bluuebunny/crossref_metadata_2025_split huggingface dataset:
PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers
Authors: Elbrecht Vasco , Leese Florian 
Published: January 2018

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that serve as a backbone for primer design is currently available.
2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR.
3) We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner.
4) With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.
Neogene amphibians and reptiles (Caudata, Anura, Gekotta, Lacertilia, Testudines) from south of Western Siberia, Russia and Northeastern Kazakhstan
Authors: Vasilyan Davit , Zazhigin Vladimir , Böhme Madelaine 
Published: January 2018

Background. Now-a-day territory of Western Siberia has the poorest diversity of amphibians and reptiles within the Palaearctic Realm, influenced by unfavourable climate. Less is known about the origin and emergence of it. Aside from better-explored European Neogene records of amphibians and reptiles, the Neogene herpetofauna of Western Asia is understudied. The few available studies on amphibian and reptile fossil assemblages need critical reviews and new interpretations considering the latest knowledge of the European record. The comparison with European record will provide data on palaeobiogeographic affiliations of the region as well as origin and emergence of the now-a-day fauna of Western Siberia. Beside these, a study providing overview about the earliest occurences of certain amphibian linages, that can be used for the calibration of the molecular clocks, is missing.
Methods and Results. The amphibian and reptile fauna from over 40 Western Siberian, Russia and Northeastern Kazakhian localities ranging from Middle Miocene to Early Pleistocene has been studied. In the study the published data has been considered and critically reviewed and newly interpreted. More then 50 amphibian and reptile taxa has been identified belonging to families Hynobiidae, Cryptobranchidae, Salamandridae, Palaeobatrachidae, Bombinatoridae, Pelobatidae, Hylidae, Bufonidae, Ranidae, Gekkonidae, Lacertidae and Emydidae. Palaeobiogeographic analysis for those group has been done. For 12 localities, palaeoprecipitation values have been estimated using the bioclimatic analysis of herpetofaunal assemblage.
Conclusions. The Neogene assemblage of Westren Sibera is dominated by groups (Palaeobatrachidae, Bombina, Hyla, Bufo bufo) with European affinities. A small part of assemblage includes Eastern Palaearctic taxa (e.g. Hynobiidae, Tylototriton, Bufotes viridis, R. arvalis). For several taxa (e.g. Mioproteus, Hyla, Bombina) the Western Siberian records of represent the most east Eurasian records of these groups. The most divers faunas are found in the Middle Miocene, whereas the poorest towards Early Pleistocene. This tendency could be referred to the progressive global cooling of the climate in Northern Hemisphere. Our results showed higher-amplitude changes of precipitation development in Western Siberia from Early Miocene to Pliocene, than earlier assumed.
Doubts concerning the analysis of data collected in areas surrounding badger culled areas of the RBCT
Authors: Hendy David 
Published: January 2018

In a report issued to the UK government in 2007 on the Randomised Badger Culling Trial (RBCT), it was stated that the incidence of bovine tuberculosis (TB) in cattle increased in areas surrounding where badgers were removed. It is known that badger culling perturbs badgers and this leads to increased TB transmission in and around these treated areas. The increase in TB in the surrounding areas was attributed to this process.
In this study of the RBCT analysis it was found that large TB increases in areas surrounding proactively treated areas depended heavily on adjustments made for pre-cull history. This work looks at the basis for applying these adjustments. Since it is not possible to remove statistical error in the data, which confidence intervals suggest may have been large, it is argued that it was unsafe to apply these adjustments. As such it is argued that TB increases due to perturbation in the report presented to the UK government in 2007 may have been grossly over-estimated.
The effects of cooling conditions on EDTA whole canine blood samples
Authors: Tobias Karen M , Serrano Leslie , Sun Xiaocun , Flatland Bente 
Published: January 2018

Background. Preanalytic factors such as time and temperature can have significant effects on laboratory test results. For example, ammonium concentration will increase 31% in blood samples stored at room temperature for 30 minutes before centrifugation. To reduce preanalytic error, blood samples may be placed in precooled tubes and chilled on ice or in ice water baths; however, the effectiveness of these modalities in cooling blood samples has not been formally evaluated. The purpose of this study was to evaluate the effectiveness of various cooling modalities on reducing temperature of EDTA whole blood samples.
Methods. Pooled samples of canine EDTA whole blood were divided into two aliquots. Saline was added to one aliquot to produce a packed cell volume (PCV) of 40% and to the second aliquot to produce a PCV of 20% (simulated anemia). Thirty samples from each aliquot were warmed to 37.7°C and cooled in 2 ml allotments under one of three conditions: in ice, in ice after transfer to a precooled tube, or in an ice water bath. Temperature of each sample was recorded at one minute intervals for 15 minutes.
Results. Within treatment conditions, sample PCV had no significant effect on cooling. Cooling in ice water was significantly faster than cooling in ice only or transferring the sample to a precooled tube and cooling it on ice. Mean temperature of samples cooled in ice water was significantly lower at 15 minutes than mean temperatures of those cooled in ice, whether or not the tube was precooled. By 4 minutes, samples cooled in an ice water bath had reached mean temperatures less than 4°C (refrigeration temperature), while samples cooled in other conditions remained above 4.0°C for at least 11 minutes. For samples with a PCV of 40%, precooling the tube had no significant effect on rate of cooling on ice. For samples with a PCV of 20%, transfer to a precooled tube resulted in a significantly faster rate of cooling than direct placement of the warmed tube onto ice.
Discussion. Canine EDTA whole blood samples cool most rapidly and to a greater degree when placed in an ice-water bath rather than in ice. Samples stored on ice water can rapidly drop below normal refrigeration temperatures; this should be taken into consideration when using this cooling modality.
EasyMirror and EasyImport: Simplifying the setup of a custom Ensembl database and webserver for any species
Authors: Challis Richard J , Kumar Sujai , Stevens Lewis , Blaxter Mark 
Published: January 2018

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce the EasyMirror and EasyImport pipelines to facilitate the setup and hosting of custom Ensembl genome browsers.
EasyMirror (https://github.com/lepbase/easy-mirror) makes it possible to set up a mirror of any Ensembl or Ensembl Genomes (including Bacteria, Metazoa, Fungi, Plants and Protists) species in four simple steps that can be run in less than an hour on a fresh Ubuntu installation. This tool exploits the modular nature of the Ensembl codebase to allow a site to be set up with none, some or all of the data hosted locally.
EasyImport (https://github.com/lepbase/easy-mirror) extends this approach to simplify the import of genomic data for any species from standard flat files into the Ensembl database schema, ready to be deployed using EasyMirror. All that is needed to get started is a genome fasta file and the gene models in GFF format.
Documentation for both pipelines is available at http://easy-import.readme.io
What is the best way for developers to learn new software tools? An empirical comparison between a text and a video tutorial
Authors: Käfer Verena , Kulesz Daniel , Wagner Stefan 
Published: January 2018

Tutorials for software developers are supposed to help them to adapt to new tools quickly. While in the early days of computing, mostly text tutorials were available, nowadays software developers can choose among a huge number of tutorials for almost any popular software tool. However, almost no research was conducted to understand how text tutorials differ from other tutorials, which tutorial types are preferred and, especially, which tutorial types yield the best learning experience in terms of efficiency and effectiveness.
To evaluate these questions, we converted a “proven” video tutorial for a novel software tool into a content-equivalent text tutorial. We then conducted an experiment in three groups where 42 undergraduate students from a software engineering course were commissioned to operate the software tool after using a tutorial: the first group was provided only with the video tutorial, the second group only with the text tutorial and the third group with both.
Surprisingly, the differences in terms of efficiency are almost negligible: we could observe that participants using only the text tutorial completed the tutorial faster than the participants with the video tutorial. However, the participants using only the video tutorial applied the learned content faster, achieving roughly the same bottom line performance. We also found that if both tutorial types are offered, participants clearly prefer video tutorials for learning new content but text tutorials for looking up “missed” information. So while it would be ideal if software tool makers would offer both tutorial types, we think that it is more efficient to produce only text tutorials – provided you manage to motivate developers to use them.
From science gateways to commercial solutions
Authors: Kiss Tamas , Terstyanszky Gabor 
Published: January 2018

The European CloudSME project that incorporated 24 European SMEs, besides five academic partners, has finished its funded phase in March 2016. This presentation will provide a summary of the results of the project, and will analyze the challenges and differences when developing “SME Gateways”, when compared to “Science Gateways”. CloudSME started in 2013 with the aim to develop a cloud-based simulation platform for manufacturing and engineering SMEs. The project was based around industry use-cases, five of which were incorporated in the project from the start, and seven additional ones that were added as an outcome of an open call in January 2015. CloudSME utilized science gateway related technologies, such as the commercial CloudBroker Platform and the WS-PGRADE/gUSE Gateway Framework that were developed in the preceding SCI-BUS project. As most important outcome, the project successfully implemented 12 industry quality demonstrators that showcase how SMEs in the manufacturing and engineering sector can utilize cloud-based simulation services. Some of these solutions are already market-ready and currently being rolled out by the software vendor companies. Some others require further fine-tuning and the implementation of commercial interfaces before being put into the market.
The CloudSME use-cases came from a very wide application spectrum. The project implemented, for example, an open marketplace for micro-breweries to optimize their production and distribution processes, an insole design validation service to be used by podiatrists and shoe manufacturers, a generic stock management solution for manufacturing SMEs, and also several “classical” high-performance computing case-studies, such as fluid dynamics simulations for model helicopter design, and dual-fuel internal combustion engine simulation. As the project generated significant impact and interest in the manufacturing sector, 10 CloudSME stakeholders established a follow-up company called CloudSME UG for the future commercialization of the results.
Besides the success stories, this talk would also like to highlight the difficulties when transferring the outcomes of an academic research project to real commercial applications. The different mindset and approach of academic and industry partners presented a real challenge for the CloudSME project, with some interesting and valuable lessons learnt. The academic way of supporting SMEs did not always work well with the rather different working practices and culture of many participants. Also, the quality of support regarding operational solutions required by the SMEs is well beyond the typical support services academic institutions are prepared for. Finally, a clear lack of trust in academic solutions when compared to commercial solutions was also imminent. The talk will highlight some of these challenges underpinned by the implementation of the CloudSME use-cases.
The piglet case: commensalism as a distinct category of intraspecific animal relationships
Authors: Skok Janko 
Published: January 2018

1. Interspecific relationships, termed symbiosis, are considered very diverse, while intraspecific relationships have just two categories.
2. The present classification fails to define all interactions among members of the same species, as demonstrated by observations of suckling behaviour in pigs.
3. Supporting latest findings on the suckling behaviour of piglets, I propose an extension of the classification for existing intraspecific animal relationships by adding a new distinct category: commensalism.
External kinetics of the kettlebell snatch in trained athletes
Authors: Ross James A , Keogh Justin W L , Wilson Cameron J , Lorenzen Christian 
Published: January 2018

Background. Kettlebell lifting has gained increased popularity as both a form of resistance training and as a sport, despite the paucity of literature validating its use as a training tool. Kettlebell sport requires participants to complete the kettlebell snatch continuously over prolonged periods of time. Kettlebell sport and weightlifting involve similar exercises, however their traditional uses suggest they are better suited to training different fitness qualities. This study examined the three dimensional ground reaction force (GRF) and force applied to the kettlebell over a six minute kettlebell snatch set in 12 kettlebell trained males.
Methods. During this set, VICON was used to record the kettlebell trajectory with nine infrared cameras while the GRF of each leg was recorded with a separate AMTI force plate. Over the course of the set, an average of 13.9 ± 3.3 repetitions per minute were performed with a 24 kg kettlebell. Significance was evaluated with a two-way ANOVA and paired t-tests, whilst Cohen’s F (ESF) and Cohen’s D (ESD) were used to determine the magnitude.
Results. The applied force at the point of maximum acceleration was 814 ± 75 N and 885 ± 86 N for the downwards and upwards phases, respectively. The absolute peak resultant bilateral GRF was 1746 ± 217 N and 1768 ± 242 N for the downwards and upwards phases, respectively. Bilateral GRF of the first and last 14 repetitions was found to be similar, however there was a significant difference in the peak applied force (F (1.11) = 7.42, p = 0.02, ESF = 0.45). Unilateral GRF was found have a significant difference for the absolute anterior-posterior (F (1.11) = 885.15 p < 0.0001, ESF = 7.00) and medio-lateral force vectors (F (1.11) = 5.31, p = 0.042, ESF = 0.67).
Discussion. Over the course of a single repetition there were significant differences in the GRF and applied force at multiple points of the kettlebells trajectory. The kettlebell snatch loads each leg differently throughout a repetition and performing the kettlebell snatch for six minutes will result in a reduction in peak applied force.
Mapping and studying an urban red fox (Vulpes vulpes) population using social media
Authors: Soysal Ahsennur , Hooper-Bui Linda M , Laws Edward A 
Published: January 2018

Foxes are timid yet resourceful animals that are integrated into many urban environments. Because they are elusive, collecting information about the number of urban foxes, their diet and spatial distribution, their interactions with the ecological community in their urban habitat, as well as residents’ response to them, is difficult. Involving stakeholders to participate in the data collection on wildlife via citizen science on social media is one way to overcome this complication, while simultaneously engaging residents in the ecology happening around them. Therefore, we used social media as the platform to engage the public to document and map the foxes in Baton Rouge, LA. Local residents were asked to post sightings and/or photographs of foxes they observed, with the location, onto our Facebook Page at Fox Finders of Baton Rouge, on Twitter at @FoxFindersBR, or on Twitter and Instagram with the hashtag #findfoxlsu. This information was added onto an ArcGIS story map. Types of public responses and engagement over time were also measured. The authors clarified people’s misconceptions about foxes when questions were asked on our Facebook Page. On-site observations and trail cameras were also used in common locations to monitor the urban foxes.
While we received only one fox sighting via Instagram and Twitter each, our Facebook Page generated 1132 “likes” and an average of 14% Page Engagement Rate during the first eight months. Along with Baton Rouge, people from 384 different cities and 16 countries have engaged with the page. In addition, 180 sightings of about 140 different foxes—including 61 photographs and eight videos—were submitted, with eight of the sightings coming from areas surrounding the city—outside the study area. Seven common fox locations in the city were identified, all of which were adjacent to a source of water. Results showed that urban foxes have become habituated to the urban environment and may serve as an umbrella species. From the many positive and enthusiastic feedback we have received on our Facebook Page, our research model successfully promoted citizen science by easily connecting residents to science, enabling them to engage with our team and local residents directly to learn about the wildlife around them, efficiently documented and mapped many local urban foxes, and provided a preliminary count of foxes for benchmark data for future studies.
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 native 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 m 2 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 checked. Comparative soil nutrient experiments were done for the substrates of the rhizomes of A. evecta, soil under the rhizomes, and bare soils to check whether the rhizomes are chemically different than other microenvironments.
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.
Discussion. Angiopteris evecta is facilitating 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, field observations suggest that A. evecta has fast decomposing leaves, which can induce the germination and the recruitment of M. calvescens in forest understories dominated by A. evecta by preventing the accumulation of leaf litter on the ground and enabling more sunlight to reach to the seed bank. The germination of trees in tropical rainforest is known to be limited by the availability for potassium, suggesting that the rhizomes of A. evecta might be favored chemically. However, further studies are needed to verify whether potassium is a limiting factor of the germination of M. calvescens. 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 in some places is especially required.