass cryopreserved with glycerol in relation to DMSO-sucrose, with Chorella sp. 22 M2 and Chlorella sp. M6 having twice as much in the first treatment. The results highlight the 23 relevance of choosing an appropriate method for storage as the materials used can affect the 3 1 biological performance of different tropical species, although is still to determine if the effects 2 observed here are long lasting in subsequent cultures of these algae.