bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of reproductive strategies between island and mainland Caribbean Gesneriaceae
Authors: Martén‐Rodríguez Silvana , Quesada Mauricio , Castro Abel‐Almarales , Lopezaraiza‐Mikel Martha , Fenster Charles B. 
Published: July 2015

Summary

The evolution of self‐pollination has long been considered an adaptive strategy to cope with low or variable pollinator service; however, alternative reproductive strategies, such as generalized pollination (>1 pollinator functional group), may also ensure plant reproductive success in environments with inadequate pollinator visitation.

Island–mainland systems provide ideal settings to assess the interaction between pollination and breeding systems in response to pollinator visitation because islands are often pollinator‐depauperate. This study compared 28 insular and 26 mainland species of Caribbean Gesneriaceae to test the hypothesis that low diversity and possibly low pollinator service on islands would lead to a greater frequency of generalized plant–pollinator interactions and/or a higher potential for autonomous self‐pollination in insular than in mainland species. We also assessed the hypothesis that epiphytic species should have greater autofertility than species occurring in other habitats.

Pollinator observations conducted in the field from 2004 to 2014 revealed bat, bee, butterfly, hummingbird, moth, and generalized pollination systems. Functional specialization in pollination systems was high in insular (71% of the species) and mainland sites (all species), but generalized and bat‐pollinated species were more common on islands. Overall, pollinator visitation rates did not differ between island and mainland; however, for hummingbird‐pollinated species, visitation rate was on average three times higher in mainland than island species. Autofertility indices (fruit set of bagged/outcross flowers) ranged from 0 to 1 and did not differ between island and mainland species. Species growing on rocks (rupiculous) and trees (epiphytic) had on average higher autofertility than terrestrial species.

Synthesis. This study revealed that alternative reproductive strategies are used in pollinator‐depauperate environments. Pollinator visitation is lower in insular hummingbird‐pollinated species (the ancestral pollination system of insular Gesneriaceae); therefore, generalized pollination may be considered a reproductive assurance mechanism evolved primarily on island environments. Contrary to the long‐standing tenet, however, autonomous self‐pollination was similar in island and mainland Gesneriaceae suggesting that: (i) generalized pollination provides a viable alternative to selfing in pollinator‐depauperate environments, (ii) autofertility as a reproductive assurance mechanism may be frequent in plant species from mainland regions in environments with unpredictable pollinator visitation and resource availability.
Seasonality in molecular and cytometric diversity of marine bacterioplankton: the re‐shuffling of bacterial taxa by vertical mixing
Authors: García Francisca C. , Alonso‐Sáez Laura , Morán Xosé Anxelu G. , López‐Urrutia Ángel 
Published: July 2015

SummaryThe ‘cytometric diversity’ of phytoplankton communities has been studied based on single‐cell properties, but the applicability of this method to characterize bacterioplankton has been unexplored. Here, we analysed seasonal changes in cytometric diversity of marine bacterioplankton along a decadal time‐series at three coastal stations in the Southern Bay of Biscay. Shannon–Weaver diversity estimates and Bray–Curtis similarities obtained by cytometric and molecular (16S rRNA tag sequencing) methods were significantly correlated in samples from a 3.5 year monthly time‐series. Both methods showed a consistent cyclical pattern in the diversity of surface bacterial communities with maximal values in winter. The analysis of the highly resolved flow cytometry time‐series across the vertical profile showed that water column mixing was a key factor explaining the seasonal changes in bacterial composition and the winter increase in bacterial diversity in coastal surface waters. Due to its low cost and short processing time as compared with genetic methods, the cytometric diversity approach represents a useful complementary tool in the macroecology of aquatic microbes.
Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons
Authors: Mishamandani Sara , Gutierrez Tony , Berry David , Aitken Michael D. 
Published: July 2015

SummaryEmerging evidence shows that hydrocarbonoclastic bacteria (HCB) may be commonly found associated with phytoplankton in the ocean, but the ecology of these bacteria and how they respond to crude oil remains poorly understood. Here, we used a natural diatom‐bacterial assemblage to investigate the diversity and response of HCB associated with a cosmopolitan marine diatom, Skeletonema costatum, to crude oil. Pyrosequencing analysis and qPCR revealed a dramatic transition in the diatom‐associated bacterial community, defined initially by a short‐lived bloom of Methylophaga (putative oil degraders) that was subsequently succeeded by distinct groups of HCB (Marinobacter, Polycyclovorans, Arenibacter, Parvibaculum, Roseobacter clade), including putative novel phyla, as well as other groups with previously unqualified oil‐degrading potential. Interestingly, these oil‐enriched organisms contributed to the apparent and exclusive biodegradation of substituted and non‐substituted polycyclic aromatic hydrocarbons (PAHs), thereby suggesting that the HCB community associated with the diatom is tuned to specializing in the degradation of PAHs. Furthermore, the formation of marine oil snow (MOS) in oil‐amended incubations was consistent with its formation during the Deepwater Horizon oil spill. This work highlights the phycosphere of phytoplankton as an underexplored biotope in the ocean where HCB may contribute importantly to the biodegradation of hydrocarbon contaminants in marine surface waters.
TrueAllele® Genotype Identification on DNA Mixtures Containing up to Five Unknown Contributors
Authors: Perlin Mark W. , Hornyak Jennifer M. , Sugimoto Garett , Miller Kevin W.P. 
Published: July 2015

AbstractComputer methods have been developed for mathematically interpreting mixed and low‐template DNA. The genotype modeling approach computationally separates out the contributors to a mixture, with uncertainty represented through probability. Comparison of inferred genotypes calculates a likelihood ratio (LR), which measures identification information. This study statistically examined the genotype modeling performance of Cybergenetics TrueAllele® computer system. High‐ and low‐template DNA mixtures of known randomized composition containing 2, 3, 4, and 5 contributors were tested. Sensitivity, specificity, and reproducibility were established through LR quantification in each of these eight groups. Covariance analysis found LR behavior to be relatively invariant to DNA amount or contributor number. Analysis of variance found that consistent solutions were produced, once a sufficient number of contributors were considered. This study demonstrates the reliability of TrueAllele interpretation on complex DNA mixtures of representative casework composition. The results can help predict an information outcome for a DNA mixture analysis.
Mediated Modeling in Water Resource Dialogues Connecting Multiple Scales
Authors: van den Belt Marjan , Blake Daniella 
Published: July 2015

AbstractWe observe a paradigm shift toward collaborative, multi‐level (from local to global) water management and suggestions for scale‐related design principles in the literature. Decision‐support tools are needed that can help achieve scale design principles. Mediated modeling (MM) refers to model building with people, rather than for people. This tool belongs to a family of participatory, systems oriented tools. This article explores their suitability for addressing challenges and principles that arise at multiple‐scales. MM can promote the understanding of cross‐level and cross‐scale links, creating salient, credible, and legitimate knowledge and encouraging boundary functions. Prerequisites for successful MM processes include an openness and willingness to collaborative learning. As new “meso‐level” institutions emerge to address complex challenges in water management collaboratively, tools like MM may play an important role in structuring dialogues, developing adaptive management capacity and advance an ecosystem services approach.
Taxonomic challenges in freshwater fishes: a mismatch between morphology andDNAbarcoding in fish of the north‐eastern part of the Congo basin
Authors: Decru Eva , Moelants Tuur , De Gelas Koen , Vreven Emmanuel , Verheyen Erik , Snoeks Jos 
Published: July 2015

AbstractThis study evaluates the utility ofDNAbarcoding to traditional morphology‐based species identifications for the fish fauna of the north‐eastern Congo basin. We comparedDNAsequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio ‘nearest‐neighbour distance/maximum intraspecific divergence’ was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNAdata exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, theDNAbarcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate whyDNAbarcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.
Recombination detection in Aspergillus fumigatus through single nucleotide polymorphisms typing
Authors: Teixeira Joana , Amorim António , Araujo Ricardo 
Published: July 2015

SummaryThe first evidence of sexual reproduction in Aspergillus fumigatus was reported in 2009. Nevertheless, it remains difficult to understand how A. fumigatus is able to reproduce through this mode in its natural environment and how frequently this occurs. The aim of this study was to analyse single nucleotide polymorphisms (SNPs) in a set of environmental and clinical isolates of A. fumigatus to detect signatures of recombination. A group of closely related Portuguese A. fumigatus isolates was characterized by mating type and the genetic diversity of the intergenic regions, microsatellites and multilocus sequence typing (MLST) genes. A group of 19 SNPs, organized in nine association groups and inherited in blocks, was identified and compared. Several variations on the association panel were detected on reference isolates of A. fumigatus AF293 and A1163, the sequence types available at MLST database and six clinical and environmental Portuguese isolates. About one to four haplotype disruptions were observed per isolate. Considering clinical and environmental isolates, sexual reproduction seems to occur more frequently than previously admitted in A. fumigatus. In this study, a practical SNP approach is proposed for detection of recombination events in larger collections of A. fumigatus.
Detecting collective behaviour in animal relocation data, with application to migrating caribou
Authors: Dalziel Benjamin D. , Corre Mael Le , Côté Steeve D. , Ellner Stephen P. 
Published: July 2015

Summary

Collective behaviour can allow populations to have emergent responses to uncertain environments, driven by simple interactions among nearby individuals. High‐throughput ethological studies, where individual behaviour is closely observed in each member of a population (typically in the laboratory or by simulation), have revealed that collective behaviour in populations requires only rudimentary cognitive abilities in individuals and could therefore represent a widespread adaptation to life in an uncertain world. However, the ecological significance of collective behaviour is not yet well understood, as most studies to date have been confined to specialized situations that allow intensive monitoring of individual behaviour.

Here, we describe a way to screen for collective behaviour in ecological data that is sampled at a coarser resolution than the underlying behavioural processes. We develop and test the method in the context of a well‐studied model for collective movement in a noisy environmental gradient. The large‐scale distribution patterns associated with collective behaviour are difficult to distinguish from the aggregated responses of independent individuals in this setting because independent individuals also align to track the gradient. However, we show that collective idiosyncratic deviations from the mean gradient direction have high predictive value for detecting collective behaviour. We describe a method of testing for these deviations using the average normalized velocity of the population.

We demonstrate the method using data from satellite tracking collars on the migration patterns of caribou (Rangifer tarandus), recovering evidence that collective behaviour is a key driver of caribou migration patterns. We find moreover that the relative importance of collective behaviour fluctuates seasonally, concurrent with the timing of migration and reproduction.

Collective behaviour is a potentially widespread dynamic property of populations that can, in some cases, be detected in coarsely sampled ecological data.
Native recolonization following control of invasive Ruellia simplex in a cypress floodplain forest
Authors: Reinhardt Adams Carrie , Wiese Christine , Lee Leah C. 
Published: July 2015

AbstractQuestionWhat factors constrain establishment of native plant species after removal of a dominant invasive plant species? Specifically, we tested whether missing soil seed banks, elevated soil nutrients and invasion by other non‐native species explained the lack of recovery of native species.LocationBald‐cypress‐dominated (Taxodium distichum) floodplain forest. Paynes Prairie Preserve State Park, Alachua County, FL, US.MethodsWe assayed the plant composition of the soil seed bank to a depth of 5 cm and analysed soil nutrient levels in a floodplain forest invaded by Ruellia simplex. We measured percentage cover of vegetation 1 yr after herbicide application to control R. simplex.ResultsMany native species (largely perennials) and very few R. simplex emerged from the seed bank assay. Herbicide application reduced cover of R. simplex, but 1 yr post‐herbicide vegetation cover lacked native perennials, and instead was largely comprised of novel invaders and early successional (annual) natives. Across locations, levels of some soil nutrients (P, Mg) and pH were higher in R. simplex‐invaded plots than in uninvaded plots. Similarly, R. simplex‐invaded plots were significantly correlated with soil K and Ca levels at some locations but not others.ConclusionIt seems most probable that watershed‐level factors, including soil nutrients and pH, as well as changes in hydrology are interacting with site‐level factors, such as remnant invasive non‐ Ruellia simplex plant propagules and vegetative propagules of R. simplex to constrain long‐term native plant community establishment. Propagule limitation from the soil seed bank is not likely a barrier to native plant recolonization in floodplain forests after removal of invasive R. simplex, as diversity and density of native species emerged from the soil seed bank was high and density of R. simplex in the soil seed bank was extremely low. It does seem likely that soil properties are influencing the plant community. A critical next step will be identification of native species tolerant of altered soil and water conditions if restoration efforts are to succeed. However, further research on all spatial levels is needed to effectively restore degraded floodplain forests, especially at the broader watershed level.
Optimizing the management of patients with spinal myeloma disease
Authors: Molloy Sean , Lai Maggie , Pratt Guy , Ramasamy Karthik , Wilson David , Quraishi Nasir , Auger Martin , Cumming David , Punekar Maqsood , Quinn Michael , Ademonkun Debo , Willis Fenella , Tighe Jane , Cook Gordon , Stirling Alistair , Bishop Timothy , Williams Cathy , Boszczyk Bronek , Reynolds Jeremy , Grainger Mel , Craig Niall , Hamilton Alastair , Chalmers Isobel , Ahmedzai Sam , Selvadurai Susanne , Low Eric , Kyriakou Charalampia ,   the UK Spinal Myeloma Working Group
Published: July 2015

SummaryMyeloma is one of the most common malignancies that results in osteolytic lesions of the spine. Complications, including pathological fractures of the vertebrae and spinal cord compression, may cause severe pain, deformity and neurological sequelae. They may also have significant consequences for quality of life and prognosis for patients. For patients with known or newly diagnosed myeloma presenting with persistent back or radicular pain/weakness, early diagnosis of spinal myeloma disease is therefore essential to treat and prevent further deterioration. Magnetic resonance imaging is the initial imaging modality of choice for the evaluation of spinal disease. Treatment of the underlying malignancy with systemic chemotherapy together with supportive bisphosphonate treatment reduces further vertebral damage. Additional interventions such as cement augmentation, radiotherapy, or surgery are often necessary to prevent, treat and control spinal complications. However, optimal management is dependent on the individual nature of the spinal involvement and requires careful assessment and appropriate intervention throughout. This article reviews the treatment and management options for spinal myeloma disease and highlights the value of defined pathways to enable the proper management of patients affected by it.
Recent advances in antibody‐based therapies for Hodgkin Lymphoma
Authors: Peggs Karl S. 
Published: July 2015

SummaryAlthough a poster child for the development and refinement of multi‐modal multi‐agent therapeutic strategies, Hodgkin Lymphoma has, until recently, lagged behind other lymphomas in terms of the use of therapeutic monoclonal antibodies. This situation has now changed dramatically, with the rapid emergence both of a toxin‐conjugated tumour‐selective anti‐CD30 antibody, and of antibodies targeting immunological checkpoints, most notably PD‐1 (also termed PDCD1). The former provides an efficient targeting vehicle for delivery of a potent synthetic anti‐mitotic drug, with ultimate efficacy independent of immunological activity. The latter are members of a class of drugs representing a new paradigm in immune‐oncological therapies that are designed to enhance pre‐existent anti‐tumour T cell activities. The role of both in the overall treatment pathway will continue to evolve over coming years. Hodgkin Lymphoma has once again become emblematic of the major trend shifts in cancer therapy.
Multiple re‐advances of a Lake Vättern outlet glacier during Fennoscandian Ice Sheet retreat, south‐central Sweden
Authors: Greenwood Sarah L. , O'Regan Matt , Swärd Henrik , Flodén Tom , Ananyev Roman , Chernykh Denis , Jakobsson Martin 
Published: July 2015

Lake Vättern represents a critical region geographically and dynamically in the deglaciation of the Fennoscandian Ice Sheet. The outlet glacier that occupied the basin and its behaviour during ice‐sheet retreat were key to the development and drainage of the Baltic Ice Lake, dammed just west of the basin, yet its geometry, extent, thickness, margin dynamics, timing and sensitivity to regional retreat forcing are rather poorly known. The submerged sediment archives of Lake Vättern represent a missing component of the regional Swedish deglaciation history. Newly collected geophysical data, including high‐resolution multibeam bathymetry of the lake floor and seismic reflection profiles of southern Lake Vättern, are used here together with a unique 74‐m sediment record recently acquired by drill coring, and with onshore LiDAR‐based geomorphological analysis, to investigate the deglacial environments and dynamics in the basin and its terrestrial environs. Five stratigraphical units comprise a thick subglacial package attributed to the last glacial period (and probably earlier), and an overlying >120‐m deglacial sequence. Three distinct retreat–re‐advance episodes occurred in southern Lake Vättern between the initial deglaciation and the Younger Dryas. In the most recent of these, ice overrode proglacial lake sediments and re‐advanced from north of Visingsö to the southern reaches of the lake, where ice up to 400 m thick encroached on land in a lobate fashion, moulding crag‐and‐tail lineations and depositing till above earlier glacifluvial sediments. This event precedes the Younger Dryas, which our data reveal was probably restricted to north‐central sectors of the basin. These dynamics, and their position within the regional retreat chronology, indicate a highly active ice margin during deglaciation, with retreat rates on average 175 m a−1. The pronounced topography of the Vättern basin and its deep proglacial‐dammed lake are likely to have encouraged the dynamic behaviour of this major Fennoscandian outlet glacier.
European glacial relict snails and plants: environmental context of their modern refugial occurrence in southern Siberia
Authors: Horsák Michal , Chytrý Milan , Hájková Petra , Hájek Michal , Danihelka Jiří , Horsáková Veronika , Ermakov Nikolai , German Dmitry A. , Kočí Martin , Lustyk Pavel , Nekola Jeffrey C. , Preislerová Zdenka , Valachovič Milan 
Published: July 2015

Knowledge of present‐day communities and ecosystems resembling those reconstructed from the fossil record can help improve our understanding of historical distribution patterns and species composition of past communities. Here, we use a unique data set of 570 plots explored for vascular plant and 315 for land‐snail assemblages located along a 650‐km‐long transect running across a steep climatic gradient in the Russian Altai Mountains and their foothills in southern Siberia. We analysed climatic and habitat requirements of modern populations for eight land‐snail and 16 vascular plant species that are considered characteristic of the full‐glacial environment of central Europe based on (i) fossil evidence from loess deposits (snails) or (ii) refugial patterns of their modern distributions (plants). The analysis yielded consistent predictions of the full‐glacial central European climate derived from both snail and plant populations. We found that the distribution of these 24 species was limited to the areas with mean annual temperature varying from −6.7 to 3.4 °C (median −2.5 °C) and with total annual precipitation varying from 137 to 593 mm (median 283 mm). In both groups there were species limited to areas with colder and drier macroclimates (e.g. snails Columella columella and Pupilla loessica, and plants Kobresia myosuroides and Krascheninnikovia ceratoides), whereas other species preferred areas with relatively warmer and/or moister macroclimates (e.g. snails Pupilla turcmenica and P. alpicola, and plants Artemisia laciniata and Carex capillaris). Analysis of climatic conditions also indicated that distributional shifts of the studied species during the Pleistocene/Holocene transition were closely related to their climatic tolerances. Our results suggest that the habitat requirements of southern Siberian populations can provide realistic insights into the reconstruction of Eurasian, especially central European, glacial environments. Data obtained from modern populations also highlight the importance of wet habitats as refugia in the generally dry full‐glacial landscape.