bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat suitability – density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)
Authors: Carrascal Luis M. , Moreno Angel C. , Delgado Alejandro , Suárez Víctor , Trujillo Domingo 
Published: January 2018

Background. Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs.
Methods. We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994.
Results. The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July-September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195-430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic.
Discussion. Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abundance during the reproductive season. The outcomes of these models can be used for the identification of potential areas for the reintroduction of the species in other suitable pine forests and to inform forest management practices.
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C
Authors: Prostova Maria A , Deviatkin Andrei A , Tcelykh Irina O , Lukashev Alexander N , Gmyl Anatoly P 
Published: January 2018

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.
Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C.
Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.
Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.
Optimizing taxonomic classification of marker gene sequences
Authors: Bokulich Nicholas A , Kaehler Benjamin D , Rideout Jai Ram , Dillon Matthew , Bolyen Evan , Knight Rob , Huttley Gavin A. , Caporaso J. Gregory 
Published: January 2018

Background. Taxonomic classification of marker-gene sequences is an important step in microbiome analysis.
Results. We present q2-feature-classifier (https://github.com/qiime2/q2-feature-classifier), a QIIME 2 plugin containing several novel machine-learning and alignment-based taxonomy classifiers that meet or exceed classification accuracy of existing methods. We evaluated and optimized several commonly used taxonomic classification methods (RDP, BLAST, BLAST+, UCLUST) and several new methods (a scikit-learn naive Bayes machine-learning classifier, and VSEARCH and SortMeRNA alignment-based methods).
Conclusions. Our results illustrate the importance of parameter tuning for optimizing classifier performance, and we make explicit recommendations regarding parameter choices for a range of standard operating conditions. q2-feature-classifier and our evaluation framework, tax-credit, are both free, open-source, BSD-licensed packages available on GitHub.
Genome rearrangements and phylogeny reconstruction in Yersinia pestis
Authors: Bochkareva Olga O , Dranenko Natalia O , Ocheredko Elena S , Kanevsky German M , Lozinsky Yaroslav N , Khalaycheva Vera A , Artamonova Irena I , Gelfand Mikhail S 
Published: January 2018

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree.
We reconstructed the evolutionary history of genome rearrangements in Y. pestis. We also reconciled phylogenetic trees for each of the three CRISPR-loci to obtain an integrated scenario of the CRISPR-cassette evolution. We detected numerous parallel inversions and gain/loss events by the analysis of contradictions between the obtained evolutionary trees. We also tested the hypotheses that large within-replichore inversions tend to be balanced by subsequent reversal events and that the core genes less frequently switch the chain by inversions. Both predictions were not confirmed.
Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.
From trash to treasure: detecting unexpected contamination in unmapped NGS data
Authors: Granata llaria , Sangiovanni Mara , Thind Amarinder Singh , Guarracino Mario Rosario 
Published: January 2018

Standard procedures for NGS data analysis involve a pre-processing step of reads quality assessment, followed by the alignment of the filtered reads to a reference genome. Typically the amount of reads that correctly maps to the specific reference genome ranges between 70% and 90%, leaving in some cases a consistent fraction of unmapped sequences. Investigating the reasons of this discrepancy may provide relevant information about the source of the so called unmapped reads. It is not unusual that genetic material of microorganisms is present in biological samples undergoing sequencing. These exogenous sequences can derive from the normal or altered tissues microbiome (upstream contamination) or from a contamination occurring during the samples processing (downstream contamination).
Here we propose DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach in which the sequences are first filtered according to quality parameters and then mapped to ribosomal, mithocondrial and foreign organism's databases. The reads that do not map on human genome are then mapped, through a local alignment algorithm (MegaBlast), to bacteria, fungi and viruses genome. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. The main novelty of DecontaMiner is the versatility of its use together with a complete, easy to use, and automatic pipeline.
DecontaMiner has been mainly used to detect contamination in human RNA-seq data, but the pipeline can be easily tailored using the configuration files and flags to process DNA-seq data, and unmapped data coming from non-human species.
The first virtual cranial endocast of a porolepiform fish and the evolution of the Dipnomorpha
Authors: Henderson Struan , Challands Tom , Giles Sam , den Blaauwen Jan 
Published: January 2018

The Dipnomorpha include the extinct Porolepiformes, in addition to Powichthys and Youngolepis and the extant Dipnoi (lungfish). As sister group to the Tetrapodomorpha, the Dipnomorpha hold a valuable place in our understanding of early sarcopterygian evolution. With complete cranial endocasts now known from most other stem sarcopterygian groups including actinistians and tetrapodomorphs (which bracket the Dipnomorpha), a thorough understanding of the porolepiform endocranium remains one of the last pieces in the puzzle towards understanding evolution of the neurocranium in stem sarcopterygians.
We present the first virtual cranial endocast of a porolepiform fish (Glyptolepis paucidens) demonstrating that it displays predominantly primitive sarcopterygian endocast characters including: lack of a bifurcation of the olfactory nerves, separate pineal and parapineal recesses, circumvention of the nasal capsule by the profundus nerve, and sessile olfactory bulbs. The union of the orbitonasal canal and the nasal capsule is consistent with that seen in Powichthys, Youngolepis and other porolepiforms, however circumvention of the nasal capsule by the profundus resembles the dipnoan Dipterus, contrasting the state observed in other porolepiforms and Powichthys.
Inconsistent with the general primitive nature of the endocast seen in Glyptolepis is the large, curved hypophyseal recess, a feature shared with Powicthys but unlike Youngolepis. Furthermore, Glyptolepis displays ventral expansion of the telencephalon - a character thought to be derived within the Dipnoi.
This new data enhances our understanding of brain and sensory evolution in sarcopterygians. In particular, it shows conservatism in stem Porolepiformes contrary to the disparate morphology of their sister-group the Dipnoi.
Multi-resolution network modelling of T-cells for precision medicine of multiple sclerosis
Authors: Gustafsson Mika 
Published: January 2018

Background: Due to the interplay between many factors, systems medicine of complex diseases is most often centered either on individual genes, or on statistical associations. Complex network analysis could potentially explain systems-wide differences between patients and controls. In order to achieve this understanding using incomplete existing data, we need these powerful coarse-graining procedures. First, disease genes have been shown to co-localise for many complex diseases in protein-interaction networks, and thereby forming disease modules, however the identification of such modules is not well-defined (Gustafsson Genome Medicine 2014). We have developed ModifieR, an R-package which combines 10 existing and new methods using statistical overlaps between multiple omics as a guiding principle. Second, upstream hub transcription factors (TFs) regulating those modules have shown to be good candidates for early predictive medicine (Gustafsson Science Transl Med 2015). Third, those TFs tend to be interconnected and form core circuits, which have a great genome-wide impact, and could be modelled by our recent dynamic ordinary differential equation based modelling tool, LASSIM (Magnusson, PLoS Comput Biol 2017, https://gitlab.com/Gustafsson-lab/ ). Each of these concepts could synergistically increase the analysis resolution. A critical problem is that parts of the models are patient-specific while parts are highly conserved across patients, which we work to resolve.
Methods: A key feature to estimate patient specific disease-relevant networks is multiple time-points omics in cells reflecting different disease-relevant stages. We hypothesise that by connecting patients at multiple stages we can infer the disease-relevant patient specific gene regulatory networks, from which we can draw statistical conclusions (extension of the work in Hellberg Cell Reports 2016). For this purpose, we are performing modelling of CD4+ T-cells in multiple sclerosis using generally applicable principles in open access pipelines. Briefly, we apply a linear transcription factor-target model based on eQTL-targeted sequencing and patients in two time-points. The model uses L1 constraints, similar to our previous models (Gustafsson Science Transl Medicine 2015, Gustafsson IEEE 2005), but is allowed to infer transcription factor activity based on target gene expression, using the CVX optimisation toolbox.
Results: We found that the inferred patient specific GRN models with L1 constraint predicted 50% of the transcriptomic changes using cross-validation. Generally, we found that the TF activity poorly correlated with its mRNA level. Moreover, we found TFs with a significantly higher effect in patients than controls.
Discussion: My research focus on three recent network medicine concepts that enable a gradually increased resolution of modelling for complex diseases, which I ultimately aim at integrating in a unifying precisions medicine toolbox.
Enumerating common molecular substructures
Authors: Engler Martin S , El-Kebir Mohammed , Mulder Jelmer , Mark Alan E , Geerke Daan P , Klau Gunnar W 
Published: January 2018

Finding and enumerating common molecular substructures is an important task in cheminformatics, where small molecules are often modeled as molecular graphs. We introduce the problem of enumerating all maximal k-common molecular fragments of a pair of molecular graphs. A k-common fragment is a common connected induced subgraph that consists of a common core and a common k-neighborhood. It is thus a generalization of the NP-hard task to enumerate all maximal common connected induced subgraphs (MCCIS) of two graphs, which corresponds to the k = 0 case.
We extend the MCCIS enumeration algorithm by Ina Koch and apply algorithm engineering techniques to solve practical instances fast for the general k > 0 case, which is relevant, for example, for automatically generating force field topologies for molecular dynamics (MD) simulations. We find that our methods achieve good performance on a real-world benchmark of all-against-all comparisons of 255 molecules.
Our software is available under the LGPL open source license at https://github.com/enitram/mogli .
Determinants of antimicrobial use practices among veterinary clinicians at The University of Tennessee Veterinary Medical Center
Authors: Ekakoro John Eddie , Okafor Chika C 
Published: January 2018

Background. Antimicrobial drugs in veterinary medical practice are primarily prescribed for the purposes of maintaining or improving health and increasing productivity. However, their value is being eroded by antimicrobial resistance (AMR). Indiscriminate use of antimicrobial drugs is suggested as one of the modifiable factors contributing to the development of AMR. To reduce indiscriminate use and to improve antimicrobial use, veterinary practices are encouraged to adopt good stewardship practices. Therefore, the objectives of this study were: to identify factors influencing clinician decisions to begin using antimicrobials as well as the choice of antimicrobials used at The University of Tennessee Veterinary Medical Center (UTVMC); to evaluate the practices, perceptions, opinions and concerns of veterinary clinicians at UTVMC concerning antimicrobial use, antimicrobial stewardship, and AMR.
Methods. This study’s protocol was approved by the University of Tennessee Knoxville IRB for the Protection of Human Subjects in Research. Survey software was used to send a questionnaire to 121 eligible participants, where all were UTVMC faculty with clinical appointments and house officers. Cumulative logit models were fitted to investigate associations between categorical explanatory variables and ordinal response variables.
Results. A response rate of 51.24% was achieved. Of the 62 respondents, 47 (75.81%) reported that bacteriological culture and antimicrobial susceptibility test results were extremely important in their antimicrobial prescription decision-making. Thirty-two (51.61%) respondents believed antimicrobials are being over-prescribed. The cephalosporin class was the most preferred antimicrobial class, while the lincosamide class was the least preferred. From the multivariable cumulative logit model, year of graduation from veterinary school (P = 0.034) and clinicians’ primary patient load (P = 0.009) were significantly associated with clinicians’ degree of concern about AMR.
Conclusions and clinical relevance. The findings suggest a need for more awareness about AMR among veterinary clinicians. Improvements in antimicrobial stewardship are needed, especially among veterinary clinicians who graduated after 1999. Educational practices that target modification of antimicrobial prescription practices of veterinary clinicians would likely improve a Good Stewardship Practice (GSP) mindset. GSP is important in prolonging the efficacy of currently available antimicrobial drugs.
Interoperability of RehabRobo-Onto
Authors: Dogmus Zeynep , Patoglu Volkan , Erdem Esra 
Published: January 2018

The leading cause of permanent disability in developed countries is due to neurological injuries, such as stroke. While physical rehabilitation therapy is indispensable for treating neurological disabilities, repetitive and high intensity therapies place high physical burden on the therapist and significantly increase the cost of such treatments. These challenges have led to design and development of various robot-assisted rehabilitation devices.
As the number of rehabilitation robots increase, the information about them also increases, but most of the time in unstructured forms (e.g., as text in publications), which make it harder to access the requested knowledge and reason about it. Also, due to interdisciplinary nature of rehabilitation robotics, sometimes requested knowledge requires integration of further knowledge from related disciplines (e.g., physical medicine). Motivated by these challenges, we have designed and developed the first formal rehabilitation robotics ontology, called RehabRobo-Onto, to represent knowledge about rehabilitation robotics in the structured form of OWL.
In this abstract, we continue our studies on RehabRobo-Onto by discussing its interoperability with the available knowledge resources, such as Foundational Model of Anatomy (FMA) and Human Disease Ontology (DO), towards personalized physical rehabilitation therapies.
Weighted growth functions of automatic groups
Authors: Vejdemo-Johansson Mikael 
Published: January 2018

The growth function is the generating function for sizes of spheres around the identity in Cayley graphs of groups. We present a novel method to calculate growth functions for automatic groups with normal form recognizing automata that recognize a single normal form for each group element, and are at most context free in complexity: context free grammars can be translated into algebraic systems of equations, whose solutions represent generating functions of their corresponding non-terminal symbols.
This approach allows us to seamlessly introduce weightings on the growth function: assign different or even distinct weights to each of the generators in an underlying presentation, such that this weighting is reflected in the growth function. We recover known growth functions for small braid groups, and calculate growth functions that weight each generator in an automatic presentation of the braid groups according to their lengths in braid generators.
On the efficiency of the Genetic Code after frameshift mutations
Authors: Geyer Regine , Madany Mamlouk Amir 
Published: January 2018

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes.
This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids: We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code - just as for the point mutations - appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other.
For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features - just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just "one in a million".