bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)
Authors: Menon Mitra , Bagley Justin C. , Friedline Christopher J. , Whipple Amy V. , Schoettle Anna W. , Leal‐Sàenz Alejandro , Wehenkel Christian , Molina‐Freaner Francisco , Flores‐Rentería Lluvia , Gonzalez‐Elizondo M. Socorro , Sniezko Richard A. , Cushman Samuel A. , Waring Kristen M. , Eckert Andrew J. 
Published: February 2018

AbstractInteractions between extrinsic factors, such as disruptive selection and intrinsic factors, such as genetic incompatibilities among loci, often contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and Pinus flexilis. Utilizing ecological niche modelling, demographic modelling and genomic cline analyses, we illustrated a divergence history with continuous gene flow. Our results supported an abundance of advanced generation hybrids and a lack of loci exhibiting steep transition in allele frequency across the hybrid zone. Additionally, we found evidence for climate‐associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. These results are consistent with extrinsic factors, such as climate, being an important isolating mechanism. A build‐up of intrinsic incompatibilities and of coadapted gene complexes is also apparent, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in facilitating speciation. Overall, our findings lend support to the hypothesis that varying strength and direction of selection pressures across the long lifespans of conifers, in combination with their other life history traits, delays the evolution of strong intrinsic incompatibilities.
Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists
Authors: Ivens Aniek B. F. , Gadau Alice , Kiers E. Toby , Kronauer Daniel J. C. 
Published: February 2018

AbstractMutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host–microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew‐producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species‐specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants’ microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar‐processing Acetobacteraceae bacteria, known from other honeydew‐feeding ants and which likely reside extracellularly in the ants’ guts. These ant–microbe associations are arguably more “open” and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.
Ultrarare marine microbes contribute to key sulphur‐related ecosystem functions
Authors: Kalenitchenko Dimitri , Le Bris Nadine , Peru Erwan , Galand Pierre E. 
Published: February 2018

AbstractThe description of a rare biosphere within microbial communities has created great interest because microbes play a fundamental role in the functioning of all ecosystems on earth. Despite recent progress in understanding the ecology of the rare biosphere, the concept itself is still discussed, and fundamental questions remain. Here, we target the seed bank compartment of the rare biosphere, assess the level of rarity at which micro‐organisms are still able to colonize an ecosystem and investigate whether rare species are functionally redundant. Using an original experimental design where wood in aquaria was inoculated with increasingly diluted coastal seawater, we show that bacteria that represented as few as 0.00000002% of the cells in the environment (or 1 cell in 10 L of seawater) were still able to grow and play key roles within the ecosystem. Our experiment further showed that some bacteria can be replaced by others that have the potential to fulfil the same metabolic tasks. This finding suggests some functional redundancy within bacterial species. However, when ultrarare bacteria were progressively removed, productivity was reduced, and below a certain threshold some processes were lost, and the function of the ecosystem was altered. Overall the study shows that bacteria that are not detected by high‐throughput sequencing approaches are nevertheless viable and able to colonize new ecosystems, suggesting the need to consider ultrarare microbes in the marine environment.
High‐Throughput DNA sequencing of ancient wood
Authors: Wagner Stefanie , Lagane Frédéric , Seguin‐Orlando Andaine , Schubert Mikkel , Leroy Thibault , Guichoux Erwan , Chancerel Emilie , Bech‐Hebelstrup Inger , Bernard Vincent , Billard Cyrille , Billaud Yves , Bolliger Matthias , Croutsch Christophe , Čufar Katarina , Eynaud Frédérique , Heussner Karl Uwe , Köninger Joachim , Langenegger Fabien , Leroy Frédéric , Lima Christine , Martinelli Nicoletta , Momber Garry , Billamboz André , Nelle Oliver , Palomo Antoni , Piqué Raquel , Ramstein Marianne , Schweichel Roswitha , Stäuble Harald , Tegel Willy , Terradas Xavier , Verdin Florence , Plomion Christophe , Kremer Antoine , Orlando Ludovic 
Published: February 2018

AbstractReconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.
Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals
Authors: Parkinson John Everett , Bartels Erich , Devlin‐Durante Meghann K. , Lustic Caitlin , Nedimyer Ken , Schopmeyer Stephanie , Lirman Diego , LaJeunesse Todd C. , Baums Iliana B. 
Published: February 2018

AbstractAs climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways, it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long‐term common garden experiments, we exposed over 30 genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of 20 genes, we designed a high‐throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying predictive and/or diagnostic thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality and bleaching susceptibility. Nevertheless, we identified several promising diagnostic biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.
Esophageal dysmotility according to Chicago classification v3.0 vs v2.0: Implications for association with reflux, bolus clearance, and allograft failure post‐lung transplantation
Authors: Tangaroonsanti A. , Vela M. F. , Crowell M. D. , DeVault K. R. , Houghton L. A. 
Published: February 2018

AbstractBackgroundProximal reflux and incomplete transit of boluses swallowed are risk factors for obstructive chronic lung allograft dysfunction (o‐CLAD) post‐lung transplantation (LTx). Likewise, so is esophagogastric junction outflow obstruction (EGJOO), but not hypo‐contractility, when diagnosed using Chicago Classification (CC) v3.0. Given, peristaltic breaks as defined using CCv2.0 can prolong esophageal clearance, both swallowed and refluxed, but which are deemed within normality using CCv3.0, our aim was to determine whether hypo‐contractility as diagnosed using CCv2.0, influences the association with reflux, along with its clearance, and that of boluses swallowed, and thus its association to allograft failure.MethodsEsophageal motility abnormalities were classified using CC v3.0 and v2.0 in 50 patients post‐LTx (26 female, 55 years (20‐73 years)).ResultsReclassification from CCv3.0 to v2.0 resulted in 7 patients with normal motility being reclassified to hypo‐contractility (n = 6) or hyper‐contractility (n = 1); 2 patients with hypo‐contractility to normal motility; and 3 patients with EGJOO without hyper‐contractility to EGJOO with hyper‐contractility. The main consequence of reclassification was that the sub‐group exhibiting hypo‐contractility became more likely to have abnormal numbers of reflux events (P = .025) and incomplete bolus transit (P = .002) than those with normal motility using CCv2.0; associations not seen using CCv3.0. Irrespective of CC used only patients with EGJOO appeared more likely to develop o‐CLAD than those with normal motility (P < .05).ConclusionsIrrespective of CC used, o‐CLAD appears linked to EGJOO. CCv2.0 however, accentuates the increased reflux and incomplete bolus transit associated with hypo‐contractility post‐LTx, suggesting that these motor abnormalities, though considered minor, may be of importance after lung transplant.
Delayed gastric emptying and altered antrum protein metabolism during activity‐based anorexia
Authors: Nobis S. , Morin A. , Achamrah N. , Belmonte L. , Legrand R. , Chan P. , do Rego J.‐L. , Vaudry D. , Gourcerol G. , Déchelotte P. , Goichon A. , Coëffier M. 
Published: February 2018

AbstractBackgroundAnorexia nervosa, a restrictive eating disorder, is often associated with gastrointestinal disorders, particularly a delayed gastric emptying. However, the mechanisms remained poorly documented. Thus, we aimed to evaluate gastric emptying and antrum protein metabolism in the Activity‐Based Anorexia model (ABA).MethodsFemales C57Bl/6 mice were randomized into 3 groups: Control, ABA, and Limited Food Access (LFA). Food access has been progressively limited from 6 h/day at day 6 to 3 h/day at day 9 and until day 17. ABA mice had free access to an activity wheel. Gastric emptying was assessed. On gastric extracts, a proteomic analysis was performed, as well as an evaluation of protein synthesis and protein oxidation.Key ResultsBoth LFA and ABA mice exhibited a delayed gastric emptying compared with Controls (P < .05). Proteomic approach revealed 15 proteins that were differentially expressed. Among these proteins, we identified 2 clusters of interest contributing to (i) the organization of muscle fiber with ACTA2, VCL, KRT19, KRT8, and DES proteins and (ii) “heat shock proteins” with STIP1, HSPD1, and HSPA8 proteins. ABA mice specifically exhibited an increased rate of gastric oxidized proteins.Conclusions and InferencesDelayed gastric emptying observed in anorectic conditions appears to be secondary to malnutrition. However, an oxidative stress is specifically present in the stomach of ABA mice. Its role remains to be further studied.
Ectomycorrhizal host specificity in a changing world: can legacy effects explain anomalous current associations?
Authors: Lofgren Lotus , Nguyen Nhu H. , Kennedy Peter G. 
Published: February 2018

SummaryDespite the importance of ectomycorrhizal (ECM) fungi in forest ecosystems, knowledge about the ecological and co‐evolutionary mechanisms underlyingECMhost associations remains limited.Using a widely distributed group ofECMfungi known to form tight associations with trees in the family Pinaceae, we characterized host specificity among three uniqueSuillus–host species pairs using a combination of field root tip sampling and experimental bioassays.We demonstrate that theECMfungusS. subaureuscan successfully colonizeQuercushosts in both field and glasshouse settings, making this species unique in an otherwise Pinaceae‐specific clade. Importantly, however, we found that the colonization ofQuercusbyS. subaureusrequired co‐planting with a Pinaceae host.While our experimental results indicate that gymnosperms are required for the establishment of newS. subaureuscolonies, Pineaceae hosts are locally absent at both our field sites. Given the historical presence of Pineaceae hosts before human alteration, it appears the currentS. subaureus–Quercusassociations represent carryover from past host presence. Collectively, our results suggest that patterns ofECMspecificity should be viewed not only in light of current forest community composition, but also as a legacy effect of host community change over time.
Biogeographic constraints to marine conservation in a changing climate
Authors: Fredston‐Hermann Alexa , Gaines Steven D. , Halpern Benjamin S. 
Published: February 2018

AbstractThe siting of protected areas to achieve management and conservation objectives draws heavily on biogeographic concepts of the spatial distribution and connectivity of species. However, the marine protected area (MPA) literature rarely acknowledges how biogeographic theories underpin MPA and MPA network design. We review which theories from biogeography have been incorporated into marine spatial planning and which relevant concepts have yet to be translated to inform the next generation of design principles. This biogeographic perspective will only become more relevant as climate change amplifies these spatial and temporal dynamics, and as species begin to shift in and out of existing MPAs. The scale of climate velocities predicted for the 21st century dwarfs all but the largest MPAs currently in place, raising the possibility that in coming decades many MPAs will no longer contain the species or assemblages they were established to protect. We present a number of design elements that could improve the success of MPAs and MPA networks in light of biogeographic processes and climate change. Biogeographically informed MPA networks of the future may resemble the habitat corridors currently being considered for many terrestrial regions.
Treatment patterns, costs, and mortality among Medicare beneficiaries with CIED infection
Authors: Greenspon Arnold J. , Eby Elizabeth L. , Petrilla Allison A. , Sohail M. Rizwan 
Published: February 2018

AbstractBackgroundCardiac implantable electronic device (CIED) infection is a serious adverse event, but there are limited contemporary real‐world data on treatment pathways and associated costs in the Medicare population following diagnosis of CIED infection. Hence, this study evaluates postinfection treatment pathways and associated healthcare expenditures and mortality among Medicare fee‐for‐service beneficiaries with CIED infection.MethodsRetrospective cohort analysis of 5,401 beneficiaries who developed a device‐related infection in the year following implantation/upgraded CIED (1/1/2010–12/31/2012). Patients were followed‐up to 12 months/death following diagnosis of infection and were divided into mutually exclusive groups based on whether they underwent CIED system removal (Group I), or no CIED system intervention (Group II; IIA with or IIB without infection hospitalization). All‐cause healthcare resource utilization/expenditures were also measured.ResultsIn the year following infection, 64.1% of patients underwent device extraction, of who 2,109 (39.0%) had their device replaced (Group IA) and 1,355 (25.1%) had their device extracted without replacement (Group IB); 62.2% of patients were hospitalized and 25.3% of patients died. Mean Medicare payments‐per‐patient for facility‐based services by group were: IA = $62,638 (standard deviation [SD]: $46,830), IB = $50,079 (SD: $45,006), IIA = $77,397 (SD: $79,130), and IIB = $22,856 (SD: $31,167).ConclusionsHospitalizations were the largest cost driver; infection‐related costs, including cost of extraction/replacement, accounted for >50% of expenditures for patients with surgical/hospital intervention. Management of CIED infection in Medicare beneficiaries is associated with high healthcare expenditures in the year following infection. Additional measures to prevent device infection are needed to improve the outcomes and reduce costs in these patients.
Maternal supplementation alone with Lactobacillus rhamnosus HN001 during pregnancy and breastfeeding does not reduce infant eczema
Authors: Wickens Kristin , Barthow Christine , Mitchell Edwin A. , Stanley Thorsten V. , Purdie Gordon , Rowden Judy , Kang Janice , Hood Fiona , van den Elsen Lieke , Forbes‐Blom Elizabeth , Franklin Isobel , Barnes Phillipa , Fitzharris Penny , Maude Robyn M. , Stone Peter , Abels Peter , Murphy Rinki , Crane Julian 
Published: February 2018

AbstractBackgroundIn a randomized placebo‐controlled trial, we previously found that the probiotic Lactobacillus rhamnosus HN001 (HN001) taken by mothers from 35 weeks of gestation until 6 months post‐partum if breastfeeding and their child from birth to age 2 years halved the risk of eczema during the first 2 years of life. We aimed to test whether maternal supplementation alone is sufficient to reduce eczema and compare this to our previous study when both the mother and their child were supplemented.MethodsIn this 2‐centre, parallel double‐blind, randomized placebo‐controlled trial, the same probiotic as in our previous study (HN001, 6 × 109 colony‐forming units) was taken daily by mothers from 14‐16 weeks of gestation till 6 months post‐partum if breastfeeding, but was not given directly to the child. Women were recruited from the same study population as the first study, where they or their partner had a history of treated asthma, eczema or hay fever.ResultsWomen were randomized to HN001 (N = 212) or placebo (N = 211). Maternal‐only HN001 supplementation did not significantly reduce the prevalence of eczema, SCORAD ≥ 10, wheeze or atopic sensitization in the infant by 12 months. This contrasts with the mother and child intervention study, where HN001 was associated with reductions in eczema (hazard ratio (HR): 0.39, 95% CI 0.19‐0.79, P = .009) and SCORAD (HR = 0.61, 95% 0.37‐1.02). However, differences in the HN001 effect between studies were not significant. HN001 could not be detected in breastmilk from supplemented mothers, and breastmilk TGF‐β/IgA profiles were unchanged.ConclusionMaternal probiotic supplementation without infant supplementation may not be effective for preventing infant eczema.
Both Wittgenstein and Kant Beg the Question
Authors: Li Jing 
Published: February 2018

AbstractI shall show that the main argument forms of Wittgenstein's Tractatus and Kant's Critique of Pure Reason are Modus Tollens. I shall then argue that the main arguments of both books beg the question by addressing only one sub‐argument in each, although it is still in controversy whether begging the question is a genuine fallacy.
Revisiting the Mechanism of Hydrolysis of Betanin
Authors: Esteves Larissa C. , Pinheiro Amanda C. , Pioli Renan M. , Penna Tatiana C. , Baader Wilhelm J. , Correra Thiago C. , Bastos Erick L. 
Published: February 2018

AbstractBetanin (betanidin 5‐O‐β‐D‐glucoside) is a water‐soluble plant pigment used as a color additive in food, drugs and cosmetic products. Despite its sensitivity to light and heat, betanin maintains appreciable tinctorial strength in low acidic and neutral conditions, where the color of other plant pigments, such as anthocyanins, quickly fades. However, betanin is an iminium natural product that experiences acid‐ and base‐catalyzed hydrolysis to form the fairly stable betalamic acid and cyclo‐DOPA‐5‐O‐β‐D‐glucoside. Here, we show that the decomposition of betanin in aqueous phosphate solution pH 2–11 is subject to general base catalysis by hydrogen phosphate ion and intramolecular general acid and base catalysis, providing new insights on the mechanism of betanin hydrolysis. UV/Vis absorption spectrophotometry, 1H NMR spectroscopy and mass spectrometry were used to investigate product formation. Furthermore, theoretical calculations support the hypothesis that the nitrogen atom of the tetrahydropyridine ring of betanin is doubly protonated, as observed for structurally simpler amino dicarboxylic acids. Our results contribute to the study of betanin and other pigments belonging to the class of betalains and to deepen the knowledge on the chemical properties of imino acids as well as on iminium‐catalyzed modifications of carbonyl compounds in water.
Three species of Ulva (Ulvophyceae) from the Persian Gulf as potential sources of protein, essential amino acids and fatty acids
Authors: Pirian Kiana , Piri Khosro , Sohrabipour Jelveh , Blomster Jaanika 
Published: February 2018

SUMMARYThree species of the cosmopolitan genus Ulva (U. paschima, U. chaugulii and U. ohnoi) from the Persian Gulf were identified using morphological and molecular markers, and were analyzed for total lipids, fatty acids, proteins and amino acid profiles. Our results show that the studied Ulva species have high protein content (9−25% dry weight), contain essential fatty acids and nearly all essential amino acids. This suggests Ulva could have potential as a form of human nutrition and animal feed with a low carbon footprint.