bluuebunny/crossref_metadata_2025 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

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

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

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

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

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

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

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

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

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.
Designing with sketches: the generative effects of knowledge preordering
Authors: Brun Juliette , Le Masson Pascal , Weil Benoit
Published: November 2016

Sketches are an essential tool for designers. They allow the externalizing of ideas and are therefore economic cognitively. Sketches also provide the designer with new insights, which play an important role in the emergence of ideas. However, some studies tend to show that sketching does not systematically have a positive effect on idea generation. Our research thus aims to analyze the generative effects of sketches by studying the way sketches support the design strategy of designers. We especially focus on the role of knowledge in comparison with concepts. Three sequences of sketches are analyzed employing C–K design theory; we show that drawings refer to both concepts and knowledge, but mostly to knowledge. In particular, sketching helps the architect mobilize knowledge distant from the initial topic. Moreover, the designer carries out through sketching an important work of knowledge structuration that we call ‘knowledge preordering’; by carefully selecting, testing and, if necessary, removing knowledge, the designer organizes a strategically built knowledge space. In particular, all elements involving modularity or determinism in the knowledge basis are abandoned. Such knowledge preordering thus allows the building of a splitting knowledge structure, which offers new rules for concept generation and enhances the production of original and disruptive ideas.
School-Based Counselling Service Use: A Year in the Life of a School Counselling Department
Authors: O'Connor Matt , Coyne Joseph
Published: November 2016

There is limited research detailing school-based counselling services and how they are utilised by students. This study presented counselling service data for a Preparatory to Grade 12 school. Specifically, it examined the number of students seen and sessions provided, and differences between users and non-users of the service. The results showed that approximately 20% of students engaged in counselling. Frequency data indicated that many students had brief contact with counselling and that there is no clear relationship for when this occurs during the term or year. There were also significant differences between users and non-users within key demographics. Implications for use of this information in school as well as recommendations for effective use of counselling service data are presented.
Double exposures: the photographic afterlives of Pasolini and Moro
Authors: Hill Sarah Patricia
Published: November 2016

Photographs play a crucial role in the ways the lives and deaths of Pier Paolo Pasolini and Aldo Moro are remembered in Italian culture. Locating photographs of the two men taken before and after their murders against the backdrop of the changes in photographic practice that took place in Italy from the period of the economic boom in the late 1950s through to the early 1970s, this article explores and compares the cultural meanings of the photographs of the bodies of these two very different but equally symbolic public figures, both alive and dead. Analysing the significance of these images in Italy in the 1970s and after, it notes how contemporary theoretical approaches to the medium – particularly in terms of understandings of mass media forms and the theoretical linking of photography and death – shaped how the photographs have been understood in relation to their social and political context. It argues that the afterimage of the photographs of the corpses of Pasolini and Moro is overlaid in Italian cultural memory over the visual record of the two men during their lives in a kind of mnemonic ‘double exposure’ that constitutes these bodies of images as collective icons of their times.
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

The 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

Global 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.
Population dynamics of two sympatric intertidal fish species (the shanny, Lipophrys pholis and long-spined scorpion fish, Taurulus bubalis) of Great Britain
Authors: Barrett C.J. , Johnson M.L. , Hull S.L.
Published: November 2016

The shanny/common blenny (Lipophrys pholis) and long-spined scorpionfish/bullhead (Taurulus bubalis) are commonly encountered, sympatric species within much of Great Britain's rocky intertidal zones. Despite being prey items of the cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) respectively, and both contributors to the diet of the near-threatened European otter (Lutra lutra), little is known on the population dynamics of the temperate specimens of Great Britain. It is further less known of the degrees of sympatricity between the two fish species and to what extent they are able to coexist. The current study examines spatio-temporal distributions and abundances at various resolutions: monthly population dynamics of both species along England's Yorkshire coast and seasonal population dynamics along the Yorkshire coast and around the Isle of Anglesey, Wales. Studies of their abundances, sizes, degrees of rock pool co-occurrence and diel activities are further examined, which indicate coexistence is maintained when interspecific co-occurrence takes place only between specimens of similar sizes, thus demoting size-related dominance hierarchies.
Canada's Arctic sector claim in historical perspective: a response to Alan MacEachern
Authors: Cavell Janice
Published: November 2016

Explorer 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

LASER 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.
HYDRODYNAMIC LIMIT OF ORDER-BOOK DYNAMICS
Authors: Gao Xuefeng , Deng S.J.
Published: November 2016

In this paper, we establish a fluid limit for a two-sided Markov order book model. The main result states that in a certain asymptotic regime, a pair of measure-valued processes representing the “sell-side shape” and “buy-side shape” of an order book converges to a pair of deterministic measure-valued processes in a certain sense. We also test the fluid approximation on data. The empirical results suggest that the approximation is reasonably good for liquidly traded stocks in certain time periods.
Characterization by X-ray powder diffraction of alpha lipoic acid
Authors: Quintana Mendoza Jose H. , Toro R. A. , Blanco Laura A. , Henao J. A.
Published: November 2016

Alpha lipoic acid (ALA) C8H14O2S2 is a naturally occurring compound that is synthesized in small amounts by plants and animals, including humans. ALA is covalently bound to specific proteins, which function as cofactors for several important mitochondrial enzyme complexes and studies suggest that they might help with type 2 diabetes. In the Cambridge Structural Database, there are four entries related to this compound: two for lipoic acid and two for complexes. In the Powder Diffraction File-4, two experimental unindexed patterns are reported. The material crystallizes in a monoclinic crystal system, space group P21/a and cell parameters a = 9.237 (1) Å, b = 9.960 (1) Å, c = 11.787 (2) Å, β = 109.13 (1)°, and V = 1024.6 (2) Å3.
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

There 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.
Scepticism about Virtue and the Five-Factor Model of Personality
Authors: PARIS PANOS
Published: November 2016

Considerable progress in personality and social psychology has been largely ignored by philosophers, many of whom still remain sceptical concerning whether the conception of character presupposed by virtue theory is descriptively adequate. Here, I employ the five-factor model of personality, currently the consensus view in personality psychology, to respond to a strong reading of the situationist challenge, whereby most people lack dispositions that are both cross-situationally consistent and temporally stable. I show that situationists rely on a false dichotomy between character traits and situations, and that evidence supports the empirical adequacy of the sorts of character traits presupposed by virtue ethics. Additionally, I suggest that the personality traits of the five-factor model are relevant to virtue theory, in so far as they are malleable, morally salient, and seem to structurally parallel Aristotelian virtues and vices. Thus,contrasituationism, the five-factor model supports the descriptive adequacy of a virtue-theoretical framework.
On the social perception of intervocalic /s/ voicing in Costa Rican Spanish
Authors: Chappell Whitney
Published: November 2016

To 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

Persistence, 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

This 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

The 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.
A Longitudinal Description of Emergency Medical Services Professionals by Race/Ethnicity
Authors: Crowe Remle P. , Levine Roger , Eggerichs Jennifer J. , Bentley Melissa A.
Published: November 2016

Objective

The objective of this paper was to compare demographics, employment variables, satisfaction, and motivation for entering the field of Emergency Medical Services (EMS) between members of under-represented races/ethnicities and members of the majority group.

Methods

A cohort of nationally certified EMS professionals was followed for 10 years through annual surveys; however, race/ethnicity was only available for 9 years (2000-2008). Descriptive statistics and 95% confidence intervals (CIs) were calculated and significance was determined by lack of CI overlap.

Results

From 2000 through 2008, the range of proportions of nationally certified EMS professionals by race/ethnicity was as follows: whites: 83.5%-86.0%, Hispanics: 4.2%-5.9%, and African-Americans: 2.5%-4.6%. There were no significant changes in the proportion of minority EMS professionals over the study period. Hispanics and African-Americans combined increased slightly from 6.7% of the population in 2000 to 9.9% in 2008. Likewise, the proportion of all under-represented races/ethnicities increased slightly from 2000 (14.0%) to 2008 (16.5%). Females were under-represented in all years. Nationally certified African-Americans were significantly more likely to be certified at the Emergency Medical Technician (EMT)-Basic level (compared with the EMT-Paramedic level) than whites in all but one survey year. The proportion of Hispanics registered at the EMT-Basic level was significantly higher than whites in three survey years. Accordingly, a larger proportion of whites were nationally registered at the EMT-Paramedic level than both African-Americans and Hispanics. A significantly larger proportion of African-Americans reported working in urban communities (population >25,000) compared with whites for nine of the 10 survey years. Similarly, a significantly larger proportion of Hispanics worked in urban communities compared with whites in 2002 and from 2005 to 2008. For satisfaction measures, there were no consistent differences between races/ethnicities. Among factors for entering EMS, the proportion of whites who reported having a friend or family member in the field was significantly higher than African-Americans in all years and significantly higher than Hispanics in four of the nine years.

Conclusion

The ethnic/racial diversity of the population of nationally certified EMS professionals is not representative of the population served and has not improved over the 2000-2008 period. Similar to other health care professions, Hispanics and African-Americans are under-represented in EMS compared with the US population. This study serves as a baseline to examine under-represented populations in EMS.

CroweRP, LevineR, EggerichsJJ, BentleyMA. A longitudinal description of Emergency Medical Services professionals by race/ethnicity. Prehosp Disaster Med. 2016;31(Suppl. 1):s30–s69.
Psychometric Properties of Turkish Adolescent Time Inventory-Time Attitude (ATI-TA) Scores
Authors: Şahin-Baltacı Hülya , Tagay Özlem , Worrell Frank C. , Mello Zena R.
Published: November 2016

The Adolescent Time Inventory (ATI; Mello & Worrell, 2007 ) is a relatively new measure developed to assess several aspects of time perspective (e.g., time orientation, time attitudes). Time attitudes, one aspect of time perspective, refer to positive and negative feelings about the past, present, and future. In the current 2-sample paper, we examined the internal consistency, structural validity, and convergent validity of scores on the time attitude subscales (TA) of the Turkish ATI ( Mello, Worrell, Şahin-Baltaci, & Tagay, 2015 ). Results from Sample 1 ( N = 244) indicated that scores on 5 of the 6 Turkish ATI-TA subscales—Past Positive, Past Negative, Present Positive, Present Negative, and Future Positive—were internally consistent, and confirmatory factor analyses provided strong support for the structural validity of a 5-factor model as well as the hypothesized 6-factor model, even though internal consistency estimates for Future Negative scores (the sixth factor) were unacceptably low. Results from Sample 2 ( N = 350) provided additional internal consistency and structural validity evidence for scores on the 5-factor model and also provided evidence of convergent validity with self-esteem, well-being, and optimism. Analyses also indicated that scores on the 2 past and 2 present subscales demonstrated configural, metric, and scalar invariance across samples, whereas the Future Positive scores only demonstrated metric invariance. We concluded that these 5 subscales can be used with Turkish adolescents and that the Future Negative subscale needs to be revised and validated in this national context.
Unraveling the Planar-Globular Transition in Gold Nanoclusters through Evolutionary Search
Authors: Kinaci Alper , Narayanan Badri , Sen Fatih G. , Davis Michael J. , Gray Stephen K. , Sankaranarayanan Subramanian K. R. S. , Chan Maria K. Y.
Published: November 2016

Au nanoclusters are of technological relevance for catalysis, photonics, sensors, and of fundamental scientific interest owing to planar to globular structural transformation at an anomalously high number of atoms i.e. in the range 12–14. The nature and causes of this transition remain a mystery. In order to unravel this conundrum, high throughput density functional theory (DFT) calculations, coupled with a global structural optimization scheme based on a modified genetic algorithm (GA) are conducted. More than 20,000 Au12, Au13, and Au14 nanoclusters are evaluated. With any DFT functional, globular and planar structures coexist across the size range of interest. The planar-globular transition is gradual at room temperature rather than a sharp transition as previously believed. The effects of anionicity, s-d band hybridization and long range interactions on the dimensional transition are quantified by using the structures adjacent to the minima. Anionicity marginally changes the relative stability of the clusters. The degree of s-d hybridization is varied via changing the Hubbard U value which corroborate that s-d hybridization alone does not stabilize planar structures. van der Waals interactions, on the other hand, stabilize globular structures. These results elucidate the balance between the different reasons of the dimensional transition in gold nanoclusters.
Comprehensive Gene expression meta-analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders
Authors: Jha Prabhash Kumar , Vijay Aatira , Sahu Anita , Ashraf Mohammad Zahid
Published: November 2016

Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes. Using INMEX bioinformatic tool, based on combined Effect Size (ES) approaches, we identified a total of 1,157 differentially expressed genes (DEGs) (697 overexpressed and 460 underexpressed genes) shared between the three diseases. EnrichR tool’s rich library was used for comprehensive functional enrichment and pathway analysis which revealed “mRNA Splicing” and “SUMO E3 ligases SUMOylate target proteins” among the most enriched terms. Network based meta-analysis identified MYC and FN1 to be the most highly ranked hub genes. Our results reveal that the alterations in biomarkers of the coagulation cascade like F2R, PROS1, SELPLG and ITGB2 were common between the three diseases. Interestingly, the study has generated a novel database of candidate genetic markers, pathways and transcription factors shared between thrombosis and MPDs, which might aid in the development of prognostic therapeutic biomarkers.
Ultraviolet optomechanical crystal cavities with ultrasmall modal mass and high optomechanical coupling rate
Authors: Zhou Wen , Yu Zejie , Ma Jingwen , Zhu Bingqing , Tsang Hon Ki , Sun Xiankai
Published: November 2016

Optomechanical crystal (OMC) cavities which exploit the simultaneous photonic and phononic bandgaps in periodic nanostructures have been utilized to colocalize, couple, and transduce optical and mechanical resonances for nonlinear interactions and precision measurements. The development of near-infrared OMC cavities has difficulty in maintaining a high optomechanical coupling rate when scaling to smaller mechanical modal mass because of the reduction of the spatial overlap between the optical and mechanical modes. Here, we explore OMC nanobeam cavities in gallium nitride operating at the ultraviolet wavelengths to overcome this problem. With a novel optimization strategy, we have successfully designed an OMC cavity, with a size of 3.83 × 0.17 × 0.13 μm3 and the mechanical modal mass of 22.83 fg, which possesses an optical mode resonating at the wavelength of 393.03 nm and the fundamental mechanical mode vibrating at 14.97 GHz. The radiation-limited optical Q factor, mechanical Q factor, and optomechanical coupling rate are 2.26 × 107, 1.30 × 104, and 1.26 MHz, respectively. Our design and optimization approach can also serve as the general guidelines for future development of OMC cavities with improved device performance.
Current induced polycrystalline-to-crystalline transformation in vanadium dioxide nanowires
Authors: Jeong Junho , Yong Zheng , Joushaghani Arash , Tsukernik Alexander , Paradis Suzanne , Alain David , Poon Joyce K. S.
Published: November 2016

Vanadium dioxide (VO2) exhibits a reversible insulator-metal phase transition that is of significant interest in energy-efficient nanoelectronic and nanophotonic devices. In these applications, crystalline materials are usually preferred for their superior electrical transport characteristics as well as spatial homogeneity and low surface roughness over the device area for reduced scattering. Here, we show applied electrical currents can induce a permanent reconfiguration of polycrystalline VO2 nanowires into crystalline nanowires, resulting in a dramatically reduced hysteresis across the phase transition and reduced resistivity. Low currents below 3 mA were sufficient to cause the local temperature in the VO2 to reach about 1780 K to activate the irreversible polycrystalline-to-crystalline transformation. The crystallinity was confirmed by electron microscopy and diffraction analyses. This simple yet localized post-processing of insulator-metal phase transition materials may enable new methods of studying and fabricating nanoscale structures and devices formed from these materials.
SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance
Authors: Li Xinyue , Du Yu , Du Pengcheng , Dai Hang , Fang Yujie , Li Zhenpeng , Lv Na , Zhu Baoli , Kan Biao , Wang Duochun
Published: November 2016

SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates. The SXT/R391 ICEs shared a common structure with a set of conserved genes, five hotspots and two variable regions, which contained more foreign genes, including drug-resistance genes. Notably, a class A β-lactamase gene was identified in nine SXT/R391 ICEs. Collectively, the ICE-carrying isolates carried resistance genes for 20 tested drugs. Six isolates were resistant to chloramphenicol, kanamycin, streptomycin, trimethoprim-sulfamethoxazole, sulfisoxazole and tetracycline, which are drug resistances commonly encoded by ICEs. Our results demonstrate abundant genetic diversity and multidrug resistance of the SXT/R391 ICEs carried by Proteus isolates, which may have significance for public health. It is therefore necessary to continuously monitor the antimicrobial resistance and related mobile elements among Proteus isolates.
Laser Light Induced Transformation of Molybdenum Disulphide-Based Nanoplatelet Arrays
Authors: Jagminas Arūnas , Niaura Gediminas , Žalnėravičius Rokas , Trusovas Romualdas , Račiukaitis Gediminas , Jasulaitiene Vitalija
Published: November 2016

One-pot hydrothermal synthesis of MoS2 nanoplatelet arrays on various substrates is perhaps the most promising approach to fabricate efficient electrocatalysts for hydrogen evolution reaction. However, the main challenges in this synthesis remain the purity and crystallinity of MoS2. In this study, we show for the first time that irradiation of amorphous, defect-rich MoS2 nanoplatelets with a green nanosecond laser at a proper irradiation dose, ca ≤0.35 J cm−2, can significantly improve the crystallinity and purity of MoS2 nanoplatelets. The effect was confirmed by Raman spectroscopy investigations demonstrating a surprising intensity increase of the A1g and "Equation missing" modes after the laser irradiation. Further increase of irradiation energy, however, resulted in the photocorrosion and destruction of MoS2 nanoplatelets. The variation of A1g and "Equation missing" Raman mode intensities ratio depending on the green light irradiation dose was also presented and is discussed below.
Peptides Labeled with Pyridinium Salts for Sensitive Detection and Sequencing by Electrospray Tandem Mass Spectrometry
Authors: Waliczek Mateusz , Kijewska Monika , Rudowska Magdalena , Setner Bartosz , Stefanowicz Piotr , Szewczuk Zbigniew
Published: November 2016

Mass spectrometric analysis of trace amounts of peptides may be problematic due to the insufficient ionization efficiency resulting in limited sensitivity. One of the possible ways to overcome this problem is the application of ionization enhancers. Herein we developed new ionization markers based on 2,4,6-triphenylpyridinium and 2,4,6-trimethylpyridinium salts. Using of inexpensive and commercially available pyrylium salt allows selective derivatization of primary amino groups, especially those sterically unhindered, such as ε-amino group of lysine. The 2,4,6-triphenylpyridinium modified peptides generate in MS/MS experiments an abundant protonated 2,4,6-triphenylpyridinium ion. This fragment is a promising reporter ion for the multiple reactions monitoring (MRM) analysis. In addition, the fixed positive charge of the pyridinium group enhances the ionization efficiency. Other advantages of the proposed ionization enhancers are the simplicity of derivatization of peptides and the possibility of convenient incorporation of isotopic labels into derivatized peptides.
Hatching asynchrony vs. foraging efficiency: the response to food availability in specialist vs. generalist tit species
Authors: Barrientos R. , Bueno-Enciso J. , Sanz J. J.
Published: November 2016

Breeding mistiming is increasingly frequent in several ecosystems in the face of current climate change. Species belonging to higher trophic levels must employ mechanisms to reduce it. One of these mechanisms is hatching asynchrony, with the eggs in a clutch hatching over a period of several days. Some authors have suggested it to be adaptive when food is unpredictable. However, these birds can also suffer associated costs. We tested whether a species with higher foraging efficiency avoid hatching asynchrony compared to its sister species. We studied hatching asynchrony and nestling provisioning in relation to food availability in sympatric populations of blue and great tits. For the first time, we show that sister species respond to food availability with different strategies. Blue tit feeding rates readily responded to the abundance of their main prey, and also reduced the impact of nestling size hierarchy on mean nestling weight, consequently increasing fledging rate. Our results suggest that levels of hatching asynchrony seem to be influenced by species-specific life history traits, as generalist foragers rely less on it. They also highlight the importance of multi-species approaches when studying the response of organisms to environmental unpredictability.