bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designing the MIRRI information system
Authors: Romano Paolo DM , Smith David , Bunk Boyke , Vasilenko Alexander , Glöckner Frank Oliver 
Published: January 2018

Culture collections (CCs) manage fundamental data about preserved microorganisms. To enable the exploitation of these resources requires standardized, and simplified, access to the associated information. To this end, a European Microbial Resource Research Infrastructure, MIRRI, was established. A prime objective of MIRRI is to unite and provide universal access to the information available in European public collections of microorganisms through a dynamic Information System, the MIRRI-IS. In this context, the desired outcome would include a repository for microbial domain Biological Resource Centre (mBRC) catalogues in a common format, the validation of catalogue contents to provide quality data, the interconnection of domain information systems for data extension, a unique portal for catalogues and associated data and an interoperable system based on Application Programming Interfaces (APIs) and service based interfaces and workflows.
The architectural design of the system foresees the adoption of a standard format for exchanging data between CCs, a Minimum Data Set for essential data, to evolve into Minimum Information about Biological Resources (MIaBRe), a user-friendly interface, as well as APIs and services/workflows for integration software.
Three systems were developed in the MIRRI preparatory phase. They have been developed to cope with distinct issues. The BacDive demonstrator aims at extending the contents of catalogues with a greater number of better defined data. The StrainInfo demonstrator is targeted towards a better integration among collection catalogues through the identification of common strains. It makes some order in strains available in various collections and makes possible the re-organization of collections and the sharing of data between catalogues. The USMI Galaxy demonstrator is aimed at supporting data curation and at integrating catalogues with external resources. It makes it possible to integrate collections' data with other bioinformatics databases by leveraging on existing tools and with little development requirements. Moreover, it allows the improvement of a collection’s data by automating links to external databases.
A five-year plan for the implementation of the MIRRI-IS has been defined. The four main lines included in the plan are data curation, interoperability, applications development and IT competence. Data curation is meant to be developed by the progressive adoption of Standard Operating Procedures, able to lead user catalogues from the current Minimum Data Set to a structured extended data set and finally to data sets fully compliant with Minimum Information about Biological Resources (MIaBRE) guidelines, still under definition. Interoperability will lead current separated catalogues to interact with an integrated repository of reference data which will finally allow user access to all catalogues through a common portal.
Towards a metadata-driven multi-community research data management service
Authors: Grunzke Richard , Hartmann Volker , Jejkal Thomas , Prabhune Ajinkya , Herold Hendrik , Deicke Aline , Hoffmann Alexander , Schrade Torsten , Meinel Gotthard , Herres-Pawlis Sonja , Stotzka Rainer , Nagel Wolfgang E. 
Published: January 2018

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is research data management in order to store data in a structured way to enable easy discovery for future reference. An integral part is the use of metadata. With it, data becomes accessible by its content instead of only its name and location. The use of metadata shall be as automatic and seamless as possible in order to foster a high usability.
Here we present the architecture and initial steps of the MASi project with its aim to build a comprehensive research data management service. First, it extends the existing KIT Data Manager framework by a generic programming interface and by a generic graphical web interface. Advanced additional features includes the integration of provenance metadata and persistent identifiers. The MASi service aims at being easily adaptable for arbitrary communities with limited effort. The requirements for the initial use cases within geography, chemistry and digital humanities are elucidated. The MASi research data management service is currently being built up to satisfy these complex and varying requirements in an efficient way.
On the connection between supersaturation in the upper airways and «humid-rainy» and «cold-dry» seasonal patterns of influenza
Authors: Ishmatov Aleksandr N 
Published: January 2018

We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.
We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:
- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;
- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;
- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.
Thus, the effect of supersaturation and condensational growth can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.
Can pond dyes help to control mosquitoes in urban gardens?
Authors: Ortiz Perea Natali , Callaghan Amanda 
Published: January 2018

Background British mosquito population distribution, abundance, species composition and potential for mosquito disease transmission are intimately linked to the physical environment. The presence of ponds and water storage can significantly increase the density of particular mosquito species in the garden. Culex pipiens is the mosquito most commonly found in UK gardens and a potential vector of West Nile Virus WNV, although the current risk of transmission is low. However any factors that significantly change the distribution and population of Cx pipiens are likely to impact subsequent risk of disease transmission. Pond dyes are used to control algal growth and improve aesthetics of still water reflecting surrounding planting. However it is well documented that females of some species of mosquito prefer to lay eggs in dark water and/or containers of different colours and we predict that dyed ponds will be attractive to Culex mosquitoes.
Methods Black pond dye was used in oviposition choice tests using wild-caught gravid Cx pipiens. Larvae from wild-caught Cx pipiens were also reared in the pond dye to determine whether it had any impact on survival. An emergence trap caught any adults that emerged from the water. Water butts (80L) were positioned around university glasshouses and woodland and treated with black pond dye or left undyed. Weekly sampling over a 6 month period through summer and autumn was performed to quantified numbers of larvae and pupae in each treatment and habitat.
Results Gravid female Culex mosquitoes preferred to lay eggs in dyed water. This was highly significant in tests conducted under laboratory conditions and in a semi-field choice test. Despite this, survivorship in black dyed water was significantly reduced compared to undyed water. Seasonal analysis of wild larval and pupal numbers in two habitats with and without dye showed no impact of dye but a significant impact of season and habitat. Mosquitoes were more successful, with significantly higher numbers of pupae, in the habitat where they had vegetation cover and shade.
Discussion Our study has raised some interesting possibilities. One is that where used, pond dyes may be encouraging mosquitoes to breed in gardens in close proximity to people. Considering the concerns over potential future spread of disease in urban environments, this as well as shading of ponds and water butts, should inform future advice over reducing mosquito breeding and spread.
A comparison of planned radiotherapy dose distributions calculated by Monte Carlo with variation of technique, statistical uncertainty and voxel size on resulting gamma pass rates
Authors: Van Delinder Kurt W 
Published: January 2018

Background: The gamma analysis index (γ) is the most commonly used method to compare a calculated and measured dose distribution. A caveat to the clinical use of γ is that the formalism does have a sensitivity to noise present in either distribution. Monte Carlo (MC) based dose calculation methods are widely accepted as the most accurate method to calculate a resulting patient dose distribution from a radiation therapy treatment plan [6]. However, noise is inherently present as random errors or statistical uncertainty within all MC based dose calculation methods and is inversely proportional to the dose calculation time [7]. A research experiment performed by Van Delinder et al. investigated the effect of decreasing voxel size and increasing statistical uncertainty for a Monte Carlo based dose calculation method using 10 clinical head and neck (H&N) IMRT treatment plans. The experimental result was a definitive increase in γ passing rates with combined decrease in voxel size [10]. In order to further clinical information regarding this phenomenon, a large comprehensive study is required using multiple treatment techniques, a different treatment site, and using a different type of radiation measurement device.
Methods/Design: A study consisting of (ntotal = 30) thirty total prostate cancer radiation therapy plans comprised of (n1 = 10) ten VMAT plans, (n2 = 10) ten IMRT plans and (n3 = 10) ten 3DCRT plans. All treatment plans consisting of three different treatment techniques are to be delivered with a total dose of 79.2 Gy prescribed to the PTV at a rate of 1.8 Gy in 44 fractions. 3DCRT will be delivered using 6 fields, IMRT delivered as 7 fields and VMAT consists of 2 arcs (CCW from 1o to 359o with a collimator angle of 170o and CW from 359o to 1o with a collimator angle of 190o). All three treatment techniques will be calculated using 6 and 10 MV energy to allow an intra-study comparison between energies. All QA plans will then be calculated with varied statistical uncertainty from 0.5%, 1%, 2%, 3%, 4% and 5%. The voxel sizes will also be varied from 3mm, 2mm and 1mm for each of the statistical uncertainty percentages. All treatment plans will be measured using ArcCHECK radiation dose measurement device and the γ will be applied within SNC Machine. Both 3%/3mm and 2%/2mm will be implemented for γ criteria for all of the treatment plans.
Discussion: The necessity for a comprehensive research experiment investigating the effects of statistical uncertainty and voxel size amongst multiple treatment techniques with additional variations is required to guarantee safe quality assurance with routine use of Monte Carlo dose calculation methods. This experimental design acts as a contrasting research experiment when combined with prior literature allowing the clinician the ability to use the direct results and develop clinical recommendations for IMRT QA involving the use of Monte Carlo based dose calculations.
Early warning indicators of grassland degradation in inner Mongolia
Authors: Qin Jie , Han Guodong , Wang Zhongwu , Hu Linxi , Zhang Jun 
Published: January 2018

Backgroung: With the implementation of the Household Production Responsibility System in China almost 30 years ago, obvious spatial heterogeneity has developed over rangeland.
Methods: We examined lifeform functional groups over 5 years on household ranches in different grazing utilization rate (30%-95%) ecosystems in Inner Mongolia to identify the early warning indicators of grassland degradation.
Results: The results showed that a similar grassland utilization threshold occurred in different types of steppe, with 78-89% utilization for meadow steppe, 81-89% for typical steppe and 70-85% for desert steppe. The vegetation composition above these utilization thresholds did not show obvious signs of degradation; therefore, the risk of degradation was difficult to determine. The spatial threshold (WD: L) had a value of 31.40:100 for meadow steppe, 8.53:100 for typical steppe and 42.21:100 for desert steppe.
Conclusion: Land managers cannot easily determine the risk of degeneration according to the vegetation composition or function group. So the spatial threshold is important for implemented strategies to prevent degradation, and our study provides new insights to improve the management and restoration of degraded grassland in Inner Mongolia.
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Authors: Gerritsen Jacoline , Hornung Bastian , Renckens Bernadette , van Hijum Sacha A.F.T. , Martins dos Santos Vitor A.P. , Rijkers Ger T. , Schaap Peter J. , de Vos Willem M. , Smidt Hauke 
Published: January 2018

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.
Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC.
Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.
Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.
Parallel and in-process compilation of individuals for genetic programming on GPU
Authors: Ayral Hakan , Albayrak Songül 
Published: January 2018

Three approaches to implement genetic programming on GPU hardware are compilation, interpretation and direct generation of machine code. The compiled approach is known to have a prohibitive overhead compared to other two.
This paper investigates methods to accelerate compilation of individuals for genetic programming on GPU hardware. We apply in-process compilation to minimize the compilation overhead at each generation; and we investigate ways to parallelize in-process compilation. In-process compilation doesn’t lend itself to trivial parallelization with threads; we propose a multiprocess parallelization using memory sharing and operating systems interprocess communication primitives. With parallelized compilation we achieve further reductions on compilation overhead. Another contribution of this work is the code framework we built in C# for the experiments. The framework makes it possible to build arbitrary grammatical genetic programming experiments that run on GPU with minimal extra coding effort, and is available as open source.
A clinical assessment of external beam focal therapy for localized prostate cancer measured by Gafchromic film
Authors: Van Delinder Kurt W 
Published: January 2018

Background: Traditionally, EBRT prostate treatments have been administered using three different techniques: three-dimensional conformal radiation therapy (3D-CRT), intensity modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT). These radiation therapy treatment techniques are often combined with additional options focusing on treating systemic disease and the entire volume of the prostate. A novel approach to EBRT is currently in development, a localized treatment administered to only the primary disease within the prostate volume termed ‘Focal Therapy’.
Methods/Design: The proposed research study is aimed to simulate 10 random EBRT prostate focal therapy treatments replicated within two treatment planning software; Monaco treatment planning system and Eclipse treatment planning system. All ten plans will be contoured simulations of focal therapy imaging sets replicated from authentic mpMRI anatomical images of focal therapy eligible prostate cancer patients. Following the completion of the 10 clinical plans, QA plans will be generated and administered via each products current commercial linacs; the TrueBeam and the Versa. All QA plans will have their radiation doses measured with Gafchromic EBT3 radiochromic film and analyzed using the gamma analysis index (γ).
Discussion: To examine the uncertainties and limitations of an EBRT focal therapy prostate cancer treatment, it’s imperative that a large study replicating many clinical cases under varying conditions should be conducted. This allows the ability for the clinician to investigate errors and uncertainties at each stage of the treatment process prior to committing to a clinical study. The experimental results can also be used as a reference for the creation of a standard guideline for the administration of focal therapy as a curative treatment for prostate cancer.
Genetic effects on life-history traits in the Glanville fritillary butterfly
Authors: Duplouy Anne , Wong Swee C , Corander Jukka , Lehtonen Rainer , Hanski Ilkka 
Published: January 2018

Background. Adaptation to local habitat conditions may lead to the natural divergence of populations in life-history traits such as body size, time of reproduction, mate signaling or dispersal capacity. Given enough time and strong enough selection pressures, populations may experience local genetic differentiation. The genetic basis of many life-history traits, and their evolution according to different environmental conditions remain however poorly understood.
Methods. We conducted an association study on the Glanville fritillary butterfly, using material from five populations along a latitudinal gradient within the Baltic Sea region, which show different degrees of habitat fragmentation. We investigated variation in ten principal components, cofounding in total 21 life-history traits, according to two environmental types, and 33 genetic SNP markers from 15 candidate genes.
Results. We found that nine SNPs from five genes showed strong trend for trait associations (p-values under 0.001 before correction). These associations, yet non-significant after multiple test corrections, with a total number of 1086 tests, were consistent across the study populations. Additionally, these nine genes also showed an allele frequency difference between the populations from the northern fragmented versus the southern continuous landscape.
Discussion. Our study provides further support for previously described trait associations within the Glanville fritillary butterfly species across different spatial scales. Although our results alone are inconclusive, they are concordant with previous studies that identified these associations to be related to climatic changes or habitat fragmentation within the Åland population.
From boss to mentor to partner : transitioning in medical education
Authors: Rossinot Helene , Brunoni Andre , Filipce Venko , Kalejs Martins , Liyanapathirana Veranja , Senkubuge Flavia , Toldi Gergely , Toth Csongor , Boufford Jo Ivey 
Published: January 2018

The relationship between the teacher and the student is changing as information becomes more readily available, and the science of education is evolving in parallel.
The question then is: what is expected from the modern teacher in medicine? As young physician professionals from all regions of the world, we asked ourselves: how should this question be answered? This paper was motivated by the shared concerns and recommendations that we, as a team of Young Physician Leaders (footnote on the program) presented at the Global Health Summit held in Berlin in October, 2015 and by our subsequent discussions.
Biases in genome reconstruction from metagenomic data
Authors: Nelson William C , Mobberley Jennifer M 
Published: January 2018

Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful technique, it is shadowed by an inability to truly determine whether assembly and binning techniques are accurate, specific, and sensitive due to a lack of complete reference genome sequences against which to check the data. Errors in genome reconstruction, such as missing or mis-attributed activities, can have a detrimental effect on downstream metabolic and ecological modeling, and thus it is important to assess the accuracy of the process.
Methods: We compared genomes reconstructed from metagenomic data to complete genome sequences of 10 organisms isolated from the same community to identify regions not captured by typical binning techniques. The nucleotide content, as %G+C and tetranucleotide frequencies, and sequence redundancy within both the genome and across the metagenome were determined for both the captured and uncaptured regions. This direct comparison allowed us to evaluate the efficacy of nucleotide composition and coverage profiles as elements of binning protocols and look for biases in sequence characteristics and gene content in regions missing from the reconstructions.
Results: We found that repeated sequences were frequently missed in the reconstruction process as were short sequences with variant nucleotide composition. Genes encoded on the missing regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function.
Conclusions: Our observation of increased mis-binning of short regions, especially those with variant nucleotide content, and repeated regions implies that factors which affect assembly efficiency also impact binning accuracy. To a large extent, mis-binned regions appear to derive from mobile elements. Our results support genome reconstruction as a robust process, and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function.