bluuebunny/crossref_metadata_2025 huggingface dataset:
Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity
Authors: Kasumovic Michael , Chen Zhiliang , Wilkins Marc R
Published: January 2018

Background: Ecological and evolutionary model organisms have provided extensive insight into the ecological triggers, adaptive benefits, and evolution of life-history driven developmental plasticity. Despite this, we still have a poor understanding of the underlying genetic changes that occur during shifts towards different developmental trajectories. The goal of this study is to determine whether we can identify underlying gene expression patterns that can describe the different life-history trajectories individuals follow in response to social cues of competition. To do this, we use the Australian black field cricket (Teleogryllus commodus), a species with sex-specific developmental trajectories moderated by the density and quality of calls heard during immaturity. In this study, we manipulated the social information males and females could hear by rearing individuals in either calling or silent treatments. We next used RNA-Seq to develop a reference transcriptome to study changes in brain gene expression at two points prior to sexual maturation. Results: We show accelerated development in both sexes when exposed to calling; changes were also seen in growth, lifespan, and reproductive effort. Functional relationships between genes and phenotypes were apparent from ontological enrichment analysis. We demonstrate that increased phenotypic expression was often associated with the expression of a greater number of genes with similar effect, thus providing a suite of candidate genes for future research in this and other invertebrate organisms. Conclusions: Our results provide interesting insight into the genomic underpinnings of developmental plasticity. We highlight the relationship between genes of known effect and behavioral and phenotypic traits that are under strong sexual selection in Teleogryllus commodus. We also demonstrate the variation in suites of genes associated with different developmental trajectories. Our results provide the opportunity for a genomic exploration of other evolutionary theories such as condition dependence and sexual conflict.
What can the inverse relationship between sex ratios and calf:cow ratios, tell us about compensatory responses to hunting, in moose populations exposed to wolf predation?
Authors: Heard Doug
Published: January 2018

Moose populations with low hunting pressure tend to have high sex ratios and low calf:cow ratios and hunted ones have low sex ratios and high calf:cow ratios. What causes this inverse relationship? I suggest that when hunting is male-biased, which it is in almost all populations; 1) the number of 10 year old or older moose and the overall sex ratio is reduced, 2) the number of wolves declines because old moose are more vulnerable to predation by wolves than prime age animals and wolf numbers are linearly related to the number of old moose, and 3) the fraction of moose calves in the population and the calf:cow ratio increases because with fewer wolves, calf survival increases. This process could partially or completely compensate for moose hunting mortality in moose-wolf ecosystems.
Behaviourally-mediated interactions of landscape pattern shape predator-prey dynamics in highly altered landscapes
Authors: DeMars Craig , Breed Greg A , Potts Jonathan , Serrouya Robert , Boutin Stan
Published: January 2018

Landscape structure plays a fundamental role in shaping predator-prey dynamics, often being a key determinant of predator-prey coexistence. Rapid alteration of landscape structure, however, can lead to changes in predator-prey interactions with the magnitude of such changes dependent upon the scale and intensity of alteration and animal behavioural responses to novel environmental stimuli. In the boreal forests of western Canada, linear features (e.g. roads, seismic lines and pipelines) from industrial activity are a ubiquitous form of landscape alteration and increasing evidence suggests their presence has impacted interactions between wolves (Canis lupus) and boreal caribou (Rangifer tarandus caribou), leading to caribou population declines. Using simulation analyses parameterized by empirical data, we demonstrate how linear features affect the ability of wolves to predate caribou and evaluate how the spatial configuration and density of linear features interacts with animal behaviour to influence caribou-wolf encounter rates. Model outputs yield insights into the spatial requirements of caribou for effectively reducing predation risk and further illustrate behavioural strategies that are theoretically optimal for caribou. We discuss how our spatially explicit modelling of predator-prey encounter rates can inform management actions aimed at minimizing anthropogenic impacts within caribou range as well as in other predator-prey systems.
The XL-mHG test for gene set enrichment
Authors: Wagner Florian
Published: January 2018

The nonparametric minimum hypergeometric (mHG) test is a popular alternative to Kolmogorov-Smirnov (KS)-type tests for determining gene set enrichment. However, these approaches have not been compared to each other in a quantitative manner. Here, I first perform a simulation study to show that the mHG test is significantly more powerful than the one-sided KS test for detecting gene set enrichment. I then illustrate a shortcoming of the mHG test, which has motivated a semiparametric generalization of the test, termed the XL-mHG test. I describe an improved quadratic-time algorithm for the efficient calculation of exact XL-mHG p-values, as well as a linear-time algorithm for calculating a tighter upper bound for the p-value. Finally, I demonstrate that the XL-mHG test outperforms the one-sided KS test when applied to a reference gene expression study, and discuss general principles for analyzing gene set enrichment using the XL-mHG test. An efficient open-source Python/Cython implementation of the XL-mHG test is provided in the xlmhg package, available from PyPI and GitHub (https://github.com/flo-compbio/xlmhg) under an OSI-approved license.
Effect of fragmentation on the Costa Rican dry forest avifauna
Authors: Barrantes Gilbert , Ocampo Diego , Ramírez-Fernández José D. , Fuchs Eric J
Published: January 2018

Deforestation and land use change have reduced the tropical dry forest in the northwestern region of Costa Rica into isolated fragments. We examined the effect of fragment area and length of the dry season (seasonality) on nestedness for the community (entire species matrix), assemblages (forest fragments), and species occupancy across fragments for the native avifauna, and for a subset of forest dependent species. Area or distance between fragments did not correlate with species richness across fragments. Similarity in bird community composition between fragments was related with habitat structure; fragments with similar forest structure have higher similarity in their avifaunas. Fragment area determined the pattern of nestedness of the bird community and species occupancy, but not the nestedness of assemblages across fragments in northwestern Costa Rican avifauna. Forest dependent species (species that require large tracts of mature forest) and assemblages of these species were nested along forest fragments ranked by seasonality gradient, but only occupancy of species nested by fragment area.
Molecular identification of new bacterial causative agent of ice-ice disease on seaweed Kappaphycus alvarezii
Authors: Achmad Marlina , Alimuddin Alimuddin , Widyastuti Utut , Sukenda Sukenda , Suryanti Emma , Harris Enang
Published: January 2018

Background. Ice-ice disease is still a big challenge for seaweed farming that is characterized with “bleaching” symptom. Bacteria are suspected as cause of ice-ice disease on seaweed Kappaphycus alvarezii. The 16S rRNA gene sequencing is current technique used for bacterial phylogeny and taxonomy studies. This study was aimed to identify bacterial onset of ice-ice disease on K. alvarezii. Methods. Eight sequenced isolates from Indonesia were identified and characterized by biochemical tests and sequenced by 16S rRNA gene as target. The isolates sequence compared to the strains of bacteria from GenBank. DNA sequences are analyzed with ClustalW program and phylogeny were performed using the result generated by Mega v.5. The micropropagules (2-4 cm) was soaked in seawater containing 106 cfu/ml of bacteria to determine the pathogenicity. Onset of ice-ice symptoms was visually observed every day. Histology are analyzed to show tissue of micropropagule post-infection by bacteria. Results. Identification of bacteria employed biochemical tests and 16 SrRNA gene sequence analysis. The results reveal eight species of bacteria, namely: Shewanella haliotis strain DW01, 2 Vibrio alginolyticus strain ATCC 17749, Stenotrophomonas maltophilia strain IAM 12323, Arthrobacter nicotiannae strain DSM 20123, Pseudomonas aeruginosa strain SNP0614, Ochrobactrum anthropic strain ATCC 49188, Catenococcus thiocycli strain TG 5-3 and Bacillus subtilis subsp.spizizenii strain ATCC 6633. In term of groups, bacteria S. haliotis, V. alginolyticus, S. maltophilia, P. aeruginosa and C. thiocycli are the in Gammaproteobacteria group and O. anthropi is in the Alphaproteobacteria group, A. nicotianae and B. subtilis is in the of Proteobacteria group both of are Actinobacteria and Firmicutes group Low GC respectively. The results showed that the fastest onset of ice-ice symptoms was caused by S. maltophilia (five hours post-infection), while the slowest it was caused by V. alginolyticus (44 hours post-infection). Other bacteria give rise to ice-ice symptoms for 15-21 hours post-infection. Thus, S. maltophilia also showed number of bleaching spot of higher than others. However, V. alginolyticus showed increased width of bleaching 2.29 mm2 greater than S. maltophilia. Discussion. Bacteria S. haliotis and V. alginolyticus were found in healthy thallus, while others were found in bleaching thallus. Indicator of bleaching this is the first study shows S. maltophilia association to ice-ice disease on K. alvarezii. Interaction of temperature with different disease-causing pathogens ice-ice on seaweed is unreported and it is thought-provoking to examine in further research. In addition, the bacteria isolated in this study is potentially used to hold the assembly seaweed ice-ice disease through the challenge test.
AmrZ is a positive regulator of swimming motility in Pseudomonas stutzeri
Authors: Baltrus David A , Dougherty Kevin , Dias Beatriz , Murillo Rachel
Published: January 2018

amrZ, a master regulator protein conserved across Pseudomonads, can be either a positive or negative regulator of swimming motility depending on the species examined. To better understand plasticity in the regulatory function of AmrZ, we characterized the mode of regulation for this protein for swimming motility in P. stutzeri. As in P. syringae, AmrZ functions as a positive regulator of motility within P. stutzeri, which suggests that the functions of this protein with regards to swimming motility have switched at least twice across Pseudomonads. We further show that divergence between P. stutzeri and P. aeruginosa alleles of AmrZ does not explain shifts in regulatory mode. Further investigation into the mechanisms underlying shifts in regulatory function for AmrZ could provide unique insights into the evolution of bacterial regulatory proteins.
Pacing during an ultramarathon running event in hilly terrain
Authors: Kerhervé Hugo A , Cole-Hunter Tom , Wiegand Aaron N , Solomon Colin
Published: January 2018

Purpose. The dynamics of speed selection as a function of distance, or pacing, are used in recreational, competitive, and scientific research situations as an indirect measure of the psycho-physiological status of an individual. The purpose of this study was to determine pacing on level, uphill and downhill sections of participants in a long (~173 km) ultramarathon performed on trails in hilly terrain. Methods. Fifteen ultramarathon runners competed in a ~173 km event (five finished at ~103 km) carrying a Global-Positioning System (GPS) device. Using the GPS data, we determined the speed, relative to average total speed, in level (LEV), uphill (UH) and downhill (DH) gradient categories as a function of total distance, as well as the correlation between overall performance and speed variability, speed loss, and total time stopped. Results. There were no significant differences in normality, variances or means in the relative speed in 173-km and 103-km participants. Relative speed decreased in LEV, UH and DH. The main component of speed loss occurred between 5% and 50% of the event distance in LEV, and between 5% and 95% in UH and DH. There were no significant correlations between overall performance and speed loss, the variability of speed, or total time stopped. Conclusions. Positive pacing was observed at all gradients, with the main component of speed loss occurring earlier (mixed pacing) in LEV compared to UH and DH. A speed reserve (increased speed in the last section) was observed in LEV and UH. The decrease in speed and variability of speed were more important in LEV and DH than in UH. The absence of a significant correlation between overall performance and descriptors of pacing is novel and indicates that pacing in ultramarathons in trails and hilly terrain differs to other types of running events.
Order and Metric Compatible Symbolic Sequence Processing
Authors: Greenhoe Daniel J
Published: January 2018

A traditional random variable X is a function that maps from a stochastic process to the real line (X,<=,d,+,.), where R is the set of real numbers, <= is the standard linear order relation on R, d(x,y)=|x-y| is the usual metric on R, and (R, +, .) is the standard field on R. Greenhoe(2015b) has demonstrated that this definition of random variable is often a poor choice for computing statistics when the stochastic process that X maps from has structure that is dissimilar to that of the real line. Greenhoe(2015b) has further proposed an alternative statistical system, that rather than mapping a stochastic process to the real line, instead maps to a weighted graph that has order and metric geometry structures similar to that of the underlying stochastic process. In particular, ideally the structure X maps from and the structure X maps to are, with respect to each other, both isomorphic and isometric.Mapping to a weighted graph is useful for analysis of a single random variable.for example the expectation EX of X can be defined simply as the center of its weighted graph. However, the mapping has limitations with regards to a sequence of random variables in performing sequence analysis (using for example Fourier analysis or wavelet analysis), in performing sequence processing (using for example FIR filtering or IIR filtering), in making diagnostic measurements (using a post-transform metric space), or in making goptimalh decisions (based on gdistanceh measurements in a metric space or more generally a distance space). Rather than mapping to a weighted graph, this paper proposes instead mapping to an ordered distance linear space Y=(R^n,<=,d,+,.,R,+,x), where (R,+,x) is a field, + is the vector addition operator on R^n x R^n, and . is the scalar-vector multiplication operator on R x R^n. The linear space component of Y provides a much more convenient (as compared to the weighted graph) framework for sequence analysis and processing. The ordered set and distance space components of Y allow one to preserve the order structure and distance geometry inherent in the underlying stochastic process, which in turn likely provides a less distorted (as compared to the real line) framework for analysis, diagnostics, and optimal decision making.
A primer for managing international collaboration and legal compliance in biobank based genomics
Authors: Klingström Tomas , Bongcam-Rudloff Erik , Reichel Jane
Published: January 2018

Resolving ethical and legal concerns is a time consuming but rarely insurmountable task when obtaining samples from biobanks. The BBMRI-LPC project has throughout its lifetime resolved numerous such issues and intense communication between involved researchers and experts have been necessary to resolve various issues. To facilitate efficient communication it is useful for non-experts to have an at least basic understanding on how the regulatory system for managing biological samples is constructed to balance the sometimes conflicting needs of privacy, trust and scientific progress.

Although laws regulating research oversight have been implemented differently in every country, there is a similarity of core principles founded on international charters. These core principles are based on the concept of consent and actions taken by the biobank in regards to sample usage rely on either an explicit or presumed consent. In interview studies among donors chief concerns among donors are focused on privacy, efficient sample utilization and if donors are given access to information generated from their samples. Despite a lack of clear evidence regarding which concern takes precedent among donors, scientific as well as public discourse has largely focused on privacy concerns and the right of donors to control the usage of their samples.

As a result biobank governance has taken a largely negative approach to uncertainties in sample utilization. This mean that sample usage is likely to be restricted if there is any uncertainty if the intended usage is in line with donor expectations. To help biobank professionals avoid making unnecessary mistakes we have developed this basic primer covering the relationship between ethics and law, the concept of informed consent and consideration for returning findings to donors.
Automation in clinical data collection in obstetrics - Enabling pooled IPD studies for fetal heart rate and activity monitoring
Authors: Saalfeld Maximilian , Weber Christopher , Lobmaier Silvia M , Weyrich Joy , Grundmann Holger J , Harboeck Christian , Daumer Martin
Published: January 2018

Cardiotocography is currently the standard surveillance tool during labour. For this reason, there are large cardiotography datasets available. Several studies gathering additional information of computerized CTG data aiming to improve surveillance during delivery and birth outcome are currently performed. Manual data collection and analysis takes a lot of human resources, is error-prone and study parameters can hardly be adjusted later on. Therefore, a software based approach was chosen to minimize the effort of preparation. The software called “CTG and patient information matcher” (CAPIM) collects relevant CTG signals for a specified patient dataset and under recognition of several parameters. CAPIM was tested with the patient database of Frauenklinik und Poliklinik of Technische Universität München (Munich, Germany). Further hospitals will follow. The cases received from CAPIM will be used to do feasibility studies for two innovative signal processing techniques as „phase-rectified signal averaging“ method on fe­tal heart rate raw data and „deceleration area“ me­thod to improve prediction of birth outcome.
Dynamics of total proteins during stress alleviation in tomato infected with cucumber mosaic virus
Authors: Tariq Rana Muhammad Sabir M , Sarwar Nighat , Haq Imran Ul , Sahi Shahbaz Talib , Gogi Muhammad Dildar
Published: January 2018

Background: Phytoalexins are the secondary metabolites produced in crop plants after the attack of necrotizing pathogens. They are aimed to support homeostasis in stressed plants. Proteins are also part of this regime that is manipulated according to the type of infection or environmental stress. Chemical elicitors substitute the traditional fungicides and safe to use. They also modify protein levels due to their direct or indirect influence on the defense pathways. Methodology: An in vitro study was conducted on tomato seedlings inoculated with cucumber mosaic virus (CMV). Plants were treated with salicylic acid and BTH at different intervals to find out the alterations in the total soluble proteins. Purpose of study was to investigate the variation in total proteins during the viral attack and role of elicitors in this case. Results: Results indicated that protein level was initially reduced (133.3 mg) in the inoculated plants prior to the application of elicitors. However, BTH alone or combined with SA significantly enhanced total soluble proteins (200.3 mg) in tomato leaves when applied on weekly intervals. Single application of Salicylic acid gave similar response as in case of non-inoculated plants, however weekly applied SA reduced the total proteins to much lower extent (83.6 mg) under the CMV stress. Discussion: Modification of total proteins in a single tomato cultivar along with homogenous environmental factors indicates the active role of chemical elicitors in the defense pathways. BTH is a structural homologue to SA but expressed a remarkable functional contrast under viral attack particularly in solanaceous crops. This novelty in plant science is worthy of discussion.
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
Authors: Moller Abraham G , Liang Chun
Published: January 2018

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns and related them to carbon cycling. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the IC21 and C34 salterns compared with the SS19, SS33, and SS37 salterns, suggesting fewer types of CRISPR spacers in the Haloquadratum-majority salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were groups of interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.
Fishing degrades size structure of coral reef fish communities
Authors: Robinson James PW , Williams Ivor D , Edwards Andrew M , McPherson Jana , Yeager Lauren , Vigliola Laurent , Brainard Russell E , Baum Julia K
Published: January 2018

Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size-structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra of coral reef fish communities at 38 US-affiliated Pacific islands, spanning from near pristine to highly human populated. Reef fish community size spectra slopes ‘steepened’ steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. In contrast, total fish community biomass was substantially lower on inhabited islands than uninhabited ones, regardless of human population density. Comparing the relationship between size spectra and reef fish biomass, we found that on populated islands size spectra steepened linearly with declining biomass, whereas on uninhabited islands size spectra and biomass were unrelated. Size spectra slopes also were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to biophysical conditions, being influenced by oceanic productivity, sea surface temperature, island type, and habitat complexity. Our results suggest that community size structure is more robust than total fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size-based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems.
Trace elements during primordial plexiform network formation in human cerebral organoids
Authors: Sartore Rafaela C , Cardoso Simone C , Lages Yuri V , Paraguassu Julia M , Madeiro da Costa Rodrigo F , Guimarães Marilia ZP , Pérez Carlos A , Rehen Stevens K
Published: January 2018

Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development. In the present work, we exposed cerebral organoids derived from human pluripotent stem cells to synchrotron radiation in order to measure how biologically valuable micronutrients are incorporated and distributed in the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves calcium, iron, phosphorus, potassium, sulfur, and zinc. Local trends in concentrations suggest a switch from passive to actively mediated transport across cell membranes. Finally, correlational analysis for pairs of elements shows spatially conserved patterns, suggesting they may physically associate, be stored in similar compartments or used in related biological processes. These findings might reflect which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood.
Integrating a thermistor flowmeter and time lapse imagery to monitor sponge (Porifera) behaviour
Authors: Strehlow Brian W , Jorgensen Damien , Webster Nicole S , Pineda Mari-Carmen , Duckworth Alan
Published: January 2018

A digital, four-channel thermistor flowmeter was developed as an experimental tool for measuring pumping rates in marine sponges, particularly those with small excurrent pores (oscula). The flowmeter is integrated with time lapse cameras and has an accuracy of ±5 mm s-1 over the range of 5–200 mm s-1, a spatial resolution of 1.4 mm, and an adjustable temporal resolution of 5 seconds. Combining flowmeters with time lapse imagery yielded valuable insights into the contractile behaviour of oscula in Cliona orientalis, revealing four distinct oscula states: (1) osculum open with extended papilla, (2) osculum closed with extended papilla, (3) osculum closed with papilla retracted, and (4) osculum closed with papilla retracted and contraction of region surrounding osculum. Osculum area was positively correlated to measured excurrent velocities, indicating that sponge pumping and osculum contraction are coordinated behaviours. Diel trends in pumping activity and osculum contraction were also observed, with sponges increasing their pumping activity to peak at midday and decreasing pumping and contracting oscula at night. Short-term elevation of the suspended sediment concentration within the seawater initially decreased pumping rates by up to 90%, ultimately resulting in closure of the oscula and cessation of pumping. The thermistor flowmeter developed here will be a valuable tool to monitor behaviour, physiology and ecophysiology of sponges.
Effect of wetland management: Are lentic wetlands refuges of plant-species diversity in the Andean-Orinoco Piedmont of Colombia?
Authors: Murillo-Pacheco Johanna I. , Rös Matthias , Escobar Federico , Castro-Lima Francisco , Verdú José R , López-Iborra Germán M
Published: January 2018

Accelerated degradation of the wetlands and fragmentation of surrounding vegetation in the Andean-Orinoco Piedmont are the main threats to diversity and ecological integrity of these ecosystems; however, information on this topic is of limited availability. In this region, we evaluated the value of 37 lentic wetlands as reservoirs of woody and aquatic plants and, analyzed diversity and changes in species composition within and among groups defined according to management given by: 1) type (swamps, heronries, rice fields, semi-natural lakes, constructed lakes and fish farms) and, 2) origins (natural, mixed and artificial). A total of 506 plant species were recorded: 80% woody and 20% aquatic. Of these, 411 species (81%) were considered species typical of the area (Meta Piedmont distribution). Diversity patterns seem to be driven by high landscape heterogeneity and wetland management. The fish farms presented the highest diversity of woody plants, while swamps ranked highest for aquatic plant diversity. Regarding wetland origin, the artificial systems were the most diverse, but natural wetlands presented the highest diversity of typical species and can therefore be considered representative ecosystems at the regional scale. Our results suggest that lentic wetlands act as refuges for native vegetation of Meta Piedmont forest, hosting 55% of the woody of Piedmont species and 29% of the aquatic species of Orinoco basin. The wetlands showed a high species turnover and the results indicated that small wetlands (mean±SD: size = 11±18.7 ha), with a small area of surrounding forest (10±8.6 ha) supported high local and regional plant diversity. To ensure long-term conservation of lentic wetlands, it is necessary to develop management and conservation strategies that take both natural and created wetlands into account.
Computational testing for automated preprocessing: a matlab toolbox for better electroencephalography data processing
Authors: Cowley Benjamin , Korpela Jussi , Torniainen Jari
Published: January 2018

EEG is a rich source of information regarding brain functioning, and is the most lightweight and affordable method of brain imaging. However, the pre-processing of EEG data is quite complicated and most existing tools present the experimenter with a large choice of methods for analysis, but no framework for method comparison to choose an optimal approach. Additionally, many tools still require a high degree of manual decision making for, e.g. the classification of artefacts in channels, epochs or segments. This introduces excessive subjectivity, is slow, and is not reproducible. Batching and well-designed automation can help to regularise EEG preprocessing, and thus minimise human effort, subjectivity, and consequent error. The Computational Testing for Automated Preprocessing (CTAP) toolbox facilitates: i) batch processing that is easy for experts and novices alike; ii) testing and comparison of automated methods. CTAP uses the existing data structure and functions from the well-known EEGLAB tool, based on Matlab, and produces extensive quality control outputs.
Detecting sedimentation impacts to coral reefs resulting from dredging the Port of Miami, Florida USA
Authors: Miller Margaret W , Karazsia Jocelyn , Groves Carolyn E , Griffin Sean , Moore Tom , Wilber Pace , Gregg Kurtis
Published: January 2018

The federal channel at Port of Miami, Florida, USA, was dredged between late 2013 and early 2015, to widen and deepen the channel. While the precise effects of the dredging on surrounding coral reefs are not well quantified, previously published remote sensing analyses, as well as agency and anecdotal reports suggest the most severe and largest area of sedimentation occurred on a coral reef feature referred to as the Inner Reef, particularly in the sector north of the channel. A regional warm-water mass bleaching event followed by a coral disease outbreak during this same time frame confounded the assessment of dredging-related impacts to coral reefs adjacent to the federal channel. In-water field assessments conducted after the completion of dredging and a time series analysis of tagged corals photographed pre-, during, and post-dredging, are used to discern dredging-related sedimentation impacts for the Inner Reef north. Results indicate increased sediment accumulation, severe in certain times and places, and an associated biological response, including significantly greater proportion of live coral tissue loss, occurred within coral reef sites located closer to the channel. Dredging projects near valuable and sensitive habitats subject to local and global stressors require monitoring methods capable of discerning non-dredging related impacts and adaptive management to ensure predicted and unpredicted project-related impacts are quantified. Anticipated increasing frequency and intensity of warming stress also suggests that manageable- but- unavoidable local stressors such as dredging should be partitioned from the warmest times of year.
Visual analogies in anatomic and clinical pathology
Authors: Kipersztok Lisa , Masukume Gwinyai , Lakhtakia Ritu
Published: January 2018

Visual medical analogies have been utilized by multiple medical disciplines for decades. Despite misgivings that some might have about such analogies, they act as excellent learning aids and will undoubtedly remain useful for decades to come. The microscope from about the seventeenth century onwards revolutionized medicine and cellular biology. In this article, we specifically consider in a pictorial essay culinary medical analogies as they pertain to the microscopic world, a gap in the literature on visual medical analogies.
Mapping irrigated areas using multi-sensor remote sensing data in a Mediterranean environment
Authors: Nino Pasquale , Vanino Silvia , Lupia Flavio , D'Urso Guido , De Michele Carlo , Pulighe Giuseppe , Bonati Guido
Published: January 2018

Water managers need map of irrigated areas (defined as the identification of their location and their areal extent) to plan a rational use of water under limited availability and to prevent the unauthorized withdrawals. Many authors have shown that the Earth Observation techniques are an effective tool for mapping irrigated areas worldwide at different spatial scales (global/regional/and local). This study presents a methodology for mapping irrigated areas in semi-arid environment based on Earth Observation techniques and by fully exploiting datasets freely available processed by open source software and tools. Data acquired with the Landsat 8 Operational Land Imager (OLI) and the new Sentinel 2A MultiSpectral Instrument (MSI) sensors were integrated to obtain cloud free dense time series allowing to monitor the vegetation development throughout the growing seasons. Irrigated areas were identified by analysing the growing patterns under water deficit conditions from NDVI values under the assumption that, in arid and semi-arid environment (like the Mediterranean Region), high trend of vegetation growth are compatible only with irrigation. The method was applied inside the Cixerri Consortium Irrigation District located in South of Sardinia (Italy).
A public data set of human balance evaluations
Authors: Santos Damiana A , Duarte Marcos
Published: January 2018

The goal of this study was to create a public data set with results of qualitative and quantitative evaluations related to human balance. Subject’s balance was evaluated by posturography using a force platform and by the Mini Balance Evaluation Systems Tests. In the posturography test, we evaluated subjects during standing still for 60 s in four different conditions where vision and the standing surface were manipulated: on a rigid surface with eyes open; on a rigid surface with eyes closed; on an unstable surface with eyes open; on an unstable surface with eyes closed. Each condition was performed three times and the order of the conditions was randomized among subjects. In addition, the following tests were employed in order to better characterize each subject: Short Falls Efficacy Scale International; International Physical Activity Questionnaire Short Version; and Trail Making Test. The subjects were also interviewed to collect information about their socio-cultural, demographic, and health characteristics. The data set comprises signals from the force platform (raw data for the force, moments of forces, and centers of pressure) of 163 subjects plus one file with information about the subjects and balance conditions and the results of the other evaluations. All the data is available at PhysioNet ( DOI: 10.13026/C2WW2W ) and at Figshare ( DOI: 10.6084/m9.figshare.3394432 ).
Ecuadorian Glass Frogs: Current state of knowledge, new research trends and conservation
Authors: Cisneros-Heredia Diego F , McDiarmid Roy W.
Published: January 2018

Ecuador has the biggest number of amphibian species per unit of area in the world (427 species in 276,840 km2). Glass frogs (Centrolenidae), with 30 species, constitute 7.06 % of the Ecuadorian anurans. However, the current state of knowledge of this family in Ecuador is still very basic. Several species of glass frogs are currently undescribed, confused with previously described taxa, not yet reported from the country but present in local museum collections, not yet discovered in Ecuador, or even described under two different names. The genus Hyalinobatrachium is poorly known in the country (four species), but at least three undescribed taxa are present in the western lowlands of Ecuador. Among the genera Cochranella and Centrolene, at least 6 new species are known from tropical and subtropical areas in western and eastern slopes of the Ecuadorian Andes. Several characters such as the patterns of skin, eye, peritoneum and pericardium color, the prepollical spine, the nuptial pad, and the presence of the bulla are discussed, especially around its taxonomic potential. At least one undescribed taxon from western lowlands of Ecuador is critically endangered, if not extinct. In the last decade, conservative estimates indicate that at least 26 species of Ecuadorian amphibians have declined or gone extinct, two of them belong to the family Centrolenidae. The reasons for this crisis are not clear but have been related to habitat destruction, climate change, and fungal disease such as the chytridiomycosis.
Food availability and flight routes for migratory birds: a GIS approach
Authors: Tattoni Clara , Soardi Erica , Zatelli Paolo , Ciolli Marco
Published: January 2018

Bird migration is a wide studied phenomenon but still many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship have not often been addressed at wide scale due to the lack of spatial models of food availability on the terrain.The aim of this work is to fill this gap with a GIS-database approach that links together spatial and non-spatial information in order to map and measure food availability in the different periods of the year in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. With this approach we were able to identify various flyways and compare them with known stopover sites, ringing stations and food availability using a mix of techniques of statistical geostatistical and interpretation of ecological data.
Response of fish species to river restoration – the role of species traits
Authors: Höckendorff Stefanie , Tonkin Jonathan D , Haase Peter , Bunzel-Drüke Margret , Zimball Olaf , Scharf Matthias , Stoll Stefan
Published: January 2018

Species are known to respond differently to restoration efforts, but we still lack a clear conceptual understanding of these differences. We analyzed the development of an entire fish community as well as the relationship between multi-metric response patterns of fish species and their ecological species traits at a comprehensively monitored river restoration project, the Lippe River in Germany. Using electrofishing data from 21 consecutive years (4 years pre- and 17 years post-restoration) from multiple restored and unrestored control reaches, we demonstrated that this restoration fully reached its targets, approximately doubling both species richness and abundance. Species richness continuously increased while fish density exhibited an overshooting response in the first years post restoration. Both richness and abundances stabilized approximately seven years after the restoration, although interannual variability remained considerable. The response of each species to the restoration was characterized using a set of six parameters. Relating the dissimilarity in species response to their ecological dissimilarity, based on 13 species traits, we found life-history and reproduction-related traits were the most important for species’ responses to restoration. Short-lived species with early female maturity and multiple spawning runs per year exhibited the strongest response, reflecting the ability of fast reproducers to rapidly colonize new habitats. Fusiform-bodied species also responded more positively than deep-bodied species, reflecting the success of this restoration to reform appropriate hydromorphological conditions (riffles and shallow bays), for which these species depend. Our results demonstrate that repeated sampling over periods longer than seven years are necessary to reliably assess river restoration outcomes. Furthermore, this study emphasizes the utility of species traits for examining restoration outcomes, particularly the metapopulation and metacommunity processes driving recovery dynamics. Focusing on species traits instead of species identity also allows for easier transfer of knowledge to other biogeographic areas and promotes coupling to functional ecology.
Introduction of seasonality concept in PSF algorithm to improve univariate time series predictions
Authors: Bokde Neeraj , Gupta Aditya , Kulat Kishore
Published: January 2018

This paper proposed a novel modification in Pattern Sequence based Forecasting (PSF) algorithm, named as Seasonal PSF. The proposed modification in PSF algorithm is done with addition of seasonality concept, such that the longer univariate time series database with combination of many sequence patterns and outliers can be converted into more relevant database in accordance with data under test of predictions. In this paper, seasonal PSF is examined on electricity load database for two years, provided by EUNITE network. The comparative analysis consists of two methodologies, multiple steps prediction and one step ahead forecasting. This analysis conclude that, seasonality based decomposition of database leads to much better performance of seasonal PSF over original PSF and benchmarked methods for univariate predictions like ARIMA and SARIMA. It is found that the maximum accuracy is achieved in minimum computational delay with Seasonal PSF. These comparisons are performed with RMSE, MAE and MAPE as error performance metrics.
Enhancing genetic algorithms using multi mutations
Authors: Hassanat Ahmad B , Alkafaween Esra’a , Alnawaiseh Nedal A , Abbadi Mohammad A , Alkasassbeh Mouhammd , Alhasanat Mahmoud B
Published: January 2018

Mutation is one of the most important stages of the genetic algorithm because of its impact on the exploration of global optima, and to overcome premature convergence. There are many types of mutation, and the problem lies in selection of the appropriate type, where the decision becomes more difficult and needs more trial and error. This paper investigates the use of more than one mutation operator to enhance the performance of genetic algorithms. Novel mutation operators are proposed, in addition to two selection strategies for the mutation operators, one of which is based on selecting the best mutation operator and the other randomly selects any operator. Several experiments on some Travelling Salesman Problems (TSP) were conducted to evaluate the proposed methods, and these were compared to the well-known exchange mutation and rearrangement mutation. The results show the importance of some of the proposed methods, in addition to the significant enhancement of the genetic algorithm’s performance, particularly when using more than one mutation operator.
How patch size and habitat complexity changes interaction strength and population dynamics: a combined individual-based and population-based modeling experiment
Authors: Li Yuanheng , Brose Ulrich , Meyer Katrin , Rall Björn C
Published: January 2018

Understanding how functional responses (non-linear prey density dependent feeding interactions) are affected by patch size and habitat complexity is crucial as functional responses are the major determinants of food web stability and subsequently biodiversity. Due to its laborious character, measuring empirical functional responses systematically across large gradients of patch sizes and habitat complexity independently is almost impossible. Here we overcame this issue by using an individual-based predator-prey model allowing to simulate functional responses in patches ranging from the size of petri dishes to natural patches in the field. Moreover we are able to vary the habitat complexity independent of the patch size. Contradicting to the pervasive type II functional response that is still assumed as the appropriate model to describe feeding interactions we found a type III functional response in our simulations, independent of patch size and habitat complexity. Moreover, half-saturation density determining the feeding success at low prey densities decrease only with increasing habitat complexity and is only marginally influenced by patch size. Subsequent population dynamic model simulations indicate that small patches do not allow for survival of the predator, caused by a mismatch of the nearly constant functional response but an increasing extinction boundary with decreasing patch size. This effect is counteracted by increasing habitat complexity allowing both, the prey and the predator to co-exist. Our results underline the need for protecting large patches with high habitat complexity to sustain biodiversity.
The evolution of logic circuits for the purpose of protein contact map prediction
Authors: Chapman Samuel D , Adami Christoph , Wilke Claus O , KC Dukka B
Published: January 2018

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.