bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic and biogeographic implications of a phylogenetic analysis of the Campanulaceae based on three chloroplast genes
Authors: Haberle Rosemarie C. , Dang Ashley , Lee Tammy , Peñaflor Cynthia , Cortes-Burns Helen , Oestreich Andrea , Raubeson Linda , Cellinese Nicoletta , Edwards Erika J. , Kim Sang-Tae , Eddie William M.M. , Jansen Robert K. 
Published: February 2019

AbstractCampanulaceae are a large, nearly cosmopolitan angiosperm family that are well‐accepted as monophyletic but whose intrafamilial and intrageneric relationships are controversial. We used DNA sequences of the chloroplast genes atpB, matK, and rbcL to infer the phylogeny of 102 taxa in 41 genera plus four outgroup taxa. Our sampling represents a wide taxonomic and geographic diversity from within the family. Results from maximum parsimony and Bayesian analyses provide strong evidence for two major clades in the family, with the platycodonoids sister to the remaining members of the family, the wahlenbergioids and campanuloids. There are two clear divisions within the campanuloids that correspond well with the historical Campanula s.str. and Rapunculus groups of Boissier and Fedorov. The phylogenetic positions of the Northern European species Wahlenbergia hederacea and the genus Jasione remain unresolved. Our results also provide evidence that the large, inclusive genera Wahlenbergia and Campanula are polyphyletic, and the smaller, segregate genera Symphyandra, Prismatocarpus, and Legousia are not monophyletic. Insights are provided into the different biogeographic origins of several oceanic island endemics. Heterochaenia, Nesocodon, and Berenice occur in a single clade, which suggests a single colonization of the Indian Ocean Mascarene Islands. Conversely, Wahlenbergia linifolia and W. angustifolia of St. Helena Island in the mid‐Atlantic are not sister taxa. The Macaronesian taxa, Canarina canariensis, and Musschia aurea, which display convergent bird‐pollination adaptations and with Azorina vidalii of the Azores, woody growth form, fall into separate major lineages. The North American Campanulaceae also do not form a monophyletic group, providing evidence that these taxa are the descendents of multiple introductions onto the North American continent.
Generic delimitations within the Sium alliance (Apiaceae tribe Oenantheae) inferred from cpDNA rps16‐5′trnK(UUU) and nrDNA ITS sequences
Authors: Spalik Krzysztof , Downie Stephen R. , Watson Mark F. 
Published: February 2019

AbstractPrevious studies of the Sium alliance within Apiaceae tribe Oenantheae, based only on nrDNA ITS sequences, revealed that the genera Sium and Berula may not be monophyletic. To confirm issues of relationships and implement nomenclatural changes, we obtained additional ITS sequences as well as independent data from the cpDNA rps16‐5′trnK(UUU) region which includes the rps16 intron and the spacer region between genes rps16 and 5′trnK. We examined 78 accessions of tribe Oenantheae including representatives of all 23 species of the Sium alliance (Afrocarum, 1 sp.; Apium pro parte/Helosciadium, 5 spp.; Berula, 1 sp.; Cryptotaenia, 4 spp.; Sium, 12 spp.). Results of Bayesian analysis and maximum parsimony analyses of partitioned and combined data revealed that the Sium alliance is strongly supported as monophyletic. Within this clade, four major subclades are resolved. Three of these subclades comprise species that were traditionally placed in Cryptotaenia, Helosciadium/Apium pro parte, and Sium s.str. (9 spp.). A restitution of the genus Helosciadium, including all Eurasian species of Apium with the exception of A. graveolens, the generitype, is supported by both molecular data and morphology. The fourth subclade, Berula sensu lato, encompasses all representatives of a widely distributed B. erecta, a monotypic African Afrocarum, and three members of Sium from Africa (S. repandum) and Saint Helena (S. bracteatum, S. burchellii). The Sium species from Saint Helena form a sister group to African representatives of B. erecta. The Berula sensu lato clade is recognized at the generic level and these four African/Saint Helena species are transferred into Berula. African and North American populations of B. erecta are distinct from their Eurasian relatives and are therefore proposed to be treated as separate species (B. thunbergii and B. incisa, respectively).
Phylogenetic relationships of Afrobrunnichia Hutch. & Dalziel (Polygonaceae) based on three chloroplast genes and ITS
Authors: Sanchez Adriana , Kron Kathleen A. 
Published: February 2019

AbstractThe subfamily Eriogonoideae (Polygonaceae) comprises 31 genera of which 20 are part of the radiation of Eriogonum and allied genera in North America. The eleven remaining genera are all woody, and include species that are vines, trees and shrubs. They are distributed in North, Central and South America, the Antilles and West Africa, and in most cases the number of species is not known, even less their relationships. Brunnichia is a woody vine native to the southeastern United States. In the past some authors have recognized species of Brunnichia as occurring in West Africa. Alternately, others recognized two genera, Brunnichia corresponding only to the American species and Afrobrunnichia to the African species. In this study two accessions of Afrobrunnichia erecta from Gabon and Ghana, representatives of Podopterus, Brunnichia ovata, and several other species of Polygonaceae are analyzed using three chloroplast genes (rbcL, matK, ndhF) and the nuclear ribosomal internal transcribed spacer (ITS). Maximum parsimony and maximum likelihood analyses strongly support Afrobrunnichia as sister to the remaining genera of Eriogonoideae; Brunnichia and Antigonon are strongly supported as sister genera. Based on these results, Afrobrunnichia is supported as a separate genus from Brunnichia. Podopterus is placed sister to Coccoloba.
No polymorphism of melatonin receptor 1A (MTNR1A) gene was found in Markhoz goat
Authors: Abdolahi Sargol , Shokrollahi Borhan , Saadati Nazila , Morammazi Salim 
Published: February 2019

AbstractMelatonin is the main hormone of seasonal breeding in sheep and goat which has an effect on reproductive organs via its receptors. Studies have shown that mutations in melatonin receptor 1A (MTNR1A) gene are related to litter size as well as the ovulation rate in sheep and goats. In this study, polymorphism of two loci in MTNR1A melatonin receptor gene was studied in order to survey their relationship with litter size in Markhoz goats. PCR primers were employed to mask polymorphisms of MTNR1A in 150 does by PCR‐RFLP method. After DNA extraction, the PCR‐RFLP was performed using Ecol31I and HpaI restriction enzymes. Results showed that these loci were not polymorphic. These results show that the fecundity of Markhoz goats is not linked to MTNR1A. No polymorphism in MTNR1A was found in Markhoz goats, therefore, it is essential to test polymorphism of other genes or loci to facilitate marker‐assisted selection techniques to improve reproduction traits in Markhoz goats.
Estimation of greenhouse gas emissions from a wastewater treatment plant using membrane bioreactor technology
Authors: Chen Ying‐Chu 
Published: February 2019

AbstractWastewater treatment plants (WWTPs) using membrane bioreactor (MBR) technology have been considered a significant source of greenhouse gas (GHG) emissions. This study chose a small‐scale wastewater treatment plant using MBR technology to estimate its potential for GHG emissions. The total GHG emissions from this wastewater treatment plant ranged from 2,802 to 11,946 kg CO2‐eq/month within the 4‐year study period, and they were mainly attributable to electricity consumption (79.94%) followed by chemical usages (17.13%) and on‐site GHG emissions (2.93%). The on‐site GHG emissions varied monthly, but most of them ranged from 80 to 160 kg CO2‐eq/month. The aeration tank was an important operating unit for GHG emissions. Off‐site GHG emissions mainly came from carbon dioxide (CO2) emissions resulting from electricity consumption. The results of this study provide useful information about the potential of GHG emissions from WWTPs using MBR technology and indicate that WWTPs can be sustainably managed.Practitioner points

Wastewater treatment plants have been considered a source of greenhouse gas emissions.

Total greenhouse gas emissions from the wastewater treatment plants using membrane bioreactor were mainly attributable to electricity consumption.

On‐site greenhouse gas emissions were relatively insignificant in this study.
Magnetic resonance imaging of stem cell–macrophage interactions with ferumoxytol and ferumoxytol‐derived nanoparticles
Authors: Nejadnik Hossein , Tseng Jessica , Daldrup‐Link Heike 
Published: February 2019

“Off the shelf” allogeneic stem cell transplants and stem cell nano‐composites are being used for the treatment of degenerative bone diseases. However, major and minor histocompatibility antigens of therapeutic cell transplants can be recognized as foreign and lead to their rejection by the host immune system. If a host immune response is identified within the first week post‐transplant, immune modulating therapies could be applied to prevent graft failure and support engraftment. Ferumoxytol (Feraheme™) is an FDA approved iron oxide nanoparticle preparation for the treatment of anemia in patients. Ferumoxytol can be used “off label” as an magnetic resonance (MR) contrast agent, as these nanoparticles provide measurable signal changes on magnetic resonance imaging (MRI). In this focused review article, we will discuss three methods to localize and identify innate immune responses to stem cell transplants using ferumoxytol‐enhanced MRI, which are based on tracking stem cells, tracking macrophages or detecting mediators of cell death: (a) monitor MRI signal changes of ferumoxytol‐labeled stem cells in the presence or absence of innate immune responses, (b) monitor influx of ferumoxytol‐labeled macrophages into stem cell implants, and (c) monitor apoptosis of stem cell implants with caspase‐3 activatable nanoparticles. These techniques can detect transplant failure at an early stage, when immune‐modulating interventions can potentially preserve the viability of the cell transplants and thereby improve bone and cartilage repair outcomes. Approaches 1 and 2 are immediately translatable to clinical practice.This article is categorized under:

Diagnostic Tools > in vivo Nanodiagnostics and Imaging
Nanotechnology Approaches to Biology > Cells at the Nanoscale
Diagnostic Tools > Biosensing
Mathematical modeling and analysis of hydroelastodynamics inside a solid tumor containing deformable tissue
Authors: Alam Meraj , Dey Bibaswan , Sekhar G. P. Raja 
Published: February 2019

AbstractPresent work reports a mathematical modeling for the interstitial hydrodynamics and mechanical behavior of the solid phase inside a solid tumor. A tumor tissue is a visco‐poroelastic deformable living biomaterial with cellular phase and extracellular matrix (ECM) as the solid phase (also small volume of blood vessels) and physiological extracellular fluid as the fluid phase. The intravascular fluid or blood and the interstitial fluid form a single fluid phase. We write down the mass and momentum balance equations for both the phases. The momentum equations are coupled due to the relative interaction (or drag) force between the phases. This study shows the well‐posedness of poroelastohydrodynamics in the weak sense under following assumptions (i) motion of interstitial fluid flow and solid phase deformation are slow and (ii) nutrient proliferation rate is much faster than the tumor cell growth. Subsequently, we use the semi‐discrete Galerkin method to establish the well‐posedness. Further, we simulate some analytical results corresponding to the one‐dimensional spherical symmetry model. Our results on the unsteady poroelastohydrodynamic model would give an idea about the time required for the necrosis formation from the initial stage of perfusion based on the system energy which can be computed using L2 and H1 norms.
Dynamic analysis of nonlinear rotating composite shafts excited by non‐ideal energy source
Authors: Kafi H. R. , Hosseini S. A. A. 
Published: February 2019

AbstractIn this article, nonlinear nonstationary vibration of a rotating composite shaft passing through critical speed excited by non‐ideal energy source is investigated. Geometrical nonlinearity, gyroscopic effect, rotary inertia and coupling due to material anisotropy are considered, while shear deformation is neglected. By using Hamilton principle, axial‐flexural‐flexural‐torsional‐rotational equations of motion for a composite shaft with variable rotational speed are derived. External source is assumed as non‐ideal that causes the interaction between external torque and vibrating system. To obtain the approximate analytical solution, perturbation theory (multiple scales method) is applied to reduce the equations in the neighborhood of the first critical speed. Although, the analysis is done for the first critical speed, one‐mode discretization is not enough. Indeed, at least two modes is required to obtain accurate results. The effects of external damping, eccentricity, angle of fibers, resistive torque, nonlinear terms, and also the effect of the extensional–torsional coupling on occurrence of Sommerfeld effect are investigated. It is shown that nonlinearity and coupling possess significant effect on the prediction of Sommerfeld phenomenon. Moreover, as observed, with appropriate implementation of layup and stacking sequence, one can obtain the best performance for the nonstationary behavior of composite shaft.
Finding the Limits of the Limes: Setting the Scene
Authors: Verhagen Philip , Joyce Jamie , Groenhuijzen Mark R. 
Published: February 2019

AbstractThe Dutch Roman limes zone has a rich history of archaeological and historical research. In this paper, we present an overview of the current state of knowledge as an introduction to other chapters in this volume dealing with the area’s demography, economy and transport system (Chaps. 2, 3, 7, 9 and 12). The main historical developments are sketched against the background of ongoing archaeological research in the area, and the main hypotheses concerning the development of settlement and the rural economy are discussed.
Footprints and Cartwheels on a Pixel Road: On the Applicability of GIS for the Modelling of Ancient (Roman) Routes
Authors: Parcero-Oubiña César , Güimil-Fariña Alejandro , Fonte João , Costa-García José Manuel 
Published: February 2019

AbstractGIS-based digital modelling tools, such as the well-known least cost paths (LCP), have been widely used in archaeology in recent years as ways of approaching forms of mobility in the past. Roman roads are among the best-known examples of ancient networks of paths and have been widely studied using such approaches. In this paper, we shall make a general reflection on the applicability of those tools for the modelling and analysis of ancient routes, with a special focus on Roman roads. Drawing from a case study in the NW Iberian Peninsula, we shall discuss certain aspects related to the potential and limits of Cumulative Costs, LCP and other related tools for the modelling and analysis of ancient roads. We will illustrate how the use of tools which explore potential mobility in less restricted ways can help to overcome some of the limitations of LCP.
Rethinking Approaches for the Study of Urban Movement at Ostia
Authors: Crawford Katherine A. 
Published: February 2019

AbstractDespite a range of existing approaches for examining movement within ancient cities, the study of movement intent has received limited attention. This paper begins to address this gap by considering how pedestrian movement can be studied at Ostia, Rome’s ancient port, by transitioning focus to what structured movement routes, namely the built environment and social activity. Using the UNA (Urban Network Analysis) Toolbox developed for ArcGIS, betweeness centrality is calculated in relation to different types of buildings. The results, when associated with Ostia’s streets, provide a visualization of potential areas of movement specific to certain social activities that occurred within the urban landscape. This provides a novel methodological approach for assessing different forms of directed movement within ancient urban landscapes.
Current Trends in Roman Demography and Empirical Approaches to the Dynamics of the Limes Populations
Authors: Séguy Isabelle 
Published: February 2019

AbstractBased on the three principal and inevitably incomplete information sources on ancient historical demography, and taking into account the particularities of the populations living around theLimes Germanicus, a largely male population of soldiers and migrants, this chapter examines the factors that may have influenced their dynamics over the short, medium and long term. It also looks at the possible consequences of increased pressure on the environment, heightened risk of epidemics linked to the rise in population concentration, long-distance communication and adverse climate changes observed from the second half of the second century AD. The proposed empirical approach aims to shed light on the factors that shaped the dynamics of these very specific populations over the long term.
Modelling the Dynamics of Demography in the Dutch Roman Limes Zone: A Revised Model
Authors: Verhagen Philip 
Published: February 2019

AbstractIn this chapter, a simulation model for better understanding the population dynamics of the limes zone is presented, building on our earlier study on the possible effects of recruitment of soldiers for the Roman army (Verhagen et al., Modelling the dynamics of demography in the Dutch limes zone. In: Multi-, inter- and transdisciplinary research in landscape archaeology. Proceedings of LAC 2014 Conference, Rome, 19–20 September 2014. Vrije Universiteit Amsterdam, Amsterdam. https://doi.org/10.5463/lac.2014.62, 2016a). In this earlier study, a number of questions were raised concerning the realism of using estimates from historical demographical sources for understanding the population dynamics of the region. In the current paper, the available data sets, approaches and hypotheses regarding fertility and mortality in the Roman period are re-assessed, together with the available archaeological evidence on the population dynamics of the region. A revised model is then presented that allows for more refined experimenting with various demographic scenarios, showing that a much larger number of parameters can be responsible for changes in population growth than is often assumed in archaeological studies. In particular, marriage strategies would seem to play an important role in regulating the number of births. The model remains a work in progress that can be further refined and linked to models of settlement and land use development.
The Role of Forts in the Local Market System in the Lower Rhine: Towards a Method of Multiple Hypothesis Testing Through Comparative Modelling
Authors: Weaverdyck Eli J. S. 
Published: February 2019

AbstractThis paper analyses rural settlement patterns in the Lower Rhine frontier zone to elucidate the role of forts in the rural economy. Von Thünen’s model of rural marketing suggests that market centres attract intensive cultivation, making them identifiable through spatial analysis of rural settlements. Environmental factors that influenced production capacity, however, can also be expected to exert a strong influence on settlement location, so a multivariate method of spatial analysis is necessary. Using a process of comparative modelling with logistic regression analysis, I test the hypotheses that rural settlements responded to the location of market centres, both civilian and military. I use univariate analysis of settlement territories to identify influential local environmental factors and combine these into a logistic regression model. Then I add a market potential (MP) variable that quantifies the accessibility of marketing opportunities from any location within a market system to see if this factor also shaped settlement patterns. Finally, I vary the centres included in the MP variable to determine whether rural settlements responded to the locations of forts in addition to civilian centres. I find that forts did not generally attract settlements and conclude that smallholders sold their produce primarily in civilian market places.
LEF1-AS1 contributes to proliferation and invasion through regulating miR-544a/ FOXP1 axis in lung cancer
Authors: Wang Ansheng , Zhao Chengling , Gao Yuan , Duan Guixin , Yang Yuming , Fan Bo , Wang Xiaojing , Wang Kangwu 
Published: February 2019

Summary
Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulators in tumor development. This study aims to investigate the potential role oflncRNALEF1-AS1, in the progression of lung cancer. Quantitative real-time PCR (qRT-PCR) and western blot assays showed that LEF1-AS1 was upregulated while miR-544a was downregulated in lung cancer specimens and cells. Overexpression of LEF1-AS1 led to the enhancement of cell proliferation and invasion, revealed by CCK-8 assay and transwell assay. A negative correlation was found between LEF1-AS1 and miR-544a. BLAST analysis and dual-luciferase assay confirmed that FOXP1 is a downstream effector of miR-544a. Therefore, the LEF1-AS1/miR-544a/FOXP1 axis is an important contributor to lung cancer progression. Collectively, our novel data uncovers a new mechanism that governs tumor progression in lung cancer and provides new targets that may be used for disease monitoring and therapeutic intervention of lung cancer.
The NMR signature of gluconoylation: a frequent N-terminal modification of isotope-labeled proteins
Authors: Schweida David , Barraud Pierre , Regl Christof , Loughlin Fionna E. , Huber Christian G. , Cabrele Chiara , Schubert Mario 
Published: February 2019

Abstract
N-terminal gluconoylation is a moderately widespread modification in recombinant proteins expressed in Escherichia coli, in particular in proteins bearing an N-terminal histidine-tag. This post-translational modification has been investigated mainly by mass spectrometry. Although its NMR signals must have been observed earlier in spectra of 13C/15N labeled proteins, their chemical shifts were not yet reported. Here we present the complete 1H and 13C chemical shift assignment of the N-terminal gluconoyl post-translational modification, based on a selection of His-tagged protein constructs (CCL2, hnRNP A1 and Lin28) starting with Met-Gly-...-(His)6. In addition, we show that the modification can hydrolyze over time, resulting in a free N-terminus and gluconate. This leads to the disappearance of the gluconoyl signals and the appearance of gluconate signals during the NMR measurements. The chemical shifts presented here can now be used as a reference for the identification of gluconoylation in recombinant proteins, in particular when isotopically labeled.