bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size matters: relationships between body size, dry weight and ash-free dry weight of common coastal, aquatic invertebrates in the Baltic Sea
Authors: Eklöf Johan , Austin Åsa , Bergström Ulf , Donadi Serena , Eriksson Britas D H K , Hansen Joakim , Sundblad Göran 
Published: January 2018

Background. Organism biomass is one of the most important variables in ecological studies, making estimations of organism weight one of the most common laboratory tasks. Biomass of small macroinvertebrates is usually estimated as dry (DW) or ash-free dry weight (AFDW); a laborious and time consuming process, that often can be speeded up using easily measured and reliable proxy variables like wet/fresh weight and/or body size. Another common way of estimating AFDW - which is the most accurate but also time-consuming estimate of biologically active tissue weight - is the use of AFDW/DW ratios or conversion factors. So far, however, these ratios typically ignore the possibility that the relative weight of biologically active vs. non-active support tissue (e.g. protective exoskeleton or shell) - and therefore, also the AFDW/DW ratio - may change with body size, as previously shown for taxa like spiders, vertebrates and trees.
Methods. We collected samples of aquatic, epibenthic macroinvertebrates (>1 mm) in 32 shallow bays along a 360 km stretch of the Swedish coast along the Baltic Sea; one of the largest brackish water bodies on Earth. We then estimated statistical relationships between the body size (length or height in mm), dry weight and ash-free dry weight for 14 of the most common taxa; five gastropods, three bivalves, three crustaceans and three insect larvae. Finally, we statistically estimated the potential influence of body size on the AFDW/DW ratio per taxon.
Results. For most of the taxa, non-linear regression models describing the power relationship between body size and i) DW and ii) AFDW fit the data well (as indicated by low SE and high R2). Moreover, for more than half of the taxa studied (including the vast majority of the shelled molluscs), body size had a negative influence on organism AFDW/DW ratios.
Discussion. The good fit of the modelled power relationships suggest that the constants reported here can be used to more quickly estimate organism dry- and ash-free dry weight based on body size, thereby freeing up considerable work resources. However, the considerable differences in constants between taxa emphasize the need for taxon-specific relationships, and the potential dangers associated with either ignoring body size or substituting relationships between taxa. The negative influence of body size on AFDW/DW ratio found in a majority of the molluscs could be caused by increasingly thicker shells with organism age, and/or spawning-induced loss of biologically active tissue in adults. Consequently, future studies utilizing AFDW/DW (and presumably also AFDW/wet weight) ratios should carefully assess the potential influence of body size to ensure more reliable estimates of organism biomass.
Randomised Badger Culling Trial: How big was the perturbation effect?
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 over-estimated.
Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling
Authors: Ahrendt Steven R , Medina Edgar Mauricio , Chang Chia-en A , Stajich Jason E 
Published: January 2018

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores.
Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus.
Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis­-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins.
Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.
Redesign of OGC Symbology Encoding standard for sharing cartography
Authors: Bocher Erwan , Ertz Olivier 
Published: January 2018

Despite most Spatial Data Infrastructures are offering service-based visualization of geospatial data, requirements are often at a very basic level leading to poor quality of maps. This is a general observation for any geospatial architecture as soon as open standards as those of the Open Geospatial Consortium (OGC) have to be applied. To improve this situation, this paper does focus on improvements at the (inter)operability side by considering standardization aspects. We propose two major redesign recommendations. First to consolidate the cartographic design knowledge at the core of the OGC Symbology Encoding standard. Secondly to build the standard in a modular way so as to be ready to host upcoming cartographic requirements.
Thus, we start by defining the main portrayal interoperability use cases that frame the concept of sharing cartography. Then we bring to light the strengths and limits of the relevant open standards to consider in this context. Finally we paint a set of recommendations to overcome the limits so as to make these use cases a reality.
Even if the definition of a cartographic-oriented standard is not able to act as a complete cartographic design framework by itself, we argue that pushing forward the standardization work dedicated to cartography is a way to share and disseminate good practices and finally to improve the quality of the visualizations.
A redesign of OGC Symbology Encoding standard for sharing cartography
Authors: Bocher Erwan , Ertz Olivier 
Published: January 2018

Despite most Spatial Data Infrastructures are offering service-based visualization of geospatial data, requirements are often at a very basic level leading to poor quality of maps. This is a general observation for any geospatial architecture as soon as open standards as those of the Open Geospatial Consortium (OGC) shall be applied. To improve the situation, this paper does focus on improvements at the portrayal interoperability side by considering standardization aspects. We propose two major redesign recommendations. First to consolidate the cartographic theory at the core of the OGC Symbology Encoding standard. Secondly to build the standard in a modular way so as to be ready to be extended with upcoming future cartographic requirements.
Thus, we start by defining portrayal interoperability by means of typical use cases that frame the concept of sharing cartography. Then we bring to light the strengths and limits of the relevant open standards to consider in this context. Finally we propose a set of recommendations to overcome the limits so as to make these use cases a true reality.
Even if the definition of a cartographic-oriented standard is not able to act as a complete cartographic design framework by itself, we argue that pushing forward the standardization work dedicated to cartography is a way to share and disseminate good practices and finally to improve the quality of the visualizations.
FUCHS - Towards full circular RNA characterization using RNAseq
Authors: Metge Franziska , Czaja-Hasse Lisa F , Reinhardt Richard , Dieterich Chistoph 
Published: January 2018

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5’ splice site is linked to an upstream 3’ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data – FUCHS: FUll CHaracterization of circular RNA using RNA- Sequencing.
Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically > 150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries.
This new knowledge will enable the user to carry out differential-motif enrichment and miRNA-seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research.
The pipeline is available as git repository: https://github.com/dieterich-lab/FUCHS
Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen
Authors: Ong Oselyne TW , Young Lauren J , Old Julie M 
Published: January 2018

Background: Reference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues.
Methods: The study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase, GAPDH; β-Actin, ACTB; 18S rRNA, 18S; 28S rRNA, 28S; and ribosomal protein L13A, RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUS software.
Results: Gene stability for juvenile and adult tissue samples combined show that GAPDH was most stable in liver and lung tissue, and 18S in small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except 28S were stable for lung and only 18S and 28S were stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTB and GAPDH) and adults (18S and 28S), and RPL13A was not stable for juvenile small intestine tissue. Except for 28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue.
Discussion: Based on expression stability, ACTB and GAPDH are suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults but RPL13A was not suitable in juveniles.
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Authors: Mishra Priyanka , Kumar Amit , Rodrigues Vereena , Shukla Ashutosh K , Sundaesan Velusamy 
Published: January 2018

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.
Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.
Principal Findings. Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses.
Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2 there by concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Authors: Mishra Priyanka , Kumar Amit , Rodrigues Vereena , Shukla Ashutosh K , Sundaesan Velusamy 
Published: January 2018

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.
Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.
Principal Findings. Based on the K2P distance, significant divergences between the inter- and intraspecific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
RelocaTE2: a high resolution transposable element polymorphism mapping tool for population resequencing
Authors: Chen Jinfeng , Wrightsman Travis , Wessler Susan R , Stajich Jason E. 
Published: January 2018

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE transposition events or polymorphisms can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools.
Methods We have developed the tool RelocaTE2 ( http://github.com/stajichlab/RelocaTE2 ) for identification of TE polymorphisms at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision.
Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrates a higher level of sensitivity and specificity when compared to other tools. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE polymorphisms and can be incorporated into analysis workflows in support of describing the complete genotype from light coverage genome sequencing.
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing
Authors: Chen Jinfeng , Wrightsman Travis , Wessler Susan R , Stajich Jason E. 
Published: January 2018

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools.
Methods We have developed the tool RelocaTE2 ( http://github.com/stajichlab/RelocaTE2 ) for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision.
Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into analysis workflows in support of describing the complete genotype from light coverage genome sequencing.