bluuebunny/crossref_metadata_2025_split huggingface dataset:
The species‐rich, paleotropical genus Memecylon (Melastomataceae): Molecular phylogenetics and revised infrageneric classification of the African species
Authors: Stone Robert Douglas 
Published: June 2014

AbstractThe internal and external transcribed spacers of nuclear ribosomal DNA were sequenced in 167 samples of Memecylon s.str. and 22 outgroup samples of Lijndenia, Mouriri, Spathandra, Votomita, and Warneckea. Maximum‐likelihood analyses of ETS, ITS1, 5.8S and ITS2 alignments yielded tree topologies that are not significantly incongruent, with one exception involving the Tanzanian sample Luke 9741. Monophyly of Memecylon s.str. is strongly supported in the separate ETS and the combined ETS + ITS1 + 5.8S + ITS2 analyses. Also supported in all analyses except 5.8S is a sister‐group relationship between a small species‐group from western and central Africa (Memecylon subg. Mouririoidea, ovary 4‐loculed) and the remaining taxa (M. subg. Memecylon, ovary unilocular). In the combined analysis, internal branches at the base of M. subg. Memecylon are short and weakly supported, yet within this large subgenus one finds a series of monophyletic groups representing different parts of the widespread paleotropical distribution (one group in western and central Africa; two separate groups in East Africa, one of these extending to southern Africa and disjunctly to western and northern Madagascar; one species‐rich group occurring exclusively on Madagascar and the neighboring Comoro and Mascarene islands; and three distinct groups in Indo‐Malesia, one of these also including the Seychelles endemic M. elaeagni). Within the western and central African clade, M. sect. Polyanthema sensu Jacques‐Félix is paraphyletic with respect to M. sect. Afzeliana, and at the morphological level it seems to be a group defined by symplesiomorphies (ovary unilocular, fruit globose). Three East African species (M. fragrans, M. greenwayi, M. semseii) are returned to Memecylon s.str. after being erroneously transferred to Lijndenia by Borhidi. The Madagascan endemic M. mocquerysii is no longer considered a taxonomic synonym of the distantly related, Tanzanian M. cogniauxii. In addition to elevating M. sect. Mouririoidea to subgeneric rank, the following changes are proposed in the infrageneric classification of African Memecylon: (1) the circumscription of sect. Polyanthema is narrowed to comprise only the members of the “M. polyanthemos complex” sensu Jacques‐Félix; (2) Engler's sections Tenuipedunculata, Cauliflora, and Obtusifolia are re‐instated with emended descriptions (in the case of sect. Cauliflora with an expanded circumscription); (3) seven new sections, Buxifolia, Diluviana, Felixiocylon, Germainiocylon, Magnifoliata, Montana, and Sitacylon, are described; (4) the purported occurrence of M. sect. Pseudonaxiandra in East Africa is rejected. A key is provided to the two subgenera and twelve sections currently recognized in African Memecylon. Further study is needed toward a sectional classification of Indo‐Malesian Memecylon, and for revision of the seven Madagascan sections recognized by Jacques‐Félix.
Molecular and morphological phylogenetic reconstruction reveals a new generic delimitation of Asian Derris (Fabaceae): Reinstatement of Solori and synonymisation of Paraderris with Derris
Authors: Sirichamorn Yotsawate , Adema Frits A.C.B. , Roos Marco C. , van Welzen Peter C. 
Published: June 2014

AbstractThe genus Derris is a problematic taxon within tribe Millettieae, because of the various generic circumscriptions proposed by different authors. Previous molecular phylogenetic studies proved Derris s.l. to be polyphyletic and thus unacceptable as a taxon. Moreover, the most recent circumscription of Derris s.str. was also not monophyletic. In this study, 29 qualitative morphological characters were analyzed together with the molecular data of our earlier studies. The combined datasets confirmed the monophyly of Solori (also known as Brachypterum) and showed it to be distinct at the generic level with the following synapomorphies: presence of stipellae, more than five flowers per brachyblast, tubular and (or) lobed floral disk, seven to twelve ovules and one‐winged pods with obvious seed chambers when dry. Paraderris appeared to be a well‐supported monophyletic group, but nested within Derris s.str. In order to maintain the monophyly of Derris s.str., Paraderris is synonymised with Derris s.str., which broadens the generic circumscription for Derris s.str. This Derris s.str. only has two synapomorphies, the liana habit and two‐winged pods. Other morphological characters used for previous generic circumscriptions of Derris s.str. appeared to be based on combinations of plesiomorphies. No infrageneric classification of Derris s.str. will be provided, because of low support for clades and lack of obvious apomorphies for several clades. Taxonomic treatment and nomenclatural changes are presented where necessary.
Taxonomy and evolutionary history of Alyssum montanum (Brassicaceae) and related taxa in southwestern Europe and Morocco: Diversification driven by polyploidy, geographic and ecological isolation
Authors: Zozomová-Lihová Judita , Marhold Karol , Španiel Stanislav 
Published: June 2014

AbstractThe Alyssum montanum–A. repens polyploid complex is a group of related perennial taxa with a diversity centre in the European (Sub)Mediterranean, controversial taxonomic treatments, and a poorly known evolutionary history. In the present study, morphological, ploidy level and genetic (AFLPs and chloroplast DNA sequences) data were collected to address the taxonomy and evolution of a sublineage of this complex distributed in southwestern Europe and Morocco. As a result, a new taxonomic treatment, differing substantially from recent concepts, is presented, including an identification key, synonymy and typifications. The recognition of several previously described but recently not accepted endemics is favoured (A. flexicaule, A. orophilum, A. rhodanense), whereas the existence of southern Iberian endemics is not supported. Most of the Iberian Peninsula is occupied by a single species for which the name A. fastigiatum is applicable. Populations from the summit areas of the Pyrenees represent a separate species, which is described here as A. cacuminum. Populations from coastal sand dunes in the Basque country (Bay of Biscay) and Galicia, recently recognised as two subspecies of A. loiseleurii, are elevated to species rank according to their genetic and morphological divergence. Alyssum atlanticum is resolved as a species confined to northern Africa and not reaching southern Spain. The distribution of A. montanum in a strict sense is much more restricted than previously reported, being delimited by the Pyrenees in the south, and the Alps in the northeast. The species complex studied here is composed of several polyploid stenoendemics confined to different mountain ranges or specific lowland habitats, and a few relatively widely distributed species. We infer that hybridisation and polyploidisation events, along with ecological and geographic isolation, have stimulated speciation in this complex. Hypotheses about the origin and evolutionary history of the species are discussed.
Molecular phylogeny of Acanthophyllum (Caryophyllaceae: Caryophylleae), with emphasis on infrageneric classification
Authors: Pirani Atefeh , Zarre Shahin , Pfeil Bernard E. , Bertrand Yann J.K. , Assadi Mostafa , Oxelman Bengt 
Published: June 2014

AbstractDespite being one of the larger genera of Caryophyllaceae with about 60 cushion‐forming subshrubby species, Acanthophyllum is represented poorly in previous molecular phylogenetic studies. The genus is an important component of the subalpine steppe flora in Central to Southwest Asia. Although the placement of Acanthophyllum in the tribe Caryophylleae and a close relationship to Allochrusa has already been suggested, the monophyly of the genus and its infrageneric taxa, as well as its relation to other closely related genera, have not been addressed. We have assembled datasets of nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 for 47 Acanthophyllum species and 63 species of 11 additional genera from Caryophylleae. Phylogenetic analyses were performed using maximum parsimony, maximum likelihood and Bayesian methods. Our analysis suggests that Allochrusa, Diaphanoptera, Ochotonophila and Scleranthopsis are nested within Acanthophyllum but that the traditionally recognized sections of Acanthophyllum are monophyletic after reassignment of a few species. Emarginate petals may be a synapomorphy for one of the two basal clades of Acanthophyllum. Moreover, non‐monophyly of the genera Gypsophila and Diaphanoptera is suggested by the present study. The age of the crown clade of Acanthophyllum s.l. is estimated to be 11.1 Ma by *BEAST species tree analysis.
Characterisation of osteoarthritis in a small animal model of type 2 diabetes mellitus
Authors: Onur T. , Wu R. , Metz L. , Dang A. 
Published: June 2014

ObjectivesOur objective in this article is to test the hypothesis that type 2 diabetes mellitus (T2DM) is a factor in the onset and progression of osteoarthritis, and to characterise the quality of the articular cartilage in an appropriate rat model.MethodsT2DM rats were obtained from the UC Davis group and compared with control Lewis rats. The diabetic rats were sacrificed at ages from six to 12 months, while control rats were sacrificed at six months only. Osteoarthritis severity was determined via histology in four knee quadrants using the OARSI scoring guide. Immunohistochemical staining was also performed as a secondary form of osteoarthritic analysis.ResultsT2DM rats had higher mean osteoarthritis scores than the control rats in each of the four areas that were analysed. However, only the results at the medial and lateral femur and medial tibia were significant. Cysts were also found in T2DM rats at the junction of the articular cartilage and subchondral bone. Immunohistochemical analysis does not show an increase in collagen II between control and T2DM rats. Mass comparisons also showed a significant relationship between mass and osteoarthritis score.ConclusionsT2DM was found to cause global degeneration in the UCD rat knee joints, suggesting that diabetes itself is a factor in the onset and progression of osteoarthritis. The immunohistochemistry stains showed little to no change in collagen II degeneration between T2DM and control rats. Overall, it seems that the animal model used is pertinent to future studies of T2DM in the development and progression of osteoarthritis. Cite this article: Bone Joint Res 2014;3:203–11
Circadian angiogenesis
Authors: Jensen Lasse Dahl , Gyllenhaal Charlotte , Block Keith 
Published: June 2014

AbstractDaily rhythms of light/darkness, activity/rest and feeding/fasting are important in human physiology and their disruption (for example by frequent changes between day and night shifts) increases the risk of disease. Many of the diseases found to be associated with such disrupted circadian lifestyles, including cancer, cardiovascular diseases, metabolic disorders and neurological diseases, depend on pathological de-regulation of angiogenesis, suggesting that disrupting the circadian clock will impair the physiological regulation of angiogenesis leading to development and progression of these diseases. Today there is little known regarding circadian regulation of pathological angiogenesis but there is some evidence that supports both direct and indirect regulation of angiogenic factors by the cellular circadian clock machinery, as well as by circulating circadian factors, important for coordinating circadian rhythms in the organism. Through highlighting recent advances both in pre-clinical and clinical research on various diseases including cancer, cardiovascular disorders and obesity, we will here present an overview of the available knowledge on the importance of circadian regulation of angiogenesis and discuss how the circadian clock may provide alternative targets for pro- or anti-angiogenic therapy in the future.
Mammalian genome evolution as a result of epigenetic regulation of transposable elements
Authors: Buckley Reuben M. , Adelson David L. 
Published: June 2014

AbstractTransposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.
A Phenomenological Fatigue Performance Model of Asphalt Mixtures Based on Fracture Energy Density
Authors: Bahadori A. M. , Mansourkhaki A. , Ameri M. 
Published: June 2014

Abstract
In this study the fatigue performance of asphalt mixtures was interpreted based on fracture energy density. Recent studies indicate that the fracture energy from indirect tension tests correlates with the field performance of asphalt concrete. The fracture energy density was obtained from indirect tensile strength tests, and the fatigue performance of asphalt mixtures was evaluated with four-point bending beam fatigue tests implemented at three different strain levels. Two different asphalt mixtures with varying binder contents were tested during this study. Test results showed that the fracture energy density could be an appropriate material property in phenomenological fatigue models. Thus a phenomenological fatigue model based on fracture energy density is presented, and this approach could be advantageous because a simple fatigue model based on fracture energy density does not require time-consuming fatigue tests. For comparison purposes, the various types of fatigue models were evaluated, and fatigue models based on fracture energy density and dissipated energy showed rather high prediction accuracy. In general, fatigue models based on the energy concept have the least dependence on material properties and can predict the fatigue lives of asphalt mixtures without changing coefficients.
Quantification of Transitions Occurring in a Hydrothermally Activated Fly Ash
Authors: Jha Bhagwanjee , Singh D. N. 
Published: June 2014

Abstract
Interaction of fly ash with NaOH results in formation of several transition compounds (viz., zeolites), which are polycrystalline in nature and their crystal wise quantification is a challenging task. In fact, various parameters (viz., oxides, minerals present in the fly ash, pH and EC of NaOH) control the outcome of such interaction at 100°C. Hence, extensive monitoring of these controlling parameters and the zeolites becomes essential. With this in view, a three-stage methodology to quantify transitions occurring in the fly ash has been proposed in this manuscript. Interestingly, it has been observed that Stage-3 of the fly ash-alkali interaction results in formation of 47 types of zeolite-crystals (viz., Na-P1, faujasite, chabazite, hydroxysodalite, and analcime), which exhibits polymerization of these zeolites and wide variation in their size (ranging from 30 to 2346 nm). This sort of transition encourages application of the residues in waste water treatment and other environmental cleanup projects.
A Dimensional Parameter for Prediction of Cooling Performance of Quenchants
Authors: Prabhu K. Narayan , Ramesh G. 
Published: June 2014

Abstract
Computer aided cooling curve analysis was carried out during immersion quenching of ISO/DIS 9950 quench probe. Water, brine solutions, polymer solutions, mineral oils, and vegetable oils were used as quench media. The results showed that the quench medium used had a significant effect on the quench probe cooling curve parameters. An empirical correlation was proposed to predict the average cooling rate from surface tension, wetting angle, thermal conductivity, and kinematic viscosity of the quench medium.
Listeria monocytogenes induces IFNβ expression through an IFI16‐, cGAS‐ and STING‐dependent pathway
Authors: Hansen Kathrine , Prabakaran Thaneas , Laustsen Anders , Jørgensen Sofie E , Rahbæk Stine H , Jensen Søren B , Nielsen Rikke , Leber Jess H , Decker Thomas , Horan Kristy A , Jakobsen Martin R , Paludan Søren R 
Published: June 2014

AbstractListeria monocytogenes is a gram‐positive facultative intracellular bacterium, which replicates in the cytoplasm of myeloid cells. Interferon β (IFNβ) has been reported to play an important role in the mechanisms underlying Listeria disease. Although studies in murine cells have proposed the bacteria‐derived cyclic‐di‐AMP to be the key bacterial immunostimulatory molecule, the mechanism for IFNβ expression during L. monocytogenes infection in human myeloid cells remains unknown. Here we report that in human macrophages, Listeria DNA rather than cyclic‐di‐AMP is stimulating the IFN response via a pathway dependent on the DNA sensors IFI16 and cGAS as well as the signalling adaptor molecule STING. Thus, Listeria DNA is a major trigger of IFNβ expression in human myeloid cells and is sensed to activate a pathway dependent on IFI16, cGAS and STING.
Deoxypyrimidine monophosphate bypass therapy for thymidine kinase 2 deficiency
Authors: Garone Caterina , Garcia‐Diaz Beatriz , Emmanuele Valentina , Lopez Luis C , Tadesse Saba , Akman Hasan O , Tanji Kurenai , Quinzii Catarina M , Hirano Michio 
Published: June 2014

AbstractAutosomal recessive mutations in the thymidine kinase 2 gene (TK2) cause mitochondrial DNA depletion, multiple deletions, or both due to loss of TK2 enzyme activity and ensuing unbalanced deoxynucleotide triphosphate (dNTP) pools. To bypass Tk2 deficiency, we administered deoxycytidine and deoxythymidine monophosphates (dCMP+dTMP) to the Tk2 H126N (Tk2−/−) knock‐in mouse model from postnatal day 4, when mutant mice are phenotypically normal, but biochemically affected. Assessment of 13‐day‐old Tk2−/− mice treated with dCMP+dTMP 200 mg/kg/day each (Tk2−/−200dCMP/dTMP) demonstrated that in mutant animals, the compounds raise dTTP concentrations, increase levels of mtDNA, ameliorate defects of mitochondrial respiratory chain enzymes, and significantly prolong their lifespan (34 days with treatment versus 13 days untreated). A second trial of dCMP+dTMP each at 400 mg/kg/day showed even greater phenotypic and biochemical improvements. In conclusion, dCMP/dTMP supplementation is the first effective pharmacologic treatment for Tk2 deficiency.
The Functional Significance of Common Polymorphisms in Zinc Finger Transcription Factors
Authors: Lockwood Sarah H , Guan Anna , Yu Abigail S , Zhang Chi , Zykovich Artem , Korf Ian , Rannala Bruce , Segal David J 
Published: June 2014

Abstract
Variants that alter the DNA-binding specificity of transcription factors could affect the specificity for and expression of potentially many target genes, as has been observed in several tumor-derived mutations. Here we examined if such trans expression quantitative trait loci (trans-eQTLs) could similarly result from common genetic variants. We chose to focus on the Cys2-His2 class of zinc finger transcription factors because they are the most abundant superfamily of transcription factors in human and have well-characterized DNA binding interactions. We identified 430 SNPs that cause missense substitutions in the DNA-contacting residues. Fewer common missense SNPs were found at DNA-contacting residues compared with non-DNA-contacting residues (P = 0.00006), consistent with possible functional selection against SNPs at DNA-contacting positions. Functional predictions based on zinc finger transcription factor (ZNF) DNA binding preferences also suggested that many common substitutions could potentially alter binding specificity. However, Hardy-Weinberg Equilibrium analysis and examination of seven orthologs within the primate lineage failed to find evidence of trans-eQTLs associated with the DNA-contacting positions or evidence of a different selection pressure on a contemporary and evolutionary timescales. The overall conclusion was that common SNPs that alter the DNA-contacting residues of these factors are unlikely to produce strong trans-eQTLs, consistent with the observations by others that trans-eQTLs in humans tend to be few and weak. Some rare SNPs might alter specificity and remained rare due to purifying selection. The study also underscores the need for large-scale eQTLs mapping efforts that might provide experimental evidence for SNPs that alter the choice of transcription factor binding sites.
Fine-Mapping and Selective Sweep Analysis of QTL for Cold Tolerance inDrosophila melanogaster
Authors: Wilches Ricardo , Voigt Susanne , Duchen Pablo , Laurent Stefan , Stephan Wolfgang 
Published: June 2014

AbstractThere is a growing interest in investigating the relationship between genes with signatures of natural selection and genes identified in QTL mapping studies using combined population and quantitative genetics approaches. We dissected an X-linked interval of 6.2 Mb, which contains two QTL underlying variation in chill coma recovery time (CCRT) in Drosophila melanogaster from temperate (European) and tropical (African) regions. This resulted in two relatively small regions of 131 kb and 124 kb. The latter one co-localizes with a very strong selective sweep in the European population. We examined the genes within and near the sweep region individually using gene expression analysis and P-element insertion lines. Of the genes overlapping with the sweep, none appears to be related to CCRT. However, we have identified a new candidate gene of CCRT, brinker, which is located just outside the sweep region and is inducible by cold stress. We discuss these results in light of recent population genetics theories on quantitative traits.
Advanced Photocatalysis with Anatase Nano-coated Multi-walled Carbon Nanotubes
Authors: Pyrgiotakis Georgios , Lee Sung-Hwan , Sigmund Wolfgang 
Published: June 2014

AbstractA novel approach is presented to synergistically enhance photocatalytic activity in a nanocomposite using the high aspect ratio of carbon nanotube (CNT) and their unique electrical properties. Composite nanoparticles were synthesized with sol-gel nano-coating on multi-walled carbon nanotubes (MWNTs). The nanostructure was characterized using SEM, TEM, XRD, Raman, FTIR and UV-VIS spectroscopies. Photocatalytic efficiencies of commercial photocatalysts (Degussa P25) and TiO2 nano-coated MWNTs were evaluated by Azo dye degradation tests. Superior photocatalytic activity was observed for the nanocomposite with UV-A and with visible light only irradiation.