bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni
Authors: Santiago-Vázquez Lory Z , Brück Thomas B , Brück Wolfram M , Duque-Alarcón Angela P , McCarthy Peter J , Kerr Russell G 
Published: October 2007

Abstract
This study examined the symbiotic microbiota of the hexacoral Cirrhipathes lutkeni using traditional plate culture, fluorescence in situ hybridization (FISH) and 16S rDNA characterization. FISH counts for the whole coral (holobiont) showed a major presence of γ-Proteobacteria (22%) and Actinobacteria (19%), followed by α-Proteobacteria (14%), Firmicutes (9%), Cytophaga-Flavobacterium (7%), β-Proteobacteria (6%) and Chloroflexi (2%). In contrast to the diversity observed by FISH, plate cultures were found to be selective for γ-Proteobacteria (22 cultures) with the exception of an Actinobacterium. The methods employed in this study detected 76% of all microbes estimated by DAPI staining of C. lutkeni homogenates. The absence of zooxanthellae in this particular hexacoral was confirmed by PCR and spectrophotometry using fresh tissue isolated from the holobiont. This is the first study describing the microbial associations of shallow-water hexacorallia, which opens further insight into coral microbial ecology and may enhance the search for novel natural products in the near future.
Subsurface clade ofGeobacteraceaethat predominates in a diversity of Fe(III)-reducing subsurface environments
Authors: Holmes Dawn E , O'Neil Regina A , Vrionis Helen A , N'Guessan Lucie A , Ortiz-Bernad Irene , Larrahondo Maria J , Adams Lorrie A , Ward Joy A , Nicoll Julie S , Nevin Kelly P , Chavan Milind A , Johnson Jessica P , Long Philip E , Lovley Derek R 
Published: October 2007

AbstractThere are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.
Correlation of patterns of denitrification instability in replicated bioreactor communities with shifts in the relative abundance and the denitrification patterns of specific populations
Authors: Gentile Margaret Elizabeth , Lynn Nyman Jennifer , Criddle Craig S 
Published: October 2007

Abstract
To assess the effects of community structure on the stability of denitrification, six chemostat cultures derived from the same denitrifying community were subjected to step increases in feed nitrate concentration and monitored for evidence that denitrification was either not occurring (indicated by the presence of nitrate) or was incomplete (indicated by the presence of nitrite or nitrous oxide). Functional stability was defined and quantified from the pattern of effluent concentration trends of nitrate and denitrification intermediates. Microbial community structure and dynamics were analyzed by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. Functional stability varied: one chemostat community lost the ability to reduce all of the influent nitrate; others continued to reduce all of the influent nitrate, but accumulated varying amounts of nitrous oxide. The microbial community structure in two of the chemostats diverged from the others, and variation of functional response among chemostats corresponded with the divergence of community structure. The Acidovorax-like terminal restriction fragment (T-RF) dominated the chemostat that accumulated nitrate, and an Acidovorax-like isolate reduced nitrate directly to dinitrogen gas in batch nitrate reduction assays. In the nitrous oxide-accumulating chemostats, the relative abundance of the Pseudomonas-like T-RF was strongly and significantly correlated with the magnitude of nitrous oxide accumulation, and a Pseudomonas-like isolate accumulated nitrous oxide in batch assays.
Mappings of finite distortion: Formation of cusps II
Authors: Takkinen Juhani 
Published: October 2007

Fors>0s>0given, we consider a planar domain Ωs\Omega _swith a rectifiable boundary but containing a cusp of degree ss, and show that there is no homeomorphismf:R2→R2f\colon \mathbb {R}^2\to \mathbb {R}^2of finite distortion withexp⁡(λK)∈Lloc1(R2)\exp (\lambda K)\in L^1_{\mathrm {loc}}(\mathbb {R}^2)so thatf(B)=Ωsf(B)=\Omega _swhenλ>4/s\lambda >4/sand BBis the unit disc. On the other hand, forλ>2/s\lambda >2/ssuch an ffexists. The critical value forλ\lambdaremains open.
Optimization of HAART with genetic algorithms and agent-based models of HIV infection
Authors: Castiglione F. , Pappalardo F. , Bernaschi M. , Motta S. 
Published: October 2007

Motivation: Highly Active AntiRetroviral Therapies (HAART) can prolong life significantly to people infected by HIV since, although unable to eradicate the virus, they are quite effective in maintaining control of the infection. However, since HAART have several undesirable side effects, it is considered useful to suspend the therapy according to a suitable schedule of Structured Therapeutic Interruptions (STI).In the present article we describe an application of genetic algorithms (GA) aimed at finding the optimal schedule for a HAART simulated with an agent-based model (ABM) of the immune system that reproduces the most significant features of the response of an organism to the HIV-1 infection.Results: The genetic algorithm helps in finding an optimal therapeutic schedule that maximizes immune restoration, minimizes the viral count and, through appropriate interruptions of the therapy, minimizes the dose of drug administered to the simulated patient.To validate the efficacy of the therapy that the genetic algorithm indicates as optimal, we ran simulations of opportunistic diseases and found that the selected therapy shows the best survival curve among the different simulated control groups.Availability: A version of the C-ImmSim simulator is available at http://www.iac.cnr.it/~filippo/c-ImmSim.htmlContact: f.castiglione@iac.cnr.it
PFRES: protein fold classification by using evolutionary information and predicted secondary structure
Authors: Chen Ke , Kurgan Lukasz 
Published: October 2007

AbstractMotivation: The number of protein families has been estimated to be as small as 1000. Recent study shows that the growth in discovery of novel structures that are deposited into PDB and the related rate of increase of SCOP categories are slowing down. This indicates that the protein structure space will be soon covered and thus we may be able to derive most of remaining structures by using the known folding patterns. Present tertiary structure prediction methods behave well when a homologous structure is predicted, but give poorer results when no homologous templates are available. At the same time, some proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination of structural similarity without sequence similarity would be beneficial for prediction of tertiary structures.Results: The proposed PFRES method for automated protein fold classification from low identity (&lt;35%) sequences obtains 66.4% and 68.4% accuracy for two test sets, respectively. PFRES obtains 6.3–12.4% higher accuracy than the existing methods. The prediction accuracy of PFRES is shown to be statistically significantly better than the accuracy of competing methods. Our method adopts a carefully designed, ensemble-based classifier, and a novel, compact and custom-designed feature representation that includes nearly 90% less features than the representation of the most accurate competing method (36 versus 283). The proposed representation combines evolutionary information by using the PSI-BLAST profile-based composition vector and information extracted from the secondary structure predicted with PSI-PRED.Availability: The method is freely available from the authors upon request.Contact: lkurgan@ece.ualberta.caSupplementary information: Supplementary data are available at Bioinformatics online.
Mining experimental evidence of molecular function claims from the literature
Authors: Crangle Colleen E. , Cherry J. Michael , Hong Eurie L. , Zbyslaw Alex 
Published: October 2007

AbstractMotivation: The rate at which gene-related findings appear in the scientific literature makes it difficult if not impossible for biomedical scientists to keep fully informed and up to date. The importance of these findings argues for the development of automated methods that can find, extract and summarize this information. This article reports on methods for determining the molecular function claims that are being made in a scientific article, specifically those that are backed by experimental evidence.Results: The most significant result is that for molecular function claims based on direct assays, our methods achieved recall of 70.7% and precision of 65.7%. Furthermore, our methods correctly identified in the text 44.6% of the specific molecular function claims backed up by direct assays, but with a precision of only 0.92%, a disappointing outcome that led to an examination of the different kinds of errors. These results were based on an analysis of 1823 articles from the literature of Saccharomyces cerevisiae (budding yeast).Availability: The annotation files for S.cerevisiae are available from ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/gene_association.sgd.gz. The draft protocol vocabulary is available by request from the first author.Contact: crangle@converspeech.com
Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G
Authors: Iwatani Yasumasa , Chan Denise S.B. , Wang F. , Stewart-Maynard Kristen , Sugiura Wataru , Gronenborn Angela M. , Rouzina Ioulia , Williams Mark C. , Musier-Forsyth Karin , Levin Judith G. 
Published: October 2007

Abstract
APOBEC3G (A3G), a host protein that inhibits HIV-1 reverse transcription and replication in the absence of Vif, displays cytidine deaminase and single-stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity, which is crucial for efficient reverse transcription. Here we report the interplay between A3G, NC and reverse transcriptase (RT) and the effect of highly purified A3G on individual reactions that occur during reverse transcription. We find that A3G did not affect the kinetics of NC-mediated annealing reactions, nor did it inhibit RNase H cleavage. In sharp contrast, A3G significantly inhibited all RT-catalyzed DNA elongation reactions with or without NC. In the case of ( − ) strong-stop DNA synthesis, the inhibition was independent of A3G's catalytic activity. Fluorescence anisotropy and single molecule DNA stretching analyses indicated that NC has a higher nucleic acid binding affinity than A3G, but more importantly, displays faster association/disassociation kinetics. RT binds to ssDNA with a much lower affinity than either NC or A3G. These data support a novel mechanism for deaminase-independent inhibition of reverse transcription that is determined by critical differences in the nucleic acid binding properties of A3G, NC and RT.
Integrating Naval Aviation Maintenance Training with Sailors' Proficiency Qualification and Its Correlation with Improved Weapon System Readiness
Authors: SNOW JOHN P. , ROSS JAMES M. , BERKIN MICHAEL G. , BOSCHEN EDWARD D. 
Published: October 2007

AbstractA core role for human systems integration is providing support of weapon systems operational effectiveness with optimal human performance (HP). When applied to the readiness of an aviation squadron, this focus on enhanced operational HP translates into ensuring that highly trained and proficient maintenance technicians are resident in these warfighting units. A key objective of the Naval Aviation Enterprise (NAE) Total Force Readiness program is to bridge Core Capabilities to Missions. This is accomplished through the linking of Navy Mission Essential Task Lists (NMETLs) to Skill Sets and Performance Standards for its future workforce. These goals can be accomplished from Initial Development to Deployment of a weapons system through its operational and support phases of the Department of Defense acquisition process using a mission/task‐centric approach to Manpower, Personnel, and Training (MPT) requirements, with NMETLs as the operational thread. This paper will describe a life‐cycle MPT analytic environment with its task‐level links to systems and human engineering disciplines. A systematic approach to accessing and training a proficient maintenance workforce is presented, focusing on task‐based maintenance training solutions for optimal unit readiness and mission capabilities. An innovative analytic framework from various skills‐based manpower analysis studies will be cited as a means to transform system and unit MPT performance for Total Force Readiness. Enhanced by a Qualified and Proficient Technician methodology, a capability (missions) and competency (proficient) future workforce with skills‐efficient maintainers will be best suited to achieving optimal readiness of weapons systems within the NAE.
Human Performance Measurement: Cultural Changes
Authors: HUGHES GEORGE , DAVIDSON KAROLE 
Published: October 2007

AbstractThere has been a high degree of cooperation and collaboration among the Navy system commands with respect to human performance under the Human Systems Performance Assessment Capability initiative. Additionally, the various warfare centers for Naval Sea Systems Command have shown the ability to team across the wide Navy organization. The steering group has shown the practitioners how to team and work together to accomplish similar objectives across different systems. Opportunities to collaborate have been identified and executed with minimal supervision and measurable contributions have been collected. One of the valuable benefits that has been gained through this effort is the ability for practitioners to share knowledge, methods, and tools with their counterparts across the Navy infrastructure. A shared common approach to addressing human performance data collection is emerging as a result. One of the real advantages of the project is a shared vision on the importance of human performance as part of the system engineering process of defining requirements through the eventual test and evaluation phases of a program.
Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)
Authors: Gómez‐Zurita Jesús , Hunt Toby , Vogler Alfried P. 
Published: October 2007

AbstractBasal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae.© The Willi Hennig Society 2007.
Incorporation of gap characters and lineage‐specific regions into phylogenetic analyses of gene families from divergent clades: an example from the kinesin superfamily across eukaryotes
Authors: Simmons Mark P. , Richardson Dale , Reddy Anireddy S. N. 
Published: October 2007

AbstractThe kinesin superfamily across eukaryotes was used to examine how incorporation of gap characters scored from conserved regions shared by all members of a gene family and incorporation of amino acid and gap characters scored from lineage‐specific regions affect gene‐tree inference of the gene family as a whole. We addressed these two questions in the context of two different densities of sequence sampling, four alignment programs, and two methods of tree construction. Taken together, our findings suggest the following. First, gap characters should be incorporated into gene‐tree inference, even for divergent sequences. Second, gene regions that are not conserved among all or most sequences sampled should not be automatically discarded without evaluation of potential phylogenetic signal that may be contained in gap and/or sequence characters. Third, among the four alignment programs evaluated using their default alignment parameters, Clustal may be expected to output alignments that result in the greatest gene‐tree resolution and support. Yet, this high resolution and support should be regarded as optimistic, rather than conservative, estimates. Fourth, this same conclusion regarding resolution and support holds for Bayesian gene‐tree analyses relative to parsimony‐jackknife gene‐tree analyses. We suggest that a more conservative approach, such as aligning the sequences using DIALIGN‐T or MAFFT, analyzing the appropriate characters using parsimony, and assessing branch support using the jackknife, is more appropriate for inferring gene trees of divergent gene families.© The Willi Hennig Society 2007.
Osmotic adjustment in three succulent species ofZygophyllaceae
Authors: Kamel M. 
Published: October 2007

AbstractThree species,Zygophyllum albumL.,Z. coccineumL. andZ. simplexL.,from familyZygophyllaceaewere collected from two locations in Egypt to study their response to environmental conditions. Organic solutes (amino acids, soluble proteins and soluble sugars) and inorganic solutes (Na+, K+, Ca2+, Mg2+, Cl−, PO43−and SO42−) were estimated to study their role in osmotic adjustment under the effect of drought and salinity. The study showed thatZ. coccineumis most tolerant for drought and salinity thanZ. simplex. Z. coccineumwas dependent on soluble proteins and soluble sugars, to increase its content of bound water, to undergo water deficit in desert.Z. simplexaccumulated inorganic solutes more thanZ.coccineumand less organic solutes. Amino acids content increased inZ. coccineumandZ. simplexsurvived in saline conditions to play a role in osmotic adjustment. Under the effect of salinity, all the studied species showed a tendency and high capacity to accumulate inorganic solutes. The main inorganic salutes were Ca2+, Mg2+and Cl−. The role of Na+was less than Ca2+and Mg2+.Z. albumandZ. simplexpreferred Mg2+more thanZ. coccineumwhich preferred Ca2+.
The role of water abundance, thermoregulation, perceived predation risk and interference competition in water access by African herbivores
Authors: Valeix Marion , Fritz Hervé , Matsika Ruwadzano , Matsvimbo Fadzai , Madzikanda Hillary 
Published: October 2007

AbstractIn African savannas, surface water can become limiting and an understanding of how animals address the trade‐offs between different constraints to access this resource is needed. Here, we describe water access by ten African herbivore species in Hwange National Park, Zimbabwe, and we explore four possible determinants of the observed behaviours: water abundance, thermoregulation, perceived predation risk and interference competition. On average, herbivores were observed to drink in 80% of visits to a waterhole. The probability of drinking was higher in 2003 (474 mm) than in 2004 (770 mm), and at the end of the dry season than at its beginning. For larger species, this probability may also be related to risks of interference competition with elephants or other herbivores. For smaller species, this probability may also be related to the perceived risk of predation. We also investigate the time spent accessing water to drink. The influence of herd size and the presence of young on the time spent accessing water for most species suggests that perceived predation risk plays a role. Thermoregulation also affects this time: during the hottest periods, herbivores spend less time in open areas, unless when wind is strong, probably owing to evapotranspired heat loss.