bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of biotic factors during plant establishment in novel communities assessed with an agent-based simulation model
Authors: Radny Janina , Meyer Katrin M 
Published: January 2018

Background. Establishment success of non-native species can be influenced by interactions with native competitors and novel enemies. Magnitude of interactions between species is mediated by traits, e.g. reflecting competitive strength or defence mechanisms. We combine the concepts to investigate the importance of species traits for successful establishment in a novel community exhibiting biotic resistance in the form of competition and herbivory.
Methods. We developed an individual-based simulation model that tracks survival rate of non-native plants in a native community. Non-native plants are characterized by high or low values of traits relevant for interaction with competitors and herbivores.
Results. Traits related to competition had a much greater impact on survival of non-native species than traits related to defence. Survival rates of strong competitors never fell below 50% while survival of weak competitors averaged about 10%. Weak competitors were also much more sensible to competitive pressures including community density, composition and asymmetry while strong competitors responded negatively to changes in competition intensity but hardly to composition or density of native community. High initial numbers of non-native individuals did decrease survival rate of strong competitors but slightly increased survival rate of weak competitors. In the current model configuration we detected only minor advantages in terms of higher survival from high defensive ability as compared to low defensive ability under enemy attack. Surprisingly, herbivory increased survival rate of species classified as weak competitors.
Discussion. High survival rates of strong competitors relate to a higher chance of establishment as compared to weak competitors. However, the negative effect of high initial numbers for strong competitive non-natives indicates a self-thinning effect, probably through creation of a highly competitive milieu. For weak competitors, our model predicted increasing survival rates at high initial densities. Positive effects of high propagule pressure have been proposed in field studies and are underlined with this model. However, our model largely overestimated mortality as compared to the preceding experiment. This could be improved by implementing more sophisticated competition modes and traits reflecting tolerance and avoidance of competition by non-native plants. This would, however, be very costly in terms of parameterization. Herbivory had a very low negative effect on survival in general and an advantage of high defence was almost untraceable. However, the positive effect of herbivory on survival of weak competitors indicated that herbivory should not be neglected in estimation of establishment success of species. Although the immediate and expected effect of herbivory might be small, side effects as weakening of resident competitors might play an important role for establishment in a new community.
A unique Morrison-Formation sauropod specimen with biconcave dorsal vertebrae
Authors: Taylor Michael P , Wedel Mathew J 
Published: January 2018

AMNH FARB 291 is a unique sauropod dinosaur specimen, excavated in 1898 from the Bone Cabin Quarry of Wyoming (Upper Jurassic; Morrison Formation). It consists of a sequence of five contiguous dorsal vertebrae, all with biconvex centra: a morphology not previously observed in any sauropod, and which is very rare even in other amniotes.
The specimen was initially catalogued as Brontosaurus, one of only half a dozen sauropods then known. But it lacks diplodocid features such as bifid neural spines, short centra and dual centroprezygapophyseal laminae. Instead, it resembles Brachiosaurus in its elongated centra, forward-shifted neural arches and lobe-like transverse processes. Centrum lengths (from anteriormost to posteriormost) are 207, 205, 232, 222 and 207 mm, about 60% those of the Brachiosaurus holotype. This specimen could represent:
1. normal development: the condyle would have ossified separately but the individual died before this could happen;
2. a developmental anomaly;
3. a Brachiosaurus with a rare variation not previously seen due to paucity of specimens;
4. a bizarre taphonomic event;
5. a unique taxon in which this is a normal, inherited trait.
Vertebrae typically ossify as rings of bone around the notochord, which sometimes persists as a tunnel through the centrum. There is a developmental continuum from biconcave centra with a persistent notochordal tube (as in most fishes), through biconcave centra with the notochord persisting as intervertebral cartilage balls, to the normal amniote condition. However, all known baby sauropod presacrals have already ossified opisthocoelous or amphiplatyan centra, so the present specimen remains mysterious.
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C
Authors: Prostova Maria A , Deviatkin Andrey 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 replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity that allows virus to adapt to 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 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) that were present in the NCBI database on February 2017 and analyzed variety and abundance of sequences in domain d of replicative element oriL and in the protein 3C.
Results. A total of 2842 full genome sequences were analyzed. Majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). 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 RNA-binding tripeptide is suggested to interact with apical region of domain d, they evolve independently in nature. Together, our data indicates plastic evolution of both interplayers of 3C-oriL recognition.
Predicting comorbidities of epilepsy patients using big data from Electronic Health Records combined with biomedical knowledge
Authors: Gerlach Thomas , Lu Chao , Fröhlich Holger 
Published: January 2018

Epilepsy is a complex brain disorder characterized by repetitive seizure events. Epilepsy patients often suffer from various and severe physical and psychological comorbidities. While general comorbidity prevalence and incidences can be estimated from epidemiological data, such an approach does not take into account that actual patient specific risks can depend on various individual factors, including medication. This motivates to develop a machine learning approach for predicting individual comorbidities. To address these needs we used Big Data from electronic health records (~100 Million raw observations),which provide a time resolved view on an individual's disease and medication history. A specific contribution of this work is an integration of these data with information from 14 biomedical sources (DisGeNET, TTD, KEGG, Wiki Pathways, DrugBank, SIDER, Gene Ontology, Human Protein Atlas, ...) to capture putative biological effects of observed diseases and applied medications. In consequence we extracted >165,000 features describing the longitudinal patient journey of >10,000 adult epilepsy patients. We used maximum-relevance-minimum-redundancy feature selection in combination with Random Survival Forests (RSF) for predicting the risk of 9 major comorbidities after first epilepsy diagnosis with high cross-validated C-indices of 76 - 89% and analyzed the influence of medications on the risk to develop specific comorbidities. Altogether we see our work as a first step towards earlier detection and better prevention of common comorbidities of epilepsy patients.
Supplementary material: https://drive.google.com/file/d/0B4OhgVPeWvGTeUNFQVJLai1HRlk/view?usp=sharing , code: https://github.com/thomasmooon/GCB2017
The dentary of Wareolestes rex and new fossil mammal material from the Middle Jurassic of Skye, Scotland
Authors: Panciroli Elsa , Benson Roger B. J. , Walsh Stig 
Published: January 2018

The Middle Jurassic was a pivotal time for many vertebrate groups: recent research suggests mammals experienced a surge in ecological diversity at this time. However, vertebrate fossils from the Middle Jurassic are rare. Until now, Middle Jurassic mammals in the UK came almost exclusively from Bathonian deposits in England, while globally the most complete specimens are mainly found in China. Ongoing fieldwork on the Isle of Skye suggests this locality is of international significance for microvertebrate skeletal remains. So far, Skye has yielded skeletal associations and fragmentary material including early mammals, tritylodontids, salamanders and basal squamates.
We report the most complete specimen of the Middle Jurassic morganucodontan Wareolestes rex, from the Bathonian Kilmaluag Formation of Skye, Scotland. The specimen was digitally reconstructed using microCT scan data. It comprises a partial left dentary with two erupted molars, one unerupted molar, and three unerupted premolars. Empty alveoli for a canine, p1 and p3 are also present.
Wareolestes was previously known from four isolated molars from Kirtlington, England, and there was debate over the position of the holotype tooth as an upper or lower molar. Comparing our new material with the holotype, we support the original diagnosis of the holotype as a lower molar, most likely m1. In the Scottish specimen, unerupted and erupted premolars, and presence of permanent molars, supports diphyodonty in Wareolestes. This has previously been suggested for other morganucodontans. Damage to the dentary of Wareolestes means questions remain regarding the sequence of replacement along the tooth row in this genus.
What is the impact of regulatory guidance and expiry of drug patents on dementia drug prescriptions in England: a trend analysis in the Clinical Practice Research Datalink
Authors: Walker Venexia M , Davies Neil M , Kehoe Patrick G , Martin Richard M 
Published: January 2018

Background: Drugs for dementia have been available in England from 1997. Since their launch, there have been several changes to national guidelines and initiatives that may have influenced prescribing. These include changes in National Institute for health and Care Excellence (NICE) guidance; several government dementia strategies; the addition of dementia to the Quality and Outcomes Framework (QOF); and the expiry of drug patents. Despite this, there has been little research into the effect of these events on prescribing. This paper examines prescribing trends in England using data from the UK Clinical Practice Research Datalink since the launch of drugs for dementia up to 1st January 2016.
Methods: We considered the monthly proportion of patients eligible for treatment, with a diagnosis of probable Alzheimer’s disease, receiving their first prescription for each drug class – namely acetylcholinesterase (AChE) inhibitors (donepezil, rivastigmine, galantamine) and N-Methyl-D-aspartate (NMDA) receptor antagonists (memantine). Trend analysis using joinpoint models was then applied to identify up to two trend changes per treatment of interest.
Results: The overall trend was for increasing prescriptions in each drug class over the period they were studied. This was indicated by the average monthly percentage change, which was 6.0% (95% CI: -6.4 to 19.9; June 1997 to December 2015) for AChE inhibitors and 15.4% (95% CI: -77.1 to 480.9; January 2003 to December 2015) for NMDA receptor antagonists. Prescriptions of AChE inhibitors increased at the end of 2012, probably in response to the patent expiry of these drugs earlier that year. The Prime Minister’s Dementia Challenge launched in May 2012 may also have contributed to the observed increase. However, neither this strategy nor patent expiry appeared to influence prescriptions of NMDA receptor antagonists. Instead trend changes in this drug class were driven by NICE guidance released in 2011 that allowed access to these drugs outside of clinical trials.
Conclusions: Dementia drug prescribing does not always respond to factors such as regulatory guidance, recommendations or patent expiry and, when it does, not necessarily in a predictable way. This suggests that improved communication with clinicians may be needed to improve the cost-effective use of drugs for dementia.
Subcutaneous microdialysis in the awake rat.
Authors: Risselada Marije , Messenger Kristen M 
Published: January 2018

Background. Microdialysis is a valued method to study the pharmacokinetics of drug distribution from an injection site or to a tumor site. The objective of this study was to assess the feasibility of prolonged use of subcutaneously implanted microdialysis catheters to assess local retention and systemic uptake of carboplatin in rats post anesthetic recovery.
Methods. Twelve rats were used: one control rat and 11 treatment rats. The control rat was used to outline the surgical implantation technique of the microdialysis catheter. Treatment rats were administered 5mg carboplatin in poloxamer 407 and divided in two treatment cohorts. Microdialysis catheters were used in both cohorts to collect extracellular fluid. Placement technique was modified between the two cohorts. Treatment cohort 1 (n=6) had the microdialysis catheter implanted in the wound bed, sutured in place and tunneled subcutaneously along the dorsum to exit dorsally in the cervical area. The ends were secured to a Velcro strip sutured to the dorsal cervical skin to avoid trauma by the rat. Treatment cohort 2 (n=5) had the catheter looped around the right hind limb, with the functional part sutured in place in the wound bed, and tunneled through a subcutaneously implanted sterile intravenous line exiting dorsally in the cervical area. The ends were maintained within the IV line and held in place with wound clips. Results. All 11 microdialysis catheters in the treatment cohorts were functional immediately after implantation, but only one out of 11 microdialysis catheters in the treatment cohorts was functional at 24hrs, and none at 48hrs. Discussion. The results of this study suggest that microdialysis catheters cannot be maintained in unanesthetized rats without further modification of the implantation protocol.
Industry payments to physician journal editors
Authors: Wong Victoria S S , Avalos Lauro N , Callaham Michael L 
Published: January 2018

Objective: To assess industry payments to physician journal editors, and determine how their financial conflict of interest rate compares to all physicians within the specialty.
Study Design and Setting: Open Payments is a United States federal program that mandates reporting of medical industry payments to physicians. We performed a retrospective analysis of prospectively collected data, reviewing August 1, 2013 to December 31, 2016 payments using the Open Payments search tool. We collected payments data on “top tier” US-based physician-editors of highly-cited medical journals including 1) total general payments from industry, 2) total “direct” research payments, and 3) associated “indirect” research funding. We compared payments to physician-editors and payments to physicians-by-specialty using existing published data.
Results: In 35 journals, 333 (74.5%) of 447 “top tier” editors met inclusion criteria as US-based physician-editors. Of these, 212 (63.7%) received any industry-associated payments in the study period. In an average year during the study period, 141 (42.3%) of physician-editors received any payments directed to themselves (rather than their institutions), 120 (36.0%) received payments >$50; 66 (19.8%) received payments >$5,000 (the threshold designated by the National Institutes of Health as a Significant Financial Interest); and 51 (15.3%) received payments >$10,000. Mean annual payment of "total general payments" was $55,157 (standard deviation 561,885, range 10-10,981,153) with median of $3,512. Median general industry payments to physician-editors were mostly higher compared to all physicians within their specialty.
Conclusions: A substantial minority of physician-editors receive direct payments from industry within any given year, though most editors received payment of some kind in the study period. There were significant outliers. More robust and specific editor financial COI declarations may be appropriate given the extent of editors’ influences on the medical literature.
Influence of alignment uncertainty on homology and phylogenetic modeling
Authors: Chang Jia-Ming , Notredame Cedric 
Published: January 2018

Most evolutionary analyses or structure modeling are based upon pre-estimated multiple sequence alignment (MSA) models. From a computational point of view, it is too complex to estimate a correct alignment. Hence, increasing or identifying signal inside sequence alignment has intensified over the last few years. During the presentation, I would like to share two approaches, homology extension and sampling, on this topic.
The first part, transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7. We show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension. Our benchmarking on BAliBASE2-ref7 alpha-helical TMPs shows a significant improvement over the most accurate methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™.
The second part, homology and evolutionary modeling are the most common applications of MSAs. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees.

References:

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic acids research 44, W339–343(2016).
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic acids research 43, W3–6 (2015).
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.Molecular biology and evolution 31, 1625–37 (2014).
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. Bmc Bioinformatics 13, S1 (2012).

Website:

PSI/TM-Coffee http://tcoffee.crg.cat/tmcoffee, TCS http://tcoffee.crg.cat/tcs
Is habitat important? Morphology and genome size of Epipactis helleborine (L.) Crantz growing in anthropogenic and natural habitats
Authors: Rewicz Agnieszka , Rewers Monika , Jędrzejczyk Iwona , Rewicz Tomasz , Kołodziejek Jeremi 
Published: January 2018

Background. The process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora (rare and law protected species) has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to i) determine and compare the phenotypic variation of E. helleborine plants in anthropogenic and natural habitats, ii) compare the genome size estimation of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species.
Methods. The research was carried out in Poland from 2011 to 2013. The study sites were located in three different geographical regions: from the Białowieża Primeval Forest, Northern East Poland, through Central Poland, to the Lower Silesia Province, Southern West Poland. We investigated eight populations of E. helleborine: four from natural habitats and four from anthropogenic habitats. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 program (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from eight populations.
Results. We observed that in anthropogenic populations: i) shoots were higher than shoots from natural populations, ii) flowers differed significantly in terms of ten biometric features between habitats, iii) the genome size differed significantly between the plants growing in natural and anthropogenic habitats.
Discussion. According to some researchers, the presence of phenotypic plasticity and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features. i.e.: high shoots, long inflorescence and long, broad leaves. We agree, however, that it is difficult to isolate a taxonomic unit for ecofen due to the lack of experimental research.