bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological facilitation of the giant tree fern Angiopteris evecta in the germination of the invasive velvet tree Miconia calvescens
Authors: Lee Jaemin 
Published: January 2018

Background. Biological facilitation is a type of relationship between two taxa that benefits at least one of the participants and harms neither. Although invasive species are widely known to compete with native taxa, recent studies suggest that invasive and native species can have positive relationships. This study aims to examine the biological facilitation of the germination of invasive Miconia calvescens by giant tree fern Angiopteris evecta, native to French Polynesia.
Methods. Field surveys were conducted to measure A. evecta and M. calvescens by applying the 10×10 m2 quadrat survey method. The density of seedlings, saplings, and matures of M. calvescens growing on the rhizomes of A. evecta and on bare soil was compared, and the correlation between the size of the rhizomes and the number of M. calvescens growing on them was verified. Two separate sets of nutrient measurements of substrates were performed to compare the nutrient of A. evecta rhizome and other environments (abiotic and potential biotic environments). Leaf decomposition rate of five dominant tree species was compared to verify whether A. evecta has quickly decomposing leaves, and therefore induce the germination of M. calvescens indirectly.
Results. Field surveys show that there is a greater number of seedlings and saplings of M. calvescens growing on the rhizomes of A. evecta as compared to bare soil. Furthermore, there is a positive correlation between the size of rhizomes and the number of M. calvescens growing on them. Substrates of A. evecta had higher phosphorus and potassium contents compared to other soils and substrates, but did not differ from bark of other tree species that could potentially offer favorable microenvironments. A. evecta has quickly decomposing leaves.
Discussion. A. evecta facilitates the germination of M. calvescens, supported by the much higher number of seedlings and saplings growing on the rhizomes and the positive correlation between the size of the rhizome and the number of M. calvescens growing on it. Microslopes on the rhizomes of A. evecta prevent leaf litter from accumulating on the rhizomes, and enable more sunlight to reach and facilitate the germination of M. calvescens seeds. Also, quickly decomposing leaves of A. evecta prevent the accumulation of leaf litter on the ground and enable more light to reach seed bank. Although the chemical components is not different from other tree species, physical structure of the rhizome and consequent higher light availability, and higher amount of potassium than bare soil would be the possible reason for the facilitation. Biological facilitation of the germination of invasive M. calvescens by native A. evecta can give better understanding on the invasion success and the relationship between the native and invasive species. Invasion of A. evecta can induce and promote further invasion of M. calvescens. Therefore, thorough management of ongoing invasion of A. evecta is particularly required.
Conus bonus! Facilitation of Conus gastropods by invasive mangroves in Mo'orea, French Polynesia
Authors: Witte Eric C 
Published: January 2018

Background. Ecosystem engineers are organisms that modify habitats and in many cases community assemblages. Mangroves (Rhizophora stylosa) on Mo’orea displace native marsh grass habitats and affect the distribution of native and non-native gastropod species. This study aimed to determine the effect of mangrove facilitation on the expansion of geographic distribution of certain cone snail species (Conus eburneus,C. frigidus C. leopardus, C. miliaris, and C. pulicaris).
Methods. Comparisons of temperature as well as cone snail abundance and diversity were conducted between marsh grasses, mangroves and sand flat habitats. The effects of short-term exposure to high temperatures on oxygen consumption were compared based on habitat parameters.
Results. While cone snails were absent from salt marshes, cone snails varied in abundance and diversity in mangrove and sand flat habitats. Cone snails were slightly more abundant in mangroves than paired sand flat habitats. Conus species assemblages were comparable in paired mangrove and sand flat habitats. One effect of mangrove ecosystem engineering is reduced thermal maxima and variance, which did not have a clear effect on oxygen consumption.
Discussion. Cone snails are excluded from salt marshes dominated by Paspalum vaginatum, however they are present in mangrove salt marshes. Habitat usage by cone snails is comparable between adjacent sites, suggesting that sand-specialized cone snails may receive the greatest benefit from mangrove facilitation due to proximity between possible habitats. Despite well documented effects of temperature variance on intertidal gastropods, this study did not find a direct effect of temperature variance on cone snails. This study contributes to efforts to understand effects of invasive ecosystem engineers on native community assemblages. Redistribution of species on a global scale has varied and complex implications; understanding these effects is crucial to predicting effects on biodiversity.
Out of place: a study of the mangrove crab Cardisoma carnifex on Mo’orea, French Polynesia
Authors: Johnson Isabel L S 
Published: January 2018

Background. Invasive plant species pose a significant threat to island biodiversity and ecosystems. Invasive mangrove trees in particular have been shown to be devastating to the shorelines of islands across the Pacific. Previous studies have assumed that the mangrove crab, Cardisoma carnifex, plays a significant role in controlling Rhizophora stylosa mangrove populations on Mo’orea, French Polynesia. Found across East Africa, Indonesia, and the Pacific, C. carnifex’s behavior can change drastically depending on the environment it’s found in.
Methods. From October-November 2016, a field study was conducted on Mo’orea to assess C. carnifex habitat and food preferences. A series of 30 meter transects were done to determine the population density of crabs in mangrove and non-mangrove sites. In addition, a set of food preference experiments were run to determine if C. carnifex preferred to eat R. stylosa leaves, propagules, Hibiscus tiliaceus leaves, flowers, and Paspalum vaginatum marsh grass.
Results. Cardisoma carnifex was found to be more prevalent in mangrove sites although the results were not statistically significant. There were no food preferences found regardless of habitat and the flow of food through both habitats was the same.
Discussion. Results do not give a clear indication of C. carnifex’s ability to impact R. stylosa populations. However, results do demonstrate C. carnifex’s opportunistic nature, suggesting that they are extremely adaptable and do not rely on one habitat or food source for survival. Cardisoma carnifex’s role in its habitat is still poorly understood and needs to be studied in more detail in the future.
The burrow morphology of mole crickets (Orthoptera: Gryllotalpidae): terminology and comparisons
Authors: Baker Edward 
Published: January 2018

Since the publication of Baker (2016) three additional burrow casts, unknown to the author, were located in the Natural History Museum, London (NHM) collection by George Beccaloni. These casts were provisionally identified as Gryllotalpa vineae. In order to establish whether this identification was correct a literature survey of the casts of mole crickets (Orthoptera: Gryllotalpidae) was conducted. Through this process a standardised terminology for mole cricket burrows has been established.
The application of eccentricity measurements to burrow structures has identified measurements that can potentially be used to discriminate those species for which suitably detailed burrow descriptions have been made available. It is demonstrated that the eccentricity of the restrictions on either side of the bulb, as well as the eccentricity of the horn opening, are useful diagnostic characters.
The influence of predator type on ‘whirling’ defensive behavior of Pholcus ancoralis (Araneae, Pholcidae), a tropical web-building spider
Authors: Striegel Theodore 
Published: January 2018

Background. The ‘whirling’ defensive behavior of Pholcus ancoralis (L. Koch, 1865) was studied in a forest and laboratory in Mo’orea, French Polynesia. This behavior involves fast web-borne gyration to dissuade predators and is widespread in the Pholcidae family.
Methods. Different local predators (Anterhyncium rufipes, Lipinia noctua, and Thorelliola ensifera) were placed in two-chambered systems with P. ancoralis individuals and qualitative data on whirling frequency and duration were obtained.
Results. Potter wasps (Anterhyncium rufipes) triggered whirling in 50% of trials and moth skinks (Lipinia noctua) triggered whirling in 20% of trials. The average durations of the behavior triggered by each were 853 and 455 seconds, respectively. Pacific horned jumping spiders (Thorelliola ensifera) triggered whirling in 10% of trials with an average duration of only 20 seconds.
Discussion. Wasps triggered whirling the most frequently and of a long average duration. This has not been seen in other studied pholcids. This difference in predator specificity of whirling may be due to differences in habitat between pholcid species.
A comparison of least squares regression and geographically weighted regression modeling of West Nile virus risk based on environmental parameters
Authors: Kala Abhishek K , Tiwari Chetan , Mikler Armin R , Atkinson Samuel F 
Published: January 2018

Background. The primary aim of the study reported here was to determine the effectiveness of utilizing local spatial variations in environmental data to uncover the statistical relationships between West Nile Virus (WNV) risk and environmental factors. Because least squares regression methods do not account for spatial autocorrelation and non-stationarity of the type of spatial data analyzed for studies that explore the relationship between WNV and environmental determinants, we hypothesized that a geographically weighted regression model would help us better understand how environmental factors are related to WNV risk patterns without the confounding effects of spatial non-stationarity.
Methods. We examined commonly mapped environmental factors using both ordinary least squares regression (LSR) and geographically weighted regression (GWR). Both types of models were applied to examine the relationship between WNV-infected dead bird counts and various environmental factors for those locations. The goal was to determine which approach yielded a better predictive model.
Results. LSR efforts lead to identifying three environmental variables that were statistically significantly related to WNV infected dead birds (adjusted R2=0.61): stream density, road density, and land surface temperature. GWR efforts increased the explanatory value of these three environmental variables with better spatial precision (adjusted R2 = 0.71).
Conclusions. The spatial granularity resulting from the geographically weighted approach provides a better understanding of how environmental spatial heterogeneity is related to WNV risk as implied by WNV infected dead birds, which should allow improved planning of public health management strategies.
Do you speak open science? Resources and tips to learn the language
Authors: Masuzzo Paola , Martens Lennart 
Published: January 2018

The internet era, large-scale computing and storage resources, mobile devices, social media, and their high uptake among different groups of people, have all deeply changed the way knowledge is created, communicated, and further deployed. These advances have enabled a radical transformation of the practice of science, which is now more open, more global and collaborative, and closer to society than ever. Open science has therefore become an increasingly important topic. Moreover, as open science is actively pursued by several high-profile funders and institutions, it has fast become a crucial matter to all researchers. However, because this widespread interest in open science has emerged relatively recently, its definition and implementation are constantly shifting and evolving, sometimes leaving researchers in doubt about how to adopt open science, and which are the best practices to follow.
This article therefore aims to be a field guide for scientists who want to perform science in the open, offering resources and tips to make open science happen in the four key areas of data, code, publications and peer-review.
Pollen extracts increase growth of a trypanosome parasite of bumble bees
Authors: Palmer-Young Evan C 
Published: January 2018

Phytochemicals produced by plants, including at flowers, function in protection against plant diseases, and have a long history of use against trypanosome infection. Floral nectar and pollen, the sole food sources for many species of insect pollinators, contain phytochemicals that have been shown to reduce trypanosome infection in bumble and honey bees when fed as isolated compounds. Nectar and pollen, however, consist of phytochemical mixtures, which can have greater antimicrobial activity than do single compounds. This study tested the hypothesis that pollen extracts would inhibit parasite growth.Extracts of six different pollens were tested for direct inhibitory activity against cell cultures of the bumble bee trypanosome gut parasite Crithidia bombi.
Surprisingly, pollen extracts increased parasite growth rather than inhibiting it. Experimental manipulations of growth media showed that supplemental monosaccharides (glucose and fructose) were sufficient to promote growth, while a common floral phytochemical (caffeic acid) with inhibitory activity against other trypanosomes had only weak inhibitory effects on Crithidia bombi. These results indicate that, although pollen is essential for bees and other pollinators, pollen may promote growth of intestinal parasites that are uninhibited by pollen phytochemicals and, as a result, can benefit from the nutrients that pollen provides.
Differential drivers of chemical defenses in three widespread pine species along a 1500-m elevational gradient: a test of the elevational gradient in plant defense hypothesis
Authors: Ferrenberg Scott , Langenhan Joseph M , Loskot Steven A , Rozal Leonardo M , Mitton Jeffry B 
Published: January 2018

1. The elevational gradient in plant defense (EGPD) hypothesis posits that natural enemy pressures increase positively alongside temperature across elevational climatic gradients, thereby selecting for enhanced defenses at lower elevations while leaving plants less defended at higher elevations. Phylogenetically constrained tests of this hypothesis in tree populations are exceedingly rare. Nevertheless, the presumed presence of poorly-defended trees has been invoked as an important driver of recent pest outbreaks at higher elevations than historically common.
2. Tree age, growth rate, and size have all been correlated with levels of tree defenses. Thus, we sought to disentangle the interacting influences of these properties from possible elevational climatic effects on monoterpene composition, concentrations, and diversity of constitutive resin within three widespread pines (Pinus contorta, Pinus ponderosa, and Pinus flexilis) across a 1532 m elevational transect in the Rocky Mountains, Colorado, USA.
3. Collectively, elevation and tree properties were relatively weak predictors of defenses in P. ponderosa and P. flexilis, but explained ~ 75% of variation in monoterpene concentration and ~ 50% of diversity in P. contorta.
4. Increasing tree age had the greatest positive influence on monoterpene concentration and diversity in P. contorta, while increasing tree size had a negative influence suggesting a potential lifelong tradeoff between tree growth and defense. Elevation had a significant, negative influence on monoterpene concentration but little to no effect on monoterpene diversity in P. contorta.
5. Overall, we found some support for the EGPD hypothesis within P. contorta, but no support within P. ponderosa or P. flexilis. Our results suggest the presence of divergent conifer defense allocation strategies and drivers even among congeners growing in shared environments. An improved understanding of the controls on tree defenses, particularly possible influences of climate-based drivers, is necessary for predicting forest pest dynamics under global change scenarios.
Strengths and weaknesses of DNA-based monitoring: Assessing macroinvertebrates in 18 Finnish streams with metabarcoding and morphology
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian 
Published: January 2018

1) DNA metabarcoding holds great promise for assessment of stream ecosystems with macroinvertebrates. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.
2) We tested metabarcoding using 18 macroinvertebrate samples from Finland using four primer sets. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Morphological identification was performed to the taxonomic level at which identification was reliable following standardized protocols.
3) We identified over twice the number of taxa, with greater species-level resolution, using DNA metabarcoding than morphology-based identification. For each sample, we detected more taxa by metabarcoding than by previous morphological methods, and all four primer sets showed similarly good performance. There was a significant linear correlation between sequence abundance and the number of taxa in each sample, but the scatter was up to two orders of magnitude. Ecological status assessment indices calculated from morphological and DNA metabarcoding datasets were mostly similar, with a few exceptions. With the recent drop in sequencing costs per sample, both methods identification are currently equally expensive.
4) We used actual samples for monitoring to demonstrate that DNA metabarcoding can achieve similar results and better taxonomic resolution than current morphological identification methods. Metabarcoding has thus already become a viable and reliable invertebrate identification method for stream assessment. However, to unlock the full potential of DNA metabarcoding for ecosystem assessment key problems in current laboratory protocols and reference databases, specified in this work, will require further attention.
Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian 
Published: January 2018

1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.
2) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardized protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring.
3) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (proxy for biomass) were significantly correlated in each sample, although adjusted R2 were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately equal priced per sample to morphology-based identification.
4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve similar assessment results as those of current protocols for morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.
Correlated mutations distinguish misfolded and properly folded proteins
Authors: Woźniak Paweł , Kotulska Malgorzata , Vriend Gert 
Published: January 2018

Knowledge about the three dimensional structure of proteins is crucial in order to learn about their behavior, stability, or role as a target in drug design. Unfortunately, traditional experimental methods used in structure determination such as X-ray crystallography and NMR are costly and time-consuming. Therefore, computational methods that allow for protein structure reconstruction from sequence only are greatly desired. One of these is the recently developed direct coupling analysis (DCA) method [1, 2] which achieves the best results in residue-residue contact prediction from multiple sequence alignments only. Predicted contacts are used as restraints in the reconstruction of the three-dimensional structure of a protein. Unfortunately, the accuracy of DCA methods is on the order of 40% among the 100 strongest predicted contacts, which is insufficient for ab initio protein structure reconstruction. However, the results of DCA can support protein structure reconstruction in a different way.
Our results show that DCA can indicate the best protein structure among its structural variants by the prediction of residue-residue contacts [3]. We counted the number of correctly predicted contacts within the strongest 100 DCA predictions for a set of obsolete PDB entries and their successors and for 22 proteins for which the Decoys 'R' Us database [4] provided properly folded and misfolded structures. These numbers were related to structure similarity scores, such as RMSD or TM-score [5]. DCA correctly predicts significantly more contacts for properly folded structures than for misfolded ones. Our method works much better for structures determined with X-ray crystallography than with the NMR spectroscopy [3]. The method will not detect misfolded proteins per se, but when a protein structure experimentalist needs to choose between alternative folds for the same protein, DCA can help.
[1] F. Morcos et al., Direct-coupling analysis of residue coevolution captures native contacts across many protein families, 2011, Proc Natl Acad Sci U S A 108(49):E1293-301.
[2] C. Feinauer et al., Improving contact prediction along three dimensions, 2014, PLoS Comput Biol., 10(10):e1003847.
[3] P.P. Wozniak, G. Vriend, M. Kotulska, Correlated mutations select misfolded from properly folded proteins, 2016, Bioinformatics, (article accepted).
[4] R. Samudrala, M. Levitt, Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction, 2000, Protein Science 9: 1399-1401.
[5] Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score, 2005, Nucleic Acids Research, 33: 2302-2309.