bluuebunny/crossref_metadata_2025_split huggingface dataset:
VSEARCH: a versatile open source tool for metagenomics
Authors: Rognes Torbjørn , Flouri Tomáš , Nichols Ben , Quince Christopher , Mahé Frédéric 
Published: January 2018

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.
Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.
Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e. format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.
Discussion. VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
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.
High non publication rate from publication professionals hinders evidence-based publication practices: a replication study in Europe
Authors: Marchington Jacqueline M 
Published: January 2018

Background: Although publication professionals plan and facilitate the timely and high-quality reporting of clinical trial results, it has been previously shown that they are not as forthcoming when it comes to publishing their own professional research. The publication rate from abstracts presented at the Annual Meeting of the International Society for Medical Publication Professionals (ISMPP) has been shown to be 2.4%. We performed a replication study based on the European Meeting of ISMPP to determine the equivalent publication rate.
Methods: ISMPP European Meeting abstract lists (November 2011–January 2016), were searched in July 2016 and extracted into a copy of the original study spreadsheet. MEDLINE was searched in August 2016 to determine the publication rate.
Results: From 2011 to 2016, 76 abstracts were submitted of which 60 were accepted (78.9%). We found three corresponding publications (publication rate 5.0%). Most studies were observational (50/60; 83.3%) and most abstracts included employees of medical communications agencies as authors (50/60; 83.3%). Most researchers were based in Europe (165/222; 74.3%) or the US (53/222; 23.9%).
Discussion: This study confirms previous findings that the publication rate of member research from ISMPP meetings in the peer-reviewed literature is low. Members of ISMPP, and of other organizations who aspire to set professional standards, should be encouraged to conduct robust research and share it with the academic community.
The Australian science gateways ecosystem
Authors: Barker Michelle 
Published: January 2018

This talk examines Australian government initiatives to facilitate the development of science gateways, and identifies the successes and challenges in this approach.
Since 2011 the Australian Government has funded the development of science gateways through the National eResearch Collaborative Tools and Resources ( NeCTAR ) program (www.nectar.org.au). NeCTAR has funded the development of twelve science gateways in diverse disciplines that provide highly collaborative, research-domain oriented, integrative research software infrastructure to meet researcher-defined needs. The virtual laboratories enable over 10,000 users to access data, models, analytical and workflow tools through a single online platform.
NeCTAR also funds the Research Cloud , which provides computing infrastructure, software and services to enable Australia’s research community to store, access, and run data, remotely, rapidly and autonomously. NeCTAR Cloud’s self-service structure allows over 7,500 users to access their own data at any time and collaborate with others from their desktop in a fast and efficient way. NeCTAR aims to enhance research collaboration through the development of eResearch infrastructure.
This paper explores the structure of the NeCTAR Virtual Laboratory program, its successes and challenges, and future plans. Key features of the program include creation of platforms where tools, models and data meeting, enabling automating and sharing of research methodologies and democratisation of access. As such, the Virtual Laboratories deliver transformative research impacts and are exemplars for sector adoption of capability. Virtual Laboratories exist in disciplines including climate and weather science, genomics, characterisation, biodiversity and climate change, astronomy, human communication science, marine studies, geophysics, endocrine disorders, and cultural studies.
Some of the enabling factors include governance structures that emphasise ownership of the Virtual Laboratories by the research community, strong user engagement in development and a support program that assists in enabling issues across the Virtual Laboratories. This has run project in areas such as provenance, authentication, security, data movement and user support. Challenges exist in sustaining a strategic approach to research software infrastructure, particularly strengthening the focus on shared research software services, improving research software quality, reliability and sustainability, and building capability within the research communities.
This paper will also provide opportunities for comparison and identification of potential alignment with other national/regional/disciplinary programs. Europe and USA have both initiated funding programs that have some similarities to the NeCTAR Virtual Laboratories program; however, these also take some different approaches on some issues.
The effects of exercise-induced heat stress on cognitive function in firefighters
Authors: Williams-Bell F. Michael , McLellan Tom M , Murphy Bernadette A 
Published: January 2018

Background. Firefighting requires tremendous cognitive demands including assessing emergency scenes, executing critical decisions, and situational awareness of their surroundings. The aim of this study was to determine the effects of differing rates of increasing core temperature on cognitive function during exercise-induced heat stress.
Methods. Nineteen male firefighters were exposed to repeated cognitive assessments, randomized and counter-balanced, in 30°C and 35°C and 50% humidity. Participants performed treadmill walking (4.5 km.h-1 and 2.5% grade) with cognitive function assessed before exercise (PRE), after mounting the treadmill (Cog 1), at core temperatures of 37.8°C (Cog 2), 38.5°C (Cog 3), and 39.0°C (Cog 4), after dismounting the treadmill (POST), and following an active cooling recovery to a core temperature of 37.8°C (REC). The cognitive tests implemented at PRE and POST were spatial working memory (SWM), rapid visual information processing (RVP), and reaction time (RTI) while paired associates learning (PAL) and spatial span (SSP) were assessed at Cog 1, Cog 2, Cog 3, and Cog 4. All five cognitive tests were assessed at REC.
Results. Planned contrasts revealed that SSP and PAL were impaired at Cog 3, with SSP also impaired at Cog 4 compared to Cog 1. REC revealed no difference compared to Cog 1, but increased errors compared to Cog 2 for PAL.
Conclusions. The decrements in cognitive function observed at a core temperature of 38.5°C are likely attributed to the cognitive resources required to maintain performance being overloaded due to increasing task complexity and external stimuli from exercise-induced heat stress. The addition of an active cooling recovery restored cognitive function to initial levels.
A comparison of models for interval-censored plant cover data, with applications to monitoring schemes
Authors: Pescott Oliver L , Jitlal Mark , Smart Simon M , Walker Kevin J , Roy David B , Freeman Stephen N 
Published: January 2018

Plant cover data collected by monitoring schemes are often expressed on interval-censored scales to reduce field effort. Existing statistical approaches to such data may not make full use of available information, or may both induce bias and assume more precision than may be warranted, e.g. by analysing mid-points and disregarding the spread of observations within a class.
We compare four approaches to modelling such data: two established methods (the proportional odds model and generalised linear mixed models) and two novel methods that explicitly accommodate the interval-censored nature of much data on plant cover. Of the latter, the first is a maximum likelihood (ML) approach that incorporates knowledge of the metric interval in which each datum lies. The second uses a Bayesian approach to incorporate interval-censoring and random effects to account for variation in annual changes between sites. All four methods are compared using data simulated with parameter values derived from analysis of a long-term monitoring dataset.
We demonstrate that model choice can influence the quality of statistical inference, particularly between models that make simplifications for convenience of fitting, and those which combine realistic distributional assumptions with accommodation of imprecise observations. A comparison of three of the methods demonstrated that all provide good accuracy and increasing precision over time. A comparison of power across the three frequentist approaches showed higher power for the novel ML approach. This is likely to be due to this non-hierarchical method underestimating residual variance. The Bayesian model is not directly comparable, but the measure of belief in a negative trend considered here was generally high, providing gradual increases in the believability of a decline with increasing time, number of sites, initial abundance, and larger effect sizes.
Our results suggest that the use of hierarchical models for plant monitoring schemes, conveniently applied in a Bayesian context, will help to bring greater realism and sensitivity to assessments of population change, and allow the use of more of the underlying information contained within cover data. Interval-censored methods will also allow for the integration of long-term plant datasets collected according to different cover scales, as well as presence/absence data.
Technology to limit the available number of chosen-plaintext
Authors: Kazawa Ichiroh 
Published: January 2018

This technology sets an upper limit on the number of available pairs for chosen-plaintext and ciphertext in any chosen-plaintext-attack (CPA).By applying the typical implementation of 128-bit encryption, all CPAs cannot use more than 16 chosen-plaintexts.It does not encrypt the plaintext directly with this technique.256 kinds of variations are created from the plaintext.
It then chooses one variation at random to encrypt.
Unless the encryption key is used in decryption, it is impossible to find out which of the 256 kinds of variations was used for the ciphertext.
A CPA when used for multiple chosen-plaintexts would need to repeat the comparison for the total amount of combinations of the chosen-plaintext.If the CPA increases the total amount of chosen-plaintexts by one, the number of generated encryption keys increased by 256 times.256^{16} (== 2^{128}) encryption keys will be generated from the 16 chosen-plaintexts.Since the the total key possibilities generated exceed the total number of encryption keys, it is not possible for CPA to win with a brute force attack.RC4 is no longer recommended.However, the compactness of RC4 in embedded devices (e.g. RF-ID) has a big advantage in regards to block ciphers such as AES.
Secret Key Size(bit length) / Variations Count(bit length) > Chosen Plaintexts Count(useable count)
** Industrial significance **
RC4 is no longer recommended.
However, the compactness of RC4 in embedded devices (e.g. RF-ID) has a big advantage in regards to block ciphers such as AES.
RC4 can regain its security with this technology.
Compacting embedded devices will lead mainly to the reduction of costs.
It is believed that this technology will contribute greatly to the IoT.
”XORveR”, is this technologies codename.
A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
Authors: Redelings Benjamin D , Holder Mark T 
Published: January 2018

We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree.
We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies.
This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project's "synthetic tree" starting at version 5. This software pipeline is called "propinquity". It relies heavily on "otcetera" - a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub.
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian 
Published: January 2018

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute disproportionate amounts of DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested.
2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate samples that were not sorted by biomass and samples that were sorted and then pooled so that each specimen contributed approximately equal amounts of biomass. DNA from all five extractions of samples from both sites was amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. The library was sequenced on a HiSeq Illumina sequencer.
3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes.
4) Our results demonstrate that even a coarse size sorting can substantially improve detection of taxa using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian 
Published: January 2018

Environmental bulk samples often contain many taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested.
Here we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate monitoring samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5x5, 5x10 and up to 10x20 mm). Tissue from each size category was extracted individually, and pooled to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene.
Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes and pooling by specimen abundance.
Our study demonstrates that even a coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
Avian community structure and habitat use of Polylepis forests along an elevation gradient
Authors: Sevillano-Rios C Steven , Rodewald Amanda D. 
Published: January 2018

Background. As one of the highest and most unique systems in the world, Polylepis forests are recognized both as center of endemism and diversity along the Andes and as a system under serious threat from human activities, fragmentation, and climate change. Effective conservation efforts are limited, in part, by our poor understanding of the habitat needs of the system’s flora and fauna.
Methods. In 2014-2015, we studied bird communities and 19 associated local and landscape attributes within five forested glacial valleys within the Cordillera Blanca and Huascaran National Park, Peru. Birds were surveyed in dry (May-August) and wet (January-April) seasons at 130 points distributed along an elevational gradient (3,300-4,700 masl) and analyzed using Canonical Correspondence Analysis (CCA).
Results. A total of 50 species of birds, including 13 species of high conservation concern, were associated with four basic habitat types: (1) Polylepis sericea forests at low elevations, (2) P. weberbaueri forests at high elevations, (3) Puna grassland and (4) shrublands. Four species of conservation priority (e.g., Poospiza alticola) were strongly associated with large forest patches (~10-ha) dominated by P. sericea at lower elevations (<3,800 masl), whereas another four (e.g., Anairetes alpinus) were associated with less disturbed forests of P. weberbaueri at upper elevations (>4,200 masl).
Discussion. Results suggest that, in addition to conserving large (>10-ha) P. sericea forests at lower elevations as the cornerstone for maintaining bird diversity, any high elevation (>4,200 masl) relicts of P. weberbaueri, irrespective of size, should be prioritized for conservation.