bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential gene expression in blastocysts following pronuclear transfer
Authors: Morrow Edward H , Ingleby Fiona C
Published: January 2018

Nuclear transfer techniques (a.k.a. mitochondrial replacement therapies) are currently under development to provide a route to eliminating particular instances of mitochondrial disease from the germline. Before these kinds of techniques are implemented clinically it is of primary concern that their safety and efficacy is established. In a recent paper, Hyslop et al (2016) utilized a specific version of pronuclear transfer (PNT) to investigate the consequences for gene expression in the developing embryo, which may indicate whether or not developmental pathways have been perturbed. However, the study was only able to include a small number of blastocysts within each treatment group, although a larger number of single cell expression profiles from each blastocyst were acquired. Using simulated datasets we show that the size and experimental design of this study cannot provide conclusive evidence that expression profiles of manipulated or control samples are indistinguishable from one another due to low power.
Drift net performance for larval fish sampling in rivers
Authors: Couch Alan J , Dyer Fiona , Lintermans Mark , Ross-Magee Pat
Published: January 2018

Deploying small-mesh drift nets in rivers is a well-established method for sampling drifting fish larvae and eggs. Quantitative comparisons are sometimes made on the basis of numbers of larvae captured per unit volume or time. In this study a GoPro ™ camera was mounted inside the drift net to record the change in flow over time (1 to 5 minute intervals for 3 hours). Although a small number of net nights (7 nights at 3 locations) were sampled, variance in the change in flow within and between sites was observed – even during soak times as little as 2 hours. In one case there was almost no change in flow over 180 minutes but at the most extreme, the flow dropped from 8.9 m3/min to 1.5 m3/min in just 160 minutes. Variance is probably due to the level of suspended particulates at different sites or times. If volumetric or temporal estimates are made on the basis of total flow only they could in some cases be misleading and at worst make comparisons almost meaningless. While there are dedicated data logging flow meters available they are prohibitively expensive for routine sampling. Researchers could consider the method used in this study to cost effectively assess the decay in net performance during sampling.
GreenScaler: Automatically training software energy models with big data
Authors: Chowdhury Shaiful Alam , Gil Stephanie , Romansky Stephen , Hindle Abram
Published: January 2018

Software energy consumption is a performance related non-functional requirement that complicates building software on mobile devices today. Energy hogging applications are a liability to both the end-user and software developer. Measuring software energy consumption is non-trivial, requiring both equipment and expertise, yet many researchers have found that software energy consumption can be modelled. Prior works have hinted that with more energy measurement data one can make more accurate energy models but this data was expensive to extract because it required energy measurement of running test cases (rare) or time consuming manually written tests. We address these concerns by automatically generating test cases to drive applications undergoing energy measurement. Automatic test generation allows a model to be continuously improved in a model building process whereby applications are extracted, tests are generated, energy is measured and combined with instrumentation to train a grander big-data model of software energy consumption. This continuous process has allowed the authors to generate and extract measurements from hundreds of applications in order to build accurate energy models capable of predicting the energy consumption of applications without end-user energy measurement. We clearly show that models built from more applications reduce energy modelling error.
Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria in wastewater treatment plants and agriculture fields of northern China
Authors: Hu Zhen , Ma Ru
Published: January 2018

Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process, which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) of northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria, due to their higher abundance and diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time and optimum environment (low NH4+ and high NO2- content) were suitable for the growth of M. oxyfera bacteria. In addition, the distribution and diversity of M. oxyfera bacterial might be related to geographical regions.
A statistical model for epigenetic control of miRNAs
Authors: Barros de Andrade e Sousa Lisa , Marsico Annalisa
Published: January 2018

microRNAs are small, non-coding RNAs involved in post-transcriptional gene regulation. Since the dysregulation of only a few miRNAs can affect many biological pathways, miRNAs are thought to play a key role in cancer development and can be used as biomarkers for cancer diagnosis and prognosis. In order to understand how miRNA dysregulation leads to a cancer phenotype it is important to determine the basic regulatory mechanisms that drive miRNA expression. Although much is known about miRNA-mediated post-transcriptional regulation, little is known about the epigenetic control of miRNAs. Here, we performed cell-line specific miRNA promoter predictions and built a classification model for expressed and non-expressed miRNAs based on several epigenetic features, e.g. histone marks and DNA methylation at both, miRNA promoters and around miRNA hairpins. We were able to classify intragenic and intergenic miRNAs with an accuracy of 79% and 85%, respectively, and identified the most important features for classification via feature selection. Surprisingly, we found that DNA methylation seems to have a dual role in regulating miRNA expression at transcriptional level: at promoters, high levels of DNA methylation correlate with transcriptional repression, while around miRNA hairpins high levels of DNA methylation have a positive impact on the expression level of the mature miRNA.
Collecting systematic, introspective reports of pharmacological effects and side-effects
Authors: Sarma Gopal P
Published: January 2018

The study of subjective, first-person experience is a topic with both philosophical and practical implications. In this article, I discuss the value of collecting a critical mass of prose or verbal descriptions of introspectively determined, subjective effects of pharmacological agents. I suggest that datasets of introspective reports fit in the modern research landscape at the intersection of biomedical informatics and the emerging discipline of contemplative neuroscience. I compare the current proposal to Descriptive Experience Sampling (DES), discuss relevant methodological and conceptual issues in the study of introspection, and provide a list of questions for directing future investigation.
A simple photographic classification of protruding ears
Authors: Lopes-Santos JA
Published: January 2018

Backgroud: Protruding ear is the most commonly found auricular populational deformity with significant social consequences. The problem is clearly perceptible in frontal facial images, but a simple photographic classification for prominence has not yet been defined. Methods: Frontal facial images of forty patients with protruding ears and 102 controls were prospectively collected. A rectangle was drawn in each ear, involving its full visible anatomy. The height of each rectangle was divided by its width in each ear. Results: Results show a trend for higher values in the protruding ears group when compared to controls for both ears. Discussion: This finding can be useful for the classification of this auricular deformity.
What should mobile app developers do about machine learning and energy?
Authors: McIntosh Andrea K , Hindle Abram
Published: January 2018

Machine learning is a popular method of learning functions from data to represent and to classify sensor inputs, multimedia, emails, and calendar events. Smartphone applications have been integrating more and more intelligence in the form of machine learning. Machine learning functionality now appears on most smartphones as voice recognition, spell checking, word disambiguation, face recognition, translation, spatial reasoning, and even natural language summarization. Excited app developers who want to use machine learning on mobile devices face one serious constraint that they did not face on desktop computers or cloud virtual machines: the end-user’s mobile device has limited battery life, thus computationally intensive tasks can harm end-user’s phone availability by draining batteries of their stored energy. How can developers use machine learning and respect the limited battery life of mobile devices? Currently there are few guidelines for developers who want to employ machine learning on mobile devices yet are concerned about software energy consumption of their applications. In this paper we combine empirical measurements of many different machine learning algorithms with complexity theory to provide concrete and theoretically grounded recommendations to developers who want to employ machine learning on smartphones.
Reanalyzing Head et al. (2015): Investigating the robustness of widespread p-hacking
Authors: Hartgerink Chris H
Published: January 2018

Head et al. (2015b) provided a large collection of p-values that, from their analytic perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. They correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that systematically more p-values are reported to two decimal places and the disputable selection of the bins .04 < p < .045 versus .045 < p < .05, I did not exclude p = .045 and p = .05, and I adjusted the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we take into account a second-decimal reporting tendency. Taking into account reporting tendencies is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, given the weight of the findings by Head et al. (2015b), it is important that these findings are robust to choices that can be debated, if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this reanalysis, this does not mean that there is no p-hacking at all. These results nuance the conclusion by Head et al. (2015b), indicating that the results are not robust and that the evidence for widespread left-skew p-hacking is ambiguous at best.
Genotyping of evolving prokaryotic populations
Authors: Zojer Markus , Schuster Lisa N , Schulz Frederik , Pfundner Alexander , Horn Matthias , Rattei Thomas
Published: January 2018

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequent alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, indels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a combination of different tools. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a vcf file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver (Afgan et al. 2016) , which is accessible at http://galaxy.csb.univie.ac.at.
Host plant affects morphometric variation of Diaphorina citri (Hemiptera: Liviidae)
Authors: Paris Thomson M. , Allan Sandra A. , Hall David G. , Hentz Matthew G. , Hetesy Gabriella , Stansly Philip A.
Published: January 2018

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is one of the most serious citrus pests worldwide due to its role as vector of huanglongbing or citrus greening disease. While some optimal plant species for ACP oviposition and development have been identified, little is known of the influence of host plants on ACP size and shape. Our goal was to determine how size and shape of ACP wing and body size varies when development occurs on different host plants in a controlled rearing environment. ACP were reared on six different rutaceous species; Bergera koenigii, Citrus aurantifolia, Citrus macrophylla, Citrus maxima, Citrus taiwanica and Murraya paniculata. Adults were examined for morphometric variation using traditional and geometric analysis based on 12 traits or landmarks. ACP reared on C. taiwanica were consistently smaller than those reared on the other plant species. Wing aspect ratio also differed between C. maxima and C. taiwanica. Significant differences in shape were detected with those reared on M. paniculata having narrower wings than those reared on C. macrophylla. This study provides evidence of wing size and shape differences of ACP based on host plant species which potentially may impact dispersal. Further study is needed to determine if behavioral and physiological differences are associated with the observed phenotypic differences.
Microbial communities mediating algal detritus turnover under anaerobic conditions
Authors: Morrison Jessica M , Murphy Chelsea L , Baker Kristina , Zamor Richard , Nikolai Steve J , Wilder Shawn , Elshahed Mostafa S , Youssef Noha H
Published: January 2018

Background. Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results. Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13-16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales. Conclusions. Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process.
10 simple rules for experimental design in ecology
Authors: Saini Neha
Published: January 2018

This article contains proposed guidelines for ensuring proper experimental design in ecology. In a sequential fashion, it is important to begin with stating a hypothesis, followed by clearly defining terms and choosing appropriate samples and parameters. Following the tips and guidelines in order will help guide the researchers thought process when designing an ecological experiment. Consult the listed citations for in-depth explanations when required. The rules may be generalized to other fields of science.
10 simple rules for developing the best experimental design in biology
Authors: Joseph Angela
Published: January 2018

These 10 simple rules were designed to help researchers develop an effective experimental design in ecology that will help yield meaningful results. These rules were based off of four articles which presented distinctive views on the expectations of experimental design along with common mistakes which are often overseen. These rules will act as a guide for researchers to determine whether or not different factors were considered in the construction of their experimental design. It will also help editors and readers deduce whether the experimental design used in an experiment was well designed or not and how it could be improved.
Foliar fungal communities strongly differ between habitat patches in a landscape mosaic
Authors: Fort Thomas , Robin Cécile , Capdevielle Xavier , Delière Laurent , Vacher Corinne
Published: January 2018

Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores.

We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the ITS2 region.

In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre.

These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.
Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae
Authors: Cabrales-Arellano Patricia , Islas-Flores Tania , Thomé Patricia E. , Villanueva Marco A.
Published: January 2018

Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian-dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, lugol's iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 µM indomethacin after 6 days of exposure, and 10-25 µM after 7 days. Strobilation under optimal conditions reached 80-100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.
Standardizing unique molecular identifiers in SAM flags would benefit more than RNA-Seq
Authors: Roberson Elisha D
Published: January 2018

Unique Molecular Identifiers (UMIs) have been incorporated into RNA-Seq experiments to overcome issues with abundance estimation from samples that may have many PCR amplification cycles. However, the use of UMIs in many different types of sequencing experiments could be beneficial, including amplicon sequencing, ATAC-Seq, and ChIP-Seq. Furthermore, UMIs help to overcome artifacts in high-coverage DNA-Seq, and would enable more accurate RNA-Seq genotyping and allele-specific expression calculation. The main advantage of using UMIs is that identical molecules that are true PCR duplicates can be discerned from unique molecules with identical break points.
How to raise H.illucens in captivity: a protocol
Authors: Marzouk Sammer
Published: January 2018

This is a study to assess the near perfect conditions in order to raise the greatest amount of Black Soldier Flies into adulthood. This is so that the amount of uses as Black Soldier flies as model organism increases. All genres of Black Soldier Flies were looked at in this study to develop the protocol. The flies that were chosen were best represented to reflect the abilities and gender of the natural amount of Black Soldier flies in the wild. Potential subjects were then tested with the different types of p variables such as food and sunlight. At this time all the Black Soldier flies were kept in specific conditions and tested with different types of habitats. These habitats reflected the living conditions of the flies in the natural plain. After all the data was compiled, it was aggregated and used to find the best living conditions for the Black Soldier fly as a model organism.
The wild tomato species Solanum chilense shows local variation in pathogen resistance between geographically distinct populations
Authors: Stam Remco , Scheikl Daniela , Tellier Aurélien
Published: January 2018

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens, however evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity is very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.
A reconstruction of the palaeoecology and environmental dynamics of the Bahariya Formation of Egypt
Authors: Ijouiher Jamale
Published: January 2018

The Bahariya formation is one of the most productive in Africa in terms of fossil material. This paper conducts a comprehensive review of the flora & fauna and creates ecological reconstruction of this assemblage based on modern analogues. There is no evidence that most of the major vertebrate components of this biome were mangrove adapted taxa & most were commuters from the surrounding mainland. The high number of theropod species is overstated as niche partitioning between them lowers the predator/prey ratios; and is a result of this habitat developing from the broader North African ecosystems with its limited vegetation. The populations of most were also limited; further offsetting the predator/prey imbalance. The rarity of ornithopods can now be seen as a result of aridity and simplified forest structure. Crustaceans can be confirmed as forming a major trophic base, but new emphasis needs to be placed on gastropods as potential ecosystem engineers. Although some questions still remain concerning missing faunal elements and the difficulty in differentiate local population patterns from general population trends in this ecosystem as a whole; Bahariya’s reportedly substantial productivity, and later over-productivity, can now be confirmed.
Community assembly and functional leaf traits mediate precipitation use efficiency of alpine grasslands along environmental gradients on the Tibetan Plateau
Authors: Li Shaowei , Wu Jianshuang
Published: January 2018

The alpine grasslands on the Tibetan Plateau are sensitive and vulnerable to climate change. However, it is still unknown how precipitation use efficiency (PUE), the ratio of ANPP to precipitation, is related to community assembly of plant species, functional groups or traits for the Tibetan alpine grasslands along actual environmental gradients. We conducted a multi-site field survey at grazing-excluded pastures across meadow, steppe and desert-steppe to measure aboveground biomass in August, 2010. We used species richness, the Shannon diversity index, and cover-weighted functional group composition (FGC) of 1-xerophytes, 2-mesophytes, and 3-hygrophytes to describe community assembly at the species level; and chose community-level leaf area index (LAIc ), specific leaf area (SLAc ), and species-mixed foliar δ13C to quantify community assembly at the functional trait level. Our results showed that PUE decreased with increasing accumulated active temperatures (AccT) when daily temperature average is higher than 5°C, but increased with increasing climatic moisture index, which was demined as the ratio of growing season precipitation (GSP) to AccT. We also found that PUE increased with increasing species richness, the Shannon diversity index, FGC and LAIc ,decreased with increasing foliar δ13C, and had no relation with SLAc at the regional scale. Neither soil total nitrogen nor organic carbon has no influence on PUE at the regional scale. The community assembly of the Shannon index, LAIc and SLAc together accounted for 46.3 % of variance in PUE, whilst climatic moisture index accounted for 47.9 % of variance in PUE at the regional scale. This implies that community structural properties and plant functional traits can mediate the sensitivity of alpine grassland productivity in response to climate change. Thus, a long-term observation on community structural and functional changes is recommended for better understanding the response of alpine ecosystems to regional climate change on the Tibetan Plateau.
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
Authors: Butterfield Cristina N , Li Zhou , Andeer Peter F , Spaulding Susan , Thomas Brian C , Singh Andrea , Hettich Robert L , Suttle Kenwyn B , Probst Alexander J , Tringe Susannah G , Northen Trent , Pan Chongle , Banfield Jillian F
Published: January 2018

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
Animal movement analysis through residence in space and time
Authors: Torres Leigh G , Orben Rachael A. , Tolkova Irina , Thompson David R
Published: January 2018

Identification and classification of behavior states in animal movement data can be complex, temporally biased, time-intensive, scale-dependent, and unstandardized across studies and taxa. Large movement datasets are increasingly common and there is a need for efficient methods of data exploration that adjust to the individual variability of each track. We present the Residence in Space and Time (RST) method to classify behavior patterns in movement data based on the concept that behavior states can be partitioned by the amount of space and time occupied in an area of constant scale. Using normalized values of Residence Time and Residence Distance within a constant search radius, RST is able to differentiate behavior patterns that are distance-intensive (e.g., area restricted search), time-intensive (e.g., rest), and transit (short time and distance). We use grey-headed albatross (Thalassarche chrysostoma) GPS tracks to demonstrate RST’s ability to classify behavior patterns and adjust to the inherent scale and individuality of each track. Next, we evaluate RST’s ability to discriminate between behavior states relative to other classical movement metrics. We then sub-sample albatross track data to illustrate RST’s response to less temporally resolved data. Finally, we evaluate RST’s performance using datasets from four taxa with diverse ecology, functional scales, ecosystems, and data-types. We conclude that RST is a robust, rapid, and flexible method for detailed exploratory analysis and meta-analyses of behavioral states in animal movement data based on its ability to integrate distance and time measurements into one descriptive metric of behavior groupings. Given the increasing amount of animal movement data collected, it is timely and useful to implement a consistent metric of behavior classification to enable efficient and comparative analyses. Overall, the application of RST to objectively explore and compare behavior patterns in movement data can enhance our fine- and broad- scale understanding of animal movement ecology.
Urban forests sustain diverse carrion beetle assemblages in the New York City metropolitan area
Authors: Fusco Nicole , Zhao Anthony , Munshi-South Jason
Published: January 2018

Urbanization is an increasingly pervasive form of land transformation that reduces biodiversity of many taxonomic groups. Beetles (Order: Coleoptera) exhibit a broad range of responses to urbanization, likely due to the high functional diversity in this order. Carrion beetles (Family: Silphidae) provide an important ecosystem service by promoting decomposition of small-bodied carcasses, and have previously been found to decline due to forest fragmentation caused by urbanization. However, New York City (NYC) and many other cities have fairly large continuous forest patches that support dense populations of small mammals, and thus may harbor relatively robust carrion beetle communities in city parks. In this study, we investigate carrion beetle community composition, abundance and diversity in forest patches along an urban-to-rural gradient spanning the urban core (Central Park, NYC) to outlying rural areas. Additionally, we conducted a more in-depth study of the carrion beetle community at a single suburban site in Westchester County, NY that was intensively surveyed in the early 1970’s. We collected a total of 2,170 carrion beetles from eight species at 13 sites along this gradient. We report little to no effect of urbanization on carrion beetle diversity, although two species were not detected in any urban parks. Nicrophorus tomentosus was the most abundant species at all sites and seemed to dominate the urban communities, potentially due to its generalist habits and shallower burying depth. Variation between species in body size, habitat specialization, and area of largest continuous forest tract also did not influence carrion beetle communities. Lastly, we found few significant differences between 10 carrion beetle relative abundance between the early 1970’s and 2015 at a single site in Westchester County, NY, although two of the rare species in the early 1970’s were not detected in 2015. These results indicate that NYC’s forested parks have the potential to sustain carrion beetle communities and the ecosystem services they provide.
Urban forests sustain diverse carrion beetle assemblages in the New York City metropolitan area
Authors: Fusco Nicole , Zhao Anthony , Munshi-South Jason
Published: January 2018

Urbanization is an increasingly pervasive form of land transformation that reduces biodiversity of many taxonomic groups. Beetles exhibit a broad range of responses to urbanization, likely due to the high functional diversity in this order. Carrion beetles (Order: Coleoptera, Family: Silphidae) provide an important ecosystem service by promoting decomposition of small-bodied carcasses, and have previously been found to decline due to forest fragmentation caused by urbanization. However, New York City (NYC) and many other cities have fairly large continuous forest patches that support dense populations of small mammals, and thus may harbor relatively robust carrion beetle communities in city parks. In this study, we investigated carrion beetle community composition, abundance and diversity in forest patches along an urban-to-rural gradient spanning the urban core (Central Park, NYC) to outlying rural areas. We conducted an additional study focusing on comparing the current carrion beetle community at a single suburban site in Westchester County, NY that was intensively surveyed in the early 1970’s. We collected a total of 2,170 carrion beetles from eight species at 13 sites along this gradient. We report little to no effect of urbanization on carrion beetle diversity, although two species were not detected in any urban parks. Nicrophorus tomentosus was the most abundant species at all sites and seemed to dominate the urban communities, potentially due to its generalist habits and shallower burying depth compared to the other beetles surveyed. Variation between species in body size, habitat specialization, and % forest area also did not influence carrion beetle communities. Lastly, we found few significant differences in relative abundance of 10 different carrion beetle species between 1974 and 2015 at a single site in Westchester County, NY, although two of the rare species in the early 1970’s were not detected in 2015. These results indicate that NYC’s forested parks have the potential to sustain carrion beetle communities and the ecosystem services they provide.
Being in the zone: Using behavioral and EEG recordings for the indirect assessment of flow
Authors: Nuñez Castellar Elena Patricia , Antons Jan-Niklas , Marinazzo Daniele , van Looy Jan
Published: January 2018

As such, video games are enjoyed most when the level and speed of the game match the players’ skills. An optimal balance between challenges and skills triggers the subjective experience of “flow”, a focused motivation leading to a feeling of spontaneous joy. Here we present the validation of a novel technique to indirectly assess the extent to which subjects experience flow during real game play by assessing attentional engagement; first behaviorally and in a second stage by means of electroencephalogram (EEG) recordings. An auditory novelty oddball paradigm was implemented as a secondary task while subjects played in three conditions: Boredom, Frustration and Flow. We found higher reaction times and error rates in the Flow condition. In a second stage we used advanced techniques to do source reconstruction and to investigate signal changes on both the temporal and frequency domain. EEG analysis revealed a response-locked fronto-central negative deflection significantly delayed during flow, likely signaling the need of re-allocation of attentional resources. Frequency domain analyses revealed significant power increase only in the alpha band for the flow condition. We believe that frontal alpha changes recorded as maximal at the mid- frontal lines during flow might be related with reward related processing
Sedation levels in dogs: a validation study
Authors: Wagner Marika C , Hecker Kent G , Pang Daniel
Published: January 2018

The aim of this study was to assess validation evidence for a sedation scale for dogs. We hypothesized that the chosen sedation scale would be unreliable when used by different raters and show poor discrimination between sedation protocols. A sedation scale was used to score 62 dogs scheduled to receive sedation at two veterinary clinics in a prospective trial. Scores recorded by a single observer were used to assess internal consistency and construct validity of the scores. To assess inter-rater reliability, video-recordings of sedation assessment were randomized and blinded for viewing by 5 raters untrained in the scale. Videos were also edited to allow assessment of inter-rater reliability of an abbreviated scale by 5 different raters. Both sedation scales exhibited excellent internal consistency and very good inter-rater reliability (full scale, ICCsingle = 0.95; abbreviated scale, ICCsingle = 0.94). The full scale discriminated between the most common protocols: dexmedetomidine-hydromorphone (11 [1-18], n = 20) and acepromazine-hydromorphone (5 [0-15], n = 36, p = 0.02). The hypothesis was rejected. Full and abbreviated scales showed excellent internal consistency and very good reliability between multiple untrained raters. The full scale differentiated between levels of sedation.
First visual record of rare purple dogwhelks (Nucella lapillus) on the Atlantic coast of Nova Scotia, Canada
Authors: Ehlers Sonja M. , Ellrich Julius A.
Published: January 2018

The dogwhelk Nucella lapillus is a rocky intertidal gastropod of the North Atlantic coast. Individual shell color varies. Common colors range between white and brown, with darker dogwhelks being more affected by heat stress than lighter-colored conspecifics. Other reported shell colors are black, mauve, pink, yellow, and orange from European coasts, red and grey from the Bay of Fundy coast of New Brunswick and Nova Scotia (Canada), and purple, black, gray, yellow, and orange from the coasts of Maine and Massachusetts (USA), with purple being considered as a rare color. On the Atlantic coast of Nova Scotia, dogwhelks are active from April until November, but information on dogwhelk shell color is missing for this coast. On 16 June 2016, we found two purple dogwhelks in the mid-to-high intertidal zone of a moderately wave-exposed rocky shore near Duncans Cove, on the Atlantic coast of Nova Scotia while collecting dogwhelks (n= 1000) for manipulative field experiments. All other dogwhelks collected on that day were of common white and brown colors. During earlier dogwhelk collections in Atlantic Nova Scotia (between 2011-2013) and field surveys in Duncans Cove (between 2014-2016), we did not find any purple dogwhelks, indicating the rareness of this color in that region. Interestingly, the purple dogwhelks were detected on a relatively cool day (12.3 ± 0.4 °C, mean ± se, n= 96 temperature measurements) compared to the intertidal temperatures of all other survey days (≥ 18.2 ± 0.5 °C), suggesting that purple dogwhelks may find it less thermally stressful to venture out of crevices and macroalgal cover under relatively cool temperatures. Our observations provide the first visual record of rare purple dogwhelks on the Atlantic coast of Nova Scotia, Canada.
Precipitation and aridity index regulating spatial patterns of vegetation production and species diversity based on alpine grassland transect, Tibetan Plateau
Authors: Sun Jian
Published: January 2018

Although the relationship between the aboveground net primary production (ANPP) and speciesdiversity (SR) have been widely reported, there is considerable disagreement about the fitting patterns of SR–ANPP, which has been variously described as ‘positive’, ‘negative’, ‘unimodal’, ‘U-shaped’ and so on. Not surprisingly, the effect-factors including precipitation, aridity index and geographic conditions (e.g.,altitude, longitude and latitude) on ANPP and SR continue to interest researchers, especially the effects at high altitude regions. We investigated ANPP and SR from 113 sampled sites (399 plots) across alpine meadow and steppe in the Tibetan Plateau, which included Tibet, Qinghai and Sichuan province. The effects of various environmental factors (precipitation, temperature, aridity index, altitude, longitude,latitude and vegetation type on SR and ANPP) were explored. The results indicate that a unimodal pattern was confirmed between ANPP and SR in alpine steppe (R 2 =0.45, P <0.0001), alpine meadow ( R 2 =0.4, P <0.0001), and all samples across alpine grassland ( R 2 =0.52, P <0.0001). For the aboveground net primary production, the appropriate precipitation and aridity is 600mm and 42, respectively. Under thesame moisture conditions, the maximum value of diversity is 0.75. Longitude ( R 2 =0.69, P <0.0001) and altitude ( R 2 =0.48, P <0.0001) have positive and negative effects on aboveground net primary production, and a similar relationship exists with diversity ( R 2 =0.44, P <0.0001 and R 2 =0.3, P <0.0001).The same patterns of diversity and production responding to precipitation and the aridity index were evident in alpine steppe and meadow, and a unimodal pattern was confirmed between ANPP and SR in both locations.
An exploratory study of the state of practice of performance testing in Java-based open source projects
Authors: Leitner Philipp , Bezemer Cor-Paul
Published: January 2018

The usage of open source (OS) software is nowadays wide- spread across many industries and domains. While the functional quality of OS projects is considered to be up to par with that of closed-source software, much is unknown about the quality in terms of non-functional attributes, such as performance. One challenge for OS developers is that, unlike for functional testing, there is a lack of accepted best practices for performance testing. To reveal the state of practice of performance testing in OS projects, we conduct an exploratory study on 111 Java-based OS projects from GitHub. We study the performance tests of these projects from five perspectives: (1) the developers, (2) size, (3) organization and (4) types of performance tests and (5) the tooling used for performance testing. First, in a quantitative study we show that writing performance tests is not a popular task in OS projects: performance tests form only a small portion of the test suite, are rarely updated, and are usually maintained by a small group of core project developers. Second, we show through a qualitative study that even though many projects are aware that they need performance tests, developers appear to struggle implementing them. We argue that future performance testing frameworks should provider better support for low-friction testing, for instance via non-parameterized methods or performance test generation, as well as focus on a tight integration with standard continuous integration tooling.