bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis on Frequency and Density of Microsatellites in Coding Sequences of Several Eukaryotic Genomes
Authors: Li Bin , Xia Qingyou , Lu Cheng , Zhou Zeyang , Xiang Zhonghuai 
Published: November 2016

Abstract
Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%–76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.
The Structure, Expression, and Function Prediction of DAZAP2, A Down-Regulated Gene in Multiple Myeloma
Authors: Shi Yiwu , Luo Saiqun , Peng Jianbin , Huang Chenghan , Tan Daren , Hu Weixin 
Published: November 2016

Abstract
In our previous studies, DAZAP2 gene expression was down-regulated in untreated patients of multiple myeloma (MM). For better studying the structure and function of DAZAP2, a full-length cDNA was isolated from mononuclear cells of a normal human bone marrow, sequenced and deposited to Genbank (AY430097). This sequence has an identical ORF (open reading frame) as the NM_014764 from human testis and the D31767 from human cell line KG-1. Phylogenetic analysis and structure prediction reveal that DAZAP2 homologues are highly conserved throughout evolution and share a polyproline region and several potential SH2/SH3 binding sites. DAZAP2 occurs as a single-copy gene with a four-exon organization. We further noticed that the functional DAZAP2 gene is located on Chromosome 12 and its pseudogene gene is on Chromosome 2 with electronic location of human chromosome in Genbank, though no genetic abnormalities of MM have been reported on Chromosome 12. The ORF of human DAZAP2 encodes a 17-kDa protein, which is highly similar to mouse Prtb. The DAZAP2 protein is mainly localized in cytoplasm with a discrete pattern of punctuated distribution. DAZAP2 may associate with carcinogenesis of MM and participate in yet-to-be identified signaling pathways to regulate proliferation and differentiation of plasma cells.
Identification of Protein Coding Regions of Rice Genes Using Alternative Spectral Rotation Measure and Linear Discriminant Analysis
Authors: Jin Jiao 
Published: November 2016

Abstract
An improved method, called Alternative Spectral Rotation (ASR) measure, for predicting protein coding regions in rice DNA has been developed. The method is based on the Spectral Rotation (SR) measure proposed by Kotlar and Lavner, and its accuracy is higher than that of the SR measure and the Spectral Content (SC) measure proposed by Tiwari et al. In order to increase the identifying accuracy, we chose three different coding characters, namely the asymmetric, purine, and stop-codon variables as parameters, and an approving result was presented by the method of Linear Discriminant Analysis (LDA).
A Novel Method for N-Terminal Acetylation Prediction
Authors: Liu Ying , Lin Yuanlie 
Published: November 2016

Abstract
The NetAcet method has been developed to make predictions of N-terminal acetylation sites, but more information of the data set could be utilized to improve the performance of the model. By employing a new way to extract patterns from sequences and using a sample balancing mechanism, we obtained a correlation coefficient of 0.85, and a sensitivity of 93% on an independent mammalian data set. A web server utilizing this method has been constructed and is available at http://166.111.24.5/acetylation.html.
Phylogeny of the Insect Homeobox Gene (Hox) Cluster
Authors: Dhawan Sangeeta , Gopinathan K.P. 
Published: November 2016

Abstract
The homeobox (Hox) genes form an evolutionarily conserved family encoding transcription factors that play major roles in segmental identity and organ specification across species. The canonical grouping of Hox genes present in the HOM-C cluster of Drosophila or related clusters in other organisms includes eight “typical” genes, which are localized in the order labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), abdominalA (abdA), and AbdominalB (AbdB). The members of Hox cluster are expressed in a distinct anterior to posterior order in the embryo. Analysis of the relatedness of different members of the Hox gene cluster to each other in four evolutionarily diverse insect taxa revealed that the loci pb/Dfd and AbdB, which are farthest apart in linkage, had a high degree of evolutionary relatedness, indicating that pb/Dfd type anterior genes and AbdB are closest to the ancestral anterior and posterior Hox genes, respectively. The greater relatedness of other posterior genes Ubx and abdA to the more anterior genes such as Antp and Scr suggested that they arose by gene duplications in the more anterior members rather than the posterior AbdB.
Feature Selection for the Prediction of Translation Initiation Sites
Authors: Li Guo-Liang , Leong Tze-Yun 
Published: November 2016

Abstract
Translation initiation sites (TISs) are important signals in cDNA sequences. In many previous attempts to predict TISs in cDNA sequences, three major factors affect the prediction performance: the nature of the cDNA sequence sets, the relevant features selected, and the classification methods used. In this paper, we examine different approaches to select and integrate relevant features for TIS prediction. The top selected significant features include the features from the position weight matrix and the propensity matrix, the number of nucleotide C in the sequence downstream ATG, the number of downstream stop codons, the number of upstream ATGs, and the number of some amino acids, such as amino acids A and D. With the numerical data generated from these features, different classification methods, including decision tree, naïve Bayes, and support vector machine, were applied to three independent sequence sets. The identified significant features were found to be biologically meaningful, while the experiments showed promising results.
Neighboring-Nucleotide Effects on the Mutation Patterns of the Rice Genome
Authors: Zhao Hui , Li Qi-Zhai , Zeng Chang-Qing , Yang Huan-Ming , Yu Jun 
Published: November 2016

Abstract
DNA composition dynamics across genomes of diverse taxonomy is a major subject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms (SNPs) generated by comparing two sequenced rice genomes from distant inbred lines (subspecies), including those from 242,811 introns and 45,462 protein-coding sequences (CDSs). Neighboring-nucleotide effects (NNEs) of these SNPs are diverse, depending on structural content-based classifications (genome-wide, intronic, and CDS) and sequence context-based categories (A/C, A/G, A/T, C/G, C/T, and G/T substitutions) of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were observed in 1−3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined effect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the magnitude of corresponding bias of nucleotide C at −1 site and G at +1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.
A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model
Authors: Chen Mao , Huang Wen-Qi 
Published: November 2016

Abstract
A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorithm is compared with other well-known methods for 10 benchmark sequences with lengths ranging from 20 to 100 monomers. The results indicate that our method is a very efficient and promising tool for the protein folding problem.
Predicting the Coupling Specificity of G-Protein Coupled Receptors to G-Proteins by Support Vector Machines
Authors: Guan Cui-Ping , Jiang Zhen-Ran , Zhou Yan-Hong 
Published: November 2016

Abstract
G-protein coupled receptors (GPCRs) represent one of the most important classes of drug targets for pharmaceutical industry and play important roles in cellular signal transduction. Predicting the coupling specificity of GPCRs to G-proteins is vital for further understanding the mechanism of signal transduction and the function of the receptors within a cell, which can provide new clues for pharmaceutical research and development. In this study, the features of amino acid compositions and physiochemical properties of the full-length GPCR sequences have been analyzed and extracted. Based on these features, classifiers have been developed to predict the coupling specificity of GPCRs to G-proteins using support vector machines. The testing results show that this method could obtain better prediction accuracy.
Narrative Theory
Authors: Puckett Kent 
Published: November 2016

Kent Puckett's Narrative Theory: A Critical Introduction provides an account of a methodology increasingly central to literary studies, film studies, history, psychology and beyond. In addition to introducing readers to some of the field's major figures and their ideas, Puckett situates critical and philosophical approaches towards narrative within a longer intellectual history. The book reveals one of narrative theory's founding claims - that narratives need to be understood in terms of a formal relation between story and discourse, between what they narrate and how they narrate it - both as a necessary methodological distinction and as a problem characteristic of modern thought. Puckett thus shows that narrative theory is not only a powerful descriptive system but also a complex and sometimes ironic form of critique. Narrative Theory offers readers an introduction to the field's key figures, methods and ideas, and it also reveals that field as unexpectedly central to the history of ideas.
Chromite chemistry as an indicator of petrogenesis and tectonic setting of the Ranomena ultramafic complex in north-eastern Madagascar
Authors: ISHWAR-KUMAR C. , RAJESH V.J. , WINDLEY B.F. , RAZAKAMANANA T. , ITAYA T. , BABU E.V.S.S.K. , SAJEEV K. 
Published: November 2016

AbstractThe Ranomena ultramafic complex in NE Madagascar consists of layered gabbro, harzburgite, orthopyroxenite, clinopyroxenite, garnet websterite and chromitite-layered peridotite. This study of the Ranomena chromite chemistry aims to better understand the petrogenesis and palaeotectonic environment of the complex. The chromite from the Ranomena chromitite is unzoned/weakly zoned and has a Cr# (Cr/(Cr + Al)) of 0.59–0.69, a Mg# (Mg/(Fe + Mg)) of 0.37–0.44, and low Al2O3(15–23 wt %) suggesting derivation from a supra-subduction zone arc setting. Calculation of parental melt composition suggests that the parental magma composition of the Ranomena chromitite was similar to that of a primitive tholeiitic basalt formed at a high degree of mantle melting, suggesting the parental melt composition was equivalent to that of an island-arc tholeiite (IAT). The parental magma of the Ranomena chromite had a FeO/MgO ratio of 0.9 to 1.8, suggesting arc derivation. The parental magma was Al- and Fe-rich, similar to a tholeiitic basaltic magma. The composition of orthopyroxene from the chromitite indicates a crystallization temperature range of 1250–1300°C at 1.0 GPa. The chemistry of the chromite in the Ranomena chromitite further suggests that the complex formed in a supra-subduction zone arc tectonic setting.
An evaluation of urine patch simulation methods for nitrous oxide emission measurement
Authors: FORRESTAL P. J. , KROL D. J. , LANIGAN G. J. , JAHANGIR M. M. R. , RICHARDS K. G. 
Published: November 2016

SUMMARYGlobal nitrous oxide (N2O) inventory estimates for pasture systems are refined based on measurements of N2O loss from simulated urine patches. A variety of methods are used for patch simulation but they frequently use a uniform wetted area (UWA), often smaller than a bovine urine patch. However, natural patches follow non-uniform infiltration patterns expanding naturally from a point of deposit with a non-wetted zone of influence. Using 2 litres of urine the UWA method was compared, using a 0·156 m2 collar, with a naturally expanding effective area (NEEA) method, using a 0·462 m2 collar under high (HL) and low (LL) N2O loss conditions. The method chosen affects urine nitrogen (N) loading to the soil. Under HL the UWA method induced a N2O-N loss of 280·6 mg/patch, significantly less than the 434·8 mg/patch loss for the NEEA method, for the same simulated urination. Under LL there was no method effect. Efforts should be made to employ patch simulation methods, which mimic natural deposits and can be achieved, at least in part, by: (a) Using a urine volume and N content similar to that of the animal of interest. (b) Allowing natural infiltration of the chosen urine volume to permit tapering towards the edges. (c) Measuring from the zone of influence in addition to the wetted area, i.e. the patch effective area.
Canada's Arctic sector claim in historical perspective: a response to Alan MacEachern
Authors: Cavell Janice 
Published: November 2016

ABSTRACTExplorer Joseph Elzéar Bernier's famous 1909 sector claim on Melville Island is often described as a key moment in the evolution of Canada's sovereignty over the Arctic archipelago. Writers such as Yolande Dorion-Robitaille and Marjolaine Saint-Pierre have argued that Bernier was unfairly deprived of the credit he deserved for his sovereignty contributions. Alan MacEachern has recently stated inPolar Recordthat civil servants in the 1920s were to blame for this supposed unfair treatment. In particular, he sees Oswald Finnie of the Department of the Interior as a man who was determined at all costs to rewrite the historical record. This article contests MacEachern's depiction of Finnie and his colleagues, based on a range of primary source documents. It also emphasises the little-known but very significant role played by James White, who first placed the sector lines on an official map five years before Bernier's 1909 proclamation. The article thus clarifies the complicated relationship between White's 1904 map, Bernier's 1909 claim, an earlier sector claim made by Bernier in 1907, and the views on the sector theory held by influential members of the Canadian civil service at the time when an official sector claim was made by Ottawa in 1925.
A comparative study of Cu–Ni Alloy using LIBS, LA-TOF, EDX, and XRF
Authors: Ahmed N. , Ahmed R. , Rafiqe M. , Baig M.A. 
Published: November 2016

AbstractLASER induced breakdown spectroscopy (LIBS) has been used for the quantitative analysis of Cu–Ni alloy of known composition (75% Cu, 25% Ni) using the one line calibration free-LIBS (OLCF-LIBS), self-calibration-LIBS (SC-LIBS), calibration free LIBS (CF-LIBS), time of flight-mass spectroscopy (TOF-MS), energy dispersive X-ray spectroscopy (EDX) and X-ray fluorescence spectroscopy (XRF). For the LIBS-based studies, the plasma was generated by focusing the beam of a Q-switched Nd:YAG laser (532 nm, pulse energy about 200 mJ, 5 ns pulse duration) while the sample was placed in air at an atmospheric pressure. Plasma temperature about (9500 ± 300) K was calculated by the Boltzmann plot method using the neutral lines of Cu and Ni whereas the electron number density was calculated (2.0 ± 0.5) × 1016 cm−3 from the Stark broadening of an isolated Cu line as well as using the relative intensities of the neutral and singly ionized optically thin lines in the Saha–Boltzmann equation. The elemental compositions determined by different LIBS methods and standard techniques are; OLCF-LIBS (69% Cu and 31% Ni), SC-LIBS (72% Cu and 28% Ni), CF-LIBS (74% Cu and 26% Ni), TOF (74% Cu and 26% Ni), EDX (75% Cu and 24.5% Ni), XRF (73% Cu and 24.7% Ni), and LA-TOF (74% Cu and 26% Ni). It is demonstrated that the CF-LIBS method gives compositions comparable with that determined by LA-TOF, EDX, or XRF, which is also in agreement with the certified reported composition.
High prevalence ofLegionellain non-passenger merchant vessels
Authors: COLLINS S. L. , STEVENSON D. , MENTASTI M. , SHAW A. , JOHNSON A. , CROSSLEY L. , WILLIS C. 
Published: November 2016

SUMMARYThere is a paucity of information on the risk from potable water in non-passenger merchant vessels (NPMVs) particularly with regard toLegionellaand other bacteria. This retrospective study examined water samples from 550 NPMVs docked in eight UK ports. A total of 1027 samples from 412 NPMVs were examined for total aerobic colony counts (ACC), coliforms,Escherichia coliand enterococci; 41% of samples yielded ACC above the action level (>1 × 103c.f.u./ml) and 4·5% contained actionable levels (>1 c.f.u./100 ml) of faecal indicator bacteria. Eight hundred and three samples from 360 NPMVs were cultured specifically forLegionellaand 58% of vessels proved positive for these organisms with 27% of samples showing levels greater than the UK upper action limit of 1 × 103c.f.u./l. Cabin showers (49%) and hospital shower (45%) were frequently positive. A subset of 106 samples was analysed by quantitative polymerase chain reaction forLegionellaand identified a further 11Legionella-positive NPMVs, returning a negative predictive value of 100%. There was no correlation between NPMV age or size and any microbial parameters (P> 0·05).Legionella pneumophilaserogroup 1 was isolated from 46% of NPMVs and sequence-based typing of 17 isolates revealed four sequence types (STs) previously associated with human disease. These data raise significant concerns regarding the management of microbial andLegionellarisks on board NPMVs and suggest that better guidance and compliance are required to improve control.
On the social perception of intervocalic /s/ voicing in Costa Rican Spanish
Authors: Chappell Whitney 
Published: November 2016

AbstractTo decipher for the first time what, if any, social meaning is indexed by nonstandard intervocalic /s/ voicing in Costa Rica, such as [paza] for pasa ‘raisin’, the present study digitally manipulates 12 utterances from six Costa Rican speakers to vary only in intervocalic [s] versus [z]. Based on 106 listeners’ responses to these stimuli, I find that intervocalic [z] indexes a lower social status for all speakers but also yields higher ratings of confidence, niceness, localness, and masculinity for male speakers. Given female speakers’ limited ability to evoke positive social meanings associated with [z], I argue that accessibility to the indexical field (Eckert, 2008) conditions men's and women's differential treatment of variation. Offering a satisfying explanation for the gender paradox (Labov, 2001:261–293), this work concludes that women agentively eschew nonstandard variants that result in no positive social gains but lead linguistic innovation when their access to the indexical field is unobstructed.
Persistence in phonological and morphological variation
Authors: Tamminga Meredith 
Published: November 2016

AbstractPersistence, the tendency to repeat a recently used variant in speech, has been observed for a range of sociolinguistic variables. This paper uses quantitative data from ING and TD in Philadelphia English to show that persistence reflects morphological structure and can therefore be a useful tool for defining variables at the phonology–morphology interface. For both ING and TD, persistence arises only when prime and target belong to the same morphological category, with additional interactions between morphological category and lexical repetition. This pattern of results suggests that both the linguistic variables and cognitive processes at play are multifactorial.
Overlap among back vowels before /l/ in Kansas City
Authors: Strelluf Christopher 
Published: November 2016

AbstractThis research examines pre-/l/ allophones of vowels in five lexical sets—GOOSE, FOOT, GOAT, STRUT, and THOUGHT—in Kansas City. It builds an acoustic profile from 5507 tokens drawn from interviews with 67 Kansas Citians born between 1955 and 1999. Results reveal a variety of overlap patterns among all five vowels, with the most widespread being overlap between the pre-/l/ allophones of FOOT, STRUT, and GOAT. Acoustically, overlap patterns generally do not show a trend of change in apparent time. However, responses to minimal pairs reveal substantial apparent-time increases in judgments of “close” or “same.” Speakers appear to adjust their productions of vowels to match their minimal pair judgments. The interaction of these productions and judgments indicates a different profile for these five vowels than has been observed in other communities and suggests that some of these vowels have become phonemically ambiguous in Kansas City.
SOME REMARKS ON THETEPONAZCUICATLOF THE PRE-HISPANIC NAHUA
Authors: Brylak Agnieszka 
Published: November 2016

AbstractThe aim of this paper is to use the example of one type of pre-Hispanic Nahua song, theteponazcuicatl,or “log-drum song,” to present the problems that arise in the classification of preconquest Nahua verbal art identified by sixteenth century Europeans according to Western criteria of categorization as songs, poetry, or the verbal component of performances. A close examination of this genre, focused on its relationship with performance and, particularly, with pre-Hispanic theater, provides insights into how sixteenth century scribes' interpretation of Nahua oral discourse and the graphic arrangement of the alphabetically transcribed text influenced in the way Nahua culture and discourse are perceived.