bluuebunny/crossref_metadata_2025_split huggingface dataset:
A discussion about reproductive modes of Pseudevernia furfuracea based on phylogenetic data
Authors: FERENCOVA Zuzana , DEL PRADO Ruth , PÉREZ-VARGAS Israel , HERNÁNDEZ-PADRÓN Consuelo , CRESPO Ana 
Published: June 2010

AbstractTwo asexual reproductive strategies of the common lichen Pseudevernia furfuracea are described. Although the species propagates mainly by isidia, some specimens also show the development of soralia. Morphological, chemical and molecular analyses were performed on three such sorediate specimens from the Canary Islands, Morocco and Turkey. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that: a) sorediate samples represent only a morphological variant of the reproductive mode and b) the separation of taxa (at species level or below) on the basis of their containing either olivetoric acid or physodic and oxyphysodic acids is not appropriate. In addition, a phylogenetic reconstruction of the genus Pseudevernia is presented for the first time. The tree shows two sister monophyletic clades, one containing American species (P. intensa, P. cladonia, P. consocians), and the second encompassing the P. furfuracea samples (including sorediate specimens). The biological and taxonomic significance of soralia in sorediate samples is discussed.
Notes on the lichen genusRhizoplacafrom continental Antarctica and on some other species from northern Victoria Land
Authors: CASTELLO M. 
Published: June 2010

AbstractFive taxa of the generaOmphalodinaandRhizoplacaknown from continental Antarctica are reassessed in order to identify a remarkable species collected from northern Victoria Land, for which the new combinationRhizoplaca macleanii(C.W. Dodge) Castello is proposed here. This poorly known species is known only from continental Antarctica. Two synonyms are discussed:Omphalodina exsulans(Th. Fr.) C. W. Dodge andO. siplei(C. W. Dodge & G. E. Baker) C. W. Dodge are synonyms ofRhizoplaca melanophthalma(DC.) Leuckert & Poelt. The correct name of another species isTephromela priestleyi(C. W. Dodge) Øvstedal. The nameO. johnstonii(C. W. Dodge) C. W. Dodge should be abandoned, type material being too scanty for a reliable identification. A contribution to the flora of the Terra Nova Bay area (northern Victoria Land) is provided, with two additional species, includingBuellia vilisTh. Fr. new to Antarctic regions, and two nomenclatural corrections.
Calongia gibelluloidesgen. sp. nov., a remarkable minute new lichenicolous conidial fungus from northern Spain
Authors: HAWKSWORTH David L. , ETAYO Javier 
Published: June 2010

AbstractThe new conidial lichenicolous fungusCalongia gibelluloidesgen. sp. nov. is described from discoloured soredial patches on thalli ofFlavoparmelia caperataand discoloured squamules of aCladoniaspecies collected in northern Spain. It is especially unusual in its minute size, the solitary conidiophores reaching at most 45 μm and bearing a cluster of conidiogenous cells that are at first enclosed by a membranous sheath, and produce 1-septate narrowly ellipsoid to elongate-reniform or elongate-soleiform fuscous conidia. The fungus has some features that recall the entomogenous hypocrealean genusGibellula,but species of that genus have synnematous conidiomata, ornamented conidiophores, phialidic conidiogenous cells, no membranous vesicle, and non-septate conidia produced in chains. The phylogenetic placement remains uncertain in the absence of a teleomorph or molecular evidence.
Preference of lichens for shady habitats is correlated with intolerance to high nitrogen levels
Authors: HAUCK Markus , WIRTH Volkmar 
Published: June 2010

AbstractBased on findings in vascular plants showing that the capacity to provide enough carbon skeletons for rapid ammonium assimilation into amino acids is a prerequisite for tolerance to eutrophication, we tested the hypothesis that lichens from shady habitats are particularly sensitive to nitrogen pollution. We tested this hypothesis using published ecological indicator values (estimates of eutrophication tolerance and light preferences on an ordinal scale) for more than 500 central European lichen species. Our results show that shade-adapted lichens are indeed at the same time intolerant to eutrophication. However, not all eutrophication-sensitive lichens inhabit shady environments, suggesting the existence of several independent mechanisms causing intolerance of high nitrogen levels in lichens. The correlation of shade adaptation with nitrogen intolerance is limited to epiphytic and saxicolous species, since terricolous lichens are out-competed by vascular plants in dense vegetation. Our results suggest that lichen communities of shady bark, wood and rock are particularly sensitive to eutrophication.
Two species of Carbacanthographis from India
Authors: SHARMA Bharati O. , MAKHIJA Urmila , KHADILKAR Pradnya 
Published: June 2010

AbstractTwo species of the lichen genus Carbacanthographis, namely C. marcescens and a new species, C. sorediata, are reported from India. The new species is characterized by a sorediate thallus, laterally carbonized exciple, submuriform ascospores, and salazinic and consalazinic acids in the thallus. A worldwide key to the species of Carbacanthographis is provided.
Distinction ofCladonia reiandC. subulatabased on molecular, chemical and morphological characteristics
Authors: DOLNIK Christian , BECK Andreas , ZARABSKA Daria 
Published: June 2010

AbstractCladonia reiandCladonia subulataare morphologically similar, but chemically different cup lichens of dry grasslands and nutrient-poor ruderal habitats. Recently,C. reihas been synonymized withC. subulataon the basis of combined morphological and chemical investigations. However, doubts remained due to a molecular divergent North American sample ofC. reicompared to EuropeanC. subulata. To clarify the situation, using molecular methods, we analysed chemically different European samples ofC. reiandC. subulata, as well as other morphologically or chemically similarCladoniaspecies. Molecular data show that European and North American samples ofC. reibelong to the same clade, which is closely related toC. fimbriataand followed by a subclade withC. coniocraeaandC. ochrochlora. The subclade ofC. subulataappears to be distinct fromC. rei. In concordance with molecular data, the presence of homosekikaic acid is the determining chemical feature forC. rei. In addition,C. humilisandC. innominataproved to be molecularly distinct species.
A new species ofStigmidiumsensu stricto onThelenella muscorum
Authors: PÉREZ-ORTEGA Sergio , HALICI M. Gökhan , KNUDSEN Kerry , CANDAN Mehmet 
Published: June 2010

AbstractStigmidium humidumis described from Spain and Turkey onThelenella muscorum(Fr.) Vain. (synChromatochlamys muscorum(Fr.) H. Mayrhofer & Poelt). The species is the firstStigmidiums. str. species on a host lichen of the familyThelenellaceaeand is compared with other species with ‘Type a’ pseudoparaphyses.
Patterning the distribution of threatened crayfish and their exotic analogues using self-organizing maps
Authors: KOPP DOROTHÉE , SANTOUL FRÉDÉRIC , POULET NICOLAS , COMPIN ARTHUR , CÉRÉGHINO RÉGIS 
Published: June 2010

SUMMARYAbility to demonstrate statistical patterns of distribution by threatened species and by their potential competitors will determine success in forecasting locations at greatest risk, and ability to target management efforts. A self-organizing map algorithm (SOM) was used to derive probabilities of presence of native (Austropotamobius pallipes) and exotic (Orconectes limosus, Pacifastacus leniusculus and Procambarus clarkii) crayfish species with respect to physical and land-cover variables in a large stream system, using a simple presence-absence dataset of species. Crayfish were sampled at 128 sites representing 86 rivers. The probability of occurrence of the native species increased at higher elevations above sea level and lower temperatures; populations appeared to be mostly confined to headwater streams where exotic competitors were unable to withstand the colder conditions. The distribution of exotic species was correlated with anthropogenic factors, such as the degree of urbanization and agricultural land area. Complementary modelling tools, such as GIS and SOMs, can help to maximize the information extracted from available data in the context of biological conservation.
Database of Active Structures From the Indo‐Asian Collision
Authors: Styron Richard , Taylor Michael , Okoronkwo Kelechi 
Published: June 2010

The ongoing collision of India and Asia has produced a vast system of folds and faults, many of which are active today, as evidenced by such recent deadly earthquakes as the 12 May 2008 Sichuan quake [Parsons et al., 2008]. Understanding these events requires knowledge of the region's geologic structures.Taylor and Yin [2009] have assembled HimaTibetMap‐ 1.0, a multiformat, comprehensive database of first‐order active structures in central Asia that may aid researchers, educators, and students in their studies of Indo‐Asian tectonics. For example, this database may be used by seismologists, geodesists, and modelers to identify structures in particular locations that contribute to active deformation, or it may be used by teachers to illustrate concepts such as continental collision or distributed deformation of continents.
AGU Congressional Science Fellow Update: Tips for Scientists
Authors: Boland Maeve 
Published: June 2010

After being selected as the AGU Congressional Science Fellow in March 2009, I packed my bags and moved from sunny Colorado to steamy Washington, D.C., in late August. By mid‐September I had completed an intensive 2‐week orientation program for incoming Science and Technology Fellows organized by the American Association for the Advancement of Science (AAAS). If I was feeling somewhat breathless at that point, it was nothing compared with the experience of searching for a congressional office in which to spend my year.Congressional Science Fellows are funded by their societies, so they are a source of free expertise to members of Congress and congressional committees. Science and Technology Fellows are in high demand, but the quality of the experience for both the fellow and the office depends on finding the right match of interests and personalities. The matchmaking process can take several weeks—and a lot of agonizing—but by the end of September, I was a member of Senator Byron Dorgan's (D‐N.D.) energy and environment team.
Bacterial community structure corresponds to performance during cathodic nitrate reduction
Authors: Wrighton Kelly C , Virdis Bernardino , Clauwaert Peter , Read Suzanne T , Daly Rebecca A , Boon Nico , Piceno Yvette , Andersen Gary L , Coates John D , Rabaey Korneel 
Published: June 2010

Abstract
Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance.
Postprandial remodeling of the gut microbiota in Burmese pythons
Authors: Costello Elizabeth K , Gordon Jeffrey I , Secor Stephen M , Knight Rob 
Published: June 2010

Abstract
The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (&gt;1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall ‘species’-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships.
Open Elite? Social Mobility, Marriage, and Family in Florence, 1282–1494*
Authors: Padgett John F. 
Published: June 2010

AbstractThis article statistically analyzes quantitative data from numerous sources in order to assess changes in marriage patterns, family structure, and rates of social mobility during the period from 1282 to 1494. During this period, three systems of social stratification coexisted — wealth, political office, and age of family — but these contending status systems were not consistent in their rankings of families. Each status system was conservative in the sense that elite families at the top of that hierarchy married each other in order to stabilize their position. But because of inconsistency in rankings, contradiction within the elite opened up the Florentine marriage system to widespread upward social mobility by new men. In their own families, successful new men aggressively imitated their economically and politically declining status superiors. Sharp class divisions thereby blurred into continuous and negotiable status gradients. These open-elite patterns of social mobility, present throughout the early Florentine Renaissance, were most extreme during the Albizzi regime, immediately following the Ciompi Revolt.
Family Matters: William of Orange and the Habsburgs after the Abdication of Charles V (1555–67)*
Authors: Geevers Liesbeth 
Published: June 2010

AbstractThe Habsburgs and the Nassaus, who collaborated during the reign of Charles V, clashed sharply during the reign of Philip II: William of Nassau, Prince of Orange, became the leader of the Dutch Revolt. Instead of focusing on religious and political matters in the Netherlands, this article examines the underlying development of both men's dynastic identity to explain this new hostility. I argue that Habsburg family affairs — the division of the dynasty into two branches — led to an increasingly Spanish dynastic identity on Philip's part, while William could not, or would not, break free from his German-focused family identity, leading to a crucial loss of common ground between the two men.
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy
Authors: Parmentier Gilles , Bastian Frederic B. , Robinson-Rechavi Marc 
Published: June 2010

Abstract
Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.
Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee.
Availability: download section of the Bgee website http://bgee.unil.ch/
Contact: marc.robinson-rechavi@unil.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
A computational genomics pipeline for prokaryotic sequencing projects
Authors: Kislyuk Andrey O. , Katz Lee S. , Agrawal Sonia , Hagen Matthew S. , Conley Andrew B. , Jayaraman Pushkala , Nelakuditi Viswateja , Humphrey Jay C. , Sammons Scott A. , Govil Dhwani , Mair Raydel D. , Tatti Kathleen M. , Tondella Maria L. , Harcourt Brian H. , Mayer Leonard W. , Jordan I. King 
Published: June 2010

Abstract
Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data.
Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes.
Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.
Contact: king.jordan@biology.gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A more precise characterization of chaperonin substrates
Authors: Raineri Emanuele , Ribeca Paolo , Serrano Luis , Maier Tobias 
Published: June 2010

Abstract
Motivation: Molecular chaperones prevent the aggregation of their substrate proteins and thereby ensure that they reach their functional native state. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level; its interactors in Escherichia coli have been identified and characterized. However, a long-standing question in the field is: What makes a protein a chaperone substrate?
Results: Here we identify, using a bioinformatics-based approach a simple set of quantities, which characterize the GroEL-substrate proteome. We define three novel parameters differentiating GroEL interactors from other cellular proteins: lower rate of evolution, hydrophobicity and aggregation propensity. Combining them with other known features to a simple Bayesian predictor allows us to identify known homologous and heterologous GroEL substrateproteins. We discuss our findings in relation to established mechanisms of protein folding and evolutionary buffering by chaperones.
Contact: tobias.maier@crg.es
Supplementary information: Supplementary data is available at Bioinformatics online.
Development of an Advisory System for Grapevine Powdery Mildew in Eastern North America: A Reassessment of Epidemic Progress
Authors: Moyer Michelle M. , Gadoury David M. , Magarey Peter A. , Wilcox Wayne F. , Seem Robert C. 
Published: June 2010

Historical data indicated that year-to-year variation in severity of powdery mildew fruit infection in New York was not directly related to annual variations in temperature or relative humidity through their known effects upon conidial germination, colony expansion, or latent period. Although severity of fruit infection varied from 0.02 to 61% among years, these environmental factors generally remained in the optimal range for the pathogen, with only slight year-to-year variations during the brief period that fruit were susceptible to infection. Vineyard experiments in New York and Australia indicated that colony growth was slower and sparser than would be expected from previous lab studies. Additional experiments indicated that transient exposure to temperatures near 4°C for a few hours had a debilitating effect on mildew colonies and produced growth similar to that observed on ontogenically-resistant tissues: slow and sparse with epidermal necrosis. Additional studies on seasonal release of ascospores from overwintering cleistothecia indicated that a large proportion of inoculum was often released prior to local grapevine budbreak at multiple sites in the eastern USA. These findings may represent key elements in forecasting potential severity of fruit infection in cool climates such as New York. Accepted for publication 28 January 2010. Published 26 May 2010.