bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants
Authors: Nelson Andrew D L , Forsythe Evan S , Devisetty Upendra K , Clausen David S , Haug-Batzell Asher K , Meldrum Ari M R , Frank Michael R , Lyons Eric , Beilstein Mark A 
Published: August 2016

AbstractTranscriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of &gt; 5000 lincRNA loci from A. thaliana. From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.
A Genetic Screen for Fission Yeast Gene Deletion Mutants Exhibiting Hypersensitivity to Latrunculin A
Authors: Asadi Farzad , Michalski Dorothy , Karagiannis Jim 
Published: August 2016

Abstract
Fission yeast cells treated with low doses of the actin depolymerizing drug, latrunculin A (LatA), delay entry into mitosis via a mechanism that is dependent on both the Clp1p and Rad24p proteins. During this delay, cells remain in a cytokinesis-competent state that is characterized by continuous repair and/or reestablishment of the actomyosin ring. In this manner, cells ensure the faithful completion of the preceding cytokinesis in response to perturbation of the cell division machinery. To uncover other genes with a role in this response, or simply genes with roles in adapting to LatA-induced stress, we carried out a genome-wide screen and identified a group of 38 gene deletion mutants that are hyper-sensitive to the drug. As expected, we found genes affecting cytokinesis and/or the actin cytoskeleton within this set (ain1, acp2, imp2). We also identified genes with roles in histone modification (tra1, ngg1), intracellular transport (apl5, aps3), and glucose-mediated signaling (git3, git5, git11, pka1, cgs2). Importantly, while the identified gene deletion mutants are prone to cytokinesis failure in the presence of LatA, they are nevertheless fully capable of cell division in the absence of the drug. These results indicate that fission yeast cells make use of a diverse set of regulatory modules to counter abnormal cytoskeletal perturbations, and furthermore, that these modules act redundantly to ensure cell survival and proliferation.
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain
Authors: Stroehlein Andreas J , Young Neil D , Korhonen Pasi K , Chang Bill C H , Sternberg Paul W , La Rosa Giuseppe , Pozio Edoardo , Gasser Robin B 
Published: August 2016

Abstract
Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation.
Autumn 2012
Authors: Lal Hamish 
Published: August 2016

Construction Law is of course a by-product of the engineering and construction sector and naturally what happens at a practical or commercial level in the sector is reflected in the cases that come up before the courts. A review of the themes and cases selected for this issue provides excellent advice and guidance for readers who are involved in the so-called Pre- Action Process; in the process of negotiating contracts, variations and settlements; in the process of signing up to agreements that include ‘good faith’ obligations; and those in the process of agreeing liquidated damages in the context of working in the Middle East. The emphasis of the Construction Law Quarterly is on practical advice and so I am especially delighted with this issue. Readers are writing to me with questions for Question Time and I would encourage more readers to let me know details of the themes and issues that require greater review and explanation. In that connection, readers in the Middle East have really shown a great desire for more comments and guidance on the local issues. In this issue, we look at liquidated damages and the idea is that in the future we will look at other relevant issues such as design liability in the Middle East. As ever, feedback is greatly appreciated and I would, personally, encourage all readers to let me have their thoughts.
Classification des sujets abordés dans dix manuels de rédaction web: vers un outil de référence pour l’enseignement universitaire
Authors: Goulet Marie-Josée , Fournier Christine 
Published: August 2016

RÉSUMÉ: Cet article présente une classification des sujets spécifiques abordés dans dix manuels de rédaction Web. Le résultat de la classification constitue une liste pratique de sujets généraux pouvant servir de base à l’enseignement de cette matière à l’université. Cette partie de l’analyse révèle notamment que l’expertise rédactionnelle est présente dans les manuels. Ainsi, la rédaction Web pourrait-elle être considérée comme une forme de rédaction professionnelle? En outre, l’analyse qualitative révèle que sept sujets spécifiques sont communs aux manuels du corpus, par exemple: l’hypertexte et la pertinence du contenu, ce qui suggère qu’un noyau de connaissances est en train de s’établir dans ce domaine. En conclusion, l’étude des dix manuels confirme que la rédaction Web est complexe et multidisciplinaire.MOTS-CLÉS: rédaction Web; enseignement de la rédaction Web; écriture Web; hypertexte; sites Web. RESUMO: Este artigo apresenta uma classificação de temas específicos em dez manuais de redação Web. O resultado da classificação é uma lista prática de tópicos gerais que podem servir de base para o ensino do tema na universidade. Essa parte da análise revela especialmente que a competência editorial está presente nos manuais. Assim, a redação na Web pode ser considerada uma forma de escrita profissional? Além disso, a análise qualitativa revela que sete temas específicos são comuns aos manuais do corpus, por exemplo: hipertexto e relevância do conteúdo, o que sugere que um núcleo de conhecimentos está sendo estabelecido nessa área. Em conclusão, o estudo de dez manuais confirma que a escrita na Web é complexa e multidisciplinar.PALAVRAS-CHAVE: redação na Web; ensino de redação na Web; escrita na Web; hipertexto; sitesWeb. ABSTRACT: This article presents a classification of specific topics in ten Web writing manuals. The result of the classification is a practical list of general topics which can be the base to the teaching of the theme at the university. This part of the analysis reveals that the editorial expertise is present in the manuals. Thus, can writing on the web be considered as a kind of professional writing? In addition, the qualitative analysis shows that seven specific topics are common to the corpus manuals, for example hypertext and content relevance, suggesting that core knowledge is being established in this domain. In conclusion, this study of ten textbooks confirms that Web writing is complex and multidisciplinary.KEYWORDS: composing on the Web; Web writing instruction; writing on the Web; hypertext; Websites.
Extensão para a educação: a experiência de capacitação a distância do Espaço do Produtor
Authors: Mota João Batista , Gomes Silvane Guimarães Silva , Leonardo Estela da Silva 
Published: August 2016

RESUMO: Este artigo apresenta e analisa os resultados da experiência do site Espaço do Produtor, desenvolvido e mantido pela Coordenadoria de Educação Aberta e a Distância (CEAD) da Universidade Federal de Viçosa (UFV). Para isso, associaram-se os resultados coletados por pesquisa realizada com os usuários em 2012 a uma revisão literária sobre o tema, particularmente sobre os cursos online oferecidos pelo site. Neles, são utilizados recursos das Tecnologias de Informação e Comunicação (TIC), a fim de estimular o autoaprendizado do usuário, dentre outras particularidades da Educação a Distância (EaD). Ao mesmo tempo, pretende-se confirmar a viabilidade técnica e institucional de se desenvolver um site para a realização de atividades de extensão de universidades públicas, fundamentando-as com dados e depoimentos da pesquisa. Entre os empecilhos para o desenvolvimento de atividades e projetos de extensão estão o alto custo e a falta de estímulo para participação de pesquisadores e de alunos. Conclui-se que, com o site, é possível alcançar um grande público, que muitas vezes, por condições geográficas ou falta de tempo, não poderia se dedicar a um curso presencial ou a distância. Além disso, o usuário consegue se aprofundar no assunto, que tem grande importância para a sua tomada de decisões presentes ou futuras na vida profissional e no dia a dia.PALAVRAS-CHAVE: cursos livres; educação a distância; espaço do produtor; extensão. ABSTRACT: This article presents and analyzes the results of the experience related to Espaço do produtor’s website (Producer space, in free translation), developed and maintained by Coordenadoria de Educação Aberta e a Distância (Cead), from Universidade Federal de Viçosa (UFV). For this purpose, we associated the results acquired by researches made with the website users in 2012, and a literature review about the theme, particularly about the online courses offered by the website. In those courses, the information and communication technologies (TIC) were used to stimulate users’ self-learning, among others e-learning particularities. At the same time, we intend to confirm the technical and institutional viability to develop a website to promote extension activities in education public institutions, grounding them with the help of data and research testimonials. Among the obstacles for the development of activities and extension projects, we found the high costs and the lack of incentive for researches and students’ participation. We conclude that it is possible to reach a large audience, that often, due to geographic condition or lack of time, could not dedicate to a classroom or distance course. Besides that, the user can go further in the matter, which has big importance for his decisions, in the present or future, for the professional or everyday life.KEYWORDS: free courses; distance learning; Espaço do produtor; extension.
Humor, ideologia e discurso: a circulação dos estereótipos do caipira em piadas na internet
Authors: Nascimento Emanuel Angelo 
Published: August 2016

RESUMO:Inscrito na Análise do Discurso (AD) de linha francesa, este artigo tem por objetivo discutir o funcionamento do discurso do humor relacionado à circulação dos estereótipos do caipira na internet. O corpus é constituído de um conjunto de piadas publicadas no portal Humortardela e no site AnimaTunes, a partir do qual analisamos, com base nos estudos de Possenti (1998, 2010), as condições de produção do discurso do humor. Para análise desse objeto de estudo no espaço digital, leva-se em conta a noção de discurso eletrônico, a partir de Orlandi (2013), além dos estudos de Bergson (2007), Raskin (1985) e Skinner (2002) sobre o riso e o humor. Mobiliza-se, ainda, os conceitos de cenas de enunciação, desenvolvidos por Maingueneau (2008), e de estereótipos, a partir de Amossy & Hershberg Pierrot (1997), a fim de compreender como as representações do caipira emergem nos processos de enunciação humorística. A partir dos resultados das análises, pretende-se verificar como as representações do caipira são interpeladas no interdiscurso e de que forma a internet contribui para a circulação dos estereótipos do caipira na rede em sua relação com o humor.PALAVRAS-CHAVE: estereótipo; caipira; internet;discurso; humor. ABSTRACT: Based on the Discourse Analysis (AD) of French orientation, this article aims at discussing the functioning of the humor discourse associated with the circulation of the stereotypes of the Brazilian caipira on the internet. Thecorpus comprises a set of jokes published on the portal Humortardela and on the website AnimaTunes, from which we analyze, based on studies of Possenti (1998, 2010), the production conditions of the humor discourse. For the analysis of this object of study on the digital environment, we take into account the notion of electronic discourse, from Orlandi (2013), as well as the studies of Bergson (2007), Raskin (1985), Skinner (2002) about laughter and humor. We also put together the concepts of scenes of enunciation, developed by Maingueneau (2008), and stereotypes, of Amossy & Hershberg Pierrot (1997), in order to understand how the representations of the caipira emerge in the processes of humor enunciation. From the analysis results, we intend to verify the way the representations of the caipira are challenged in interdiscourse and how the internet contributes for the circulation of the caipira stereotypes on the web in its relation with humor. KEYWORDS: stereotype; caipira; internet; discourse; humor.
Política pública de turismo do Amazonas a partir do Modelo de Fluxos Múltiplos
Authors: Nascimento Vânia Lúcia Quadros , Simonian Ligia Terezinha Lopes , Farias Filho Milton Cordeiro 
Published: August 2016

Este artigo apresenta os resultados parciais de uma pesquisa sobre a formulação da política pública de turismo.O objetivo foi identificar os fatores e os atores que influenciaram o processo de formulação da política pública de turismo do Estado do Amazonas. Utilizou-se como referencial teórico o Modelo de Fluxos Múltiplos de Kingdon. As evidências estão baseadas em pesquisa documental e entrevistas semiestruturadas com a gestora estadual de turismo. Os resultados apontam que as alternativas para o desenvolvimento do turismo
no Estado foram concretizadas no Plano “Victória Régia” e que elas dependeram dos fluxos de problemas, de políticas públicas e da política e da atuação dos participantes ativos. Conclui-se que alguns dos atores listados no Plano não se comportaram do modo como prevê o Modelo utilizado e que as orientações e determinações do Ministério do Turismo brasileiro influenciaram os fluxos de políticas públicas e/ou da política.
Comparison of owner satisfaction between stifle joint orthoses and tibial plateau leveling osteotomy for the management of cranial cruciate ligament disease in dogs
Authors: Hart Juliette L. , May Kimberly D. , Kieves Nina R. , Mich Patrice M. , Goh Clara S. S. , Palmer Ross H. , Duerr Felix M. 
Published: August 2016

Abstract
OBJECTIVE To compare owner satisfaction between custom-made stifle joint orthoses and tibial plateau leveling osteotomy (TPLO) for the management of medium- and large-breed dogs with cranial cruciate ligament disease (CCLD).
DESIGN Owner survey.
SAMPLE 819 and 203 owners of dogs with CCLD that were managed with a custom-made stifle joint orthosis or TPLO, respectively.
PROCEDURES Client databases of an orthosis provider and veterinary teaching hospital were reviewed to identify potential survey respondents. An online survey was developed to evaluate owner-reported outcomes, complications, and satisfaction associated with the nonsurgical (orthosis group) and surgical (TPLO group) interventions. Survey responses were compared between groups.
RESULTS The response rate was 25% (203/819) and 37% (76/203) for the orthosis and TPLO groups, respectively. The proportion of owners who reported that their dogs had mild or no lameness and rated the intervention as excellent, very good, or good was significantly greater for the TPLO group than for the orthosis group. However, ≥ 85% of respondents in both groups reported that they would choose the selected treatment again. Of 151 respondents from the orthosis group, 70 (46%) reported skin lesions associated with the device, 16 (11%) reported that the dog subsequently underwent surgery, and 10 (7%) reported that the dog never tolerated the device.
CONCLUSIONS AND CLINICAL RELEVANCE Results indicated high owner satisfaction rates for both interventions. Owners considering nonsurgical management with an orthosis should be advised about potential complications such as persistent lameness, skin lesions, patient intolerance of the device, and the need for subsequent surgery.
STUDIES OF THE ORIGIN OF HIGH-FREQUENCY QUASI-PERIODIC OSCILLATIONS OF MASS-ACCRETING BLACK HOLES IN X-RAY BINARIES WITH NEXT-GENERATION X-RAY TELESCOPES
Authors: Beheshtipour Banafsheh , Hoormann Janie K. , Krawczynski Henric 
Published: August 2016

ABSTRACT
Observations with RXTE (Rossi X-ray Timing Explorer) revealed the presence of high-frequency quasi-periodic oscillations (HFQPOs) of the X-ray flux from several accreting stellar-mass black holes. HFQPOs (and their counterparts at lower frequencies) may allow us to study general relativity in the regime of strong gravity. However, the observational evidence today does not yet allow us to distinguish between different HFQPO models. In this paper we use a general-relativistic ray-tracing code to investigate X-ray timing spectroscopy and polarization properties of HFQPOs in the orbiting Hotspot model. We study observational signatures for the particular case of the 166 Hz quasi-periodic oscillation (QPO) in the galactic binary GRS 1915+105. We conclude with a discussion of the observability of spectral signatures with a timing-spectroscopy experiment such as the LOFT (Large Observatory for X-ray Timing) and polarization signatures with space-borne X-ray polarimeters such as IXPE (Imaging X-ray Polarimetry Explorer), PolSTAR (Polarization Spectroscopic Telescope Array), PRAXyS(Polarimetry of Relativistic X-ray Sources), or XIPE (X-ray Imaging Polarimetry Explorer). A mission with high count rate such as LOFT would make it possible to get a QPO phase for each photon, enabling the study of the QPO-phase-resolved spectral shape and the correlation between this and the flux level. Owing to the short periods of the HFQPOs, first-generation X-ray polarimeters would not be able to assign a QPO phase to each photon. The study of QPO-phase-resolved polarization energy spectra would thus require simultaneous observations with a first-generation X-ray polarimeter and a LOFT-type mission.
REVISED MODEL OF THE STEADY-STATE SOLAR WIND HALO ELECTRON VELOCITY DISTRIBUTION FUNCTION
Authors: Yoon Peter H. , Kim Sunjung , Choe G. S. , moon Y.-J. 
Published: August 2016

ABSTRACT
A recent study discussed the steady-state model for solar wind electrons during quiet time conditions. The electrons emanating from the Sun are treated in a composite three-population model—the low-energy Maxwellian core with an energy range of tens of eV, the intermediate ∼102–103 eV energy-range (“halo”) electrons, and the high ∼103–105 eV energy-range (“super-halo”) electrons. In the model, the intermediate energy halo electrons are assumed to be in resonance with transverse EM fluctuations in the whistler frequency range (∼102 Hz), while the high-energy super-halo electrons are presumed to be in steady-state wave–particle resonance with higher-frequency electrostatic fluctuations in the Langmuir frequency range (∼105 Hz). A comparison with STEREO and WIND spacecraft data was also made. However, ignoring the influence of Langmuir fluctuations on the halo population turns out to be an unjustifiable assumption. The present paper rectifies the previous approach by including both Langmuir and whistler fluctuations in the construction of the steady-state velocity distribution function for the halo population, and demonstrates that the role of whistler-range fluctuation is minimal unless the fluctuation intensity is arbitrarily raised. This implies that the Langmuir-range fluctuations, known as the quasi thermal noise, are important for both halo and super-halo electron velocity distribution.
ON THE CHEMISTRY OF HYDRIDES OF N ATOMS AND O+ IONS
Authors: Awad Zainab , Viti Serena , Williams David A. 
Published: August 2016

ABSTRACT
Previous work by various authors has suggested that the detection by Herschel/HIFI of nitrogen hydrides along the low-density lines of sight toward G10.6-0.4 (W31C) cannot be accounted for by gas-phase chemical models. In this paper we investigate the role of surface reactions on dust grains in diffuse regions, and we find that formation of the hydrides by surface reactions on dust grains with efficiency comparable to that for H2 formation reconciles models with observations of nitrogen hydrides. However, similar surface reactions do not contribute significantly to the hydrides of O+ ions detected by Herschel/HIFI that are present along many sight lines in the Galaxy. The O+ hydrides can be accounted for by conventional gas-phase chemistry either in diffuse clouds of very low density with normal cosmic-ray fluxes or in somewhat denser diffuse clouds with high cosmic-ray fluxes. Hydride chemistry in dense dark clouds appears to be dominated by gas-phase ion–molecule reactions.