bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerium Oxygen Apatite (Ce4.67[SiO4]3O) X-Ray Diffraction Pattern Revisited
Authors: Tas A. Cuneyt , Akinc Mufit 
Published: January 2013

AbstractA new X-ray diffraction pattern for the compound cerium oxygen apatite, Ce4.67[SiO4]3O is suggested. The compound was prepared by the solid state reaction of the oxides, CeO2 and SiO2 and has a hexagonal crystal structure with the lattice constants a = 9.6578 Å and c = 7.1187 Å. The sample of the most recent PDF pattern 31-0336* (Visser, 1978) for this compound is believed to be contaminated with significant quantities of N owing to the fact that it was prepared by mixing Ce2O3 and Si3N4 and its very close resemblance to the pattern displayed in the PDF 33-0333 given for the cerium “nitrogen” apatite, Ce5[SiO4]3N.
X-Ray Powder Diffraction Pattern for Reaction-HIPed A118Ti2Mg3
Authors: Gayle Frank W. , Biancaniello Francis S. , Schaefer Robert J. , Jiggets Rodney D. 
Published: January 2013

AbstractThe cubic Al18Ti2Mg3 phase (184 atoms/unit cell, Z = 8, space group Fdm) has been fabricated by reaction hot isostatic pressing. Quantitative energy dispersive X-ray analysis showed the phase to have nearly ideal stoichiometry. Interplanar spacings and diffraction peak intensities have been determined by X-ray diffraction. The experimental data show good agreement with the pattern calculated using atomic site positional parameters for A118Cr2Mg3, confirming that A118Cr2Mg3 is the prototype for A118Ti2Mg3.
X-Ray and Optical Data for a Vanadium-rich Dravite from Silver Knob, Mariposa County, California, U.S.A.
Authors: Foit Franklin F. 
Published: January 2013

AbstractX-ray powder diffraction and optical data are presented for a vanadium-rich dravite from Silver Knob, Mariposa County, California, U.S.A. The limited compositional variability observed for vanadium-rich dravite is due to the presence of a Tschermaks substitution whereby the substitution of Al for Si in the tetrahedral ring is charge balanced by trivalent for divalent cation substitution in the octahedral sites in the structure. Vanadium-rich dravite is uniaxial negative with ε = 1.646(2) and ω = 1.676(2). Refined unit cell dimensions are a = 15.9599(10) and c = 7.1889(2); F30 = 111(0.009; 30); M20 = 80; and Dx = 3.07. An indexed X-ray powder diffraction pattern is also presented.
Epiphytic diatom communities of Terra Nova Bay, Ross Sea, Antarctica: structural analysis and relations to algal host
Authors: Majewska Roksana , Gambi Maria Cristina , Totti Cecilia Maria , De Stefano Mario 
Published: January 2013

AbstractEpiphytic diatoms are important constituents of the Southern Ocean coastal water ecosystem, being a key element in many of the Antarctic trophic chains. However, only limited information exists relating to these microalgal communities. Here we describe our findings of a study on epiphytic diatoms from Terra Nova Bay (Ross Sea, Antarctica) based on material collected during the summer campaigns spanning from 1990–2004. Observations of diatoms associated with three rhodophyte species (Iridaea cordata(Turner) Bory,Phyllophora antarcticaGepp & Gepp, andPlocamium cartilagineum(L.) Dixon) were carried out with the use of a scanning electron microscope. A total of 73 diatom taxa (32 genera) were distinguished, of which 20 taxa exceeded 3% of total abundance.Cocconeis fasciolata(Ehrenberg) Brown,Navicula perminutaGrunow, andFragilariopsis nana(Steemann Nielsen) Paasche appeared in every sample. The analysis of similarities (ANOSIM) test as well as non-metric multidimensional scaling analysis indicated the nature of host organism as a major factor influencing associated diatom community structure, whereas depth, site, and time of sampling seemed to be less important. The epizooic communities associated with sessile fauna epiphytic on macroalgae differed significantly from those associated with macroalgal surface. A pronounced difference between the communities epiphytic on various host macroalgae species was also observed, although most of the dissimilarities occurred between diatom taxa of the same growth form.
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages
Authors: Nelson Craig E , Goldberg Stuart J , Wegley Kelly Linda , Haas Andreas F , Smith Jennifer E , Rohwer Forest , Carlson Craig A 
Published: January 2013

Abstract
Increasing algal cover on tropical reefs worldwide may be maintained through feedbacks whereby algae outcompete coral by altering microbial activity. We hypothesized that algae and coral release compositionally distinct exudates that differentially alter bacterioplankton growth and community structure. We collected exudates from the dominant hermatypic coral holobiont Porites spp. and three dominant macroalgae (one each Ochrophyta, Rhodophyta and Chlorophyta) from reefs of Mo’orea, French Polynesia. We characterized exudates by measuring dissolved organic carbon (DOC) and fractional dissolved combined neutral sugars (DCNSs) and subsequently tracked bacterioplankton responses to each exudate over 48 h, assessing cellular growth, DOC/DCNS utilization and changes in taxonomic composition (via 16S rRNA amplicon pyrosequencing). Fleshy macroalgal exudates were enriched in the DCNS components fucose (Ochrophyta) and galactose (Rhodophyta); coral and calcareous algal exudates were enriched in total DCNS but in the same component proportions as ambient seawater. Rates of bacterioplankton growth and DOC utilization were significantly higher in algal exudate treatments than in coral exudate and control incubations with each community selectively removing different DCNS components. Coral exudates engendered the smallest shift in overall bacterioplankton community structure, maintained high diversity and enriched taxa from Alphaproteobacteria lineages containing cultured representatives with relatively few virulence factors (VFs) (Hyphomonadaceae and Erythrobacteraceae). In contrast, macroalgal exudates selected for less diverse communities heavily enriched in copiotrophic Gammaproteobacteria lineages containing cultured pathogens with increased VFs (Vibrionaceae and Pseudoalteromonadaceae). Our results demonstrate that algal exudates are enriched in DCNS components, foster rapid growth of bacterioplankton and select for bacterial populations with more potential VFs than coral exudates.
Ecology of marine Bacteroidetes: a comparative genomics approach
Authors: Fernández-Gómez Beatriz , Richter Michael , Schüler Margarete , Pinhassi Jarone , Acinas Silvia G , González José M , Pedrós-Alió Carlos 
Published: January 2013

Abstract
Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.
Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes
Authors: Zimmerman Amy E , Martiny Adam C , Allison Steven D 
Published: January 2013

Abstract
Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004–0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04–98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.
Vocabulary Use Across Genres: Implications for Students With Complex Communication Needs
Authors: Clendon Sally A. , Sturm Janet M. , Cali Kathleen S. 
Published: January 2013

Purpose
This study examined the vocabulary words and multiword sequences used by 124 typically developing kindergarten and 1st-grade students when they wrote about self-selected topics. The study extends previous research by examining the vocabulary used in different genres.

Method
A total of 457 writing samples were analyzed. The samples were classified according to 9 genres and were analyzed using the Child Language Analysis (MacWhinney, 2006) software program.

Results

The authors found that 140 words represented 70% of the vocabulary produced. The most common genre types were narrative recounts and opinions. The patterns of frequency for words and multiword sequences varied across genres. The degree of variation was greater for particular vocabulary words. For instance, the word
going
was used predominantly in 1 genre. In contrast, the word
mom
was used in every genre except 3. The structure words tended to be used with high frequency across genres.

Conclusion
The word lists generated can be used to inform vocabulary selection, organization, and instruction for students with complex communication needs who are beginning writers.

Supplemental Material

https://doi.org/10.23641/asha.6170273
Morphological Analysis in Context Versus Isolation: Use of a Dynamic Assessment Task With School-Age Children
Authors: Ram Gayatri , Marinellie Sally A. , Benigno Joann , McCarthy John 
Published: January 2013

Purpose
The current study investigated the ability of typically developing children in Grades 3 and 5 to use morphological analysis to determine the meanings of derived words with and without context clues. Also of interest was the relation between children’s reading practices and their performance in determining the meanings of derived words.

Method
Children provided definitions for 20 low-frequency derived words that were presented to them in isolation and in context. Responses were scored on a scale of 0 to 5 based on the children’s performance on the Dynamic Assessment of Morphological Analysis—Modified (DATMA–M), which was created by the authors.

Results
Results indicated a large variability in the children’s performance on the DATMA–M. Children in Grade 5 achieved significantly higher scores as compared to children in Grade 3. Overall, children performed better in the context condition than the isolation condition. Significant correlations were found for reading frequency and DATMA–M scores. There was no significant difference in performance between the isolation and context conditions after controlling for reading frequency.

Conclusion
The findings of this study emphasize the need for continued research to enable speech-language pathologists to use assessments such as the DATMA–M to obtain insights into the morphological analytical skills of school-age children.
Readability of Questionnaires Assessing Listening Difficulties Associated With (Central) Auditory Processing Disorders
Authors: Atcherson Samuel R. , Richburg Cynthia M. , Zraick Richard I. , George Cassandra M. 
Published: January 2013

PurposeEight English-language, student- or parent proxy-administered questionnaires for (central) auditory processing disorders, or (C)APD, were analyzed for readability. For student questionnaires, readability levels were checked against the approximate reading grade levels by intended administration age per the questionnaires' developers. For proxy questionnaires, results were compared to the reading grade level for the average U.S. adult and the minimum 5th- to 6th-grade reading level for health materials as recommended by adult health literacy experts.MethodThis was a descriptive study that was based on the results of a commercially available readability calculations software package. Text-based files of the 8 questionnaires were analyzed using 3 readability formulas: FORCAST (Caylor & Sticht, 1973), Flesch Reading Ease (FRE; Flesch, 1948), and Gunning’s Fog index (FOG; Gunning, 1952).ResultsThe FORCAST formula, the most appropriate for nonnarrative-type materials, indicated that all 8 questionnaires were written at reading levels between the 8th and 10th grades. The FRE and FOG formulas, designed for narrative-type materials, were generally in good agreement with one another but varied widely between the upper 4th- and 12th-grade levels.ConclusionIn an effort to decrease respondent burden, developers should consider readability as another testable psychometric construct. Clinicians should take into account the functional health literacy skills of adult proxy respondents when giving self-administered questionnaires.
Differentiating Children With and Without Language Impairment Based on Grammaticality
Authors: Eisenberg Sarita L. , Guo Ling-Yu 
Published: January 2013

PurposeThis study compared the diagnostic accuracy of a general grammaticality measure (i.e., percentage grammatical utterance; PGU) to 2 less comprehensive measures of grammaticality—a measure that excluded utterances without a subject and/or main verb (i.e., percentage sentence point; PSP) and a measure that looked only at verb tense errors (i.e., percentage verb tense usage; PVT)—in differentiating children with and without language impairment.MethodTwo groups of 3-year-olds, 17 with language impairment and 17 with typical language, participated in a picture description task. PGU, PSP, and PVT were computed. Receiver operating characteristic curve analyses were conducted to determine the best cutoff value for each measure.ResultsAll 3 measures demonstrated a sensitivity of 100%. PGU showed a specificity of 88%, and both PSP and PVT showed a specificity of 82%. In addition, PGU showed a larger positive likelihood ratio than the other 2 measures.ConclusionPGU, PSP, and PVT were all sensitive to language impairment. However, PGU was less likely than PSP and PVT to misclassify children with typical language. The resultant diagnostic accuracy makes PGU an appropriate measure to use to screen for language impairment.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
Authors: Clark Scott C. , Egan Rob , Frazier Peter I. , Wang Zhong 
Published: January 2013

Abstract
Motivation: Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification, and none are designed to evaluate metagenome assemblies.
Results: In this article, we present an Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synthetic errors in both single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearrangements and chimeric assemblies presented in metagenomes. At the genome level with real-world data, ALE identifies three large misassemblies from the Spirochaeta smaragdinae finished genome, which were all independently validated by Pacific Biosciences sequencing. At the single-base level with Illumina data, ALE recovers 215 of 222 (97%) single nucleotide variants in a training set from a GC-rich Rhodobacter sphaeroides genome. Using real Pacific Biosciences data, ALE identifies 12 of 12 synthetic errors in a Lambda Phage genome, surpassing even Pacific Biosciences’ own variant caller, EviCons. In summary, the ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process.
Availability: ALE is released as open source software under the UoI/NCSA license at http://www.alescore.org. It is implemented in C and Python.
Contact: pf98@cornell.edu or ZhongWang@lbl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
Authors: Thomas Niclas , Heather James , Ndifon Wilfred , Shawe-Taylor John , Chain Benjamin 
Published: January 2013

Abstract
Summary: High-throughput sequencing provides an opportunity to analyse the repertoire of antigen-specific receptors with an unprecedented breadth and depth. However, the quantity of raw data produced by this technology requires efficient ways to categorize and store the output for subsequent analysis. To this end, we have defined a simple five-item identifier that uniquely and unambiguously defines each TcR sequence. We then describe a novel application of finite-state automaton to map Illumina short-read sequence data for individual TcRs to their respective identifier. An extension of the standard algorithm is also described, which allows for the presence of single-base pair mismatches arising from sequencing error. The software package, named Decombinator, is tested first on a set of artificial in silico sequences and then on a set of published human TcR-β sequences. Decombinator assigned sequences at a rate more than two orders of magnitude faster than that achieved by classical pairwise alignment algorithms, and with a high degree of accuracy (&gt;88%), even after introducing up to 1% error rates in the in silico sequences. Analysis of the published sequence dataset highlighted the strong V and J usage bias observed in the human peripheral blood repertoire, which seems to be unconnected to antigen exposure. The analysis also highlighted the enormous size of the available repertoire and the challenge of obtaining a comprehensive description for it. The Decombinator package will be a valuable tool for further in-depth analysis of the T-cell repertoire.
Availability and implementation: The Decombinator package is implemented in Python (v2.6) and is freely available at https://github.com/uclinfectionimmunity/Decombinator along with full documentation and examples of typical usage.
Contact: b.chain@ucl.ac.uk
Nodes and arcs: concept map, semiotics, and knowledge organization
Authors: Friedman Alon , Smiraglia Richard P. 
Published: January 2013

PurposeThe purpose of the research reported here is to improve comprehension of the socially‐negotiated identity of concepts in the domain of knowledge organization. Because knowledge organization as a domain has as its focus the order of concepts, both from a theoretical perspective and from an applied perspective, it is important to understand how the domain itself understands the meaning of a concept.Design/methodology/approachThe paper provides an empirical demonstration of how the domain itself understands the meaning of a concept. The paper employs content analysis to demonstrate the ways in which concepts are portrayed in KO concept maps as signs, and they are subjected to evaluative semiotic analysis as a way to understand their meaning. The frame was the entire population of formal proceedings in knowledge organization – all proceedings of the International Society for Knowledge Organization's international conferences (1990‐2010) and those of the annual classification workshops of the Special Interest Group for Classification Research of the American Society for Information Science and Technology (SIG/CR).FindingsA total of 344 concept maps were analyzed. There was no discernible chronological pattern. Most concept maps were created by authors who were professors from the USA, Germany, France, or Canada. Roughly half were judged to contain semiotic content. Peirceian semiotics predominated, and tended to convey greater granularity and complexity in conceptual terminology. Nodes could be identified as anchors of conceptual clusters in the domain; the arcs were identifiable as verbal relationship indicators. Saussurian concept maps were more applied than theoretical; Peirceian concept maps had more theoretical content.Originality/valueThe paper demonstrates important empirical evidence about the coherence of the domain of knowledge organization. Core values are conveyed across time through the concept maps in this population of conference papers.