bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)
Authors: Koglin Sven , Trense Daronja , Wink Michael , Sauer-Gürth Hedwig , Tietze Dieter Thomas 
Published: December 2017

Background
In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed.

Methods
Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R.

Results
Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found.

Discussion
Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.
Three‐Dimensional Time Domain Simulation of Tsunami‐Generated Electromagnetic Fields: Application to the 2011 Tohoku Earthquake Tsunami
Authors: Minami Takuto , Toh Hiroaki , Ichihara Hiroshi , Kawashima Issei 
Published: December 2017

AbstractWe present a new finite element simulation approach in time domain for electromagnetic (EM) fields associated with motional induction by tsunamis. Our simulation method allows us to conduct three‐dimensional simulation with realistic smooth bathymetry and to readily obtain broad structures of tsunami‐generated EM fields and their time evolution, benefitting from time domain implementation with efficient unstructured mesh. Highly resolved mesh near observation sites enables us to compare simulation results with observed data and to investigate tsunami properties in terms of EM variations. Furthermore, it makes source separations available for EM data during tsunami events. We applied our simulation approach to the 2011 Tohoku tsunami event with seawater velocity from linear‐long and linear‐Boussinesq approximations. We revealed that inclusion of dispersion effect is necessary to explain magnetic variations at a northwest Pacific seafloor site, ~1,500 km away from the epicenter, while linear‐long approximation is enough at a seafloor site ~200 km east‐northeast of the epicenter. Our simulations provided, for the first time, comprehensive views of spatiotemporal structures of tsunami‐generated EM fields for the 2011 Tohoku tsunami, including large‐scale electric current circuits in the ocean. Finally, subtraction of the simulated magnetic fields from the observed data revealed symmetric magnetic variations on the western and eastern sides of the epicenter for 30 min since the earthquake origin time. These imply a pair of southward and northward electric currents in the ionosphere that exist on the western and eastern sides of the source region, respectively, which was likely to be caused by tsunami‐generated atmospheric acoustic/gravity waves reaching the ionosphere.
A New One‐Equation Model of Fluid Drag for Irregularly Shaped Particles Valid Over a Wide Range of Reynolds Number
Authors: Dioguardi F. , Mele D. , Dellino P. 
Published: December 2017

AbstractA new drag law for irregularly shaped particles is presented here. Particles are described by a shape factor that takes into account both sphericity and circularity, which can be measured via the most commonly used image particle analysis techniques. By means of the correlation of the drag coefficient versus the particle Reynolds number and the shape factor, a new drag formula, which is valid over a wide range of Reynolds number (0.03–10,000), is obtained. The new model is able to reproduce the drag coefficient of particles measured in terminal velocity experiments with a smaller scatter compared to other laws commonly used in multiphase flow engineering and volcanology. Furthermore, the new formula uses only one equation, whereas previous models, to insure validity over an ample range, made use of a step function that introduces a discontinuity at the switch of equations. Finally, this drag law works in the whole range of variation, from extremely irregular particles to perfect sphere. A code of the iterative algorithm for the drag coefficient calculation and terminal velocity is included in the supporting information both as a Fortran routine and a Matlab function.
Quasi‐Steady Evolution of Hillslopes in Layered Landscapes: An Analytic Approach
Authors: Glade R. C. , Anderson R. S. 
Published: December 2017

AbstractLandscapes developed in layered sedimentary or igneous rocks are common on Earth, as well as on other planets. Features such as hogbacks, exposed dikes, escarpments, and mesas exhibit resistant rock layers adjoining more erodible rock in tilted, vertical, or horizontal orientations. Hillslopes developed in the erodible rock are typically characterized by steep, linear‐to‐concave slopes or “ramps” mantled with material derived from the resistant layers, often in the form of large blocks. Previous work on hogbacks has shown that feedbacks between weathering and transport of the blocks and underlying soft rock can create relief over time and lead to the development of concave‐up slope profiles in the absence of rilling processes. Here we employ an analytic approach, informed by numerical modeling and field data, to describe the quasi‐steady state behavior of such rocky hillslopes for the full spectrum of resistant layer dip angles. We begin with a simple geometric analysis that relates structural dip to erosion rates. We then explore the mechanisms by which our numerical model of hogback evolution self‐organizes to meet these geometric expectations, including adjustment of soil depth, erosion rates, and block velocities along the ramp. Analytical solutions relate easily measurable field quantities such as ramp length, slope, block size, and resistant layer dip angle to local incision rate, block velocity, and block weathering rate. These equations provide a framework for exploring the evolution of layered landscapes and pinpoint the processes for which we require a more thorough understanding to predict their evolution over time.
Cosmopolitanism
Authors: Woodward Ian 
Published: December 2017

AbstractCosmopolitanism is understood as a philosophical ideal and sociocultural process whereby people feel connection not only to local others who are ethnically or culturally like themselves, but to geographically and culturally distant others. Cosmopolitanism is an attitude which favors understanding points of universal human commonality and a political imperative which prioritizes reflexive dialogue and cooperation across nations. As a set of sociocultural practices and institutional priorities, it also comes with political complications and ethical dilemmas. Social scientifically, questions also exist about the best ways to conceptualize, identify, and measure the concept.
Intercultural Communication in the Global Workplace, Critical Approaches
Authors: Holmes Prue 
Published: December 2017

AbstractThe critical intercultural turn in intercultural communication and cross‐cultural management research has begun to question dominating traditional (positivist) approaches. Therefore, preparing people for the global workplace requires understanding of intercultural communication informed by critical scholarship: questioning the theory and practices of the “metropole” (or developed “North”), it also requires complementary research, education, and training that gives voice to those in the “global South” who may be marginalized, disenfranchised, poor, and exploited. Community diversity and interconnectivity, whether through communication technologies or movement of people, have placed new demands on preparing critical intercultural citizens for communication in the global workplace: people who can appreciate similarity and difference; who are capable of taking nonessentialist approaches to cultures, languages, and communities; who understand the role of the intercultural speaker; and who acknowledge the multiple languages and lingua franca Englishes at play, and the translingual, transcultural practices this recognition entails.
Third‐Culture Individuals
Authors: Barker Gina G. 
Published: December 2017

Abstract

This entry provides an overview of third‐culture individuals, defined as men and women who lived in a country other than that of their nationality during their developmental years. Becoming socialized into their home culture and host culture(s) simultaneously, they form a multicultural identity. Since this identity is derived largely from their atypical, mobile upbringing involving multiple transitions as children of corporate employees, military or government personnel, missionaries or aid workers, people with this background generally refer to themselves as
third‐culture kids
. They are also described as
hidden immigrants
,
global nomads
,
cultural chameleons,
and
cultural composites
. A formal theory of third‐culture individuals has yet to emerge, but researchers have recently begun testing assertions made in popular and professional literature about third‐culture individuals' intercultural competence, enhanced adaptability, social sensitivity, open‐mindedness, and cultural marginality. This research has produced evidence that their unique intercultural adaptation allows them to acquire specialized intercultural communication skills.
Intercultural Communication Study in Japan
Authors: Takai Jiro 
Published: December 2017

AbstractIntercultural communication in Japan as an academic field has often been misunderstood, having been associated more with English language teaching than with research in its own right. Japan does not recognize communication as an independent discipline, and because of this, intercultural majors within Japanese universities are likely to be misconstrued, hence students who wish to pursue a career in the field need to obtain their education overseas. In spite of this, the community of intercultural scholars is active in both research and teaching. This entry briefly describes the history of intercultural communication in Japan, its status as an academic field, its scholarly societies, and research and practice.
Intercultural Communication Study in Latin America
Authors: Medina‐López‐Portillo Adriana 
Published: December 2017

AbstractThis entry makes a distinction between the concepts ofinterculturalidad(interculturality) andintercultural communicationin Latin America. Interculturalidad is the product of the social, economic, political, and cultural challenges that the indigenous communities have encountered since the Europeans arrived to the Americas. Intercultural communication is a term and approach borrowed from the discipline that originated in the United States. In this entry are examples of institutions and academic disciplines offering undergraduate and graduate education, academic professional organizations, publications in which research articles are published, and major research themes and topics in interculturality and intercultural communication in Latin America. The entry includes specific names of authors and publication titles.
Intercultural Communication Study in South Africa
Authors: Bornman Elirea 
Published: December 2017

Abstract
This entry deals with issues related to intercultural communication in South Africa. The focus falls first on the state of the discipline and issues related to teaching and research. Attention is then given to the nature of South African society and the implications of culture and group membership in determining intergroup communication. Issues related to language and identity as well as the extent and nature of contact and interaction between groups are discussed, and attention is given to the African worldview and its emphasis on human connectedness. The entry examines various barriers to intercultural communication such as nonverbal communication and paralinguistics, ethnocentrism, and xenophobia as well as contrasting communication styles, and then concludes with a call to local and international researchers to tackle the largely unexplored terrain of communication within African contexts and to assist in solving the manifold problems associated with intercultural communication in those settings.
Cultural Dimensions, Hofstede
Authors: Taras Vas 
Published: December 2017

Abstract
This entry provides a description and analysis of Hofstede's model of culture. It presents an overview of the dimensions included in the model, describes the process by which the model was developed, and reviews the key features of the model, as well as noting its strengths and weaknesses. The entry will be of interest to students of culture who seek to better understand the origin, content, and limitations of Hofstede's model of culture and its dimensions.
Communication Modes,Arab
Authors: Feghali Ellen Kussman , Braithwaite Charles A. 
Published: December 2017

AbstractThis entry takes the position that understanding important communicative characteristics found across Arab‐speaking communities facilitates effective intercultural interaction. After clarifying the term “Arab,” the entry explicates such pan‐Arab communication modes as the use ofInshallahand other God expressions, the invoking ofwasta, and the pervasiveness ofwejbet.
Communication Modes,Asian
Authors: Chang Hui‐Ching 
Published: December 2017

AbstractThis entry presents results and arguments accompanying studies of Asian communication modes. Three research foci are identified: how philosophical traditions inform Asian communicative practices; how the individualism/collectivism cultural value framework helps situate Asian communication; and how an Asiacentric focus helps us better theorize links between culture and communication. Along these lines, scholars also challenge problematics in classifying “Asian” as an encompassing category; the risk of essentializing Asian culture as endorsing collectivistic values; and the position that the link between culture and individual behavior can be taken for granted. Treating Asian culture as an ever‐changing, open system and Asian modes of communication as situationally negotiated allows better understanding of dynamic Asian modes of communication in global society.
Cultural Identifications Theory
Authors: Chen Yea‐Wen 
Published: December 2017

Abstract
This entry provides an introduction to cultural identifications theory (also known as cultural identity theory, cultural identity negotiation theory, or CIT). This theory began as cultural identity theory, an interpretive theory that examines, understands, and describes the communitive processes through which individuals come to know, construct, and negotiate their cultural group identities in intercultural communication interactions. Now—responding to postcolonial and postmodern critiques—it has evolved into cultural identity negotiation theory, or theorizing cultural identifications, which is a critical/interpretive theory that understands and interrogates processes and forms of cultural identifications as historical, relational, and cultural constructions. This introduction traces the theoretical evolutions of the CIT framework and synthesizes ongoing commitments of the theory.
Conversational Norms Across Cultures
Authors: Kim Min‐Sun 
Published: December 2017

Abstract

As intensive communication with speakers of differing backgrounds and assumptions is now the rule, conversing competently across cultures is becoming a major concern for many. It is important to be aware of
how
language is used in another culture and to understand the culturally specific patterns of communication. Normative conduct is a major component of the system of culture, and the notion of conversational norms has already proven a powerful tool for understanding social interactions. This entry describes main conversational norms across cultures, focusing on different styles (“how”) and approach vs. avoidance (“how much”). Speakers' negative evaluations of cultural others are typically attributed to misidentification of the meanings associated with different ways of speaking. Recognizing and respecting different communication styles is the first step in developing intercultural competence. Knowledge of conversational norms in different cultures can provide new insights into the dynamics of social interactions and help build such competence.
Pedagogy across Cultures
Authors: Grove Cornelius N. 
Published: December 2017

Abstract

With Greek roots meaning “the child” and “to lead,”
pedagogy
today may refer to the theory and practice of classroom instruction, or more broadly to the bringing about of a child's development into adulthood. This entry adopts the broader meaning, and applies a cross‐cultural perspective by relying on the voluminous research findings of anthropologists and others who, since the 1970s in East Asia and the West (especially the United States), have explored cultural factors in homes and schools to uncover the values and concepts that people
think with
when they think about child development. In the discussion of schools, the organizing principle is the distinction between the knowledge‐focused and learner‐focused approaches to instruction. The discussion of homes is shaped by differences in how East Asian and Western parents conceive of their newborn and their responsibility for her learning, and how their child comes to regard learning.
Personal Space across Cultures
Authors: Høgh‐Olesen Henrik 
Published: December 2017

Abstract

This entry provides an introduction to the research related to the concept of personal space (PS) and the field of human spatial behavior. PS is defined as an emotionally tinged
integrity zone
surrounding the body and functioning as a portable territory, serving both protective and communicative functions. The integrity zone has no fixed size but varies according to variables such as age, gender, personality, relation, and culture. The key theoretical traditions and models are presented and the field's methodological techniques and measurements are discussed.
Proxemics
—cultural differences—constitutes one of the main areas of interest, dividing cultures into either contact or low‐contact cultures. Examples of
proxetics
—human spatial behavior studied in terms of universal spacing patterns and cultural similarities—are presented. Finally, future directions for the study of PS in the digital age are outlined.
AComparative Immunohistochemical Study of Anal Canal Epithelium in Humans and Swine, Focusing on the Anal Transitional Zone Epithelium and the Anal Glands
Authors: Muranaka Futoshi , Nakajima Tomoyuki , Iwaya Mai , Ishii Keiko , Higuchi Kayoko , Ogiwara Naoko , Miyagawa Shinichi , Ota Hiroyoshi 
Published: December 2017

ABSTRACTTo better understand the cellular origins and differentiation of anal canal epithelial neoplasms, the immunohistochemical profiles of the anal canal epithelium in humans and swine were evaluated. Formalin‐fixed tissue sections were immunostained for mucin (MUC: MUC2, MUC5AC, MUC5B), desmoglein 3 (DGS3), p63, CDX2, SOX2, and α‐smooth muscle actin (α‐SMA). The anal transitional zone (ATZ) epithelium covered the anal sinus and consisted of a stratified epithelium with mucous cells interspersed within the surface lining. Anal glands opened into the anal sinus. Ducts and acini of intraepithelial or periepithelial mucous type were the main structures of human anal glands, whereas those of swine were compound tubuloacinar mixed glands. Distal to the ATZ epithelium, non‐keratinized stratified squamous epithelium merged with the keratinized stratified squamous epithelium of the perianal skin. MUC5AC expression predominated over MUC5B expression in the ATZ epithelium, while MUC5B expression was higher in the anal glands. SOX2 was positive in the ATZ epithelium, anal glands, and squamous epithelium except in the perianal skin. In humans, DGS3 was expressed in the ATZ epithelium, anal gland ducts, and squamous epithelium. p63 was detected in the ATZ epithelium, anal glands, and squamous epithelium. Myoepithelial cells positive for α‐SMA and p63 were present in the anal glands of swine. Colorectal columnar cells were MUC5B+/MUC2+/CDX2+/MUC5AC−/SOX2−. The ATZ epithelium seems to be a distinctive epithelium, with morphological and functional features allowing smooth defecation. The MUC5AC+/SOX2+/MUC2−/CDX2− profile of the ATZ epithelium and anal glands is a useful feature for diagnosing adenocarcinoma arising from these regions. Anat Rec, 301:796–805, 2018. © 2017 Wiley Periodicals, Inc.
Diabetic Status Influences the Storage of Melatonin in Human Salivary Glands
Authors: Isola Michela , Lilliu Maria Alberta , Loy Francesco , Isola Raffaella 
Published: December 2017

ABSTRACTRecently we reported on the detailed localization of melatonin (and its receptors) in human salivary glands, revealing that serous cells are able to store and secrete melatonin into saliva. Since we found that type 2 diabetic patients display reduced melatonin content in saliva, our next step was to examine the presence of melatonin in salivary glands removed from type 2 diabetic subjects. The resulting data were compared with those previously obtained by identical procedures in non‐diabetics, to establish if the diabetic status may affect melatonin distribution. Bioptic samples of diabetic parotid and submandibular glands were fixed, dehydrated, embedded in Epon Resin and processed to demonstrate melatonin reactivity by the immunogold staining method. The labeling density (expressed as the number of gold particles per μm2/granule) and the percentage of melatonin‐positive granules were assessed in diabetic samples. These values were compared with those in non‐diabetic samples and differences were evaluated. In parotid and submandibular diabetic glands the reactivity for melatonin was specifically associated with secretory granules and small vesicles in serous cells. Melatonin reactivity was higher in parotid than in submandibular glands. Our data were in line with those obtained in our previous study on non‐diabetic glands. Diabetic salivary glands showed a higher labeling density and a lower number of melatonin‐positive granules compared to non‐diabetic glands. Taken together, these data might explain the decreased salivary melatonin content and the associated oral problems observed in diabetics. Anat Rec, 301:711–716, 2018. © 2017 Wiley Periodicals, Inc.